Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 6 of 74
Found at i:1475749 original size:54 final size:52
Alignment explanation
Indices: 1475645--1475749 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 52
1475635 ACAACAACAG
*
1475645 TAATTATAATCACAATGTGAAGTATAGTGTAGTACATACCAAATTCATATAA
1 TAATTATAATCACAATGTGAAGTATAGTGTAGTACATACCAAAATCATATAA
*
1475697 TAATATATAATCACAATGTGAAAGTATAGTGTAGTAGATACCAATAAT-ATATA
1 TAAT-TATAATCACAATGTG-AAGTATAGTGTAGTACATACCAA-AATCATATA
1475750 TTGCATGAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
52 4 0.08
53 15 0.31
54 27 0.56
55 2 0.04
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (52 bp):
TAATTATAATCACAATGTGAAGTATAGTGTAGTACATACCAAAATCATATAA
Found at i:1478256 original size:36 final size:36
Alignment explanation
Indices: 1478209--1478282 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1478199 CAATTTGTAC
1478209 TTAAATTGTATTACCCAATAAGGATCTTTATGGAAT
1 TTAAATTGTATTACCCAATAAGGATCTTTATGGAAT
1478245 TTAAATTGTATTACCCAATAAGGATCTTTATGGAAT
1 TTAAATTGTATTACCCAATAAGGATCTTTATGGAAT
1478281 TT
1 TT
1478283 CAATGTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (36 bp):
TTAAATTGTATTACCCAATAAGGATCTTTATGGAAT
Found at i:1482770 original size:22 final size:21
Alignment explanation
Indices: 1482731--1482813 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
1482721 TTAAAAAAAT
1482731 TATAACATGTAATAATCATATAC
1 TATAACATG--ATAATCATATAC
1482754 TCATAACATGATAATCACGTA-AC
1 T-ATAACATGATAATCA--TATAC
* *
1482777 TGTAACGT-ATAATCATATAAC
1 TATAACATGATAATCATAT-AC
1482798 TATAACATGATAATCA
1 TATAACATGATAATCA
1482814 CATGTCATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.04
21 15 0.30
22 19 0.38
23 4 0.08
24 10 0.20
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (21 bp):
TATAACATGATAATCATATAC
Found at i:1482790 original size:21 final size:22
Alignment explanation
Indices: 1482731--1482816 Score: 86
Period size: 21 Copynumber: 3.9 Consensus size: 22
1482721 TTAAAAAAAT
*
1482731 TATAACATG-TAATAATCATATAC
1 TATAACATGATAATCA-CATA-AC
*
1482754 TCATAACATGATAATCACGTAAC
1 T-ATAACATGATAATCACATAAC
* * *
1482777 TGTAACGT-ATAATCATATAAC
1 TATAACATGATAATCACATAAC
1482798 TATAACATGATAATCACAT
1 TATAACATGATAATCACAT
1482817 GTCATTCATC
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
21 17 0.33
22 14 0.27
23 4 0.08
24 11 0.22
25 5 0.10
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (22 bp):
TATAACATGATAATCACATAAC
Found at i:1494444 original size:6 final size:6
Alignment explanation
Indices: 1494417--1494475 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
1494407 ATCCTCTAAC
* * * * *
1494417 TCCTCT TCCTCAA T-CTCT TCTTCC TCTTCT TCCTCT TCTTCT TCCTCT
1 TCCTCT TCCTC-T TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
1494465 TCCTCT TCCTC
1 TCCTCT TCCTC
1494476 CAAATCACCC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (6 bp):
TCCTCT
Found at i:1494445 original size:9 final size:9
Alignment explanation
Indices: 1494431--1494472 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
1494421 CTTCCTCAAT
1494431 CTCTTCTTC
1 CTCTTCTTC
1494440 CTCTTCTTC
1 CTCTTCTTC
1494449 CTCTTCTTC
1 CTCTTCTTC
* *
1494458 TTCCTCTTC
1 CTCTTCTTC
1494467 CTCTTC
1 CTCTTC
1494473 CTCCAAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (9 bp):
CTCTTCTTC
Found at i:1499042 original size:2 final size:2
Alignment explanation
Indices: 1499035--1499073 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1499025 TTATATGTTT
1499035 TA TA TA TA 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 TA TA TA TA T
1499074 TCACCGTTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1507565 original size:42 final size:44
Alignment explanation
Indices: 1507523--1507612 Score: 108
Period size: 49 Copynumber: 1.9 Consensus size: 44
1507513 AAAGCCAAAT
**
1507523 AAGAGTCTAGAGATTCATGGAAGGGAATTTAAATTTTCAAATATACTTA
1 AAGAGTCTAGAGATTCACAGAAGGGAATTTAAATTTTC--A-A-AC-TA
*
1507572 AAGAGTGTAGAGATTCACAGAAGGGAATTTAAATTTTCAAA
1 AAGAGTCTAGAGATTCACAGAAGGGAATTTAAATTTTCAAA
1507613 ATCTTCCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 1 0.03
46 1 0.03
47 1 0.03
49 35 0.92
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (44 bp):
AAGAGTCTAGAGATTCACAGAAGGGAATTTAAATTTTCAAACTA
Found at i:1508744 original size:6 final size:6
Alignment explanation
Indices: 1508735--1508776 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1508725 TAATATAATA
*
1508735 TTAAAT TTAAA- TTAAAT TTTAAT TTAAAAT TTAATAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAA-AT TTAAA
1508777 ATTCAGTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 15 0.48
7 11 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:1510046 original size:24 final size:24
Alignment explanation
Indices: 1510010--1510073 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1510000 AAATTTTTAT
*
1510010 TAAATTTTTTAATTTTAATTATAA
1 TAAATTTTTTAATTATAATTATAA
*
1510034 TAATTTTTTTAATTATAATTATAA
1 TAAATTTTTTAATTATAATTATAA
1510058 TAAATTTTATT-ATTAT
1 TAAATTTT-TTAATTAT
1510074 TTTTAATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 34 0.94
25 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TAAATTTTTTAATTATAATTATAA
Found at i:1512715 original size:137 final size:136
Alignment explanation
Indices: 1512466--1512868 Score: 610
Period size: 137 Copynumber: 3.0 Consensus size: 136
1512456 ACATAATGAA
* * * *
1512466 CTCAACATTTACAGTTACTGGTTTCTAGATCTGATCAGTGAAATTTCTCAAGTGCTTTGTATTGT
1 CTCAACATTTGCAGTTACTGGTTTCTAAATCTGATCTGTGAAATTTCTCAAGTGCTTTATATTGT
*
1512531 ATTCATATATTGCATAATCCTTTTCATAGCTGACTAGCATGATAGTTTAATGACATTATTGAACT
66 ATTCATTTATTGCATAATCCTTTTCATAGCTGACT-GCATGA-AGTTTAATGACATTATTGAACT
1512596 CTTCATTT
129 CTTCATTT
*
1512604 CTCAACATTTGCAGTTACTGGTTT-TGAAATCT-ATCTGTGAAATTTCTCAAGTGCTTTATGTTG
1 CTCAACATTTGCAGTTACTGGTTTCT-AAATCTGATCTGTGAAATTTCTCAAGTGCTTTATATTG
*
1512667 TATTCATTTATTGCATAATCCTTTTCATAGCTGACTGGCATGACAGTTTACTGACATTATTGAAC
65 TATTCATTTATTGCATAATCCTTTTCATAGCTGACT-GCATGA-AGTTTAATGACATTATTGAAC
1512732 TCTTCATTT
128 TCTTCATTT
*
1512741 CTCAACATTTGCAATTACTGGTTTCTAAATCTGATCTGTGAAATTTCTCAAGTGCTTTATATTGT
1 CTCAACATTTGCAGTTACTGGTTTCTAAATCTGATCTGTGAAATTTCTCAAGTGCTTTATATTGT
*
1512806 ATTCATTTATTGCATAATCC--TTC---GCTGACTG-AT--AGTTTAATGGCATTATTGAACTCT
66 ATTCATTTATTGCATAATCCTTTTCATAGCTGACTGCATGAAGTTTAATGACATTATTGAACTCT
1512863 TCATTT
131 TCATTT
1512869 TTTCTAATTT
Statistics
Matches: 249, Mismatches: 13, Indels: 16
0.90 0.05 0.06
Matches are distributed among these distances:
128 28 0.11
131 2 0.01
132 1 0.00
133 7 0.03
136 3 0.01
137 128 0.51
138 80 0.32
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (136 bp):
CTCAACATTTGCAGTTACTGGTTTCTAAATCTGATCTGTGAAATTTCTCAAGTGCTTTATATTGT
ATTCATTTATTGCATAATCCTTTTCATAGCTGACTGCATGAAGTTTAATGACATTATTGAACTCT
TCATTT
Found at i:1516575 original size:214 final size:216
Alignment explanation
Indices: 1516162--1516591 Score: 607
Period size: 214 Copynumber: 2.0 Consensus size: 216
1516152 AAGGAATTCA
* * *
1516162 GAACTCTAAATAATTAGAACAACAAAATGTAGGACAACCAACATTAGTACCAAACGCCTACTAAT
1 GAACTCTAAAAAATTAG-A-AACAAAATGAAGGACAACCAACATTAGTACCAAACGCCTAATAAT
* * *
1516227 GCAAAAACCTTGTGCTACTTCTCTTTTTTTTTTTTTTTTCTAACGTTTTCTTATTACAGCTCCAT
64 GCAAAAACCTTGTGCTAC-TCTC------TTTTTTTTTCCTAACGTTTTCTAATAACAGCTCCAT
*
1516292 TATGATACGTAAAACTGCTTTTATTAACTTATATCTACAATGTGCTCTGTAGATTCAGAAGAATT
122 TATGATACGTAAAACTGCTTTTATTAACTTATATCTACAATGTGCTCTGTAGATTCAGAACAATT
1516357 TGTAAACATAACGATAAATACACAAGTTAG
187 TGTAAACATAACGATAAATACACAAGTTAG
* *
1516387 GAACTCTAAAAAATTAG-AACAAAGTGAAGGACAACCAACATTAGTACCAAACGTCTAATAATGC
1 GAACTCTAAAAAATTAGAAACAAAATGAAGGACAACCAACATTAGTACCAAACGCCTAATAATGC
** *
1516451 AAAAACCTTGTGCTAC-CTC-TTTTTTTTCCTAA-GTTTGTTCTAATAATGGTTCCATTATGATA
66 AAAAACCTTGTGCTACTCTCTTTTTTTTTCCTAACG-TT-TTCTAATAACAGCTCCATTATGATA
* *
1516513 CGTAAAACTGCTTTTATTAACTTATATCTACAATGTGCTCTGTGGATTCAGAACAGTTTGTAAAC
129 CGTAAAACTGCTTTTATTAACTTATATCTACAATGTGCTCTGTAGATTCAGAACAATTTGTAAAC
1516578 ATAACGATAAATAC
194 ATAACGATAAATAC
1516592 CCAAATTATT
Statistics
Matches: 189, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
212 1 0.01
213 14 0.07
214 96 0.51
220 3 0.02
222 59 0.31
225 16 0.08
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (216 bp):
GAACTCTAAAAAATTAGAAACAAAATGAAGGACAACCAACATTAGTACCAAACGCCTAATAATGC
AAAAACCTTGTGCTACTCTCTTTTTTTTTCCTAACGTTTTCTAATAACAGCTCCATTATGATACG
TAAAACTGCTTTTATTAACTTATATCTACAATGTGCTCTGTAGATTCAGAACAATTTGTAAACAT
AACGATAAATACACAAGTTAG
Found at i:1531163 original size:30 final size:31
Alignment explanation
Indices: 1531115--1531173 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1531105 TTTTGTTTGA
*
1531115 AGGACCTTTTTAAAAGCATTGTTAGACAACT
1 AGGACCTTTTTAAAAGCATTGTTAAACAACT
*
1531146 AGGAGCTTTTT-AAAGCATTGTTAAACAA
1 AGGACCTTTTTAAAAGCATTGTTAAACAA
1531174 GTTTATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (31 bp):
AGGACCTTTTTAAAAGCATTGTTAAACAACT
Found at i:1533625 original size:20 final size:20
Alignment explanation
Indices: 1533579--1533636 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
1533569 TTTCGGAAAT
1533579 AAATTTTTA-AAAAATCATA
1 AAATTTTTAGAAAAATCATA
* **
1533598 AAACTTTTAGAAAAATTTTA
1 AAATTTTTAGAAAAATCATA
* * *
1533618 TAATTTTTTGAAAATTCAT
1 AAATTTTTAGAAAAATCAT
1533637 TTTCGAAAGG
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (20 bp):
AAATTTTTAGAAAAATCATA
Found at i:1533796 original size:34 final size:35
Alignment explanation
Indices: 1533745--1533814 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
1533735 TCTAAAATTC
*
1533745 ATTTTTGAAAACATTTATTTTCAAAAAGTTATATG
1 ATTTTTCAAAACATTTATTTTCAAAAAGTTATATG
* **
1533780 ATTTTTCAAAA-ATTTATTTTGAAAATTTTATATG
1 ATTTTTCAAAACATTTATTTTCAAAAAGTTATATG
1533814 A
1 A
1533815 AAAAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (35 bp):
ATTTTTCAAAACATTTATTTTCAAAAAGTTATATG
Found at i:1540594 original size:23 final size:21
Alignment explanation
Indices: 1540568--1540612 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
1540558 TTCAATTTGA
1540568 ATTAAATTTAAATATTAAATTAT
1 ATTAAATTTAAA-ATT-AATTAT
1540591 ATTAAATTTAAAATTAATTAT
1 ATTAAATTTAAAATTAATTAT
1540612 A
1 A
1540613 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 3 0.14
23 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAATTTAAAATTAATTAT
Found at i:1540795 original size:22 final size:23
Alignment explanation
Indices: 1540770--1540813 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1540760 AATAAATTTT
1540770 AATTTAGA-TTAAATT-AAATAAA
1 AATTT-GATTTAAATTCAAATAAA
1540792 AATTTGATTTAAATTCAAATAA
1 AATTTGATTTAAATTCAAATAA
1540814 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 12 0.60
23 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATTTGATTTAAATTCAAATAAA
Found at i:1543574 original size:43 final size:42
Alignment explanation
Indices: 1543458--1543567 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
1543448 ATAGGACTGC
*
1543458 ACTCCCAACTAATATATACCATAGACGATAATTTCAGTCCCT
1 ACTCCCAACTAATATATACTATAGACGATAATTTCAGTCCCT
1543500 ACTCCCAACTAATATATACTATAGACGATAATTTCAGTCCCAT
1 ACTCCCAACTAATATATACTATAGACGATAATTTCAGTCCC-T
* *
1543543 ACTCCCAACTAATAAATAGTATAGA
1 ACTCCCAACTAATATATACTATAGA
1543568 AAATAATGAC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
42 40 0.62
43 24 0.38
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.28
Consensus pattern (42 bp):
ACTCCCAACTAATATATACTATAGACGATAATTTCAGTCCCT
Found at i:1548005 original size:8 final size:8
Alignment explanation
Indices: 1547992--1548020 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1547982 ATTGCCGAAA
1547992 TTTTTTCT
1 TTTTTTCT
1548000 TTTTTTC-
1 TTTTTTCT
1548007 TTTTTTCT
1 TTTTTTCT
1548015 TTTTTT
1 TTTTTT
1548021 TTTGTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1548012 original size:15 final size:15
Alignment explanation
Indices: 1547992--1548020 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1547982 ATTGCCGAAA
1547992 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
1548007 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
1548021 TTTGTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:1550250 original size:24 final size:24
Alignment explanation
Indices: 1550223--1550269 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1550213 ACGTTCAGTT
1550223 TTTA-CTCTTAGTTTTTCACACAGA
1 TTTATCTCTTAGTTTTTC-CACAGA
*
1550247 TTTATTTCTTAGTTTTTCCACAG
1 TTTATCTCTTAGTTTTTCCACAG
1550270 CAACAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTATCTCTTAGTTTTTCCACAGA
Found at i:1553858 original size:15 final size:16
Alignment explanation
Indices: 1553838--1553871 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1553828 ATAATTTATT
1553838 TATTTATTAAAA-TTA
1 TATTTATTAAAATTTA
1553853 TATTTATTAAAATTTA
1 TATTTATTAAAATTTA
1553869 TAT
1 TAT
1553872 AATTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTATTAAAATTTA
Found at i:1553876 original size:19 final size:18
Alignment explanation
Indices: 1553830--1553877 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
1553820 AAAATATAAT
*
1553830 AATTTATTTATTTATTAA
1 AATTTATATATTTATTAA
1553848 AA--T-TATATTTATTAA
1 AATTTATATATTTATTAA
1553863 AATTTATATAATTTA
1 AATTTATAT-ATTTA
1553878 ATTATTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 13 0.52
16 1 0.04
17 1 0.04
18 5 0.20
19 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTATATATTTATTAA
Found at i:1560864 original size:3 final size:3
Alignment explanation
Indices: 1560856--1560888 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1560846 ATTTCTCTTT
1560856 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1560889 TCCAACATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1568146 original size:31 final size:33
Alignment explanation
Indices: 1568100--1568162 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
1568090 TACAATAATT
* *
1568100 TTTTATATAAAATTTACTATTTAATTTTCTTTC
1 TTTTATATAAAATTTACTACTTAATCTTCTTTC
*
1568133 TTTTAT-T-AAATTTACTGCTTAATCTTCTTT
1 TTTTATATAAAATTTACTACTTAATCTTCTTT
1568163 TTGTACCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 20 0.74
32 1 0.04
33 6 0.22
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (33 bp):
TTTTATATAAAATTTACTACTTAATCTTCTTTC
Found at i:1569707 original size:22 final size:23
Alignment explanation
Indices: 1569664--1569708 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1569654 GACATTTGAT
* *
1569664 TTTAAAATTTTTTTAATATATTA
1 TTTAAAAATTATTTAATATATTA
1569687 TTTAAAAATTATTT-ATATATTA
1 TTTAAAAATTATTTAATATATTA
1569709 CGTGTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAAAAATTATTTAATATATTA
Found at i:1569796 original size:20 final size:21
Alignment explanation
Indices: 1569748--1569801 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1569738 AAAATAAGTA
1569748 AAATATTATATTAATTATTTTT
1 AAATATT-TATTAATTATTTTT
1569770 AAA-ATTTAGTT-ATTA-TTTT
1 AAATATTTA-TTAATTATTTTT
1569789 AAATATTTTATTA
1 AAATA-TTTATTA
1569802 TAATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 9 0.32
22 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AAATATTTATTAATTATTTTT
Found at i:1569802 original size:20 final size:20
Alignment explanation
Indices: 1569748--1569812 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 20
1569738 AAAATAAGTA
*
1569748 AAATATTATATTAATTATTTTT
1 AAATATTTTATT-ATTA-TTTT
1569770 AAA-A-TTTAGTTATTATTTT
1 AAATATTTTA-TTATTATTTT
*
1569789 AAATATTTTATTA-TAATTT
1 AAATATTTTATTATTATTTT
1569808 AAATA
1 AAATA
1569813 CTATGACATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 17 0.45
20 11 0.29
21 7 0.18
22 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AAATATTTTATTATTATTTT
Found at i:1576823 original size:34 final size:34
Alignment explanation
Indices: 1576784--1576852 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1576774 CATTTAGATT
*
1576784 TCCAAATCTAGTAGCATAAGCATAAGCTTTCTAG
1 TCCAAATCTAGCAGCATAAGCATAAGCTTTCTAG
* *
1576818 TCCAAATCTAGCAGTATATGCATAAGCTTTCTAG
1 TCCAAATCTAGCAGCATAAGCATAAGCTTTCTAG
1576852 T
1 T
1576853 GGTTACCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (34 bp):
TCCAAATCTAGCAGCATAAGCATAAGCTTTCTAG
Found at i:1584454 original size:38 final size:40
Alignment explanation
Indices: 1584407--1584482 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1584397 CATTTTAATA
*
1584407 TAAATTATAA-TAAATAATTTTTAT-ATA-AAATATAACT
1 TAAATTATAATTAAATAATTTATATAATATAAATATAACT
*
1584444 TAAATATATAATTTTAATAATTTATATAATATAAATATA
1 TAAAT-TATAA-TTAAATAATTTATATAATATAAATATA
1584483 TAAATCGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 5 0.16
38 5 0.16
40 12 0.38
41 3 0.09
42 7 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (40 bp):
TAAATTATAATTAAATAATTTATATAATATAAATATAACT
Found at i:1585255 original size:20 final size:19
Alignment explanation
Indices: 1585213--1585256 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1585203 AAAAGTTTAA
*
1585213 TTTTTAATATTTACAATTT
1 TTTTTAATATTTACAATTC
* *
1585232 TTTTTAATGTTTTCATATTC
1 TTTTTAATATTTACA-ATTC
1585252 TTTTT
1 TTTTT
1585257 GGTACTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTAATATTTACAATTC
Found at i:1586482 original size:22 final size:21
Alignment explanation
Indices: 1586430--1586482 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1586420 ATAATTATTT
* *
1586430 TATATAT-AATTTTATTTAAA
1 TATATATAAATTATATTAAAA
*
1586450 TATATTTTAAATTATATTAAAA
1 TATA-TATAAATTATATTAAAA
1586472 TAATATATAAA
1 T-ATATATAAA
1586483 AGTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.15
21 2 0.08
22 17 0.65
23 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATATAAATTATATTAAAA
Found at i:1605967 original size:64 final size:64
Alignment explanation
Indices: 1605895--1606021 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
1605885 AAAAAACTGG
*
1605895 TAATAGTTATAACTACT-AATGAATGGAATGGAAATGAAGATTGACATGGGTCAGGGACTGCTCA
1 TAATAGTTATAACTA-TGAATGAATGAAATGGAAATGAAGATTGACATGGGTCAGGGACTGCTCA
1605959 TAATAGTTATAACTATGAATGAATGAAATGGAAATGAAGATTGACATGGGTCAGGGACTGCTC
1 TAATAGTTATAACTATGAATGAATGAAATGGAAATGAAGATTGACATGGGTCAGGGACTGCTC
1606022 GTGAATGTGA
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (64 bp):
TAATAGTTATAACTATGAATGAATGAAATGGAAATGAAGATTGACATGGGTCAGGGACTGCTCA
Found at i:1606046 original size:39 final size:39
Alignment explanation
Indices: 1605992--1606075 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
1605982 TGAAATGGAA
* **
1605992 ATGAAGATTGACATGGGTCAGGGACTGCTCGTGAATGTG
1 ATGAAGATTAACATGGGTCAGGGACTGCTAATGAATGTG
1606031 ATGAAGATTAACATGGGTCAGGGACTGCTAATGAATGTG
1 ATGAAGATTAACATGGGTCAGGGACTGCTAATGAATGTG
1606070 ATGAAG
1 ATGAAG
1606076 TGGAGTAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.25
Consensus pattern (39 bp):
ATGAAGATTAACATGGGTCAGGGACTGCTAATGAATGTG
Found at i:1607468 original size:8 final size:8
Alignment explanation
Indices: 1607455--1607479 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1607445 ACATAAGGAT
1607455 GGGAAGCG
1 GGGAAGCG
1607463 GGGAAGCG
1 GGGAAGCG
1607471 GGGAAGCG
1 GGGAAGCG
1607479 G
1 G
1607480 CTCTCGCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.64, T:0.00
Consensus pattern (8 bp):
GGGAAGCG
Found at i:1608486 original size:23 final size:23
Alignment explanation
Indices: 1608456--1608505 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1608446 TTTCATTAAT
*
1608456 TTTTTTAATCATAATTACAATAA
1 TTTTTTAATCACAATTACAATAA
*
1608479 TTTTTTAATCACAATTATAATAA
1 TTTTTTAATCACAATTACAATAA
1608502 TTTT
1 TTTT
1608506 ATTACTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTAATCACAATTACAATAA
Found at i:1612758 original size:2 final size:2
Alignment explanation
Indices: 1612751--1612787 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1612741 CATTCTCGCA
*
1612751 TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1612788 GACGTGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1625512 original size:47 final size:46
Alignment explanation
Indices: 1625430--1625522 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 46
1625420 TTAAAATTTG
* *
1625430 ATTTAAATTTTTTTAATTTAAATTTAATTCAAAATAAAAATTAAATT
1 ATTTAAATTTATTTAATTTAAATTTAATTAAAAATAAAAA-TAAATT
*
1625477 ATTTAAATTTATTTAA-TTATAA-TTGATTAATAAATAAAAATAAATT
1 ATTTAAATTTATTTAATTTA-AATTTAATTAA-AAATAAAAATAAATT
1625523 TAATTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 15 0.37
47 26 0.63
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (46 bp):
ATTTAAATTTATTTAATTTAAATTTAATTAAAAATAAAAATAAATT
Found at i:1633705 original size:1 final size:1
Alignment explanation
Indices: 1633699--1633723 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1633689 CATCTAATGC
1633699 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1633724 CATTGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1652848 original size:21 final size:21
Alignment explanation
Indices: 1652824--1652867 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1652814 ATATATGTAT
*
1652824 AAATCATGTTTAATAATTTTA
1 AAATCATATTTAATAATTTTA
*
1652845 AAATTATATTTAATAATTTTA
1 AAATCATATTTAATAATTTTA
1652866 AA
1 AA
1652868 TAAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAATCATATTTAATAATTTTA
Found at i:1652879 original size:21 final size:21
Alignment explanation
Indices: 1652832--1652880 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1652822 ATAAATCATG
*
1652832 TTTAATAATTTTAAAATTATA
1 TTTAATAATTTTAAAATTAAA
1652853 TTTAATAATTTT-AAA-TAAA
1 TTTAATAATTTTAAAATTAAA
1652872 -TTAATAATT
1 TTTAATAATT
1652881 CATTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
19 3 0.11
20 3 0.11
21 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATAATTTTAAAATTAAA
Found at i:1654279 original size:14 final size:13
Alignment explanation
Indices: 1654252--1654299 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
1654242 TTCAAGTTTC
1654252 AATTAATTTAAATTA
1 AATT-ATTT-AATTA
1654267 AATTATTTGAATTA
1 AATTATTT-AATTA
*
1654281 TAATTCTTTAATTA
1 -AATTATTTAATTA
1654295 AATTA
1 AATTA
1654300 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 14 0.48
15 11 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
AATTATTTAATTA
Found at i:1654485 original size:20 final size:20
Alignment explanation
Indices: 1654452--1654509 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1654442 TCATTTATAC
1654452 TAAAAT-ATTGAATAAAAAAT
1 TAAAATAATT-AATAAAAAAT
**
1654472 TAAAATAATTAATAATTAAT
1 TAAAATAATTAATAAAAAAT
**
1654492 TAATTTAATTAATTAAAA
1 TAAAATAATTAA-TAAAA
1654510 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAATAATTAATAAAAAAT
Found at i:1658183 original size:34 final size:33
Alignment explanation
Indices: 1658120--1658184 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
1658110 TAAAAATCTA
**
1658120 TAATAAAATAAATTTTTATAAATTTATTAAATT
1 TAATAAAATAAATTTTTATAAATCAATTAAATT
*
1658153 TAATATAAATAAATTTATT-TGAATCAATTAAA
1 TAATA-AAATAAATTT-TTATAAATCAATTAAA
1658185 AAAATAGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 5 0.19
34 20 0.74
35 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
TAATAAAATAAATTTTTATAAATCAATTAAATT
Found at i:1662502 original size:2 final size:2
Alignment explanation
Indices: 1662495--1662536 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1662485 TCTTTTTCTG
1662495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1662537 CAACAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1665082 original size:84 final size:84
Alignment explanation
Indices: 1664941--1665109 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
1664931 TTAATAGAAA
1664941 ACCATCAATCTTTGTATCAAAACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATCAAC
1 ACCATCAATCTTTGTATCAAAACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATCAAC
1665006 CAAGCTAGAATTTCTACTT
66 CAAGCTAGAATTTCTACTT
1665025 ACCATCAATCTTTGTATCAAAACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATCAAC
1 ACCATCAATCTTTGTATCAAAACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATCAAC
*
1665090 CAAGGTAGAATTTCTACTT
66 CAAGCTAGAATTTCTACTT
1665109 A
1 A
1665110 ACTTTGTTCT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (84 bp):
ACCATCAATCTTTGTATCAAAACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATCAAC
CAAGCTAGAATTTCTACTT
Found at i:1665091 original size:42 final size:42
Alignment explanation
Indices: 1664961--1665095 Score: 118
Period size: 42 Copynumber: 3.2 Consensus size: 42
1664951 TTTGTATCAA
1664961 AACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATC
1 AACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATC
* * * ** * * *
1665003 AACCAAGCT-AGAATTTC-TACTTACCAT-CAATCTTTGTA-TCA-A
1 AACCAAGGTCA-AA-GTCGT-CGT-GGATGC-TTCTTTGAATTCATC
1665045 AACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATC
1 AACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATC
1665087 AACCAAGGT
1 AACCAAGGT
1665096 AGAATTTCTA
Statistics
Matches: 67, Mismatches: 16, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
40 9 0.13
41 9 0.13
42 31 0.46
43 9 0.13
44 9 0.13
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
AACCAAGGTCAAAGTCGTCGTGGATGCTTCTTTGAATTCATC
Found at i:1669682 original size:11 final size:11
Alignment explanation
Indices: 1669666--1669690 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1669656 AGCTTTCCCC
1669666 CATTAGAAAAG
1 CATTAGAAAAG
1669677 CATTAGAAAAG
1 CATTAGAAAAG
1669688 CAT
1 CAT
1669691 CATATATAGA
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:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (11 bp):
CATTAGAAAAG
Found at i:1675969 original size:20 final size:21
Alignment explanation
Indices: 1675933--1675984 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1675923 CTCGAAATTA
1675933 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
1675955 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
1675976 AT-AAATATT
1 ATAAAATATT
1675985 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:1675975 original size:21 final size:22
Alignment explanation
Indices: 1675933--1675984 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1675923 CTCGAAATTA
1675933 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
1675955 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
1675976 AT-AAATATT
1 ATAAAATATT
1675985 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:1675993 original size:16 final size:16
Alignment explanation
Indices: 1675972--1676030 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
1675962 ATTATTTTTT
*
1675972 AAATATAAATATTTAA
1 AAATATAAATATATAA
* *
1675988 AAATATCACTATATAA
1 AAATATAAATATATAA
*
1676004 ATATATATAAATA-AAAA
1 A-A-ATATAAATATATAA
1676021 AAAT-TAAATA
1 AAATATAAATA
1676031 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.17
15 2 0.06
16 15 0.43
17 5 0.14
18 7 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:1677009 original size:15 final size:15
Alignment explanation
Indices: 1676989--1677020 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1676979 CAAGGTTTTT
*
1676989 CATCAATAAAATGCG
1 CATCAATAAAAAGCG
1677004 CATCAATAAAAAGCG
1 CATCAATAAAAAGCG
1677019 CA
1 CA
1677021 GACAATCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (15 bp):
CATCAATAAAAAGCG
Found at i:1677424 original size:24 final size:24
Alignment explanation
Indices: 1677383--1677459 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
1677373 CCGACTCTTG
*
1677383 CACCAGTTCATCCACCACCCAAGC
1 CACCAGTTCATCCTCCACCCAAGC
* *
1677407 CTCCAGTTCACCCTCCACCCAAGC
1 CACCAGTTCATCCTCCACCCAAGC
* *
1677431 CACCAGTTCATCCTCCAACTAAGC
1 CACCAGTTCATCCTCCACCCAAGC
1677455 CACCA
1 CACCA
1677460 ACTCATCCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.49, G:0.08, T:0.16
Consensus pattern (24 bp):
CACCAGTTCATCCTCCACCCAAGC
Found at i:1677465 original size:24 final size:24
Alignment explanation
Indices: 1677418--1677532 Score: 70
Period size: 24 Copynumber: 4.8 Consensus size: 24
1677408 TCCAGTTCAC
* * **
1677418 CCTCCACCCAAGCCACCAGTTCAT
1 CCTCCAACTAAGCCACCAACTCAT
1677442 CCTCCAACTAAGCCACCAACTCAT
1 CCTCCAACTAAGCCACCAACTCAT
* ** * *
1677466 CCCCCGGCTAAGCCACC-AGTGCAC
1 CCTCCAACTAAGCCACCAACT-CAT
* * * * *
1677490 CCACCAACTTACCCACCATCGCAT
1 CCTCCAACTAAGCCACCAACTCAT
**
1677514 CCTCCGGCTAAGCCACCAA
1 CCTCCAACTAAGCCACCAA
1677533 GTTACCCAAA
Statistics
Matches: 65, Mismatches: 24, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
23 2 0.03
24 63 0.97
ACGTcount: A:0.27, C:0.49, G:0.10, T:0.14
Consensus pattern (24 bp):
CCTCCAACTAAGCCACCAACTCAT
Found at i:1677479 original size:48 final size:48
Alignment explanation
Indices: 1677427--1677531 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
1677417 CCCTCCACCC
* * * * *
1677427 AAGCCACCAGTTCATCCTCCAACTAAGCCACCAACTCATCCCCCGGCT
1 AAGCCACCAGTGCACCCACCAACTAACCCACCAACGCATCCCCCGGCT
* * *
1677475 AAGCCACCAGTGCACCCACCAACTTACCCACCATCGCATCCTCCGGCT
1 AAGCCACCAGTGCACCCACCAACTAACCCACCAACGCATCCCCCGGCT
1677523 AAGCCACCA
1 AAGCCACCA
1677532 AGTTACCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.28, C:0.47, G:0.11, T:0.14
Consensus pattern (48 bp):
AAGCCACCAGTGCACCCACCAACTAACCCACCAACGCATCCCCCGGCT
Found at i:1707976 original size:15 final size:15
Alignment explanation
Indices: 1707956--1707985 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1707946 GTAATTTTTC
1707956 ATTTTCGTTAGCTAA
1 ATTTTCGTTAGCTAA
1707971 ATTTTCGTTAGCTAA
1 ATTTTCGTTAGCTAA
1707986 TTTAGCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
ATTTTCGTTAGCTAA
Found at i:1712591 original size:34 final size:34
Alignment explanation
Indices: 1712552--1712620 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1712542 ACAACAAAAA
1712552 GAAAGAGTTTGGAATGAAGGGTTTACCTGTGTTT
1 GAAAGAGTTTGGAATGAAGGGTTTACCTGTGTTT
1712586 GAAAGAGTTTGGAATGAAGGGTTTACCTGTGTTT
1 GAAAGAGTTTGGAATGAAGGGTTTACCTGTGTTT
1712620 G
1 G
1712621 CAAGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.06, G:0.33, T:0.35
Consensus pattern (34 bp):
GAAAGAGTTTGGAATGAAGGGTTTACCTGTGTTT
Found at i:1716264 original size:15 final size:14
Alignment explanation
Indices: 1716239--1716272 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1716229 AAAATTTTAA
1716239 TAAAA-ATATTTGTT
1 TAAAATATATTT-TT
1716253 TAAAATATATTTTT
1 TAAAATATATTTTT
1716267 TAAAAT
1 TAAAAT
1716273 TTATATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TAAAATATATTTTT
Found at i:1716294 original size:22 final size:22
Alignment explanation
Indices: 1716265--1716317 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1716255 AAATATATTT
1716265 TTTA-AAATTTATATA-CTTAA
1 TTTATAAATTTATATATCTTAA
* *
1716285 TTTATGAAA-TAATATATTTTAA
1 TTTAT-AAATTTATATATCTTAA
1716307 TTTATAAATTT
1 TTTATAAATTT
1716318 GGTCATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.15
21 9 0.35
22 13 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATAAATTTATATATCTTAA
Found at i:1722501 original size:14 final size:14
Alignment explanation
Indices: 1722482--1722518 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1722472 ATTTTTTTTA
1722482 ATATTAAAAAATTT
1 ATATTAAAAAATTT
1722496 ATATTAAATAAATTT
1 ATATTAAA-AAATTT
1722511 -TATTAAAA
1 ATATTAAAA
1722519 TAAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.68
15 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAAAAAATTT
Found at i:1722519 original size:15 final size:14
Alignment explanation
Indices: 1722483--1722528 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
1722473 TTTTTTTTAA
1722483 TATTAAA-AAATTT
1 TATTAAATAAATTT
1722496 ATATTAAATAAATTT
1 -TATTAAATAAATTT
1722511 TATTAAAATAAATATT
1 TATT-AAATAAAT-TT
1722527 TA
1 TA
1722529 AATTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATTAAATAAATTT
Found at i:1726238 original size:2 final size:2
Alignment explanation
Indices: 1726231--1726261 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1726221 TCCATATAGA
1726231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1726262 CACATATACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1727629 original size:3 final size:3
Alignment explanation
Indices: 1727621--1727645 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1727611 TAACAATTAA
1727621 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1727646 GGAGTATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1728652 original size:7 final size:7
Alignment explanation
Indices: 1728640--1728666 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1728630 GCGCAGATAG
1728640 TGATGAC
1 TGATGAC
1728647 TGATGAC
1 TGATGAC
1728654 TGATGAC
1 TGATGAC
1728661 TGATGA
1 TGATGA
1728667 AGAAGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (7 bp):
TGATGAC
Found at i:1729439 original size:15 final size:15
Alignment explanation
Indices: 1729419--1729451 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1729409 TTTCGATTGT
*
1729419 CAGTATCCCCCGACC
1 CAGTATCCCCAGACC
1729434 CAGTATCCCCAGACC
1 CAGTATCCCCAGACC
1729449 CAG
1 CAG
1729452 AAGAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.48, G:0.15, T:0.12
Consensus pattern (15 bp):
CAGTATCCCCAGACC
Found at i:1729888 original size:3 final size:3
Alignment explanation
Indices: 1729880--1729915 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1729870 TAGGGCTTGT
1729880 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
1729916 AGTTGTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
TGC
Found at i:1730480 original size:13 final size:14
Alignment explanation
Indices: 1730462--1730491 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1730452 CTAATTGAAT
1730462 AAATTTT-AAAATA
1 AAATTTTAAAAATA
1730475 AAATTTTAAAAATA
1 AAATTTTAAAAATA
1730489 AAA
1 AAA
1730492 AAGGAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTTTAAAAATA
Found at i:1746553 original size:129 final size:129
Alignment explanation
Indices: 1746323--1746585 Score: 379
Period size: 129 Copynumber: 2.0 Consensus size: 129
1746313 CAGATGGGGT
*
1746323 TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTATATCTGCAGCACTTGTTTGCC
1 TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTATATCTGCAGCACTTGTTGGCC
* * * *
1746388 CCTCAGAAAGGCTTCACTTGGGAGCTGGCGGCATGCGAAGTCACACACCAGATGGCAGTTTGAG
66 CCTCAGAAAGGCTTCACTTGGGAGCAGGCGGCATGCGAAGTCACACAACACATGGCAGTTTGAC
* * *
1746452 TGGTGACGAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTTTGT-TGGCAGCACTTAG-TGG
1 TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTATATCT-GCAGCACTT-GTTGG
* * *
1746515 CCTCTCAGAAAGGCTTCA-TTGGGGAGCAGGCGGCATGCGCAGTCACACAAGACATGGCAGTTTG
64 CCCCTCAGAAAGGCTTCACTT-GGGAGCAGGCGGCATGCGAAGTCACACAACACATGGCAGTTTG
1746579 AC
128 AC
1746581 TGGTG
1 TGGTG
1746586 GAAATGGAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
128 3 0.03
129 116 0.97
130 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (129 bp):
TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTATATCTGCAGCACTTGTTGGCC
CCTCAGAAAGGCTTCACTTGGGAGCAGGCGGCATGCGAAGTCACACAACACATGGCAGTTTGAC
Found at i:1747599 original size:14 final size:14
Alignment explanation
Indices: 1747565--1747600 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1747555 CGTACATAGT
*
1747565 ATATATGTATATAA
1 ATATATATATATAA
*
1747579 ATATATATATATAC
1 ATATATATATATAA
1747593 ATATATAT
1 ATATATAT
1747601 GCTCTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:1758328 original size:17 final size:18
Alignment explanation
Indices: 1758295--1758330 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1758285 TTCATAAAAG
*
1758295 TCATAATTATACAGAATA
1 TCATAATCATACAGAATA
1758313 TCATAATCAT-CAGAATA
1 TCATAATCATACAGAATA
1758330 T
1 T
1758331 AAATTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (18 bp):
TCATAATCATACAGAATA
Found at i:1760058 original size:23 final size:21
Alignment explanation
Indices: 1760027--1760136 Score: 90
Period size: 23 Copynumber: 5.2 Consensus size: 21
1760017 TTATTTATTA
1760027 TTTTT-TTTATCTTGTAATTTT
1 TTTTTATTTATC-TGTAATTTT
1760048 TTTTTGATTTATCT-T-ATTTT
1 TTTTT-ATTTATCTGTAATTTT
*
1760068 ATTTTTAATTATCTGTTAATTTT
1 -TTTTTATTTATCTG-TAATTTT
1760091 TTTTTCATTTATCTG--A--TT
1 TTTTT-ATTTATCTGTAATTTT
*
1760109 TTTTTATTTATCTGATTATTCTT
1 TTTTTATTTATCTG-TAATT-TT
1760132 TTTTT
1 TTTTT
1760137 TCTTTTTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 24
0.74 0.02 0.24
Matches are distributed among these distances:
17 9 0.12
18 7 0.09
20 14 0.19
21 11 0.15
22 7 0.09
23 26 0.35
ACGTcount: A:0.17, C:0.06, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTATTTATCTGTAATTTT
Found at i:1760066 original size:20 final size:19
Alignment explanation
Indices: 1760043--1760121 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 19
1760033 TTATCTTGTA
1760043 ATTTTTTTTTGATTTATCTT
1 ATTTTTTTTT-ATTTATCTT
*
1760063 ATTTTATTTTTAATTATCTGTT
1 ATTTT-TTTTTATTTATC--TT
*
1760085 AATTTTTTTTTCATTTATCTG
1 -ATTTTTTTTT-ATTTATCTT
1760106 A--TTTTTTTATTTATCT
1 ATTTTTTTTTATTTATCT
1760122 GATTATTCTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
17 8 0.16
18 7 0.14
20 12 0.24
21 6 0.12
22 7 0.14
23 11 0.22
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTTTTTATTTATCTT
Found at i:1760089 original size:43 final size:42
Alignment explanation
Indices: 1760024--1760119 Score: 122
Period size: 43 Copynumber: 2.2 Consensus size: 42
1760014 AATTTATTTA
* * *
1760024 TTATTTTTTTTATCTTGTAATTTTTTTTTGATTTATCTTATT
1 TTATTTTTATTATCTTGTAATTTTTTTTTCATTTATCTGATT
1760066 TTATTTTTAATTATC-TGTTAATTTTTTTTTCATTTATCTGATT
1 TTATTTTT-ATTATCTTG-TAATTTTTTTTTCATTTATCTGATT
*
1760109 TTTTTATTTAT
1 TTATT-TTTAT
1760120 CTGATTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 10 0.21
43 34 0.72
44 3 0.06
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (42 bp):
TTATTTTTATTATCTTGTAATTTTTTTTTCATTTATCTGATT
Found at i:1760112 original size:17 final size:17
Alignment explanation
Indices: 1760090--1760125 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1760080 CTGTTAATTT
1760090 TTTTTTCATTTATCTGA
1 TTTTTTCATTTATCTGA
*
1760107 TTTTTTTATTTATCTGA
1 TTTTTTCATTTATCTGA
1760124 TT
1 TT
1760126 ATTCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTTTCATTTATCTGA
Found at i:1760134 original size:43 final size:42
Alignment explanation
Indices: 1760024--1760138 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 42
1760014 AATTTATTTA
* * *
1760024 TTATTTTT-TTTATCT-TGTAATTTTTTTTTGATTTATCTTATT
1 TTATTTTTAATTATCTGT-TAATTTTTTTTTCATTTATCTGA-T
1760066 TTATTTTTAATTATCTGTTAATTTTTTTTTCATTTATCTGA-
1 TTATTTTTAATTATCTGTTAATTTTTTTTTCATTTATCTGAT
* *
1760107 TT-TTTTTATTTATCTGATTATTCTTTTTTTTC
1 TTATTTTTAATTATCTG-TTAAT-TTTTTTTTC
1760139 TTTTTTTGGG
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
40 13 0.20
41 6 0.09
42 17 0.27
43 27 0.42
44 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.71
Consensus pattern (42 bp):
TTATTTTTAATTATCTGTTAATTTTTTTTTCATTTATCTGAT
Found at i:1760997 original size:27 final size:27
Alignment explanation
Indices: 1760954--1761006 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1760944 CGCTTCAAAA
* *
1760954 TTTTTTTTAATTTATTAATTTTATTTG
1 TTTTTTTTAATTGATTAAGTTTATTTG
*
1760981 TTTTTTTT-ATTAGATTAGGTTTATTT
1 TTTTTTTTAATT-GATTAAGTTTATTT
1761007 AATATTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (27 bp):
TTTTTTTTAATTGATTAAGTTTATTTG
Found at i:1761158 original size:59 final size:58
Alignment explanation
Indices: 1761107--1761518 Score: 395
Period size: 59 Copynumber: 6.8 Consensus size: 58
1761097 AAAAAAAAAA
* *
1761107 TTCAAAAAAAAGGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATT
1 TTCAAAAAAAA-TATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGT
* *
1761167 TTCAAAAAAAA-GTTTTTGAGAAAAAGTTGAAAGTATCAATACTTTCAACTTTTCTTAAAAATCA
1 TTCAAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATC-A-A---T----TTTTCTTAAAAAT-A
1761231 AAGT
55 AAGT
* * *
1761235 TTCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATTAAAATT
1 TTC--AAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAAAT-AAAGT
*
1761298 TTC--AAAAAATATTTTTAGTGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGT
1 TTCAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAGT
* * **
1761356 TTCAAAAAAAAACATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGT
1 TTC-AAAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAGT
* * * * *
1761417 TTC-TAAAAAATATTTTTGGGAAAAAGTTAAAAATATCAATTTTCCTTAAAAATAAATT
1 TTCAAAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGT
*
1761475 TTC--AAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTTTC
1 TTCAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTC
1761519 CTGCACAAAA
Statistics
Matches: 302, Mismatches: 29, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
57 36 0.12
58 44 0.15
59 85 0.28
60 14 0.05
61 50 0.17
62 6 0.02
63 13 0.04
66 1 0.00
67 13 0.04
68 7 0.02
69 1 0.00
70 9 0.03
71 22 0.07
72 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (58 bp):
TTCAAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAGT
Found at i:1761391 original size:120 final size:119
Alignment explanation
Indices: 1761107--1761516 Score: 440
Period size: 120 Copynumber: 3.4 Consensus size: 119
1761097 AAAAAAAAAA
** * ** *
1761107 TTCAAAAAAAAGGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTTTC-
1 TTCAAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCT
* * *
1761170 AAAAAAAAGTTTTTGAGAAAAAGTTGAAAGTATCAATACTTTCAACTTTTCTTAAAAATCAAAGT
65 AAAAAATA-TTTTTGGGAAAAAGTT--AA--A--AATA---TCAATTTTTCTTAAAAATCAAAGT
* *
1761235 TTCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATTAAAATTTT
1 TTC-AAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAA-TAAAAGTTT
* * *
1761300 C-AAAAAATATTTTTAGTG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAAGT
63 CTAAAAAATATTTTT-GGGAAAAAGTTAAAAATATCAATTTTTCTTAAAAATCAAAGT
* *
1761356 TTCAAAAAAAAACATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAGTTTCT
1 TTCAAAAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCT
* *
1761421 AAAAAATATTTTTGGGAAAAAGTTAAAAATATCAATTTTCCTTAAAAAT-AAATT
65 AAAAAATATTTTTGGGAAAAAGTTAAAAATATCAATTTTTCTTAAAAATCAAAGT
*
1761475 TTC---AAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTT
1 TTCAAAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTT
1761517 TCCTGCACAA
Statistics
Matches: 253, Mismatches: 21, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
116 33 0.13
117 3 0.01
119 20 0.08
120 87 0.34
121 26 0.10
124 3 0.01
126 1 0.00
128 4 0.02
129 46 0.18
130 13 0.05
131 17 0.07
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (119 bp):
TTCAAAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCTA
AAAAATATTTTTGGGAAAAAGTTAAAAATATCAATTTTTCTTAAAAATCAAAGT
Found at i:1761476 original size:17 final size:18
Alignment explanation
Indices: 1761443--1761477 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1761433 TGGGAAAAAG
1761443 TTAAAAATATCAATTTTCC
1 TTAAAAATA-CAATTTTCC
1761462 TTAAAAATA-AATTTTC
1 TTAAAAATACAATTTTC
1761478 AAAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAAATACAATTTTCC
Found at i:1769934 original size:7 final size:8
Alignment explanation
Indices: 1769923--1769961 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
1769913 AAAAATGGAA
1769923 AAAAAATC
1 AAAAAATC
1769931 AAAAAATC
1 AAAAAATC
*
1769939 AAAAAATGG
1 AAAAAAT-C
1769948 AAAAAATC
1 AAAAAATC
1769956 AAAAAA
1 AAAAAA
1769962 AATGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAATC
Found at i:1769942 original size:17 final size:18
Alignment explanation
Indices: 1769922--1769971 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1769912 AAAAAATGGA
1769922 AAAAAAAT-CAAAAAATC
1 AAAAAAATGCAAAAAATC
*
1769939 -AAAAAATGGAAAAAATC
1 AAAAAAATGCAAAAAATC
1769956 AAAAAAAATG-AAAAAA
1 -AAAAAAATGCAAAAAA
1769972 GAGGACTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 6 0.21
19 8 0.28
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (18 bp):
AAAAAAATGCAAAAAATC
Found at i:1769943 original size:19 final size:19
Alignment explanation
Indices: 1769902--1769944 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1769892 TACTATGCTT
* * **
1769902 AAAAATAATGAAAAAATGG
1 AAAAAAAATCAAAAAATCA
1769921 AAAAAAAATCAAAAAATCA
1 AAAAAAAATCAAAAAATCA
1769940 AAAAA
1 AAAAA
1769945 TGGAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAAAAATCAAAAAATCA
Found at i:1769962 original size:27 final size:25
Alignment explanation
Indices: 1769902--1769971 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 25
1769892 TACTATGCTT
*
1769902 AAAAATAATGAAAAAATGGAAAAAA
1 AAAAAAAATGAAAAAATGGAAAAAA
*
1769927 AATCAAAAAATCAAAAAATGGAAAAAA
1 AA--AAAAAATGAAAAAATGGAAAAAA
1769954 TCAAAAAAAATGAAAAAA
1 --AAAAAAAATGAAAAAA
1769972 GAGGACTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
27 34 0.89
29 2 0.05
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (25 bp):
AAAAAAAATGAAAAAATGGAAAAAA
Found at i:1771200 original size:41 final size:40
Alignment explanation
Indices: 1770959--1771226 Score: 313
Period size: 42 Copynumber: 6.5 Consensus size: 40
1770949 GATTGTCAAT
* *
1770959 GAGCAATTTATTTTCCAAAGTTTCGTTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGTTT-GGTGCCTCTGTTTAGAG
*
1771000 GAGCAATTTAC-TTCCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGT-TTGGTGCCTCTGTTTAGAG
* * * *
1771040 GAGTAATTTACTTTCTCAAAGTCGTGGTGCCTTTATTTAGAG
1 GAGCAATTTACTTTC-CAAAGT-TTGGTGCCTCTGTTTAGAG
* *
1771082 AAGCAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTAC-TTTCCAAAGT-TTGGTGCCTCTGTTTAGAG
* *
1771124 GAGCAATTTATTTTTCTAAAGTTGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTA-CTTTCCAAAGTT-TGGTGCCTCTGTTTAGAG
* * *
1771166 GAGCAATTTACTTTCCAAAGTTTCGTTACGTCTGTTTAGAG
1 GAGCAATTTACTTTCCAAAGTTT-GGTGCCTCTGTTTAGAG
*
1771207 GAGCAATTTACTTTTCAAAG
1 GAGCAATTTACTTTCCAAAG
1771227 GCACCAATTT
Statistics
Matches: 198, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
40 36 0.18
41 57 0.29
42 101 0.51
43 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (40 bp):
GAGCAATTTACTTTCCAAAGTTTGGTGCCTCTGTTTAGAG
Found at i:1771342 original size:41 final size:41
Alignment explanation
Indices: 1771231--1771436 Score: 250
Period size: 43 Copynumber: 4.9 Consensus size: 41
1771221 TCAAAGGCAC
1771231 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
1 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
* *
1771272 CAATTTACTTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAG
1 CAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
*
1771314 CAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
1 CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
* * * * * *
1771355 CAATTTATTATTTTTAAAGTTGTTGAGCCTCTGATTAGAGGAG
1 CAATTTA--CTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
* * * *
1771398 CCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGA
1 CAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAGA
1771437 TGAGGTTTGG
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
41 45 0.31
42 43 0.30
43 56 0.39
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
CAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
Found at i:1771361 original size:145 final size:145
Alignment explanation
Indices: 1771085--1771361 Score: 443
Period size: 145 Copynumber: 1.9 Consensus size: 145
1771075 TTTAGAGAAG
**
1771085 CAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCTAAAGTTGTG
1 CAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCTAAAGTCATG
* *
1771150 GTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTTCGTTACGTCTGTTTAGAGGAGCAATT
66 GTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAG-TTCGTTACCTCTGTTTAGAGGAGCAATT
1771215 TACTTTTCAAAGGCAC
130 TACTTTTCAAAGGCAC
*
1771231 CAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTC-AAAGTCAT
1 CAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCTAAAGTCAT
*
1771294 GGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAA
65 GGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAGTTCGT--TACCTCTGTTTAGAGGAGCAA
1771358 TTTA
128 TTTA
1771362 TTATTTTTAA
Statistics
Matches: 122, Mismatches: 6, Indels: 7
0.90 0.04 0.05
Matches are distributed among these distances:
143 4 0.03
145 100 0.82
146 18 0.15
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (145 bp):
CAATTTACTTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCTAAAGTCATG
GTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAGTTCGTTACCTCTGTTTAGAGGAGCAATTT
ACTTTTCAAAGGCAC
Found at i:1771810 original size:26 final size:27
Alignment explanation
Indices: 1771759--1771830 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
1771749 TGTTAATATT
*
1771759 TATATGTATT-TTAT-TTATATAGTTA
1 TATATTTATTATTATATTATATAGTTA
*
1771784 TATATTTATTATTATATTATA-ATTTA
1 TATATTTATTATTATATTATATAGTTA
*
1771810 TTTATTTATTATTATTATTAT
1 TATATTTATTATTA-TATTAT
1771831 TTATCTTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 9 0.22
26 21 0.51
27 11 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
TATATTTATTATTATATTATATAGTTA
Found at i:1771869 original size:44 final size:43
Alignment explanation
Indices: 1771809--1771909 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 43
1771799 ATTATAATTT
* *
1771809 ATTTAT-TTATTATTATTATTATTTATCT-TGTAATATTTTTTTGG
1 ATTTATCTTATTATTATTATTAATTATCTGT-TAAT-TTTTTTT-C
*
1771853 ATTTATCTTATT-TTATTTTTAATTATCTGTTAATTTTTTTTC
1 ATTTATCTTATTATTATTATTAATTATCTGTTAATTTTTTTTC
*
1771895 ATTTATCTGATTATT
1 ATTTATCTTATTATT
1771910 TTTTTTCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
42 11 0.22
43 9 0.18
44 24 0.48
45 6 0.12
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (43 bp):
ATTTATCTTATTATTATTATTAATTATCTGTTAATTTTTTTTC
Found at i:1771911 original size:21 final size:20
Alignment explanation
Indices: 1771806--1771914 Score: 71
Period size: 22 Copynumber: 5.2 Consensus size: 20
1771796 TATATTATAA
*
1771806 TTTATTTAT-TTATTATTATT
1 TTTATTTATCTGATTATT-TT
* *
1771826 ATTATTTATCTTGTAATATTTT
1 TTTATTTATC-TG-ATTATTTT
*
1771848 TTTGGATTTATCTTATT-TTATT
1 TTT--ATTTATCTGATTATT-TT
*
1771870 TTTAATTATCTG-TTAATTTTT
1 TTTATTTATCTGATT-A-TTTT
1771891 TTTCATTTATCTGATTATTTT
1 TTT-ATTTATCTGATTATTTT
1771912 TTT
1 TTT
1771915 TCTTTTTTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
19 2 0.03
20 15 0.22
21 14 0.20
22 23 0.33
23 8 0.12
24 7 0.10
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTATTTATCTGATTATTTT
Found at i:1772803 original size:24 final size:24
Alignment explanation
Indices: 1772767--1772813 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1772757 GCCGCTCCAG
* *
1772767 ATTTTTTTTTTTTTGGATTTATTT
1 ATTTATTTGTTTTTGGATTTATTT
**
1772791 ATTTATTTGTTTTTTTATTTATT
1 ATTTATTTGTTTTTGGATTTATT
1772814 AGATTAGGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (24 bp):
ATTTATTTGTTTTTGGATTTATTT
Found at i:1773144 original size:59 final size:57
Alignment explanation
Indices: 1772942--1773206 Score: 336
Period size: 57 Copynumber: 4.5 Consensus size: 57
1772932 AAAAAAGGGG
* * *
1772942 TTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAATTTCCAAAAAAATA
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTCC-AAAAAATA
* *
1773002 TTTTTAGGGAAAAGTTGAAAGTATCAAATTTCCTTAAAAATAAATTTTCAAAAAA-A
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAATA
* * * *
1773058 GGGTTTT-GAAGAAAATTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAATA
1 --TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAA-TTTCCAAAAAATA
* * *
1773119 TTTTTGGGGAAAAGTTGAAAATATCAATTTTCCTTAAAAATAAATTTCTAAAAAATA
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAATA
1773176 TTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1773207 TTCTGCACAA
Statistics
Matches: 179, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.01
57 48 0.27
58 44 0.25
59 37 0.21
60 48 0.27
61 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (57 bp):
TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAATA
Found at i:1773151 original size:117 final size:117
Alignment explanation
Indices: 1772918--1773206 Score: 422
Period size: 117 Copynumber: 2.5 Consensus size: 117
1772908 TATTATTTTT
* *
1772918 TTAAAAA-AAATTTCAAAAAAGGGGTTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAA
1 TTAAAAATAAATTTCAAAAAAAGGGTTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAA
*
1772982 TCAAAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAAATTTCC
65 TCAAAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAATATCAAATTTCC
* * *
1773035 TTAAAAATAAATTTTCAAAAAAAGGGTTTTGAAGAAAATTTGAAAGTATCAATTTTCCTTGAAAA
1 TTAAAAATAAA-TTTCAAAAAAAGGGTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA
* * *
1773100 TCAAAGTTTCC-AAAAAATATTTTTGGGGAAAAGTTGAAAATATCAATTTTCC
65 TCAAAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAATATCAAATTTCC
* **
1773152 TTAAAAATAAATTTCTAAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1 TTAAAAATAAATTTCAAAAAAAGGGTTTTTA-GGAAAAGTTGAAAGTATCAATTTT
1773207 TTCTGCACAA
Statistics
Matches: 154, Mismatches: 15, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
115 5 0.03
116 32 0.21
117 56 0.36
118 42 0.27
119 19 0.12
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (117 bp):
TTAAAAATAAATTTCAAAAAAAGGGTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
CAAAATTTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAATATCAAATTTCC
Found at i:1773209 original size:59 final size:59
Alignment explanation
Indices: 1772942--1773206 Score: 340
Period size: 59 Copynumber: 4.5 Consensus size: 59
1772932 AAAAAAGGGG
* * * *
1772942 TTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAATTTCCAAAAAAATA
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTT-CAAAAAAATA
* * **
1773002 TTTTTAGGGAAAAGTTGAAAGTATCAAATTTCCTTAAAAAT-AAATTTTCAAAAAAAGG
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAATA
* * * * *
1773060 GTTTT-GAAGAAAATTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAATA
1 TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAATA
* * *
1773119 TTTTTGGGGAAAAGTTGAAAATATCAATTTTCCTTAAAAAT-AAA-TTTCTAAAAAATA
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAATA
1773176 TTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1 TTTTTAGGGAAAAGTTGAAAGTATCAATTTT
1773207 TTCTGCACAA
Statistics
Matches: 178, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
57 42 0.24
58 45 0.25
59 53 0.30
60 38 0.21
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (59 bp):
TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTCAAAAAAATA
Found at i:1777474 original size:12 final size:12
Alignment explanation
Indices: 1777457--1777493 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1777447 TATCAGCTTG
1777457 AATTTTTATTAA
1 AATTTTTATTAA
1777469 AATTTTTATT-A
1 AATTTTTATTAA
1777480 AATTATTT-TTAA
1 AATT-TTTATTAA
1777492 AA
1 AA
1777494 AGAAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTTTTATTAA
Found at i:1778474 original size:18 final size:18
Alignment explanation
Indices: 1778440--1778478 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1778430 TTTTATTTTA
*
1778440 TTTTTATTAATTTAATAT
1 TTTTTATTAATTAAATAT
1778458 TTTTTATT-ATTAAAATAT
1 TTTTTATTAATT-AAATAT
1778476 TTT
1 TTT
1778479 AAAGTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATTAATTAAATAT
Found at i:1782798 original size:23 final size:22
Alignment explanation
Indices: 1782757--1782799 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1782747 ATAAATTTCT
*
1782757 TTTTAAGTTTAAAATTATCAAA
1 TTTTAAGTTTAAAACTATCAAA
*
1782779 TTTTAAGTTTAACTACTATCA
1 TTTTAAGTTTAA-AACTATCA
1782800 TCTAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
TTTTAAGTTTAAAACTATCAAA
Found at i:1789070 original size:15 final size:15
Alignment explanation
Indices: 1789050--1789080 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1789040 TTGAGTTCAT
1789050 TTGAAGATGAGAAAG
1 TTGAAGATGAGAAAG
1789065 TTGAAGATGAGAAAG
1 TTGAAGATGAGAAAG
1789080 T
1 T
1789081 GGGAGGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (15 bp):
TTGAAGATGAGAAAG
Found at i:1792591 original size:14 final size:14
Alignment explanation
Indices: 1792574--1792603 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1792564 TTTCCTCACG
1792574 TTTTTTATTTAATT
1 TTTTTTATTTAATT
1792588 TTTTTTATTTAATT
1 TTTTTTATTTAATT
1792602 TT
1 TT
1792604 ATAGTTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTAATT
Found at i:1792639 original size:3 final size:3
Alignment explanation
Indices: 1792631--1792672 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1792621 CGATGGTCCA
1792631 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1792673 AATAAGGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1793437 original size:21 final size:22
Alignment explanation
Indices: 1793391--1793437 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1793381 CAGGCCAGCA
1793391 AAAGCAACAAGAGCAAGAAGAG
1 AAAGCAACAAGAGCAAGAAGAG
*
1793413 -AAGCAAACAATAG-AA-AAGAG
1 AAAGC-AACAAGAGCAAGAAGAG
1793433 AAAGC
1 AAAGC
1793438 CAGTGTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.62, C:0.13, G:0.23, T:0.02
Consensus pattern (22 bp):
AAAGCAACAAGAGCAAGAAGAG
Found at i:1798859 original size:14 final size:14
Alignment explanation
Indices: 1798842--1798874 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1798832 AATATGTTTG
1798842 AATAAAAAAATAAA
1 AATAAAAAAATAAA
1798856 AATAAAAAAATAAA
1 AATAAAAAAATAAA
1798870 AATAA
1 AATAA
1798875 GTATAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:1804307 original size:38 final size:39
Alignment explanation
Indices: 1804264--1804338 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
1804254 TTTACCTTTA
1804264 AATAAGTACTGATTAAATTTTAG-TTAGATATTTTTATG
1 AATAAGTACTGATTAAATTTTAGATTAGATATTTTTATG
* *
1804302 AATAAGTATTGATTAAATTTTTGATTAGATATTTTTA
1 AATAAGTACTGATTAAATTTTAGATTAGATATTTTTA
1804339 ATAATTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 21 0.62
39 13 0.38
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.49
Consensus pattern (39 bp):
AATAAGTACTGATTAAATTTTAGATTAGATATTTTTATG
Found at i:1804864 original size:24 final size:24
Alignment explanation
Indices: 1804837--1804884 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1804827 AAGAGTTTAT
*
1804837 ATTTAATACACTATCAGTATATAA
1 ATTTAATACACTATCAGTAAATAA
* * *
1804861 ATTTTATATACTATTAGTAAATAA
1 ATTTAATACACTATCAGTAAATAA
1804885 GATGATACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTTAATACACTATCAGTAAATAA
Found at i:1805721 original size:24 final size:24
Alignment explanation
Indices: 1805694--1805745 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
1805684 AAAACTAAAG
1805694 AAGTTG-ATTTTCTTTGTGCTAA-TT
1 AAGTTGAATTTT-TTTGTGC-AATTT
1805718 AAG-TGAATTTTTTTGTGCAATTT
1 AAGTTGAATTTTTTTGTGCAATTT
1805741 AAGTT
1 AAGTT
1805746 TTGCTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.08
23 14 0.56
24 9 0.36
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (24 bp):
AAGTTGAATTTTTTTGTGCAATTT
Found at i:1805742 original size:23 final size:24
Alignment explanation
Indices: 1805700--1805744 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1805690 AAAGAAGTTG
1805700 ATTTTCTTTGTGCTAATTAAGTGA
1 ATTTTCTTTGTGCTAATTAAGTGA
1805724 ATTTT-TTTGTGC-AATTTAAGT
1 ATTTTCTTTGTGCTAA-TTAAGT
1805745 TTTGCTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.53
Consensus pattern (24 bp):
ATTTTCTTTGTGCTAATTAAGTGA
Found at i:1809554 original size:23 final size:22
Alignment explanation
Indices: 1809506--1809589 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 22
1809496 GTATATTTAG
*
1809506 ATAATTTT-TTA-ATAAATATA
1 ATAATTTTATTATTTAAATATA
*
1809526 TTAATTTTAATTAATTTAAA-ATA
1 ATAATTTT-ATT-ATTTAAATATA
1809549 ATAATTTTATTATTT-AATA-A
1 ATAATTTTATTATTTAAATATA
*
1809569 A-AAATTTATT-TATTAAATATA
1 ATAATTTTATTAT-TTAAATATA
1809590 TAAAAAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
18 1 0.02
19 10 0.19
20 15 0.29
21 6 0.12
22 5 0.10
23 11 0.21
24 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTTTATTATTTAAATATA
Found at i:1819751 original size:7 final size:7
Alignment explanation
Indices: 1819741--1819778 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1819731 CCCGATCCTT
1819741 GATCCAA
1 GATCCAA
1819748 GATCCAA
1 GATCCAA
1819755 GATCCAA
1 GATCCAA
1819762 GATCCAA
1 GATCCAA
1819769 GATCCAA
1 GATCCAA
1819776 GAT
1 GAT
1819779 AGAGAGATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (7 bp):
GATCCAA
Found at i:1820511 original size:2 final size:2
Alignment explanation
Indices: 1820504--1820534 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1820494 CCCTTATCTA
1820504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1820535 ACAGTATACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1821620 original size:17 final size:18
Alignment explanation
Indices: 1821598--1821631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1821588 TAACAAATCA
1821598 ATATA-TAAAAATTTTAT
1 ATATATTAAAAATTTTAT
*
1821615 ATATATTATAAATTTTA
1 ATATATTAAAAATTTTA
1821632 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATTAAAAATTTTAT
Found at i:1834055 original size:2 final size:2
Alignment explanation
Indices: 1834048--1834078 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1834038 CCCTTATCTA
1834048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1834079 ACAGTATACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1835158 original size:17 final size:18
Alignment explanation
Indices: 1835136--1835169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1835126 TAACAAATCA
1835136 ATATA-TAAAAATTTTAT
1 ATATATTAAAAATTTTAT
*
1835153 ATATATTATAAATTTTA
1 ATATATTAAAAATTTTA
1835170 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATTAAAAATTTTAT
Found at i:1844108 original size:105 final size:105
Alignment explanation
Indices: 1843985--1844197 Score: 372
Period size: 105 Copynumber: 2.0 Consensus size: 105
1843975 CATCATAAGC
*
1843985 TCCTAACCAAGAAATAATTCTAATTATTCATAAAAGGCAACATAACATTATTCCAACCAACCACA
1 TCCTAACCAAGAAATAATTCTAATTATTCATAAAAGGCAACATAAAATTATTCCAACCAACCACA
* *
1844050 TTGAGAACATTCATTATGTTAGTGGCATCCAGTATTTTCA
66 TTGAAAACATTCATTATATTAGTGGCATCCAGTATTTTCA
* * *
1844090 TCCTAACCAAGAAATAATTCTGATTATTCATTAAAGGGAACATAAAATTATTCCAACCAACCACA
1 TCCTAACCAAGAAATAATTCTAATTATTCATAAAAGGCAACATAAAATTATTCCAACCAACCACA
1844155 TTGAAAACATTCATTATATTAGTGGCATCCAGTATTTTCA
66 TTGAAAACATTCATTATATTAGTGGCATCCAGTATTTTCA
1844195 TCC
1 TCC
1844198 AAATGTTTGA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (105 bp):
TCCTAACCAAGAAATAATTCTAATTATTCATAAAAGGCAACATAAAATTATTCCAACCAACCACA
TTGAAAACATTCATTATATTAGTGGCATCCAGTATTTTCA
Found at i:1848853 original size:17 final size:17
Alignment explanation
Indices: 1848831--1848864 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1848821 AAGATGCACC
*
1848831 TGTAAAAAAATAAAACT
1 TGTAAAAAAAAAAAACT
1848848 TGTAAAAAAAAAAAACT
1 TGTAAAAAAAAAAAACT
1848865 AAAAACAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
TGTAAAAAAAAAAAACT
Found at i:1851457 original size:31 final size:31
Alignment explanation
Indices: 1851386--1851486 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
1851376 TGTGGATTTG
* * **
1851386 AAAATTTATATATTTGTATTATATAAAATAT
1 AAAATATATATATTTATATTATATTTAATAT
* *
1851417 -TAATAATATATATTTATATTATATTTTATAT
1 AAAAT-ATATATATTTATATTATATTTAATAT
1851448 AAAATATATATA-TTATAATT-TATATTAATAT
1 AAAATATATATATTTAT-ATTATAT-TTAATAT
1851479 AAAATATA
1 AAAATATA
1851487 AAATAAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
30 10 0.17
31 45 0.78
32 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
AAAATATATATATTTATATTATATTTAATAT
Found at i:1851485 original size:29 final size:29
Alignment explanation
Indices: 1851412--1851504 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 29
1851402 TATTATATAA
1851412 AATATTAATAATATATATT-T-ATATTATATTT
1 AATA-TAA-AATATATATTATAAT-TTATA-TT
*
1851443 TATATAAAATATATATATTATAATTTATATT
1 AATAT-AAA-ATATATATTATAATTTATATT
* * * *
1851474 AATATAAAATATAAAATAAAATTTTTATT
1 AATATAAAATATATATTATAATTTATATT
1851503 AA
1 AA
1851505 AATTTTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 19 0.37
30 5 0.10
31 20 0.38
32 6 0.12
33 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATAAAATATATATTATAATTTATATT
Found at i:1851486 original size:38 final size:38
Alignment explanation
Indices: 1851406--1851491 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
1851396 TATTTGTATT
***
1851406 ATATAAAATATTAATAATATATATTTATATTATATTTT
1 ATATAAAATATTAATAATATATATTTATATTATATAAA
*
1851444 ATATAAAATA-TATATATTATA-ATTTATATTAATATAAA
1 ATATAAAATATTA-ATAATATATATTTATATT-ATATAAA
1851482 ATATAAAATA
1 ATATAAAATA
1851492 AAATTTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 11 0.26
38 31 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
ATATAAAATATTAATAATATATATTTATATTATATAAA
Found at i:1851532 original size:24 final size:24
Alignment explanation
Indices: 1851505--1851553 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1851495 TTTTTATTAA
*
1851505 AATTTTAAATTATGTTATTTTTAT
1 AATTTTAAATTATATTATTTTTAT
* *
1851529 AATTTTTATTTATATTATTTTTAT
1 AATTTTAAATTATATTATTTTTAT
1851553 A
1 A
1851554 TAATATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATTTTAAATTATATTATTTTTAT
Found at i:1851537 original size:15 final size:15
Alignment explanation
Indices: 1851519--1851552 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1851509 TTAAATTATG
*
1851519 TTATTTTTATAATTT
1 TTATTTATATAATTT
*
1851534 TTATTTATATTATTT
1 TTATTTATATAATTT
1851549 TTAT
1 TTAT
1851553 ATAATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATATAATTT
Found at i:1851919 original size:14 final size:14
Alignment explanation
Indices: 1851900--1851927 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1851890 TGTAAGCAAC
1851900 ATCTTTCTCTTAAA
1 ATCTTTCTCTTAAA
1851914 ATCTTTCTCTTAAA
1 ATCTTTCTCTTAAA
1851928 TATGATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCTTTCTCTTAAA
Found at i:1852533 original size:10 final size:10
Alignment explanation
Indices: 1852508--1852534 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1852498 AAAAAAAGTC
1852508 AAAAAAATAA
1 AAAAAAATAA
1852518 AAAAAAATAA
1 AAAAAAATAA
1852528 AAAAAAA
1 AAAAAAA
1852535 GTTGATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Done.