Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 21
Found at i:1514085 original size:35 final size:34
Alignment explanation
Indices: 1514001--1514087 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1513991 AATATAATTT
*
1514001 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1514035 TAAATAATAAAAAAATTACAATAACATGTATTAAATGG
1 TAAAT-ACAACAAAATTACAAT-A-A-GTATTAAATGG
1514073 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1514088 AGAAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 22 0.49
36 2 0.04
37 4 0.09
38 12 0.27
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1514100 original size:13 final size:13
Alignment explanation
Indices: 1514082--1514106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1514072 GTAATAAACA
1514082 AAATTAAGAAAAT
1 AAATTAAGAAAAT
1514095 AAATTAAGAAAA
1 AAATTAAGAAAA
1514107 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (13 bp):
AAATTAAGAAAAT
Found at i:1520262 original size:24 final size:23
Alignment explanation
Indices: 1520220--1520264 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1520210 TAACTGCACA
*
1520220 AAAAAATTAATTAAATAAATATT
1 AAAAAATTAAATAAATAAATATT
*
1520243 AAAAAATTAAAATAATTAAATA
1 AAAAAATT-AAATAAATAAATA
1520265 AAATAGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATTAAATAAATAAATATT
Found at i:1520284 original size:32 final size:29
Alignment explanation
Indices: 1520222--1520297 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
1520212 ACTGCACAAA
*
1520222 AAAATTAATTAAAT-AAATATTAAAAAATT
1 AAAA-TAATTAAATAAAATAGTAAAAAATT
1520251 AAAATAATTAAATAAAATAGTAACCAAATATT
1 AAAATAATTAAATAAAATAGTAA--AAA-ATT
*
1520283 AAATATAATAAAATA
1 AAA-ATAATTAAATA
1520298 TACCTTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 9 0.22
29 12 0.30
31 3 0.08
32 6 0.15
33 10 0.25
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAATAATTAAATAAAATAGTAAAAAATT
Found at i:1521316 original size:14 final size:14
Alignment explanation
Indices: 1521297--1521338 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
1521287 ATGTGAGGGG
1521297 GTTTGAGAGAAAGA
1 GTTTGAGAGAAAGA
1521311 GTTTGAGAGAAAGA
1 GTTTGAGAGAAAGA
1521325 GTTTGAGAGAAAGA
1 GTTTGAGAGAAAGA
1521339 TGAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
GTTTGAGAGAAAGA
Found at i:1521566 original size:16 final size:17
Alignment explanation
Indices: 1521547--1521584 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1521537 TAGGGTTAAT
1521547 CACCTTTAG-GACCCTC
1 CACCTTTAGCGACCCTC
*
1521563 CACC-TTAGCTACCCTC
1 CACCTTTAGCGACCCTC
1521579 CACCTT
1 CACCTT
1521585 AGCTGTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 14 0.74
17 1 0.05
ACGTcount: A:0.18, C:0.47, G:0.08, T:0.26
Consensus pattern (17 bp):
CACCTTTAGCGACCCTC
Found at i:1521585 original size:16 final size:16
Alignment explanation
Indices: 1521557--1521588 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1521547 CACCTTTAGG
1521557 ACCCTCCACCTTAGCT
1 ACCCTCCACCTTAGCT
1521573 ACCCTCCACCTTAGCT
1 ACCCTCCACCTTAGCT
1521589 GTGTATGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.06, T:0.25
Consensus pattern (16 bp):
ACCCTCCACCTTAGCT
Found at i:1521930 original size:2 final size:2
Alignment explanation
Indices: 1521923--1521952 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1521913 CAAACTATCC
1521923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1521953 TCTTTCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1524342 original size:21 final size:21
Alignment explanation
Indices: 1524289--1524369 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
1524279 GCACTGAAAT
1524289 TTATCCCGAAGGACCA-T-TA
1 TTATCCCGAAGGACCACTGTA
* * *
1524308 -TGTCTCGTAGGACCACTGTA
1 TTATCCCGAAGGACCACTGTA
* * *
1524328 TTGTCCCGAATGACCATTGTA
1 TTATCCCGAAGGACCACTGTA
1524349 TTATCCCGAAGGACCACTGTA
1 TTATCCCGAAGGACCACTGTA
1524370 ACCCTCGACT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 12 0.24
19 1 0.02
20 2 0.04
21 34 0.69
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
TTATCCCGAAGGACCACTGTA
Found at i:1524625 original size:29 final size:29
Alignment explanation
Indices: 1524604--1524659 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1524594 TCACTTAATC
*
1524604 TCATATCATATAACATGTATCACATAGAT
1 TCATATCATATAACATATATCACATAGAT
* *
1524633 TCATATCATGTAATATATATCACATAG
1 TCATATCATATAACATATATCACATAG
1524660 CACATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (29 bp):
TCATATCATATAACATATATCACATAGAT
Found at i:1530579 original size:29 final size:29
Alignment explanation
Indices: 1530547--1530602 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1530537 TCACTTAATC
*
1530547 TCATATCATATAACATGTATCACATAGAT
1 TCATATCATATAACATATATCACATAGAT
*
1530576 TCATATCATGTAACATATATCACATAG
1 TCATATCATATAACATATATCACATAG
1530603 CACATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (29 bp):
TCATATCATATAACATATATCACATAGAT
Found at i:1542717 original size:35 final size:36
Alignment explanation
Indices: 1542678--1542758 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
1542668 AACACAATCA
*
1542678 TCAATTACATTCTAAACCCCAAATTCC-AAAATACT
1 TCAATTACATTCTAAACCCCAAAGTCCAAAAATACT
**
1542713 TCAATTACATTCTAAACCTTAAAGTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAAGTCCAAAAATACT
*
1542749 TTAATTACAT
1 TCAATTACAT
1542759 GACCAACCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 24 0.59
36 17 0.41
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAAGTCCAAAAATACT
Found at i:1542873 original size:21 final size:21
Alignment explanation
Indices: 1542821--1542873 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1542811 CTTGAAGCAG
*
1542821 TAACCCTAAACCCTCAAAACA
1 TAACCCTAAATCCTCAAAACA
1542842 TAACCCTAAATCCTCAAAACA
1 TAACCCTAAATCCTCAAAACA
1542863 TAACCCTAAAT
1 TAACCCTAAAT
1542874 GCTAAAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (21 bp):
TAACCCTAAATCCTCAAAACA
Found at i:1543458 original size:146 final size:149
Alignment explanation
Indices: 1543273--1543571 Score: 487
Period size: 146 Copynumber: 2.0 Consensus size: 149
1543263 GTTAAAAACT
* *
1543273 ATTTAAATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAAC
1 ATTTAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAAC
*
1543338 TCAAAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCATAT-AAAAAAA-TTCAAGT
66 TCAAAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCAAGT
*
1543401 CAACTATTTTATTAACTGA
131 CAACTATTTTATAAACTGA
*
1543420 ATTT-AATTAGAATAAAATGATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAAC
1 ATTTAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAAC
** * *
1543484 TTGAAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTTCGAG
66 TCAAAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATC-AAAAAAATTTCAAG
1543549 TCAACTATTTTATAAACTGA
130 TCAACTATTTTATAAACTGA
1543569 ATT
1 ATT
1543572 GAGTATTTAG
Statistics
Matches: 140, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
146 102 0.73
147 4 0.03
148 7 0.05
149 27 0.19
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (149 bp):
ATTTAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAAC
TCAAAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCAAAAAAATTTCAAGT
CAACTATTTTATAAACTGA
Found at i:1543778 original size:35 final size:35
Alignment explanation
Indices: 1543739--1543818 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
1543729 GGGGTTGGGT
* *
1543739 ATGTAATTGAAGTATTTT-GAAATTTGAGGTTTATA
1 ATGTAATTGAAGCATTTTAG-AATTTGAGGTTTAAA
* *
1543774 ATGTAATTGAAGCATTTTAGATTTTGGGGTTTAAA
1 ATGTAATTGAAGCATTTTAGAATTTGAGGTTTAAA
1543809 ATGTAATTGA
1 ATGTAATTGA
1543819 TGACTGTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATTTGAGGTTTAAA
Found at i:1545302 original size:38 final size:37
Alignment explanation
Indices: 1545239--1545623 Score: 313
Period size: 37 Copynumber: 10.4 Consensus size: 37
1545229 CAATATAATG
* *
1545239 TAGTTTTTGAAAAT-ATTTTTAAAAACATATAATGTA
1 TAGTTTTTGAAAATGATTTTTGAAAACATATAATATA
*
1545275 TAGTTTTTAGAAAATGGTTTTTGAAAACATATAATATA
1 TAGTTTTT-GAAAATGATTTTTGAAAACATATAATATA
* *
1545313 TA-TTTTTTAAAATCAGTTTTTGAAAACATAT-ATA-A
1 TAGTTTTTGAAAATGA-TTTTTGAAAACATATAATATA
* ** * *
1545348 TATGATTTTGAAAACACACTTTTGAAAACGTATAATATA
1 TA-GTTTTTGAAAA-TGATTTTTGAAAACATATAATATA
**
1545387 TAG-TTTTGAAAACACATTTTTGAAAACATATAATATA
1 TAGTTTTTGAAAA-TGATTTTTGAAAACATATAATATA
*** * * *
1545424 TAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATA
1 TAGTTT-TTGAAAATGATTTTTGAAAACATATAATATA
* ** * **
1545462 AAG-TTTTGAAAACACATTTTGGAAAATGTATAATATA
1 TAGTTTTTGAAAA-TGATTTTTGAAAACATATAATATA
** * *
1545499 TAGTTTTAAAAAAATGGTTTTTGAAAACGTATAATATA
1 TAGTTTT-TGAAAATGATTTTTGAAAACATATAATATA
*
1545537 TAG-TTTTGAAAATACAATTTTTGAAAACATATAATATA
1 TAGTTTTTGAAAAT--GATTTTTGAAAACATATAATATA
** *
1545575 TAGATTTTT-AAAGCGGTTTTTGAAAACATAT--TATA
1 TAG-TTTTTGAAAATGATTTTTGAAAACATATAATATA
1545610 TAGTTTTTGAAAAT
1 TAGTTTTTGAAAAT
1545624 ATAATATATG
Statistics
Matches: 283, Mismatches: 48, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
34 5 0.02
35 13 0.05
36 25 0.09
37 123 0.43
38 99 0.35
39 14 0.05
40 4 0.01
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (37 bp):
TAGTTTTTGAAAATGATTTTTGAAAACATATAATATA
Found at i:1545467 original size:75 final size:75
Alignment explanation
Indices: 1545253--1545622 Score: 398
Period size: 75 Copynumber: 5.0 Consensus size: 75
1545243 TTTTGAAAAT
* * ** * * * *
1545253 ATTTTTAAAAACATATAATGTATAGTTTTTAGAAAATGGTTTTTGAAAACATATAATATATATTT
1 ATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATATAGTT
*
1545318 TTTAAAATCA-
66 TTGAAAA-CAC
* * * *
1545328 GTTTTTGAAAACATAT-ATAATATGATTTTGAAAACACAC---TTTTGAAAACGTATAATATATA
1 ATTTTTGAAAACATATAAT-ATAT-AGTTT-AAAAAAAACGGTTTTTGAAAACGTATAATATATA
1545389 GTTTTGAAAACAC
63 GTTTTGAAAACAC
*
1545402 ATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATAAAGTT
1 ATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATATAGTT
1545467 TTGAAAACAC
66 TTGAAAACAC
* ** * *
1545477 ATTTTGGAAAATGTATAATATATAGTTTTAAAAAAATGGTTTTTGAAAACGTATAATATATAGTT
1 ATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATATAGTT
*
1545542 TTGAAAATAC
66 TTGAAAACAC
** * *
1545552 AATTTTTGAAAACATATAATATATAGATTT--TTAAAGCGGTTTTTGAAAAC--ATATTATATAG
1 -ATTTTTGAAAACATATAATATATAG-TTTAAAAAAAACGGTTTTTGAAAACGTATAATATATAG
1545613 TTTTTGAAAA
64 -TTTTGAAAA
1545623 TATAATATAT
Statistics
Matches: 251, Mismatches: 33, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
72 7 0.03
73 16 0.06
74 59 0.24
75 137 0.55
76 26 0.10
77 6 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.39
Consensus pattern (75 bp):
ATTTTTGAAAACATATAATATATAGTTTAAAAAAAACGGTTTTTGAAAACGTATAATATATAGTT
TTGAAAACAC
Found at i:1545618 original size:22 final size:22
Alignment explanation
Indices: 1545590--1545632 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1545580 TTTTAAAGCG
*
1545590 GTTTTTGAAAACATATTATATA
1 GTTTTTGAAAACATAATATATA
*
1545612 GTTTTTGAAAATATAATATAT
1 GTTTTTGAAAACATAATATAT
1545633 GTTATATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
GTTTTTGAAAACATAATATATA
Found at i:1545630 original size:20 final size:22
Alignment explanation
Indices: 1545590--1545631 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1545580 TTTTAAAGCG
*
1545590 GTTTTTGAAAACATATTATATA
1 GTTTTTGAAAACATATAATATA
1545612 GTTTTTG-AAA-ATATAATATA
1 GTTTTTGAAAACATATAATATA
1545632 TGTTATATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (22 bp):
GTTTTTGAAAACATATAATATA
Found at i:1547943 original size:12 final size:12
Alignment explanation
Indices: 1547926--1547960 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1547916 TGGGGTTGGA
1547926 ATTTTTATTTTC
1 ATTTTTATTTTC
*
1547938 ATTTTTATTTTG
1 ATTTTTATTTTC
*
1547950 ATTATTATTTT
1 ATTTTTATTTT
1547961 TATCTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTATTTTC
Found at i:1552178 original size:18 final size:18
Alignment explanation
Indices: 1552155--1552189 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1552145 TTTAAAGAAA
1552155 TTTTTGA-GAAATCTTGTG
1 TTTTTGATGAAAT-TTGTG
1552173 TTTTTGATGAAATTTGT
1 TTTTTGATGAAATTTGT
1552190 TATAGATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (18 bp):
TTTTTGATGAAATTTGTG
Found at i:1552599 original size:21 final size:21
Alignment explanation
Indices: 1552528--1552604 Score: 86
Period size: 23 Copynumber: 3.6 Consensus size: 21
1552518 AAACCCGATG
* * *
1552528 GGTGTATCGGTACAC-CTCAG
1 GGTGTATCGATACACATTCAA
1552548 GGTGTATCGATACACATTCAA
1 GGTGTATCGATACACATTCAA
1552569 GGAATGTATCGATACACATTCATA
1 GG--TGTATCGATACACATTCA-A
1552593 -GTGTATCGATAC
1 GGTGTATCGATAC
1552605 CTAGGTATCT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 14 0.28
21 16 0.32
23 19 0.38
24 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (21 bp):
GGTGTATCGATACACATTCAA
Found at i:1556351 original size:18 final size:18
Alignment explanation
Indices: 1556310--1556352 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1556300 AACTCCAACG
*
1556310 TTCTTCTTTTTCTCCGTC
1 TTCTTCTTTGTCTCCGTC
*
1556328 TCCTTCTTTGTCT-CGTCC
1 TTCTTCTTTGTCTCCGT-C
1556346 TTCTTCT
1 TTCTTCT
1556353 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.35, G:0.07, T:0.58
Consensus pattern (18 bp):
TTCTTCTTTGTCTCCGTC
Found at i:1558843 original size:2 final size:2
Alignment explanation
Indices: 1558836--1558885 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1558826 TACGTATGTG
*
1558836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1558877 TA TA -A TA TA
1 TA TA TA TA TA
1558886 AGTATAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1558891 original size:11 final size:10
Alignment explanation
Indices: 1558836--1558897 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 10
1558826 TACGTATGTG
1558836 TATATATATATA
1 TATA-ATATA-A
1558848 TATATATATATA
1 TATA-ATATA-A
1558860 TATATATATACA
1 TATA-ATATA-A
1558872 TATAATATAA
1 TATAATATAA
1558882 TATAAGTATAA
1 TATAA-TATAA
1558893 TATAA
1 TATAA
1558898 ACATATAAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
10 6 0.12
11 15 0.31
12 27 0.56
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
TATAATATAA
Found at i:1559735 original size:18 final size:19
Alignment explanation
Indices: 1559688--1559736 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1559678 AGATAAGTCT
*
1559688 TCTTATTCTCTCCCTTTTAC
1 TCTT-TTCTTTCCCTTTTAC
*
1559708 TATCTTTCTTTCCCTTTT-C
1 TCT-TTTCTTTCCCTTTTAC
1559727 TCTTTTCTTT
1 TCTTTTCTTT
1559737 TTGGTTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 14 0.56
21 1 0.04
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTTTTCTTTCCCTTTTAC
Found at i:1560446 original size:38 final size:38
Alignment explanation
Indices: 1560385--1560500 Score: 196
Period size: 38 Copynumber: 3.0 Consensus size: 38
1560375 CATTCTTAAC
*
1560385 TTCCCTTCTTTTTGTCTCCTAGCTTGATTACTCATTTGA
1 TTCCCTTC-TTTTGTCTCTTAGCTTGATTACTCATTTGA
*
1560424 TTCCCTGCTTTTGTCTCTTAGCTTGATTACTCATTTGA
1 TTCCCTTCTTTTGTCTCTTAGCTTGATTACTCATTTGA
*
1560462 TTACCTTCTTTTGTCTCTTAGCTTGATTACTCATTTGA
1 TTCCCTTCTTTTGTCTCTTAGCTTGATTACTCATTTGA
1560500 T
1 T
1560501 ATCGGACTCA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
38 66 0.90
39 7 0.10
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (38 bp):
TTCCCTTCTTTTGTCTCTTAGCTTGATTACTCATTTGA
Found at i:1567850 original size:38 final size:37
Alignment explanation
Indices: 1567792--1569039 Score: 393
Period size: 38 Copynumber: 33.7 Consensus size: 37
1567782 TTCTTAAAAC
*
1567792 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* * ** **
1567830 AAGATTAGTCTCACTGGAGATTGTTTTTCTTAAAACA-
1 AAGATTA-TCTCACTTGAGATAGTTTCACTCGAAACAG
** * * *
1567867 ATATTTTATCTCGCTTGAGATGGTTTCAGTCGAAACAG
1 A-AGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** * * *
1567905 AAGATTCATTTCACTCAAGATTGTTTTC-CT-TAAA-AC
1 AAGATT-ATCTCACTTGAGATAG-TTTCACTCGAAACAG
* *
1567941 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAA
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** **
1567979 AAGATTTATCTCACTTGAGATTGTTTTGCTTAAAACA-
1 AAGA-TTATCTCACTTGAGATAGTTTCACTCGAAACAG
** * *
1568016 AATTTTATCTCCCTTGAGATAGTTTCACTCAAAACAG
1 AAGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** * ** * *
1568053 AAGATTCATTTCACTCAAGATAATTTTTCT-TAAA-AC
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* *
1568089 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAATAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* * ** * *
1568127 AAGATTATTCTCACTGGAGATTGTTTTTCT-TAAA-AC
1 AAGATTA-TCTCACTTGAGATAGTTTCACTCGAAACAG
* * * *
1568163 AAGATTTTACCTCGCTTAAGATGGTTTCACTCGAAACAG
1 AAGA--TTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** * * * *
1568202 AAGATTCATTTCACTCAAGATTGATTT-TCT-TAAA-AC
1 AAGATT-ATCTCACTTGAGATAG-TTTCACTCGAAACAG
* * * *
1568238 AAGATTCATCTCGCTTGATATAGTTTCACTCAAAATAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** **
1568276 AAGATTTATCTCACTTGAGATTGTTTGTTCTTAAAACA-
1 AAGA-TTATCTCACTTGAGATAGTTT-CACTCGAAACAG
** * *
1568314 AATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAG
1 AAGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** ** *
1568351 AAGATTCATTTCACTCAAGATCA-TTTTTCT-TATAAC--
1 AAGATT-ATCTCACTTGAGAT-AGTTTCACTCGA-AACAG
*
1568387 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* * * * ** * *
1568425 AAGATCAGTCTCGCTGGAGATTGTTTTTCT-TAAA-AC
1 AAGATTA-TCTCACTTGAGATAGTTTCACTCGAAACAG
* * * *
1568461 AAGATTTTACCTCGCTTGATATGGTTTCACTCGAAACAG
1 AAGA--TTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** * ** * *
1568500 AAGATTCATTTCACTCAAGATTGTTTTTCT-TAAA-AC
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* * *
1568536 AAGATTCATATCGCTTGAGATAGTTTTCACTCGAAACAT
1 AAGATT-ATCTCACTTGAGATAG-TTTCACTCGAAACAG
* ** **
1568575 AA-ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACA-
1 AAGA--TTATCTCACTTGAGATAGTTTCACTCGAAACAG
** * * * * *
1568612 AACTTTATCTCACTTGAGACAATTTTTACTAGAAATAAG
1 AAGATTATCTCACTTGAGA-TAGTTTCACTCGAAA-CAG
* * ** * ** * *
1568651 ACA-TTTCATTTCACTCAAGATTGTTTTTCT-TAAA-AC
1 A-AGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* *
1568687 AAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* * * *
1568725 AAGATTTATCTCA-TTGGAGATTCGTTT-TCT-TAAA-AT
1 AAGA-TTATCTCACTT-GAGA-TAGTTTCACTCGAAACAG
* * * *
1568761 AAGATTTTACCTCGCTTGAGATGGTTTCACTCGAAATAG
1 AAGA--TTATCTCACTTGAGATAGTTTCACTCGAAACAG
* ** * ** * *
1568800 AAGATTCATTTCACTCAAGATTGTTTTTCT-TAAA-AC
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
* *
1568836 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAATAG
1 AAGATT-ATCTCACTTGAGATAGTTTCACTCGAAACAG
** **
1568874 AAGATTTATCTCACTTGAGATTA-TTTTTCTTAAAACA-
1 AAGA-TTATCTCACTTGAGA-TAGTTTCACTCGAAACAG
** * *
1568911 AATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAG
1 AAGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
*
1568948 AAGATTTATCTCACTTGAGAT--TGT---T--AAACA-
1 AAGA-TTATCTCACTTGAGATAGTTTCACTCGAAACAG
** * * *
1568978 AATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAG
1 AAGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
** *
1569015 AATTTTATCTCACTTGAGATTGTTT
1 AAGATTATCTCACTTGAGATAGTTT
1569040 TTCTTAAAAC
Statistics
Matches: 877, Mismatches: 256, Indels: 155
0.68 0.20 0.12
Matches are distributed among these distances:
29 15 0.02
30 2 0.00
31 6 0.01
33 1 0.00
34 1 0.00
35 11 0.01
36 253 0.29
37 193 0.22
38 311 0.35
39 71 0.08
40 13 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (37 bp):
AAGATTATCTCACTTGAGATAGTTTCACTCGAAACAG
Found at i:1567851 original size:74 final size:74
Alignment explanation
Indices: 1567755--1569051 Score: 1461
Period size: 74 Copynumber: 17.5 Consensus size: 74
1567745 TATTTAATAT
* * *
1567755 GAAGATTTATCTTACTTGAGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTC
1 GAAGA-TTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
1567819 ACTCGAAACA
65 ACTCGAAACA
* * *
1567829 GAAGATTAGTCTCACTGGAGATTGTTTTTCTTAAAACAATATTTTATCTCGCTTGAGATGGTTTC
1 GAAGATTA-TCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
*
1567894 AGTCGAAACA
65 ACTCGAAACA
* * * *
1567904 GAAGATTCATTTCACTCAAGATTGTTTTCCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTC
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
1567968 ACTCGAAACA
65 ACTCGAAACA
* * * *
1567978 AAAGATTTATCTCACTTGAGATTGTTTTGCTTAAAACAA-ATTTTATCTCCCTTGAGATAGTTTC
1 GAAGA-TTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
*
1568042 ACTCAAAACA
65 ACTCGAAACA
* * ** *
1568052 GAAGATTCATTTCACTCAAGATAATTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTC
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
*
1568116 ACTCGAAATA
65 ACTCGAAACA
* * * *
1568126 GAAGATTATTCTCACTGGAGATTGTTTTTCTTAAAACAAGATTTTACCTCGCTTAAGATGGTTTC
1 GAAGATTA-TCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
1568191 ACTCGAAACA
65 ACTCGAAACA
* * * * *
1568201 GAAGATTCATTTCACTCAAGATTGATTTTCTTAAAACAAGA-TTCATCTCGCTTGATATAGTTTC
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
* *
1568265 ACTCAAAATA
65 ACTCGAAACA
*
1568275 GAAGATTTATCTCACTTGAGATTGTTTGTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTT
1 GAAGA-TTATCTCACTCGAGATTGTTT-TTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTT
*
1568339 CACTCAAAACA
64 CACTCGAAACA
* * ** * *
1568350 GAAGATTCATTTCACTCAAGATCATTTTTCTTATAACAAGA-TTCATCTCGCTTGAGATAGTTTC
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
1568414 ACTCGAAACA
65 ACTCGAAACA
* * * * * *
1568424 GAAGATCAGTCTCGCTGGAGATTGTTTTTCTTAAAACAAGATTTTACCTCGCTTGATATGGTTTC
1 GAAGATTA-TCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
1568489 ACTCGAAACA
65 ACTCGAAACA
* * * *
1568499 GAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTCATATCGCTTGAGATAGTTTT
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAG-TTT
1568563 CACTCGAAACA
64 CACTCGAAACA
* * * * * *
1568574 TAA-ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-ACTTTATCTCACTTGAGACAATTT
1 GAAGA--TTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGA-TAGTT
* * *
1568637 TTACTAGAAATAA
63 TCACTCGAAA-CA
* * * *
1568650 GACA-TTTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTT
1 GA-AGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTT
*
1568713 CACTCAAAACA
64 CACTCGAAACA
* * * * *
1568724 GAAGATTTATCTCATTGGAGATTCG-TTTTCTTAAAATAAGATTTTACCTCGCTTGAGATGGTTT
1 GAAGA-TTATCTCACTCGAGATT-GTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTT
*
1568788 CACTCGAAATA
64 CACTCGAAACA
* * *
1568799 GAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTC
1 GAAGATT-ATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
*
1568863 ACTCGAAATA
65 ACTCGAAACA
* *
1568873 GAAGATTTATCTCACTTGAGATTATTTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTC
1 GAAGA-TTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
*
1568937 ACTCGAAATA
65 ACTCGAAACA
*
1568947 GAAGATTTATCTCACTTGAGATTG------TT-AAACAA-ATTTTATCTCGCTTGAGATAGTTTC
1 GAAGA-TTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTC
* *
1569004 ACTCAAAATA
65 ACTCGAAACA
** *
1569014 GAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 GAAGATTATCTCACTCGAGATTGTTTTTCTTAAAACAA
1569052 ACTACACCTC
Statistics
Matches: 1037, Mismatches: 144, Indels: 85
0.82 0.11 0.07
Matches are distributed among these distances:
66 18 0.02
67 43 0.04
68 2 0.00
72 2 0.00
73 16 0.02
74 504 0.49
75 400 0.39
76 50 0.05
77 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (74 bp):
GAAGATTATCTCACTCGAGATTGTTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTCA
CTCGAAACA
Found at i:1568081 original size:149 final size:148
Alignment explanation
Indices: 1567773--1569052 Score: 1766
Period size: 149 Copynumber: 8.6 Consensus size: 148
1567763 ATCTTACTTG
*
1567773 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* * *
1567837 GTCTCACTGGAGATTGTTTTTCTTAAAACAATATTTTATCTCGCTTGAGATGGTTTCAGTCGAAA
66 -TCTCACTTGAGATTGTTTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
1567902 CAGAAGATTCATTTCACTCA
129 CAGAAGATTCATTTCACTCA
* * *
1567922 AGATTGTTTTCCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* * *
1567987 TCTCACTTGAGATTGTTTTGCTTAAAACAAATTTTATCTCCCTTGAGATAGTTTCACTCAAAACA
66 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
1568052 GAAGATTCATTTCACTCA
131 GAAGATTCATTTCACTCA
* *
1568070 AGATAATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGA-TTA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* * * *
1568134 TTCTCACTGGAGATTGTTTTTCTTAAAACAAGATTTTACCTCGCTTAAGATGGTTTCACTCGAAA
66 -TCTCACTTGAGATTGTTTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
1568199 CAGAAGATTCATTTCACTCA
129 CAGAAGATTCATTTCACTCA
* * *
1568219 AGATTGA-TTTTCTTAAAACAAGATTCATCTCGCTTGATATAGTTTCACTCAAAATAGAAGATTT
1 AGATT-ATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
*
1568283 ATCTCACTTGAGATTGTTTGTTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCAAAA
65 ATCTCACTTGAGATTGTTT-TTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
1568348 CAGAAGATTCATTTCACTCA
129 CAGAAGATTCATTTCACTCA
* * *
1568368 AGATCATTTTTCTTATAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TCA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* * * * *
1568432 GTCTCGCTGGAGATTGTTTTTCTTAAAACAAGATTTTACCTCGCTTGATATGGTTTCACTCGAAA
66 -TCTCACTTGAGATTGTTTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
1568497 CAGAAGATTCATTTCACTCA
129 CAGAAGATTCATTTCACTCA
* * *
1568517 AGATTGTTTTTCTTAAAACAAGATTCATATCGCTTGAGATAGTTTTCACTCGAAACATAA-ATTT
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAG-TTTCACTCGAAACAGAAGA-TT
* * * * * *
1568581 TATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTATCTCACTTGAGACAATTTTTACTAGAA
64 TATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTATCTCGCTTGAGA-TAGTTTCACTCGAA
* *
1568646 ATAAGACA-TTTCATTTCACTCA
128 A-CAGA-AGATTCATTTCACTCA
* *
1568668 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* * *
1568733 TCTCA-TTGGAGATTCG-TTTTCTTAAAATAAGATTTTACCTCGCTTGAGATGGTTTCACTCGAA
66 TCTCACTT-GAGATT-GTTTTTCTTAAAACAA-ATTTTATCTCGCTTGAGATAGTTTCACTCGAA
*
1568796 ATAGAAGATTCATTTCACTCA
128 ACAGAAGATTCATTTCACTCA
* *
1568817 AGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTA
1 AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
* *
1568882 TCTCACTTGAGATTATTTTTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAATA
66 TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
* *
1568947 GAAGATTTATCTCACT--
131 GAAGATTCATTTCACTCA
* * * * * * *
1568963 TGA-GA---TTGTT-AAACAA-ATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAA-TTTT
1 AGATTATTTTTCTTAAAACAAGA-TTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
1569021 ATCTCACTTGAGATTGTTTTTCTTAAAACAAA
65 ATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1569053 CTACACCTCA
Statistics
Matches: 1019, Mismatches: 89, Indels: 55
0.88 0.08 0.05
Matches are distributed among these distances:
140 35 0.03
141 40 0.04
142 4 0.00
146 2 0.00
147 3 0.00
148 196 0.19
149 534 0.52
150 128 0.13
151 76 0.07
152 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (148 bp):
AGATTATTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTA
TCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAACA
GAAGATTCATTTCACTCA
Found at i:1569014 original size:67 final size:66
Alignment explanation
Indices: 1568906--1569038 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 66
1568896 ATTTTTCTTA
*
1568906 AAACAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTATCTCACTTGAGATTG
1 AAACAAATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAA-ATTTATCTCACTTGAGATTG
1568971 TT
65 TT
*
1568973 AAACAAATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAATTTTATCTCACTTGAGATTGT
1 AAACAAATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAAATTTATCTCACTTGAGATTGT
1569038 T
66 T
1569039 TTTCTTAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 21 0.33
67 43 0.67
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (66 bp):
AAACAAATTTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAAATTTATCTCACTTGAGATTGT
T
Found at i:1581633 original size:49 final size:49
Alignment explanation
Indices: 1581575--1581709 Score: 189
Period size: 49 Copynumber: 2.8 Consensus size: 49
1581565 TTATATTTCT
* * *
1581575 AGCATGTTATCTGACGTTTGTGTGATAGTGATGCTATTATATGATACTG
1 AGCATGTTATCTGACGTCTGTGTGATAGTGGTGCTATGATATGATACTG
* ** *
1581624 AGCATGTTATCTGATGTCTGTGTGACGGTGGTGCTATGATATGATATTG
1 AGCATGTTATCTGACGTCTGTGTGATAGTGGTGCTATGATATGATACTG
* *
1581673 AGCACGTAATCTGACGTCTGTGTGATAGTGGTGCTAT
1 AGCATGTTATCTGACGTCTGTGTGATAGTGGTGCTAT
1581710 AGTACCAGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 74 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (49 bp):
AGCATGTTATCTGACGTCTGTGTGATAGTGGTGCTATGATATGATACTG
Found at i:1581638 original size:107 final size:107
Alignment explanation
Indices: 1581438--1581657 Score: 244
Period size: 107 Copynumber: 2.1 Consensus size: 107
1581428 TATGTCAGAA
* * * * * *
1581438 TGGTGCCACTAGCAGCTGCATTATATTTCTAGCAGGTTATGTGATGTCTGTGTGGCGGTGGTACT
1 TGGTGCCACTAGCAGCCGCATTATATTTCTAGCAGGTTATCTGACGTCTGTGTGACAGTGATACT
* *
1581503 ACTATACGATACTTGGCACATAACCTGATGTTTGGGTGATGG
66 ACTATACGATACTTGGCACATAACCTGATGTCTGGGTGACGG
* * * * *
1581545 TGGTGGCACTAGCAGCCGCATTATATTTCTAGCATGTTATCTGACGTTTGTGTGATAGTGATGCT
1 TGGTGCCACTAGCAGCCGCATTATATTTCTAGCAGGTTATCTGACGTCTGTGTGACAGTGATACT
* * ** * * *
1581610 ATTATATGATAC-TGAGCATGTTATCTGATGTCTGTGTGACGG
66 ACTATACGATACTTG-GCACATAACCTGATGTCTGGGTGACGG
1581652 TGGTGC
1 TGGTGC
1581658 TATGATATGA
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
106 2 0.02
107 89 0.98
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.35
Consensus pattern (107 bp):
TGGTGCCACTAGCAGCCGCATTATATTTCTAGCAGGTTATCTGACGTCTGTGTGACAGTGATACT
ACTATACGATACTTGGCACATAACCTGATGTCTGGGTGACGG
Found at i:1589817 original size:19 final size:19
Alignment explanation
Indices: 1589790--1589827 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1589780 CGATCGACGT
1589790 ATATAAACTTCATAAACAA
1 ATATAAACTTCATAAACAA
*
1589809 ATATGAACTTCATAAACAA
1 ATATAAACTTCATAAACAA
1589828 CATGAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (19 bp):
ATATAAACTTCATAAACAA
Found at i:1591249 original size:20 final size:20
Alignment explanation
Indices: 1591224--1591261 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1591214 TGAAAAAATA
*
1591224 ATTGGTGTATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1591244 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1591262 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:1597807 original size:22 final size:21
Alignment explanation
Indices: 1597766--1597808 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1597756 GAGTTTATTT
*
1597766 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTCAAACA
1597787 TCATTTTT-ATATTTTACAAACA
1 TCATTTTTCA-ATTTT-CAAACA
1597809 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (21 bp):
TCATTTTTCAATTTTCAAACA
Found at i:1606828 original size:11 final size:11
Alignment explanation
Indices: 1606809--1606839 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1606799 TGTTTAGCAT
*
1606809 CTCTTGTTGTC
1 CTCTCGTTGTC
1606820 CTCTCGTTGTC
1 CTCTCGTTGTC
1606831 CTCTCGTTG
1 CTCTCGTTG
1606840 GGTGCTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.19, T:0.48
Consensus pattern (11 bp):
CTCTCGTTGTC
Found at i:1607524 original size:19 final size:19
Alignment explanation
Indices: 1607500--1607537 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1607490 CAAAACTACC
1607500 GACAAATATGAACTTCACA
1 GACAAATATGAACTTCACA
1607519 GACAAATATGAACTTCACA
1 GACAAATATGAACTTCACA
1607538 AACACCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (19 bp):
GACAAATATGAACTTCACA
Found at i:1610842 original size:139 final size:138
Alignment explanation
Indices: 1610691--1611013 Score: 334
Period size: 139 Copynumber: 2.3 Consensus size: 138
1610681 CTCTTATTTG
* * *
1610691 ATTATTCAATTCAATAATTAATTAAAATTAATTAGGATTAATATTAGAGTTTTCATTTTAGGTAT
1 ATTATTCGATTCAATAATTAATTAAAATTAATTAGGATTAATATTAGAGTCTTCATTTCAGGTAT
* * * *
1610756 AATTTCA-AATTTAATCCTTTTAATTTAGGA-AATTTTTTAATTTGGTAATCTCTTTTGCTCGAG
66 AATTTCATAA-CTAATCC-TTTAATTTAGGAGAATCTTTT-ATTTGGTAATCGCTTATGCTCGAG
*
1610819 GTTCCGA-ATTA
128 GCTCC-ACATTA
* * ** *
1610830 ATTATTCGATTCAACAAGTCCTTAAAATTGAA-TATG-TTAATACTTAGAGTCTTCATTTCAGGT
1 ATTATTCGATTCAATAATTAATTAAAATT-AATTAGGATTAATA-TTAGAGTCTTCATTTCAGGT
* * * *
1610893 TTAATTTCATAACTAGTCCTTTAATTTAGGAGAATCTTTTATTTGGTCATCGCTTATGCTTGAGG
64 ATAATTTCATAACTAATCCTTTAATTTAGGAGAATCTTTTATTTGGTAATCGCTTATGCTCGAGG
* *
1610958 CTCCACTTTT
129 CTCCACATTA
* * * *
1610968 ACTATTCGATTCAATAATTTATTAAAAATGAGTT-GGATTAATATTA
1 ATTATTCGATTCAATAATTAATT-AAAATTAATTAGGATTAATATTA
1611014 AAGCCTATAT
Statistics
Matches: 149, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
137 1 0.01
138 67 0.45
139 77 0.52
140 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (138 bp):
ATTATTCGATTCAATAATTAATTAAAATTAATTAGGATTAATATTAGAGTCTTCATTTCAGGTAT
AATTTCATAACTAATCCTTTAATTTAGGAGAATCTTTTATTTGGTAATCGCTTATGCTCGAGGCT
CCACATTA
Found at i:1611371 original size:20 final size:20
Alignment explanation
Indices: 1611346--1611388 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1611336 GGGTGGCCGT
1611346 TATTGATCTTGGTAAATCGA
1 TATTGATCTTGGTAAATCGA
1611366 TATTGATCTTGGTAAATCGA
1 TATTGATCTTGGTAAATCGA
1611386 TAT
1 TAT
1611389 CCTTTTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (20 bp):
TATTGATCTTGGTAAATCGA
Found at i:1627839 original size:3 final size:3
Alignment explanation
Indices: 1627833--1627906 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
1627823 GTAGTAGTAG
1627833 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1627881 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1627907 TCAAACATCG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1628407 original size:134 final size:131
Alignment explanation
Indices: 1628109--1628530 Score: 496
Period size: 134 Copynumber: 3.2 Consensus size: 131
1628099 ATTCTTTAGG
* * * *
1628109 GAAGATTGAATCAGGGTAGACTTGTT--TGTTACTTAGGGAATATCAAATATTGAAAGAGAAGGA
1 GAAGATTGAATCAAGGCAGACTTGTTCATGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGA
* * ** * *
1628172 TATGTTCCGCTTCTTCTTGTGGGAAAATC-ATATCTGGATGTTGATTCATTCAAATATCACTCA-
66 TATGTTCCACTTCTTCTTGAGGGAAAATCAATATGGGGATGTTGATTCATTCCACTATCACTCAG
1628235 T
131 T
*
1628236 GAAAGATTGAAT-AGAGGCAGACTTGTTTCATTGTTACTCAGGGAATATCAAATCTTGAAAGAGA
1 G-AAGATTGAATCA-AGGCAGACTTG-TTCA-TGTTACTTAGGGAATATCAAATCTTGAAAGAGA
* * * * *
1628300 GGGATCTATTCCACTTCTTCTTGAGGAAAAATCAGATATGGGGATGTTGATTCATTCCACTGTTA
62 GGGATATGTTCCACTTCTTCTTGAGGGAAAATCA-ATATGGGGATGTTGATTCATTCCACTATCA
1628365 CTCAGT
126 CTCAGT
* *
1628371 GAAGATTGAATCAAGGCAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTAGAAAGAGAGG
1 GAAGATTGAATCAAGGCAGACTTGTT-CA-TGTTACTTAGGGAATATCAAATCTTGAAAGAGAGG
* * * *
1628436 GATTTGTTCCACTT-TGTCTTGAGGGAATATCATATCTGGGGACGTTGATTCATTCCACTATCAC
64 GATATGTTCCACTTCT-TCTTGAGGGAAAATCA-ATATGGGGATGTTGATTCATTCCACTATCAC
*
1628500 TCAGG
127 TCAGT
* *
1628505 GAAGATTGAATCGAGGCTGACTTGTT
1 GAAGATTGAATCAAGGCAGACTTGTT
1628531 TTTCTTGTCT
Statistics
Matches: 251, Mismatches: 32, Indels: 17
0.84 0.11 0.06
Matches are distributed among these distances:
127 2 0.01
128 19 0.08
129 2 0.01
132 58 0.23
133 3 0.01
134 164 0.65
135 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (131 bp):
GAAGATTGAATCAAGGCAGACTTGTTCATGTTACTTAGGGAATATCAAATCTTGAAAGAGAGGGA
TATGTTCCACTTCTTCTTGAGGGAAAATCAATATGGGGATGTTGATTCATTCCACTATCACTCAG
T
Found at i:1630251 original size:4 final size:4
Alignment explanation
Indices: 1630242--1630344 Score: 90
Period size: 4 Copynumber: 25.8 Consensus size: 4
1630232 TTTTCCTTAT
* * *
1630242 TTTC TTTC TTATC TATC TTTTC TTTC TTTA TTTC TTTC ATTT- TTTC ATTTT
1 TTTC TTTC TT-TC TTTC -TTTC TTTC TTTC TTTC TTTC -TTTC TTTC -TTTC
*
1630293 TTTC -TT- TTTC TTTC TTTC -TT- TTTC TTTC TTTC TTTTT TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
1630338 TTTC TTT
1 TTTC TTT
1630345 GTTCGTTCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
3 11 0.14
4 55 0.68
5 15 0.19
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1630300 original size:6 final size:6
Alignment explanation
Indices: 1630291--1630431 Score: 72
Period size: 6 Copynumber: 21.8 Consensus size: 6
1630281 TTTTTTCATT
*
1630291 TTTTTC TTTTTC TTTCTTTC TTTTTC TTTCTTTC TTTTTT TTCTTTC TTTCTT-
1 TTTTTC TTTTTC -TT-TTTC TTTTTC -TT-TTTC TTTTTC TT-TTTC TTT-TTC
* * *
1630344 TGTTCGTTC TTTTTC TTTTTC TTTTCC TTTTCCC TTTCTT- TTTTT- TTTTTA
1 T-TT--TTC TTTTTC TTTTTC TTTTTC TTTT-TC TTT-TTC TTTTTC TTTTTC
* * * *
1630395 TTTTTA TTTATTT TTTTTA TTTTATT TTTTTC TTTTT
1 TTTTTC TTT-TTC TTTTTC TTTT-TC TTTTTC TTTTT
1630432 TAGTGTTGTA
Statistics
Matches: 112, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
5 7 0.06
6 59 0.53
7 32 0.29
8 13 0.12
9 1 0.01
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:1630374 original size:17 final size:14
Alignment explanation
Indices: 1630241--1630429 Score: 112
Period size: 14 Copynumber: 13.6 Consensus size: 14
1630231 ATTTTCCTTA
1630241 TTTTCTTTCTTATCT
1 TTTTCTTTCTT-TCT
* *
1630256 ATCT-TTTCTTTC-
1 TTTTCTTTCTTTCT
*
1630268 -TTTATTTCTTTCATT
1 TTTTCTTTCTTTC--T
*
1630283 TTTTCATTTTTTTCT
1 TTTTC-TTTCTTTCT
1630298 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
1630312 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
1630326 TTTT-TTTCTTTCT
1 TTTTCTTTCTTTCT
*
1630339 TTCTT-TGTTCGTTCT
1 TT-TTCT-TTCTTTCT
1630354 TTTTC-TT-TTTCT
1 TTTTCTTTCTTTCT
*
1630366 TTTCCTTTTCCCTTTCT
1 TTTTC-TTT--CTTTCT
* *
1630383 TTTT-TTTTTTTAT
1 TTTTCTTTCTTTCT
* *
1630396 TTTTATTTATTT-T
1 TTTTCTTTCTTTCT
*
1630409 TTTTATTT-TATT-T
1 TTTTCTTTCT-TTCT
1630422 TTTTCTTT
1 TTTTCTTT
1630430 TTTAGTGTTG
Statistics
Matches: 144, Mismatches: 14, Indels: 34
0.75 0.07 0.18
Matches are distributed among these distances:
11 2 0.01
12 17 0.12
13 42 0.29
14 45 0.31
15 20 0.14
16 3 0.02
17 15 0.10
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:1630398 original size:13 final size:13
Alignment explanation
Indices: 1630382--1630432 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1630372 TTTCCCTTTC
1630382 TTTTTT-TTTTTT
1 TTTTTTATTTTTT
* *
1630394 ATTTTTATTTATT
1 TTTTTTATTTTTT
*
1630407 TTTTTTATTTTAT
1 TTTTTTATTTTTT
*
1630420 TTTTTTCTTTTTT
1 TTTTTTATTTTTT
1630433 AGTGTTGTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 5 0.16
13 26 0.84
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTT
Found at i:1630431 original size:19 final size:19
Alignment explanation
Indices: 1630382--1630431 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1630372 TTTCCCTTTC
1630382 TTTTTTTTTTTTATTTTTA
1 TTTTTTTTTTTTATTTTTA
*
1630401 TTTATTTTTTTTA-TTTTA
1 TTTTTTTTTTTTATTTTTA
1630419 TTTTTTTCTTTTT
1 TTTTTTT-TTTTT
1630432 TAGTGTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTTTATTTTTA
Found at i:1632833 original size:77 final size:81
Alignment explanation
Indices: 1632682--1632833 Score: 181
Period size: 77 Copynumber: 1.9 Consensus size: 81
1632672 AGAAAGTAAG
*
1632682 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
1 CATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
*
1632747 TGAGTTTTTAAATAAA
66 TGAATTTTTAAATAAA
* * * * *
1632763 CATT-AAAGATTGTAATTCAGATTATAAGTC-TTT-ATTG-TATATTTAATT-TGAATTAATTAA
1 CATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATTGATATATATAATTCAGAA-TAATTAA
1632823 AT-AATATTTTA
65 ATGAAT-TTTTA
1632834 TTTATTAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 5 0.08
77 24 0.39
78 4 0.06
79 3 0.05
80 22 0.35
81 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (81 bp):
CATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATTGATATATATAATTCAGAATAATTAAA
TGAATTTTTAAATAAA
Found at i:1653399 original size:157 final size:159
Alignment explanation
Indices: 1653220--1653532 Score: 594
Period size: 157 Copynumber: 2.0 Consensus size: 159
1653210 GAACTACTTT
1653220 TTTTTTGTTTTTTTAAACAAAGAGGAATTTTTTTCTTTTTCACATGACTTCTTTTCTAACACCAC
1 TTTTTTGTTTTTTTAAACAAAGAGGAATTTTTTTCTTTTTCACATGACTTCTTTTCTAACACCAC
1653285 AAAAATTCTTTTGTTCATGGAGC-A-TATACACTGGATAAATTGTTCATTTTTCCTGAAAAGAAT
66 AAAAATTCTTTTGTTCATGGAGCAATTATACACTGGATAAATTGTTCATTTTTCCTGAAAAGAAT
1653348 AGAAAATAGGAATAAAATAAAAAAACTAC
131 AGAAAATAGGAATAAAATAAAAAAACTAC
1653377 TTTTTTGTTTTTTTAAACAAAGAGGAATTTTTTTCTTTTTCACATGACTTCTTTTCTAACACCAC
1 TTTTTTGTTTTTTTAAACAAAGAGGAATTTTTTTCTTTTTCACATGACTTCTTTTCTAACACCAC
1653442 AAAAATTCTTTTGTTCATGGAGCATGATTATACACTGGATAAATTGTTCATTTTTCCTGAAAAGA
66 AAAAATTCTTTTGTTCATGGAGCA--ATTATACACTGGATAAATTGTTCATTTTTCCTGAAAAGA
1653507 ATAGAAAATAGGAATAAAATAAAAAA
129 ATAGAAAATAGGAATAAAATAAAAAA
1653533 TCTCGGGTTT
Statistics
Matches: 152, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
157 88 0.58
160 1 0.01
161 63 0.41
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (159 bp):
TTTTTTGTTTTTTTAAACAAAGAGGAATTTTTTTCTTTTTCACATGACTTCTTTTCTAACACCAC
AAAAATTCTTTTGTTCATGGAGCAATTATACACTGGATAAATTGTTCATTTTTCCTGAAAAGAAT
AGAAAATAGGAATAAAATAAAAAAACTAC
Found at i:1654820 original size:21 final size:19
Alignment explanation
Indices: 1654788--1654829 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1654778 TTAAAAATTA
1654788 TGATGAACAGTAGTGATAC
1 TGATGAACAGTAGTGATAC
*
1654807 TGATGCAATCAGTATTGATAC
1 TGATG-AA-CAGTAGTGATAC
1654828 TG
1 TG
1654830 CTATGGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (19 bp):
TGATGAACAGTAGTGATAC
Found at i:1655748 original size:46 final size:46
Alignment explanation
Indices: 1655364--1655745 Score: 443
Period size: 46 Copynumber: 8.4 Consensus size: 46
1655354 AAATGAATGA
* * * * *
1655364 ATAAATAAAAATG-ATTAATGGTGCATTATCAGTATGAAAGGAAGCC
1 ATAAATGAAAATGCA-TAACGGTGCATTATCGGCATGAAAGGATGCC
* *
1655410 ATAAATGAAAATGCTTAACGGTGCATTATCGGCATGAAAGGATTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
1655456 ATAAATGAAAATGTATAACGGTGCATTATCGACATGAAAGAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
1655502 ATAAATGAAAATGCATAACGGTGCAGTATCGGCATGAAAGGCTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
1655548 ATAAATGAAAATGCATAATGATGCATTATCGGCATGAAAGGATGAC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
1655594 ATAAATGAAAATGCATAAAGGTGCATTATCGGCATG-AA-G--G-C
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** * *
1655635 ATAAATAAAAATGTGTAACGGTGCATTATCGACATGAAAGGATTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * ** * *
1655681 ACAAATGAAATTGCATAACAATACATAATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
1655727 ACAAATAAAAATACATAAC
1 ATAAATGAAAATGCATAAC
1655746 AATGTATTAA
Statistics
Matches: 286, Mismatches: 44, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
41 32 0.11
42 3 0.01
43 1 0.00
44 1 0.00
45 2 0.01
46 247 0.86
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:1658828 original size:11 final size:11
Alignment explanation
Indices: 1658812--1658836 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1658802 CACTTAACCG
1658812 AAATAAAATAA
1 AAATAAAATAA
1658823 AAATAAAATAA
1 AAATAAAATAA
1658834 AAA
1 AAA
1658837 ATACAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:1659138 original size:66 final size:66
Alignment explanation
Indices: 1659024--1659187 Score: 247
Period size: 66 Copynumber: 2.5 Consensus size: 66
1659014 TTTTCCTTTG
*
1659024 GATCTTTTTTAGCTTTGAAAACTTATCCGAAATAATAACCAGTAAAGTAGCATTTTCTCCTAACA
1 GATCTTTTTTAGCTTTGAAAGCTTATCCGAAATAATAACCAGTAAAGTAGCATTTTCTCCTAACA
1659089 A
66 A
* * * * * *
1659090 TATCTTTTTTAGCTTTGAAAGCTTATTCGAAATAATAATCGGTGAAGTAGCATTTTCTCCTAACC
1 GATCTTTTTTAGCTTTGAAAGCTTATCCGAAATAATAACCAGTAAAGTAGCATTTTCTCCTAACA
*
1659155 G
66 A
*
1659156 GATCTTTTTTAGCTTTAAAAGCTTATCCGAAA
1 GATCTTTTTTAGCTTTGAAAGCTTATCCGAAA
1659188 GAAAGATGGA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (66 bp):
GATCTTTTTTAGCTTTGAAAGCTTATCCGAAATAATAACCAGTAAAGTAGCATTTTCTCCTAACA
A
Found at i:1667556 original size:7 final size:7
Alignment explanation
Indices: 1667544--1667569 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1667534 AGTTAGGAAA
1667544 ATATTAT
1 ATATTAT
1667551 ATATTAT
1 ATATTAT
1667558 ATATTAT
1 ATATTAT
1667565 ATATT
1 ATATT
1667570 CTACGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTAT
Found at i:1670776 original size:11 final size:12
Alignment explanation
Indices: 1670752--1670781 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1670742 ATATCCCCGG
1670752 TTTTAAATATTT
1 TTTTAAATATTT
*
1670764 TTTTAACTATTT
1 TTTTAAATATTT
1670776 TTTTAA
1 TTTTAA
1670782 TATAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTAAATATTT
Found at i:1672559 original size:45 final size:43
Alignment explanation
Indices: 1672502--1672891 Score: 251
Period size: 45 Copynumber: 9.6 Consensus size: 43
1672492 TTCTTATTAA
*
1672502 CATGAAATGATGCCATAGATGAAATGCATATGGGTGCATTATTTG
1 CATGAAA-GATGCCATAGAT-AAATGCATATGGGTGCATTATTGG
* *
1672547 CATGAAAGGATGCCATAGTTTAAATGCATATGGGTGCATTATGGG
1 CATGAAA-GATGCCATAG-ATAAATGCATATGGGTGCATTATTGG
*
1672592 CAT-AAA-A-G----A-AT-AATGTATATGGGTGCATTATTGG
1 CATGAAAGATGCCATAGATAAATGCATATGGGTGCATTATTGG
* * * *
1672626 CCA-GAAATGATGCCATAGCTGAAATGCATATGGGTGCATTGTCGA
1 -CATGAAA-GATGCCATAGAT-AAATGCATATGGGTGCATTATTGG
1672671 CAT-AAA-A-G----A-AT-AATGCATATGGGTGCATTATTGG
1 CATGAAAGATGCCATAGATAAATGCATATGGGTGCATTATTGG
* * *
1672705 CATGAAAGGATGCCATAGCTTAAATACATATGGGTGCATTATCGG
1 CATGAAA-GATGCCATAG-ATAAATGCATATGGGTGCATTATTGG
**
1672750 CAT-AAA-A-G----A-AT-AATGCATATATGTGCATTATTGG
1 CATGAAAGATGCCATAGATAAATGCATATGGGTGCATTATTGG
* *
1672784 CATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTATCGG
1 CATGAAA-GATGCCATAGAT-AAATGCATATGGGTGCATTATTGG
*
1672829 CAT-AAA-A-G----A-ATAAA-ACATATGGGTGCATTATTGG
1 CATGAAAGATGCCATAGATAAATGCATATGGGTGCATTATTGG
*
1672863 CATGAAAGGATGCCATAAATAAAATGCAT
1 CATGAAA-GATGCCATAGAT-AAATGCAT
1672892 GAAAGGCTAC
Statistics
Matches: 266, Mismatches: 32, Indels: 94
0.68 0.08 0.24
Matches are distributed among these distances:
34 87 0.33
35 19 0.07
36 2 0.01
37 8 0.03
38 4 0.02
41 4 0.02
42 8 0.03
43 4 0.02
44 18 0.07
45 111 0.42
46 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (43 bp):
CATGAAAGATGCCATAGATAAATGCATATGGGTGCATTATTGG
Found at i:1672891 original size:79 final size:79
Alignment explanation
Indices: 1672524--1672879 Score: 570
Period size: 79 Copynumber: 4.5 Consensus size: 79
1672514 CCATAGATGA
* * *
1672524 AATGCATATGGGTGCATTATTTGCATGAAAGGATGCCATAGTTTAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
*
1672589 GGGCATAAAAGAAT
66 CGGCATAAAAGAAT
* * *
1672603 AATGTATATGGGTGCATTATTGGCCA-GAAATGATGCCATAGCTGAAATGCATATGGGTGCATTG
1 AATGCATATGGGTGCATTATTGG-CATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTA
*
1672667 TCGACATAAAAGAAT
65 TCGGCATAAAAGAAT
* *
1672682 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTTAAATACATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1672747 CGGCATAAAAGAAT
66 CGGCATAAAAGAAT
**
1672761 AATGCATATATGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1672826 CGGCATAAAAGAAT
66 CGGCATAAAAGAAT
**
1672840 AAAACATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1672880 AATAAAATGC
Statistics
Matches: 253, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
78 2 0.01
79 249 0.98
80 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CGGCATAAAAGAAT
Found at i:1672984 original size:46 final size:46
Alignment explanation
Indices: 1672934--1673098 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
1672924 TATGTAAAAT
1672934 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
* * *
1672980 GCATGAAAGAATGCCATAAATAAAAGGCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
* *
1673026 GCATAAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAT
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
* *
1673072 TCATGAAAGGATGCCATAATTAAAATG
1 GCATGAAAGGATGCCATAAATAAAATG
1673099 AAATTTAACG
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 108 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
Found at i:1672985 original size:20 final size:20
Alignment explanation
Indices: 1672960--1673085 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
1672950 TAAATAAAAT
1672960 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1672980 GCATGAAAGAATGCCATAAATAAAAG
1 GCATGAAAGGATG-CAT---T--AAG
*
1673006 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1673026 GCATAAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1673052 GCATGAAAGGATGCATTAAT
1 GCATGAAAGGATGCATTAAG
*
1673072 TCATGAAAGGATGC
1 GCATGAAAGGATGC
1673086 CATAATTAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 42 0.49
21 6 0.07
22 2 0.02
24 2 0.02
25 6 0.07
26 28 0.33
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1673000 original size:118 final size:119
Alignment explanation
Indices: 1672852--1673065 Score: 313
Period size: 118 Copynumber: 1.8 Consensus size: 119
1672842 AACATATGGG
* * * * * **
1672852 TGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGCTACATTAAGGCATGTAAG
1 TGCATTATAGGCATGAAAGAATGCCATAAATAAAAGGCATGAAAAGATACATTAAGGCATAAAAG
* **
1672917 GATGATATATGTAAAATGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGA
66 GATGACATAAATAAAATGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGA
*
1672971 TGCATTA-AGGCATGAAAGAATGCCATAAATAAAAGGCATGAAAAGATGCATTAAGGCATAAAAG
1 TGCATTATAGGCATGAAAGAATGCCATAAATAAAAGGCATGAAAAGATACATTAAGGCATAAAAG
*
1673035 GATGCCATAAATAAAATGCATGAAAGGATGC
66 GATGACATAAATAAAATGCATGAAAGGATGC
1673066 ATTAATTCAT
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
118 76 0.92
119 7 0.08
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.21
Consensus pattern (119 bp):
TGCATTATAGGCATGAAAGAATGCCATAAATAAAAGGCATGAAAAGATACATTAAGGCATAAAAG
GATGACATAAATAAAATGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGA
Found at i:1673004 original size:72 final size:72
Alignment explanation
Indices: 1672861--1673019 Score: 228
Period size: 72 Copynumber: 2.2 Consensus size: 72
1672851 GTGCATTATT
* * * *
1672861 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGCTACATTAAGGCATGTAAGGATGATATA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACATTAAGGCATGAAAGAATGACATA
**
1672926 TGTAAAA
66 AATAAAA
* * *
1672933 TGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCATA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACATTAAGGCATGAAAGAATGACATA
1672998 AATAAAA
66 AATAAAA
*
1673005 GGCATGAAAAGATGC
1 GGCATGAAAGGATGC
1673020 ATTAAGGCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (72 bp):
GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACATTAAGGCATGAAAGAATGACATA
AATAAAA
Found at i:1673065 original size:26 final size:26
Alignment explanation
Indices: 1672861--1673019 Score: 126
Period size: 26 Copynumber: 6.6 Consensus size: 26
1672851 GTGCATTATT
1672861 GGCATGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATGCCATAAATAAAA
* * *
1672887 TGCATGAAA-G--G-C-TACAT-TAA
1 GGCATGAAAGGATGCCATAAATAAAA
* ** **
1672907 GGCATGTAAGGATGATATATGTAAAA
1 GGCATGAAAGGATGCCATAAATAAAA
*
1672933 TGCATGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATGCCATAAATAAAA
*
1672959 TGCATGAAAGGATG-CAT---T--AA
1 GGCATGAAAGGATGCCATAAATAAAA
*
1672979 GGCATGAAAGAATGCCATAAATAAAA
1 GGCATGAAAGGATGCCATAAATAAAA
*
1673005 GGCATGAAAAGATGC
1 GGCATGAAAGGATGC
1673020 ATTAAGGCAT
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
20 23 0.23
21 8 0.08
22 2 0.02
23 2 0.02
24 1 0.01
25 7 0.07
26 59 0.58
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (26 bp):
GGCATGAAAGGATGCCATAAATAAAA
Found at i:1675287 original size:232 final size:232
Alignment explanation
Indices: 1674867--1675332 Score: 761
Period size: 232 Copynumber: 2.0 Consensus size: 232
1674857 TGGTGACATA
*
1674867 TGCCTTAATAAAGTTAAAGACTTACAAGAGGAATTATCTACGCATGATTTAGAGTCGACCGTAGT
1 TGCCTCAATAAAGTTAAAGACTTACAAGAGGAATTATCTACGCATGATTTAGAGTCGACCGTAGT
* *
1674932 CGAATGTCTTAAAATATGTGACATTATAATTTGTATAGTGAGCGGTACTATAGTTGTGTTAATTA
66 CGAATGTCTTAAAAGACGTGACATTATAATTTGTATAGTGAGCGGTACTATAGTTGTGTTAATTA
* * * *
1674997 TAAAAGTTTTATGCTAATCTAAAGAGAAAAATGATTGAGTAACCAAAAAGTGGTAAAGTTTTCTT
131 CAAAAGTTTTATGCTAATCTAAAGAAAAAAATGATTGAGTAACCAAAAAGTAGTAAAGTTTTCTG
*
1675062 AAAGTATCGCTTTGGAAGTAAGTATTGCTGTTGGGAC
196 AAAGTATCGCTTTGGAAGTAAGTATTGCGGTTGGGAC
* *
1675099 TGCCTCAATAAAGTTAAAGACTTACAAGAGGAATTATCTATGCATGATTTAGAGTCGACTGTAGT
1 TGCCTCAATAAAGTTAAAGACTTACAAGAGGAATTATCTACGCATGATTTAGAGTCGACCGTAGT
** ** *
1675164 CGAATGTCTTAAAAGACGTGATGTTATAATTTGTATAGTGAGCGGTTTTATTGTTGTGTTAATTA
66 CGAATGTCTTAAAAGACGTGACATTATAATTTGTATAGTGAGCGGTACTATAGTTGTGTTAATTA
* *
1675229 CAAAAGTTTTATGCTGATCTAAAGAAAAAAATGATTGAGTAACCAGAAAGTAGTAAAGTTTTCTG
131 CAAAAGTTTTATGCTAATCTAAAGAAAAAAATGATTGAGTAACCAAAAAGTAGTAAAGTTTTCTG
* *
1675294 AAAGTTTCTCTTTGGAAGTAAGTATTGCGGTTGGGAC
196 AAAGTATCGCTTTGGAAGTAAGTATTGCGGTTGGGAC
1675331 TG
1 TG
1675333 AGTTTGAGAA
Statistics
Matches: 215, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
232 215 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (232 bp):
TGCCTCAATAAAGTTAAAGACTTACAAGAGGAATTATCTACGCATGATTTAGAGTCGACCGTAGT
CGAATGTCTTAAAAGACGTGACATTATAATTTGTATAGTGAGCGGTACTATAGTTGTGTTAATTA
CAAAAGTTTTATGCTAATCTAAAGAAAAAAATGATTGAGTAACCAAAAAGTAGTAAAGTTTTCTG
AAAGTATCGCTTTGGAAGTAAGTATTGCGGTTGGGAC
Found at i:1676927 original size:45 final size:43
Alignment explanation
Indices: 1676863--1677229 Score: 250
Period size: 45 Copynumber: 8.9 Consensus size: 43
1676853 ATAAAAGAAT
*
1676863 AATGCATATGGGTGCATTATTGGAATGAAAGGATGCCATAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-T-A
* * * *
1676908 AATGCATATGGGTGCATTATTGGTAAGAAATGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-T-A
* *
1676953 AATGCATATGGGTGCATTGTTGGCCT-AAA--A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTA
* **
1676987 AATGCATATGGGTGCATTATTGACATGAAAGGATGTGATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-T-A
* * *
1677032 AATGCATATGAGTGCATTATCGACAT-AAA--A-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTA
1677066 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAG-T-A
* * *
1677111 AATACATATGGGTTCATTATCGGCAT--AA-GA-G--A-A-T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTA
*
1677145 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAAATAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT-AGT-A
* * *
1677190 AATGCATGAAAGGATGCATTA-AGGCATGAAAGGATGCCAT
1 AATGCAT--ATGGGTGCATTATTGGCATGAAAGGATGCCAT
1677230 GATTAAAATG
Statistics
Matches: 261, Mismatches: 26, Indels: 69
0.73 0.07 0.19
Matches are distributed among these distances:
34 69 0.26
35 6 0.02
36 5 0.02
37 4 0.02
38 6 0.02
39 3 0.01
40 3 0.01
41 5 0.02
42 5 0.02
43 5 0.02
44 6 0.02
45 116 0.44
46 18 0.07
47 10 0.04
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTA
Found at i:1677003 original size:79 final size:79
Alignment explanation
Indices: 1676908--1677184 Score: 410
Period size: 79 Copynumber: 3.5 Consensus size: 79
1676898 CCATAGCTAA
* * * *
1676908 AATGCATATGGGTGCATTATTGGTAAGAAATGATGTCATAGCTGAAATGCATATGGGTGCATTGT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
* *
1676973 TGGCCTAAAAGAAT
66 CGGCATAAAAGAAT
* * *
1676987 AATGCATATGGGTGCATTATTGACATGAAAGGATGTGATAGCTGAAATGCATATGAGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
*
1677052 CGACATAAAAGAAT
66 CGGCATAAAAGAAT
* * * *
1677066 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATACATATGGGTTCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
*
1677131 CGGCATAAGAGAAT
66 CGGCATAAAAGAAT
*
1677145 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA
1677185 AATAAAATGC
Statistics
Matches: 179, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 179 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGCATATGGGTGCATTAT
CGGCATAAAAGAAT
Found at i:1678568 original size:134 final size:134
Alignment explanation
Indices: 1678320--1678740 Score: 456
Period size: 134 Copynumber: 3.1 Consensus size: 134
1678310 ATTGTTCTTC
* * * *
1678320 AGGGAAGATTGAATCG-GAGTAGACTTGCTCCATTATTACT-AGGGAATATCAAATCTTGAAAGA
1 AGGGAAGATTGAATCGAG-GCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGA
* * * * * * *
1678383 GAGAG-GTATATTTCCCTTCTCCTTGAGGGGAAATCAGATATGGGAACATTGATTCATTCCACTG
65 GAGAGACT-TGTTTCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACATTGATTCATTCCACTG
1678447 TCACTA
129 TCACTA
* * * *
1678453 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAAGGAATATAAAATCTTAAAAGTG
1 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
* * * * * *
1678518 AGAGACTTGTTTCACATCTTCTTAAGGGTAAATCAGATCTGGGGGCATTGATTCATTCCACTATG
66 AGAGACTTGTTTCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACATTGATTCATTCCACTGTC
* *
1678583 AGTT
131 ACTA
* * *
1678587 ATGGAAGATTGAATC-ATGTCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGA
1 AGGGAAGATTGAATCGA-GGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGA
* * ** * * *
1678651 GAGGGACATGTTTCGTTTCTTCTTGAGGGAAAATTAGATCTGGGGACGTTGATTAATTCCACTGT
65 GAGAGACTTGTTTCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACATTGATTCATTCCACTGT
1678716 CACTCA
130 CACT-A
* *
1678722 A-GGAATATTAAATCGAGGC
1 AGGGAAGATTGAATCGAGGC
1678741 TAACTTATTT
Statistics
Matches: 235, Mismatches: 47, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
133 35 0.15
134 197 0.84
135 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (134 bp):
AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAG
AGAGACTTGTTTCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACATTGATTCATTCCACTGTC
ACTA
Found at i:1680819 original size:19 final size:20
Alignment explanation
Indices: 1680792--1680834 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1680782 AACTGGCCCG
*
1680792 ACCCGAATCGAGACAA-CCA
1 ACCCCAATCGAGACAACCCA
*
1680811 ACCCCAATCGAGTCAACCCA
1 ACCCCAATCGAGACAACCCA
1680831 ACCC
1 ACCC
1680835 TACCTGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.37, C:0.44, G:0.12, T:0.07
Consensus pattern (20 bp):
ACCCCAATCGAGACAACCCA
Found at i:1688904 original size:65 final size:67
Alignment explanation
Indices: 1688807--1688941 Score: 150
Period size: 65 Copynumber: 2.0 Consensus size: 67
1688797 AAAAAATATC
**
1688807 TTATCTAATTAATTCAAATTAAATATACATT-AAAGAATTACAATCTGAATTACAATC-TTTAAT
1 TTATCTAATTAATTCAAATTAAATATACATTAAAAGAATTACAATCAAAATTACAATCTTTTAAT
*
1688870 GT
66 CT
* * * * * * *
1688872 TTATTTAATTATTTCGAATTAATTATTA-ATTAAAAGAGTTATAATCAAAATTACATTCTTTTAA
1 TTATCTAATTAATTCAAATTAAATA-TACATTAAAAGAATTACAATCAAAATTACAATCTTTTAA
1688936 TCT
65 TCT
1688939 TTA
1 TTA
1688942 CTTACTATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
65 24 0.42
66 23 0.40
67 10 0.18
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (67 bp):
TTATCTAATTAATTCAAATTAAATATACATTAAAAGAATTACAATCAAAATTACAATCTTTTAAT
CT
Found at i:1698620 original size:17 final size:18
Alignment explanation
Indices: 1698584--1698626 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1698574 CAAATTTACG
1698584 TTAGAAACTGAACTCAAT
1 TTAGAAACTGAACTCAAT
*
1698602 TTAGAAATTGAAC-CAAT
1 TTAGAAACTGAACTCAAT
1698619 TTAGAAAC
1 TTAGAAAC
1698627 CATATTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (18 bp):
TTAGAAACTGAACTCAAT
Found at i:1698783 original size:20 final size:20
Alignment explanation
Indices: 1698758--1698798 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1698748 TTAACTTTTT
1698758 GTCAAAGTCAACGGTCAACA
1 GTCAAAGTCAACGGTCAACA
*
1698778 GTCAAAGTCAATGGTCAACA
1 GTCAAAGTCAACGGTCAACA
1698798 G
1 G
1698799 CCAACGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
GTCAAAGTCAACGGTCAACA
Found at i:1698875 original size:29 final size:29
Alignment explanation
Indices: 1698843--1698898 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1698833 AGTTAACTTA
*
1698843 AATGGGTTGACTTAGACCAAGTTGACTAG
1 AATGGGTTGACTCAGACCAAGTTGACTAG
* *
1698872 AATGGGTTGACTCGGACCGAGTTGACT
1 AATGGGTTGACTCAGACCAAGTTGACT
1698899 CGGTGACTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (29 bp):
AATGGGTTGACTCAGACCAAGTTGACTAG
Found at i:1703093 original size:18 final size:19
Alignment explanation
Indices: 1703052--1703095 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1703042 TTTGGTTCAC
* *
1703052 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCA-TA
1703072 GGAATAAAAGATTACC-TA
1 GGAATAAAAGATTACCATA
1703090 GGAATA
1 GGAATA
1703096 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCATA
Found at i:1711367 original size:14 final size:14
Alignment explanation
Indices: 1711340--1711375 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1711330 TTTTCCCATG
1711340 TCTTTTTC-TGTTT
1 TCTTTTTCTTGTTT
*
1711353 TCTTTTTCTTTTTT
1 TCTTTTTCTTGTTT
1711367 TCTTTTTCT
1 TCTTTTTCT
1711376 GAACTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (14 bp):
TCTTTTTCTTGTTT
Found at i:1718776 original size:6 final size:6
Alignment explanation
Indices: 1718767--1720071 Score: 1887
Period size: 6 Copynumber: 222.5 Consensus size: 6
1718757 TACGTATACG
1718767 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACAC-
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * *
1718814 TACACC TACACC TACACC TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1718862 TACACA TACACA TACACA T--ACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * * *
1718908 TACACA TACACA TACACA TACACA TACACC TACACC TACACC TACACC
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1718956 TACACC TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1719004 TACACA TACACA TACACA TACACA TACACC TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * * *
1719052 TACACA TACACA T--ACA TACACA TACACC TAC-CC TACACC TACACC
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719097 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * * * * *
1719145 TACACA TACACC TACACC TACACC TACACC TACACC TACACC TAC-C-
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1719191 CACACA TACACA T-CACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* *
1719238 TACACA TACACC T-CACC TACACA TACACA TACACA TACAC- -ACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719283 TACACA TACACA TACACA TACACA TAC-CA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1719330 TACACACA TACACA TACACA TACACA TACAC- -ACACA TACAC- CACACA
1 T--ACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719377 TACACA TACACCA TACACA TACACA TACAC- -ACACA TACACA TACACA
1 TACACA TACA-CA TACACA TACACA TACACA TACACA TACACA TACACA
1719424 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719472 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719520 TACACA TACACA TACACA TACACA TACACA T--AC- TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719565 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719613 TACACA TACACACA TACACA TAC-CA TACACA TACACA TACACA TACACA
1 TACACA T--ACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719662 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACCACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TA-CACA
*
1719711 TACACA TACACA TAC-CA TAC-CA TACACA TACACA TCCACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
1719757 TACACA T-CACA TACACA TACACA TACACA TACACA T-CACA TACAC-
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1719802 -ACACA TACACA TACACA TACACA TACACC TACACA TACACA TACACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1719849 -ACACA TACACCA CACACA TACACA TACACA T--ACA TACACCA TACACA
1 TACACA TACA-CA TACACA TACACA TACACA TACACA TACA-CA TACACA
* *
1719896 TACACA TACACA TACACA TACACA TACCACC TACACC TACACA TACAC-
1 TACACA TACACA TACACA TACACA TA-CACA TACACA TACACA TACACA
* * * * * *
1719944 -A-ACA TACACC TACACC TACACC TACACC TACACA TACACC TACACC
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * * * * *
1719990 TACACA TACACC TACACC TACACA CACACC TACCCC TACAC- TAC-CA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
*
1720036 T--ACA TAC-CA TACACA TACACA TACGCA TACACA TAC
1 TACACA TACACA TACACA TACACA TACACA TACACA TAC
1720072 CCTACGCCTA
Statistics
Matches: 1217, Mismatches: 35, Indels: 94
0.90 0.03 0.07
Matches are distributed among these distances:
3 3 0.00
4 37 0.03
5 73 0.06
6 1064 0.87
7 28 0.02
8 12 0.01
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.16
Consensus pattern (6 bp):
TACACA
Found at i:1720081 original size:6 final size:6
Alignment explanation
Indices: 1720072--1720431 Score: 422
Period size: 6 Copynumber: 60.0 Consensus size: 6
1720062 ATACACATAC
* * *
1720072 CCTACG CCTAC- CCTACG CCTACA CCTACG CCTACA CCTACA CCTACG
1 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
* * * * *
1720119 CACACACA CCTACG CC-A-- CCTACA CCTACG CCTACG CATACA CCTACG
1 C-C-TACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1720166 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1720214 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
* * * * * * *
1720262 CCTACG CACCTACA CATACA CCTACA CCTATG CATACG CATACG CCTACG
1 CCTACG --CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
* *
1720312 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACA CCTACG CATACG
1 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
* * ** * * *
1720360 CATACG CATACG TATATG CCTACG CCTACG CATATG CCTACG CCTACG
1 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
* *
1720408 CATACG CCTACG CCTACG CATACG
1 CCTACG CCTACG CCTACG CCTACG
1720432 TATACGCATA
Statistics
Matches: 310, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
3 2 0.01
4 1 0.00
5 6 0.02
6 291 0.94
7 2 0.01
8 8 0.03
ACGTcount: A:0.23, C:0.46, G:0.13, T:0.17
Consensus pattern (6 bp):
CCTACG
Found at i:1720436 original size:6 final size:6
Alignment explanation
Indices: 1719410--1720622 Score: 350
Period size: 6 Copynumber: 203.8 Consensus size: 6
1719400 CATACACACA
* * * * * * * *
1719410 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1719458 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * *
1719506 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATA--
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1719552 C-TACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * *
1719599 CATACA CATACA CATACA CATACACA CATACA CATAC- CATACA CATACA
1 CATACG CATACG CATACG CAT--ACG CATACG CATACG CATACG CATACG
* * * * * * * *
1719648 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * *
1719696 CATACA CATACCA CATACA CATACA CATAC- CATAC- CATACA CATACA
1 CATACG CATA-CG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * * *
1719743 CATCCA CATACA CATACA CAT-CA CATACA CATACA CATACA CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * * *
1719790 CAT-CA CATA-- CACACA CATACA CATACA CATACA CATACA CCTACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1719835 CATACA CATACA CA-ACA CATACAC CACACA CATACA CATACA CATA--
1 CATACG CATACG CATACG CATAC-G CATACG CATACG CATACG CATACG
* * * * * * *
1719881 CATACAC CATACA CATACA CATACA CATACA CATACA CATAC- CACCTACA
1 CATAC-G CATACG CATACG CATACG CATACG CATACG CATACG CA--TACG
* * * * * * * * * * * *
1719931 CCTACA CATACA CA-A-- CATACA CCTACA CCTACA CCTACA CCTACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * * * * * * * *
1719976 CATACA CCTACA CCTACA CATACA CCTACA CCTACA CACACA CCTACC
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * *
1720024 CCTACA C-TAC- CATA-- CATAC- CATACA CATACA CATACG CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * * * *
1720067 CATAC- CCTACG CCTAC- CCTACG CCTACA CCTACG CCTACA CCTACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1720113 CCTACG CACACA CACCTACG CCACCTACA CCTACG CCTACG CATACA CCTACG
1 CATACG CATACG CA--TACG -CA--TACG CATACG CATACG CATACG CATACG
* * * * * * * *
1720166 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1720214 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG CCTACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1720262 CCTACG CACCTACA CATACA CCTACA CCTATG CATACG CATACG CCTACG
1 CATACG CA--TACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * * *
1720312 CCTACG CCTACG CCTACG CCTACG CCTACG CCTACA CCTACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * *
1720360 CATACG CATACG TATATG CCTACG CCTACG CATATG CCTACG CCTACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * *
1720408 CATACG CCTACG CCTACG CATACG TATACG CATACG CATACG TATATG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * *
1720456 CATACG CATACG CATTCG CATTCG CATTCG TATACG CATACG CATATG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * *
1720504 CATACG CTTACG CTTACG CAGAAG CATACG CAGACG CATACG CTTACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * * *
1720552 CAGACG CAGACG CAGACG CAGACG CAGACG CAGACG CAGACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* *
1720600 CAGACG CATACG CAGACG CATAC
1 CATACG CATACG CATACG CATAC
1720623 ATATAATACT
Statistics
Matches: 1080, Mismatches: 94, Indels: 66
0.87 0.08 0.05
Matches are distributed among these distances:
3 4 0.00
4 14 0.01
5 53 0.05
6 969 0.90
7 18 0.02
8 15 0.01
9 7 0.01
ACGTcount: A:0.37, C:0.39, G:0.08, T:0.17
Consensus pattern (6 bp):
CATACG
Found at i:1723896 original size:133 final size:134
Alignment explanation
Indices: 1723654--1723980 Score: 442
Period size: 133 Copynumber: 2.4 Consensus size: 134
1723644 GCAATATGAT
* * * * * *
1723654 GAGGGATCTGTTCCGCATCTTCTTGAACGAAA-ATCATATATGGGGGAGGTTGATCCATTATACT
1 GAGGGATTTGTTCCGCTTCTTC-TGGAGGAAATATCATATATAGGGGA-GTTGATCCATTCTACT
* * *
1723718 GTCACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
64 GTCACTCAGAGAAGATTGAATCGAGGTAGACTTGTTCAACTGTCACTCAGGGAATATAAAATCTT
*
1723783 TAAAGA
129 GAAAGA
* *
1723789 GAGGGATTTGTTCCACTTCTTCTGGAGGAAATATCATATATAGGGGAGTTGATCCATTCTATTGT
1 GAGGGATTTGTTCCGCTTCTTCTGGAGGAAATATCATATATAGGGGAGTTGATCCATTCTACTGT
*
1723854 CACTCA-AGAAGATTGAATCGAGGTATACTTGTTCAACTGTCACTCAGGGAATATAAAATCTTGA
66 CACTCAGAGAAGATTGAATCGAGGTAGACTTGTTCAACTGTCACTCAGGGAATATAAAATCTTGA
1723918 AAGA
131 AAGA
* * * * * * *
1723922 TAGGGATTTGTTCCGCTTCTTCAGGAGGGAATATCAGATCTAGGGAAGTTGATTCATTC
1 GAGGGATTTGTTCCGCTTCTTCTGGAGGAAATATCATATATAGGGGAGTTGATCCATTC
1723981 CAGTTACTCA
Statistics
Matches: 170, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
133 108 0.64
134 29 0.17
135 33 0.19
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (134 bp):
GAGGGATTTGTTCCGCTTCTTCTGGAGGAAATATCATATATAGGGGAGTTGATCCATTCTACTGT
CACTCAGAGAAGATTGAATCGAGGTAGACTTGTTCAACTGTCACTCAGGGAATATAAAATCTTGA
AAGA
Found at i:1724741 original size:233 final size:233
Alignment explanation
Indices: 1724289--1726051 Score: 2040
Period size: 233 Copynumber: 7.6 Consensus size: 233
1724279 CATGCGAAAA
* * * *
1724289 CATCATGCCCGAAGGACTTA-TGGATGGCCTGAAGGACTTACCAAA-TTT-GAGAATAGTTTACT
1 CATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTA-TAAATTTTGGA-AATAGTTTACT
* * *
1724351 AGGTAAGAAA-TTTTCTTACTTTAAAAAAAA-TCAA-TTTACATATTTTAATGAGAAACCTTTCT
63 AGGTAAGAAACCTTTCTTACTTTAAAAAAAATTCAATTTTA-AGATTTAAATGAGAAACCTTTCT
* * * * * *
1724413 CATTTTTTTGAGAGACACGTGAAAAAAAATCCTTCCCAAAGGTCTTATAGATGACCCGAAGGACT
127 CA-TTTTTTGAGAGACATGTG--AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACT
* * *
1724478 TATCATCTTGCTCGAAAGACTTATAGATGACCTGGAGGATTTAAG
189 TATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* ** * * *
1724523 CATCATACTCGGGAGACTTCCCGATGGCCCGAAGGACTTA-ACCAACTTTGGAAATAGTTTACTA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA--AATTTTGGAAATAGTTTACTA
*
1724587 GGTAAGAAACCTTTCTTACTTTAAAAAAAATT-AATTTTAAGATTTAAATGAGAAATCTTTCTCA
64 GGTAAGAAACCTTTCTTACTTTAAAAAAAATTCAATTTTAAGATTTAAATGAGAAACCTTTCTCA
* * * * * *
1724651 CTTTTTGAGATACATGTGAAAACATCCTACCCGAATGTCTTATGGATGACACGAAGGACTTATTA
129 TTTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
1724716 TCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
194 TCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* * * *
1724756 TATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACCTATAAAATTTGGAAATAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* * *
1724821 TAAGAAACCTTTCTTACTTTTTTTAATAAAAATTTCAATTTTCAGATTTAAATGAAAAACCTTTC
66 TAAGAAACCTTTCTTAC----TTTAA-AAAAAATTCAATTTTAAGATTTAAATGAGAAACCTTTC
* * * * *
1724886 ACATTTTCTGAGAGAGATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAATGACTTA
126 TCATTTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
* * * *
1724951 TCATCTTGCTCAAAATACTTATAGAGATGACACGAAGGATTTAAG
191 TCATCTTGCTCGAAAGAC-T-TACAGATGACCCGAAGGATTTAAG
* * * * * *
1724996 TATCATGCTTGAAAGACTTACTGATGGTCCAAATGACTTATAAAATTTGGAAATAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* * *
1725061 TAAGAAACC-TTCTTACTTTTCAAAAAAATTCAATTTTCATATTTAAATGAGAAACCTTTCTCAT
66 TAAGAAACCTTTCTTAC-TTTAAAAAAAATTCAATTTTAAGATTTAAATGAGAAACCTTTCTCAT
* * ** * * *
1725125 TTTTTTAGAGACATGTGAAATCATCCTGTCCAAAGGACTTATGGATGGCCCAAAGGACTTATCAT
130 TTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
* *
1725190 CTTGATTGAAAGACTTACAGATGACCCGAAGGATTTAAG
195 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* * *
1725229 CAT-ATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTATAAATTTTGAAAAGAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* * ** * * * * *
1725293 TGAGAAACCTTTCTTAATTTTCCAAAAACTTCAATTTTCAGATTTAAATGAGAAAACTTACACAT
66 TAAGAAACCTTTCTT-ACTTTAAAAAAAATTCAATTTTAAGATTTAAATGAGAAACCTTTCTCAT
* * * * * *
1725358 TTTCTGAGAAAGATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGTCCGAAGAACTTATCAT
130 TTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
1725423 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
195 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* * * ** * * *
1725462 CATCATGCTCGAATGACTTAATCATGGCATGTAGGAGTTATAAATTTTGGAAATAGTTTACTAAG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* ** *
1725527 TAAGAAACCTTTCTCACTTT---CCAAA---AATTTTAA-ATTT-AATCGAGGAACCTTTCTCAT
66 TAAGAAACCTTTCTTACTTTAAAAAAAATTCAATTTTAAGATTTAAAT-GAGAAACCTTTCTCAT
** * * * *
1725584 TTTTTGAGTCACTTGTGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGAACTTATAAT
130 TTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
* *
1725649 CTTGTTCGAAAGACTTATAGATGACCCGAAGGATTTAAG
195 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* * *
1725688 CATCATCCTCGAAAGACTCACTGATGGCCCGAAGGACTTATAAA-TTTGGAAATAGTTTACTTGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* * * *
1725752 TAAGAAATCCTTTCTTACTTTTAAAAAATTTCAATTTTCAA-ATTTAAATGAGAATCCTTTCACA
66 TAAGAAA-CCTTTCTTACTTTAAAAAAAATTCAATTTT-AAGATTTAAATGAGAAACCTTTCTCA
* * * * * * *
1725816 TTTTTCGAGATACATTTGAAAACATCCTACCCTAAGGTCTTATGGATGGGCCGAAGGAGTTATTA
129 TTTTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
* * *
1725881 TCTTGCTCGAAAGATTTACAGATGACCCGAAGGGTTTAAT
194 TCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
* * * * *
1725921 AATCATGCTCGAAAGACTTACTGATGGTCCAAAGGACTTATAAATTTTGGAAATAATTTACTAGT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
* *
1725986 TAAGAAACC-TTCATTACTTT-TAAAAAATTTAAGTTTTAAGATTTAAATGAGAAACCTTTCTCA
66 TAAGAAACCTTTC-TTACTTTAAAAAAAATTCAA-TTTTAAGATTTAAATGAGAAACCTTTCTCA
1726049 TTT
129 TTT
1726052 ATTTAACTTA
Statistics
Matches: 1307, Mismatches: 188, Indels: 69
0.84 0.12 0.04
Matches are distributed among these distances:
225 28 0.02
226 156 0.12
227 7 0.01
229 2 0.00
230 2 0.00
232 121 0.09
233 460 0.35
234 126 0.10
235 142 0.11
236 55 0.04
237 12 0.01
238 96 0.07
239 8 0.01
240 92 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (233 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
TAAGAAACCTTTCTTACTTTAAAAAAAATTCAATTTTAAGATTTAAATGAGAAACCTTTCTCATT
TTTTGAGAGACATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATC
TTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAG
Found at i:1725222 original size:41 final size:40
Alignment explanation
Indices: 1725168--1725268 Score: 103
Period size: 41 Copynumber: 2.5 Consensus size: 40
1725158 AGGACTTATG
* * * *
1725168 GATGGCCCAAAGGACTTATCATCTTGATTGAAAGACTTACA
1 GATGACCCGAAGGACTTATCAT-ATGATCGAAAGACTTACA
* * * *
1725209 GATGACCCGAAGGATTTAAGCATATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATATGATCGAAAGACTTACA
*
1725250 GATGTCCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
1725269 AAATTTTGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.02
41 43 0.90
42 4 0.08
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (40 bp):
GATGACCCGAAGGACTTATCATATGATCGAAAGACTTACA
Found at i:1725799 original size:459 final size:458
Alignment explanation
Indices: 1724289--1726051 Score: 2007
Period size: 459 Copynumber: 3.8 Consensus size: 458
1724279 CATGCGAAAA
* * * *
1724289 CATCATGCCCGAAGGACTTA-TGGATGGCCTGAAGGACTTACCAAATTT-GAGAATAGTTTACTA
1 CATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTA-TAAATTTGGA-AATAGTTTACTA
* * * * * * *
1724352 GGTAAGAAA-TTTTCTTAC-TTTAAAAAAA-ATCAATTTACATATTTTAATGAGAAACCTTTCTC
63 GGTAAGAAACCTTTCTTACTTTTAAAAAAATTTCAATTTTCAGATTTAAATGAGAAAACTTTCAC
* * * * * *
1724414 ATTTTTTTGAGAGACACGTGAAAAAAAATCCTTCCCAAAGGTCTTATAGATGACCCGAAGGACTT
128 A-TTTTCTGAGAGACATGTG--AAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTT
* * * * **
1724479 ATCATCTTGCTCGAAAGACTTATAGATGACCTGGAGGATTTAAGCATCATACTCGGGAGACTT-C
190 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
1724543 CCGATGGCCCGAAGGACTTA-ACCAACTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACT
255 TC-ATGG-CCAAAGGACTTATA--AATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACT
* * *
1724607 TTAAAAAAAATTAATTTTAAGATTTAAATGAGAAATCTTTCTCACTTTTTGAGATACATGTGAAA
316 TT---CAAAA-TAATTTTAA-ATTTAAATGAGAAACCTTTCTCATTTTTTGAG-TACATGTGAAA
* * * * *
1724672 ACATCCTACCCGAATGTCTTATGGATGACACGAAGGACTTATTATCTTGCTCGAAAGACTTACAG
375 ACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATAATCTTGTTCGAAAGACTTACAG
1724737 ATGACCCGAAGGATTTAAG
440 ATGACCCGAAGGATTTAAG
* * *
1724756 TATCATGCTTGAAAGACTTACTGATGGCCCGAAGGACCTATAAAATTTGGAAATAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT-AAATTTGGAAATAGTTTACTAGG
1724821 TAAGAAACCTTTCTTACTTTTTTTAATAAAAATTTCAATTTTCAGATTTAAATGA-AAAACCTTT
65 TAAGAAACCTTTCTTAC---TTTTAA-AAAAATTTCAATTTTCAGATTTAAATGAGAAAA-CTTT
* *
1724885 CACATTTTCTGAGAGAGATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAATGACTT
125 CACATTTTCTGAGAGACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTT
* * * * * *
1724950 ATCATCTTGCTCAAAATACTTATAGAGATGACACGAAGGATTTAAGTATCATGCTTGAAAGACTT
190 ATCATCTTGCTCGAAAGAC-T-TACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTT
* * * *
1725015 ACTGATGGTCCAAATGACTTATAAAATTTGGAAATAGTTTACTAGGTAAGAAACC-TTCTTACTT
253 ACTCATGG-CCAAAGGACTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTAC-T
*
1725079 TTCAAAAAAATTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTTAGAG-ACATGTGA
316 TTC---AAAA-T-AATTTT-AAATTTAAATGAGAAACCTTTCTCA-TTTTTT-GAGTACATGTGA
* ** * * * *
1725143 AATCATCCTGTCCAAAGGACTTATGGATGGCCCAAAGGACTTATCATCTTGATT-GAAAGACTTA
373 AAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATAATCTTG-TTCGAAAGACTTA
1725207 CAGATGACCCGAAGGATTTAAG
437 CAGATGACCCGAAGGATTTAAG
* * *
1725229 CAT-ATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTATAAATTTTGAAAAGAGTTTACTAGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA-TTTGGAAATAGTTTACTAGG
* * ** * *
1725293 TGAGAAACCTTTCTTAATTTTCCAAAAACTTCAATTTTCAGATTTAAATGAGAAAACTTACACAT
65 TAAGAAACCTTTCTTACTTTTAAAAAAATTTCAATTTTCAGATTTAAATGAGAAAACTTTCACAT
* * * * *
1725358 TTTCTGAGAAAGATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGTCCGAAGAACTTATCAT
130 TTTCTGAGAGACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCAT
* *
1725423 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAATGACTTAATCATG
195 CTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTCATG
* * * *
1725488 G-CATGTAGGAGTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTCACTTTCCAAA
260 GCCA--AAGGACTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTCAAAA
* *
1725552 -AATTTTAAATTT-AATCGAGGAACCTTTCTCATTTTTTGAGTCACTTGTGAAAACATCCTACCC
323 TAATTTTAAATTTAAAT-GAGAAACCTTTCTCATTTTTTGAGT-ACATGTGAAAACATCCTACCC
* * *
1725615 GAAGGTCTTATAGATGGCCCGAAGAACTTATAATCTTGTTCGAAAGACTTATAGATGACCCGAAG
386 GAAGGTCTTATGGATGGCCCGAAGGACTTATAATCTTGTTCGAAAGACTTACAGATGACCCGAAG
1725680 GATTTAAG
451 GATTTAAG
* * *
1725688 CATCATCCTCGAAAGACTCACTGATGGCCCGAAGGACTTATAAATTTGGAAATAGTTTACTTGGT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTGGAAATAGTTTACTAGGT
* **
1725753 AAGAAATCCTTTCTTACTTTT-AAAAAATTTCAATTTTCAAATTTAAATGAGAATCCTTTCACAT
66 AAGAAA-CCTTTCTTACTTTTAAAAAAATTTCAATTTTCAGATTTAAATGAGAAAACTTTCACAT
* * * * * * *
1725817 TTT-TCGAGATACATTTGAAAACATCCTACCCTAAGGTCTTATGGATGGGCCGAAGGAGTTATTA
130 TTTCT-GAGAGACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
* * ** *
1725881 TCTTGCTCGAAAGATTTACAGATGACCCGAAGGGTTTAATAATCATGCTCGAAAGACTTACTGAT
194 TCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTCAT
* *
1725946 GGTCCAAAGGACTTATAAATTTTGGAAATAATTTACT-AGTTAAGAAACC-TTCATTACTTTTAA
259 GG-CCAAAGGACTTATAAATTTTGGAAATAGTTTACTAAG-TAAGAAACCTTTC-TTAC-TTT-C
1726009 AAAATTTAAGTTTTAAGATTTAAATGAGAAACCTTTCTCATTT
319 AAAA--TAA-TTTTAA-ATTTAAATGAGAAACCTTTCTCATTT
1726052 ATTTAACTTA
Statistics
Matches: 1111, Mismatches: 137, Indels: 97
0.83 0.10 0.07
Matches are distributed among these distances:
457 3 0.00
458 17 0.02
459 315 0.28
460 59 0.05
461 5 0.00
463 3 0.00
464 4 0.00
465 6 0.01
466 107 0.10
467 69 0.06
468 118 0.11
469 8 0.01
471 65 0.06
472 113 0.10
473 182 0.16
474 34 0.03
475 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (458 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTGGAAATAGTTTACTAGGT
AAGAAACCTTTCTTACTTTTAAAAAAATTTCAATTTTCAGATTTAAATGAGAAAACTTTCACATT
TTCTGAGAGACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATC
TTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTCATGG
CCAAAGGACTTATAAATTTTGGAAATAGTTTACTAAGTAAGAAACCTTTCTTACTTTCAAAATAA
TTTTAAATTTAAATGAGAAACCTTTCTCATTTTTTGAGTACATGTGAAAACATCCTACCCGAAGG
TCTTATGGATGGCCCGAAGGACTTATAATCTTGTTCGAAAGACTTACAGATGACCCGAAGGATTT
AAG
Found at i:1727892 original size:3 final size:3
Alignment explanation
Indices: 1727884--1727987 Score: 187
Period size: 3 Copynumber: 35.7 Consensus size: 3
1727874 TGTATAATCT
1727884 ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1727931 ATA ATA ATA AT- ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1727977 ATA ATA ATA AT
1 ATA ATA ATA AT
1727988 TTATTAACCT
Statistics
Matches: 98, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 6 0.06
3 92 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1731665 original size:19 final size:20
Alignment explanation
Indices: 1731643--1731680 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1731633 AGTTTTCTTG
*
1731643 ATCATG-AAACCTTTTGTCC
1 ATCATGAAAAACTTTTGTCC
1731662 ATCATGAAAAACTTTTGTC
1 ATCATGAAAAACTTTTGTC
1731681 ATGAACATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
ATCATGAAAAACTTTTGTCC
Found at i:1734682 original size:2 final size:2
Alignment explanation
Indices: 1734675--1734713 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1734665 TAATAAAGGA
1734675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1734714 GCATGTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1735362 original size:9 final size:9
Alignment explanation
Indices: 1735343--1735377 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1735333 GAGTTCAAAT
1735343 AAAAAGAAA
1 AAAAAGAAA
1735352 AAAATAGAAA
1 AAAA-AGAAA
*
1735362 AAAAAGAAG
1 AAAAAGAAA
1735371 AAAAAGA
1 AAAAAGA
1735378 GAATTTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1735367 original size:19 final size:20
Alignment explanation
Indices: 1735343--1735380 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1735333 GAGTTCAAAT
*
1735343 AAAAAGAA-AAAAATAGAAA
1 AAAAAGAAGAAAAAGAGAAA
1735362 AAAAAGAAGAAAAAGAGAA
1 AAAAAGAAGAAAAAGAGAA
1735381 TTTCAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAAAGAAGAAAAAGAGAAA
Found at i:1743414 original size:2 final size:2
Alignment explanation
Indices: 1743407--1743437 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1743397 ATTCTTCAAT
1743407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1743438 TAAACACGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1744234 original size:55 final size:54
Alignment explanation
Indices: 1744041--1744553 Score: 482
Period size: 55 Copynumber: 9.4 Consensus size: 54
1744031 GAATTACATA
* * ** * * * ** *
1744041 GGTTGCACATATAGTTCCAATATGGTAATTCACAAACTCATTGTGAATTACGTA
1 GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
* * * * *
1744095 GGTTGCACACATAGTGCAAATACAGTAATTCAAAAACTCATTATGAATTACT-TA
1 GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATT-TTGTG
* *
1744149 GGTTGCGCACATAGTACCAATAC-GAAAATTCATAAACTCATTATGAATTTTGTG
1 GGTTGCACACATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTTGTG
*
1744203 GTGTTACACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
1 G-GTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
* *
1744258 AGGTTG-A-ACATAGTGCCCATAC-GAAAATTCATAAAATCATTATGAA-TTTGTG
1 -GGTTGCACACATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTTGTG
* * * * *
1744310 ACGTTGCACACATAGTGCTAATACATAAATCCATAAACTCATTAT-AAATTTGTTG
1 -GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTG-TG
* * * *
1744365 AGGTTGGACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTTA
1 -GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTG-TG
* * * * * * *
1744421 GGTTTCATACATAGAGCCAATACGGAAATTAATAAACTCATTATAAATTTCGTG
1 GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
** * **
1744475 ATATTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCATG
1 -GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
* * *
1744530 AGATTGCACACACAGTGTCAATAC
1 -GGTTGCACACATAGTGCCAATAC
1744554 GGAAGTTGCA
Statistics
Matches: 387, Mismatches: 58, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
52 12 0.03
53 40 0.10
54 124 0.32
55 202 0.52
56 9 0.02
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (54 bp):
GGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
Found at i:1744378 original size:162 final size:160
Alignment explanation
Indices: 1744040--1744553 Score: 541
Period size: 162 Copynumber: 3.1 Consensus size: 160
1744030 TGAATTACAT
* * ** * * * *
1744040 AGGTTGCACATATAGTTCCAATATGGTAATTCACAAACTCATTGTGAATTACGTAGGTTGCACAC
1 AGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTAGGTTG-ACAC
* * ** * * * *
1744105 ATAGTGCAAATAC-AGTAATTCA-AAAACTCATTATGAATTACTTAGGTTGCGCACATAGTACCA
65 ATAGTGCCAATACGA-AAATTCATAAAA-TCATTATGAATTTGTGACGTTGCACACATAGTGCCA
1744168 ATACGAAAATTCATAAACTCATTATGAATTTTGTG
128 ATAC-AAAATTCATAAACTCATTATGAATTTT-TG
* *
1744203 -GTGTTACACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTGAGGTTGA-A
1 AG-GTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGT-AGGTTGACA
* *
1744266 CATAGTGCCCATACGAAAATTCATAAAATCATTATGAATTTGTGACGTTGCACACATAGTGCTAA
64 CATAGTGCCAATACGAAAATTCATAAAATCATTATGAATTTGTGACGTTGCACACATAGTGCCAA
* *
1744331 TACATAAATCCATAAACTCATTATAAATTTGTTG
129 TACA-AAATTCATAAACTCATTATGAATTT-TTG
* * * *
1744365 AGGTTGGACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTTAGGTTTCATA
1 AGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCG-TAGG-TTGACA
* * * * * **
1744430 CATAGAGCCAATACGGAAATTAATAAACTCATTATAAATTTCGTGATATTGCACACATAGTGCCA
64 CATAGTGCCAATACGAAAATTCATAAAATCATTATGAATTT-GTGACGTTGCACACATAGTGCCA
*
1744495 ATACAAAAATTCATAAACTCATTATGAATTTCATG
128 ATAC-AAAATTCATAAACTCATTATGAATTT-TTG
* * *
1744530 AGATTGCACACACAGTGTCAATAC
1 AGGTTGCACACATAGTGCCAATAC
1744554 GGAAGTTGCA
Statistics
Matches: 295, Mismatches: 44, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
161 1 0.00
162 128 0.43
163 54 0.18
164 42 0.14
165 69 0.23
166 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (160 bp):
AGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTAGGTTGACACA
TAGTGCCAATACGAAAATTCATAAAATCATTATGAATTTGTGACGTTGCACACATAGTGCCAATA
CAAAATTCATAAACTCATTATGAATTTTTG
Found at i:1744557 original size:110 final size:109
Alignment explanation
Indices: 1744040--1744553 Score: 549
Period size: 110 Copynumber: 4.7 Consensus size: 109
1744030 TGAATTACAT
* * **** * * *
1744040 AGGTTGCACATATAGTTCCAATATGGTAATTCACAAACTCATTGTGAATTACGT-AGGTTGCACA
1 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACA
* * * *
1744104 CATAGTGCAAATACAGTAATTCAA-AAACTCATTATGAATTAC-TT
66 CATAGTGC-AATACAGAAATT-AATAAACTCATTATAAATTTCGTG
* * * * *
1744148 AGGTTGCGCACATAGTACCAATACGAAAATTCATAAACTCATTATGAATTTTGTG-GTGTTACAC
1 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAG-GTTGCAC
* * *
1744212 ACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTTGTG
65 ACATAGTG-CAATACAGAAATTAATAAACTCATTATAAATTTCGTG
* * * *
1744258 AGGTTG-A-ACATAGTGCCCATACGAAAATTCATAAAATCATTATGAATTT-GTGACGTTGCACA
1 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACA
* **
1744320 CATAGTGCTAATACATAAATCCATAAACTCATTATAAATTT-GTTG
66 CATAGTGC-AATACAGAAATTAATAAACTCATTATAAATTTCG-TG
* * * *
1744365 AGGTTGGACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTTAGGTTTCATA
1 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACA
* *
1744430 CATAGAGCCAATACGGAAATTAATAAACTCATTATAAATTTCGTG
66 CATAGTG-CAATACAGAAATTAATAAACTCATTATAAATTTCGTG
** * *
1744475 ATATTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCATGAGATTGCACA
1 AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACA
*
1744540 CACAGTGTCAATAC
66 CATAGTG-CAATAC
1744554 GGAAGTTGCA
Statistics
Matches: 345, Mismatches: 48, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
106 2 0.01
107 54 0.16
108 86 0.25
109 80 0.23
110 121 0.35
111 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (109 bp):
AGGTTGCACACATAGTGCCAATACAAAAATTCATAAACTCATTATGAATTTCGTGAGGTTGCACA
CATAGTGCAATACAGAAATTAATAAACTCATTATAAATTTCGTG
Found at i:1749978 original size:4 final size:4
Alignment explanation
Indices: 1749964--1750044 Score: 51
Period size: 4 Copynumber: 20.2 Consensus size: 4
1749954 AATTACTTTA
* * ** *
1749964 ATTT A-TT ATTT ATTT ATTTT ATCCTT ATAT -TTT ATTT ATAT CCTT ATCT
1 ATTT ATTT ATTT ATTT A-TTT AT--TT ATTT ATTT ATTT ATTT ATTT ATTT
* *
1750013 -TTT ACTT AATT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1750045 ATCTTTATCT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
3 7 0.12
4 43 0.74
5 4 0.07
6 4 0.07
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:1750005 original size:19 final size:18
Alignment explanation
Indices: 1749976--1750016 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1749966 TTATTATTTA
1749976 TTTATTTTATCCTTATAT
1 TTTATTTTATCCTTATAT
*
1749994 TTTATTTATATCCTTATCT
1 TTTATTT-TATCCTTATAT
1750013 TTTA
1 TTTA
1750017 CTTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATTTTATCCTTATAT
Found at i:1750063 original size:19 final size:19
Alignment explanation
Indices: 1749944--1750064 Score: 50
Period size: 19 Copynumber: 6.0 Consensus size: 19
1749934 TATAAATTTC
*
1749944 TCTTTATCTTAATTACTTTAA
1 TCTTTATCTT--TTATTTTAA
* *
1749965 TTTATTATTTATTTATTTT-A
1 TCT-TTATCT-TTTATTTTAA
* *
1749985 TCCTTATATTTTA-TTTATA
1 TCTTTATCTTTTATTTTA-A
* *
1750004 TCCTTATCTTTTA-CTTAA
1 TCTTTATCTTTTATTTTAA
* *
1750022 TTATTTATTTATTTATTTATTTAA
1 -TCTTTATCT-TTTA--T-TTTAA
1750046 TCTTTATCTTTTATTTTAA
1 TCTTTATCTTTTATTTTAA
1750065 AAATAATTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
17 3 0.04
18 5 0.07
19 32 0.42
20 7 0.09
21 8 0.11
22 9 0.12
23 8 0.11
24 4 0.05
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTTTATCTTTTATTTTAA
Found at i:1770946 original size:19 final size:19
Alignment explanation
Indices: 1770922--1770964 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1770912 TCCAGCTCAC
*
1770922 AACACCTCCAATAAGACAA
1 AACACCTCCAATAAGAAAA
*
1770941 AACACCTCTAATAAGAAAA
1 AACACCTCCAATAAGAAAA
1770960 AACAC
1 AACAC
1770965 AAACACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.28, G:0.05, T:0.12
Consensus pattern (19 bp):
AACACCTCCAATAAGAAAA
Found at i:1775598 original size:13 final size:13
Alignment explanation
Indices: 1775580--1775606 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1775570 TTGTTCCACT
1775580 TCCAAACGCGATA
1 TCCAAACGCGATA
1775593 TCCAAACGCGATA
1 TCCAAACGCGATA
1775606 T
1 T
1775607 GCTATCGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.19
Consensus pattern (13 bp):
TCCAAACGCGATA
Found at i:1776289 original size:90 final size:89
Alignment explanation
Indices: 1776132--1776303 Score: 290
Period size: 90 Copynumber: 1.9 Consensus size: 89
1776122 CCTAACACAC
*
1776132 CCTTTTATAACCAAGGTACCCTAATCATAGTAGGGTTTTATTATTTTAAATTAATTAAATCTATA
1 CCTTTTATAACCAAGGTACCCTAATCATAGTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
*
1776197 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTTAATAAT
* * *
1776221 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAACCAAGGTACCCTAATCATAGTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
1776286 ATTTAATTAATTGAAATT
65 ATTTAATTAATTGAAATT
1776304 ACATATTTGG
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 32 0.42
90 45 0.58
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (89 bp):
CCTTTTATAACCAAGGTACCCTAATCATAGTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTTAATAAT
Found at i:1793441 original size:28 final size:29
Alignment explanation
Indices: 1793409--1793465 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1793399 CTAAAAATCC
* *
1793409 TATGTT-TATTCAATCCCCCACTTTTTGG
1 TATGTTATATACAATCCCCAACTTTTTGG
1793437 TATGTTATATACAATCCCCAACTTTTTGG
1 TATGTTATATACAATCCCCAACTTTTTGG
1793466 CCGGTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (29 bp):
TATGTTATATACAATCCCCAACTTTTTGG
Found at i:1793472 original size:29 final size:29
Alignment explanation
Indices: 1793419--1793475 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1793409 TATGTTTATT
* * *
1793419 CAATCCCCCACTTTTTGGTATGTTATATA
1 CAATCCCCAACTTTTTGGCAGGTTATATA
*
1793448 CAATCCCCAACTTTTTGGCCGGTTATAT
1 CAATCCCCAACTTTTTGGCAGGTTATAT
1793476 CCTAACCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (29 bp):
CAATCCCCAACTTTTTGGCAGGTTATATA
Found at i:1798164 original size:64 final size:62
Alignment explanation
Indices: 1798041--1798183 Score: 148
Period size: 64 Copynumber: 2.3 Consensus size: 62
1798031 TCTTTAACAT
* * *
1798041 GTGCATCGATGCACTATCCATGCATCGATGCACCAATCACCTTCGATCTTTTCGTTTTAAGGGG
1 GTGCATCGATGCAC-ATCCATGCATCGATGCACCAATCACATTCGATCTTTTCGTTTTAA-AGA
** *
1798105 GTGCATCGATGCAC-TCCTTATGCATCGATGCACCAATTGCATTCG-T-TGTTTCTTCTTTAAAG
1 GTGCATCGATGCACATCC--ATGCATCGATGCACCAATCACATTCGATCT-TTTCGT-TTTAAAG
1798167 A
62 A
*
1798168 GTGCATCGATACACAT
1 GTGCATCGATGCACAT
1798184 TAAATTTGCA
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
62 4 0.06
63 20 0.30
64 43 0.64
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACATCCATGCATCGATGCACCAATCACATTCGATCTTTTCGTTTTAAAGA
Found at i:1801479 original size:23 final size:23
Alignment explanation
Indices: 1801453--1801551 Score: 78
Period size: 23 Copynumber: 4.3 Consensus size: 23
1801443 CACCACAGCT
*
1801453 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* **
1801476 CGTAGAATTGCACCGAAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1801499 CGTAGAATTACACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1801522 TGTA-AAATGTC-CCTAAG-GACCA
1 CGTAGAAATG-CACCGAAGTG-CCA
1801544 CGTAGAAA
1 CGTAGAAA
1801552 ATTCCTTAAG
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
21 1 0.02
22 13 0.22
23 45 0.76
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1806455 original size:23 final size:23
Alignment explanation
Indices: 1806429--1806488 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1806419 TCGTATAAAA
*
1806429 GCACCAAAGTGCCACGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
*
1806452 GCACCGAAGTGCCGCGTAGAATT
1 GCACCGAAGTGCCACGTAGAATT
*
1806475 GCACTGAAGTGCCA
1 GCACCGAAGTGCCA
1806489 TAGAAAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (23 bp):
GCACCGAAGTGCCACGTAGAATT
Found at i:1808168 original size:17 final size:19
Alignment explanation
Indices: 1808129--1808175 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1808119 TTTAAGGGGG
**
1808129 TGCATCGATGCACACCTTA
1 TGCATCGATGCACACAATA
1808148 TGCATCGATGCAC-CAAT-
1 TGCATCGATGCACACAATA
1808165 TGCATTCGATG
1 TGCA-TCGATG
1808176 TTTCTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 8 0.32
19 13 0.52
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACACAATA
Found at i:1808187 original size:64 final size:62
Alignment explanation
Indices: 1808064--1808205 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 62
1808054 TCTTTAACAT
* * * *
1808064 GTGCATTGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCAC-ACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* * ** *
1808128 GTGCATCGATGCACACCTTATGCATCGATGCACCAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACACC-CATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
*
1808191 GTGCATCGATACACA
1 GTGCATCGATGCACA
1808206 TTGAATGTGC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
63 23 0.35
64 43 0.65
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCACACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:1811551 original size:23 final size:23
Alignment explanation
Indices: 1811525--1811585 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1811515 CTCGTATAAA
1811525 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1811548 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
**
1811571 TATACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1811586 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1813167 original size:20 final size:23
Alignment explanation
Indices: 1813142--1813195 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
1813132 CTTTGAAGTA
1813142 CATCGATACATTC-T-ACA-GTG
1 CATCGATACATTCTTAACATGTG
*
1813162 CATCGATGCATTCTTTAACATGTG
1 CATCGATACATTC-TTAACATGTG
1813186 CATCGATACA
1 CATCGATACA
1813196 CAAATCACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
22 1 0.04
23 3 0.11
24 12 0.43
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (23 bp):
CATCGATACATTCTTAACATGTG
Found at i:1816644 original size:23 final size:23
Alignment explanation
Indices: 1816629--1816686 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1816619 GTATAAATGT
1816629 ACCGAAGTGCCACGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
1816652 ACCGAAGTGCCGCGTAGAATTGC
1 ACCGAAGTGCCACGTAGAATTGC
*
1816675 ATCGAAGTGCCA
1 ACCGAAGTGCCA
1816687 TATAAAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
ACCGAAGTGCCACGTAGAATTGC
Found at i:1818277 original size:20 final size:22
Alignment explanation
Indices: 1818241--1818298 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
1818231 TCCCCTTTGA
**
1818241 AGTGCATCGATATATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1818261 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1818284 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1818299 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1818398 original size:64 final size:63
Alignment explanation
Indices: 1818286--1818426 Score: 144
Period size: 64 Copynumber: 2.2 Consensus size: 63
1818276 TCTTTAACAT
* * * *
1818286 GTGCATCGATGCACTACCCATGCATCGATATACCAATCACCTTGGATGT-T-TTCATTTTAAGGT
1 GTGCATCGATGCACTACCCATGCATCAATATACCAATCACATTCGATGTCTCTTC--TTTAAAG-
1818349 G
63 G
* * ***
1818350 GTGCATCGATGCACT-CCTTATGCATCAATGTACCAATTGTATTCGATGTCTCTTCTTTAAAGG
1 GTGCATCGATGCACTACC-CATGCATCAATATACCAATCACATTCGATGTCTCTTCTTTAAAGG
1818413 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1818427 CAATTGCATT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
63 17 0.26
64 44 0.68
65 1 0.02
66 3 0.05
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCAATATACCAATCACATTCGATGTCTCTTCTTTAAAGG
Found at i:1818442 original size:44 final size:44
Alignment explanation
Indices: 1818370--1818466 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
1818360 GCACTCCTTA
* * * **
1818370 TGCATCAATGTACCAATTGTATTCGATGTCTCTTCTTTAAAGGG
1 TGCATCGATGCACCAATTGCATTCGATGTCTCTTCTTTAAAGAC
* *
1818414 TGCATCGATGCACCAATTGCATTTGATGTTTCTTCTTTAAAGAC
1 TGCATCGATGCACCAATTGCATTCGATGTCTCTTCTTTAAAGAC
1818458 TGCATCGAT
1 TGCATCGAT
1818467 ACACATTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (44 bp):
TGCATCGATGCACCAATTGCATTCGATGTCTCTTCTTTAAAGAC
Found at i:1819711 original size:17 final size:17
Alignment explanation
Indices: 1819689--1819721 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1819679 AGAAATGGTG
1819689 AAAAAGAAAGAAAAAAT
1 AAAAAGAAAGAAAAAAT
*
1819706 AAAAAGAATGAAAAAA
1 AAAAAGAAAGAAAAAA
1819722 GAAGTTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAT
Found at i:1819755 original size:5 final size:5
Alignment explanation
Indices: 1819739--1819768 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1819729 ATGTTTATAT
1819739 TTTTA GTTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT
1819769 TGGAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1821442 original size:18 final size:18
Alignment explanation
Indices: 1821421--1821518 Score: 87
Period size: 18 Copynumber: 5.5 Consensus size: 18
1821411 TAATTAATTA
*
1821421 TTTATTTTATCCTGATCT
1 TTTATTTTATCCTTATCT
1821439 TTTATTTTTATCCTTATCT
1 TTTA-TTTTATCCTTATCT
*
1821458 TTTA--TT-TCATTAT-T
1 TTTATTTTATCCTTATCT
*
1821472 TATATATTTTATCTTTATCT
1 T-T-TATTTTATCCTTATCT
* * *
1821492 TTTATTTTATTCTAATAT
1 TTTATTTTATCCTTATCT
1821510 TTTATTTTA
1 TTTATTTTA
1821519 AAACCAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.03
15 7 0.11
16 4 0.06
18 27 0.41
19 24 0.36
20 2 0.03
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTATTTTATCCTTATCT
Found at i:1821449 original size:19 final size:19
Alignment explanation
Indices: 1821421--1821464 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1821411 TAATTAATTA
1821421 TTTA-TTTTATCCTGATCT
1 TTTATTTTTATCCTGATCT
*
1821439 TTTATTTTTATCCTTATCT
1 TTTATTTTTATCCTGATCT
1821458 TTTATTT
1 TTTATTT
1821465 CATTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATTTTTATCCTGATCT
Found at i:1821474 original size:19 final size:18
Alignment explanation
Indices: 1821421--1821517 Score: 62
Period size: 19 Copynumber: 5.4 Consensus size: 18
1821411 TAATTAATTA
*
1821421 TTTA-TTTTATCCTGATCT
1 TTTATTTTTAT-CTTATCT
1821439 TTTATTTTTATCCTTATCT
1 TTTATTTTTAT-CTTATCT
*
1821458 TTTA-TTTCA--TTAT-T
1 TTTATTTTTATCTTATCT
*
1821472 TATATATTTTATCTTTATCT
1 TTTAT-TTTTATC-TTATCT
* *
1821492 TTTA-TTTTATTCTAATAT
1 TTTATTTTTA-TCTTATCT
1821510 TTTATTTT
1 TTTATTTT
1821518 AAAACCAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 4 0.06
15 4 0.06
16 4 0.06
18 21 0.33
19 26 0.41
20 4 0.06
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTATTTTTATCTTATCT
Found at i:1821484 original size:53 final size:52
Alignment explanation
Indices: 1821413--1821516 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
1821403 TTTAAGTTTA
* * *
1821413 ATTAATTATTTATTTTATCCTGATCTTTTATTTTTATCCTTATCTTTTATTTC
1 ATTAATTATATATTTTATCCTGATCTTTTA-TTTTATCCTAATATTTTATTTC
* * * *
1821466 ATTATTTATATATTTTATCTTTATCTTTTATTTTATTCTAATATTTTATTT
1 ATTAATTATATATTTTATCCTGATCTTTTATTTTATCCTAATATTTTATTT
1821517 TAAAACCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 18 0.41
53 26 0.59
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (52 bp):
ATTAATTATATATTTTATCCTGATCTTTTATTTTATCCTAATATTTTATTTC
Found at i:1822753 original size:15 final size:15
Alignment explanation
Indices: 1822733--1822765 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1822723 CGATGTCCGA
1822733 TTGAATATGAATGTC
1 TTGAATATGAATGTC
1822748 TTGAATATGAATGTC
1 TTGAATATGAATGTC
1822763 TTG
1 TTG
1822766 TGTTATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (15 bp):
TTGAATATGAATGTC
Found at i:1823210 original size:17 final size:17
Alignment explanation
Indices: 1823168--1823212 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1823158 AAATAACTCG
*
1823168 ATTCATAAATGAACTAC
1 ATTCATAAATGAAATAC
*
1823185 -TTCCCTAAATGAAATAC
1 ATT-CATAAATGAAATAC
1823202 ATTCATAAATG
1 ATTCATAAATG
1823213 CAATGCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (17 bp):
ATTCATAAATGAAATAC
Found at i:1825118 original size:24 final size:26
Alignment explanation
Indices: 1825091--1825147 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
1825081 ATATATATAT
*
1825091 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
1825115 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
1825139 ATATATATA
1 ATA-ATATA
1825148 TACCCGGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 4 0.15
23 2 0.07
24 18 0.67
25 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:1825133 original size:19 final size:19
Alignment explanation
Indices: 1825109--1825148 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1825099 AATAAATTTA
1825109 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
1825128 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
1825147 AT
1 AT
1825149 ACCCGGCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:1825191 original size:12 final size:12
Alignment explanation
Indices: 1825147--1825212 Score: 89
Period size: 12 Copynumber: 5.6 Consensus size: 12
1825137 AAATATATAT
*
1825147 ATACCCGGCCCG
1 ATACCCGGCCCA
*
1825159 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
1825171 ATA-CCGACCCA
1 ATACCCGGCCCA
*
1825182 ATACCCGACCCA
1 ATACCCGGCCCA
1825194 ATACCCGGCCCA
1 ATACCCGGCCCA
1825206 ATACCCG
1 ATACCCG
1825213 TTTAAATAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:1825210 original size:24 final size:24
Alignment explanation
Indices: 1825147--1825212 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
1825137 AAATATATAT
* * *
1825147 ATACCCGGCCCGATTCCCGGCCCA
1 ATACCCGGCCCAATACCCGACCCA
*
1825171 ATA-CCGACCCAATACCCGACCCA
1 ATACCCGGCCCAATACCCGACCCA
1825194 ATACCCGGCCCAATACCCG
1 ATACCCGGCCCAATACCCG
1825213 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (24 bp):
ATACCCGGCCCAATACCCGACCCA
Done.