Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001519.1 Hibiscus syriacus cultivar Beakdansim tig00002967_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: 75413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:946 original size:12 final size:12
Alignment explanation
Indices: 929--953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
919 TAACGCATAC
929 GTGTCGTATTTG
1 GTGTCGTATTTG
941 GTGTCGTATTTG
1 GTGTCGTATTTG
953 G
1 G
954 GATATCGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (12 bp):
GTGTCGTATTTG
Found at i:1201 original size:20 final size:20
Alignment explanation
Indices: 1178--1216 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1168 ACTCAGTTTC
1178 TAAAATTCGCAACGCGATTG
1 TAAAATTCGCAACGCGATTG
*
1198 TAAAATTCGCAATGCGATT
1 TAAAATTCGCAACGCGATT
1217 TTGAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (20 bp):
TAAAATTCGCAACGCGATTG
Found at i:1270 original size:21 final size:21
Alignment explanation
Indices: 1216--1270 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
1206 GCAATGCGAT
* *
1216 TTTGAAAATGTGTTGCGATAG
1 TTTGAAAACGTGTTGCGAGAG
1237 -TT--AAACTGTGTTGCGAGAG
1 TTTGAAAAC-GTGTTGCGAGAG
1256 TTTGAAAACGTGTTG
1 TTTGAAAACGTGTTG
1271 TTGTGATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.11
19 11 0.39
20 4 0.14
21 6 0.21
22 4 0.14
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.36
Consensus pattern (21 bp):
TTTGAAAACGTGTTGCGAGAG
Found at i:1711 original size:21 final size:21
Alignment explanation
Indices: 1687--1737 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1677 AATTTAGAAA
* **
1687 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTAAACT
*
1708 ATCGCAACGTGAACTTAAACT
1 ATCGCAACGCGAACTTAAACT
1729 ATCGCAACG
1 ATCGCAACG
1738 AATTTGGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAAACT
Found at i:1818 original size:41 final size:41
Alignment explanation
Indices: 1768--1858 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
1758 GAAAATCGTG
* *
1768 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCA
1 TTGCGATTTTGTATTATCGCGTTGCAATAGTCAGAATAGCA
*
1809 TTGCGATTTTGTATTATCGCGTTGCAATAGTCAGAATAGCG
1 TTGCGATTTTGTATTATCGCGTTGCAATAGTCAGAATAGCA
1850 TTGCGATTT
1 TTGCGATTT
1859 ATTCGCGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCAATAGTCAGAATAGCA
Found at i:1833 original size:21 final size:21
Alignment explanation
Indices: 1762--1833 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1752 TAATTTGAAA
*
1762 ATCGTGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
1783 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
1803 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
1824 ATCGCGTTGC
1 ATCGCGTTGC
1834 AATAGTCAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 21 0.54
22 3 0.08
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:3537 original size:23 final size:23
Alignment explanation
Indices: 3501--3545 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3491 ATTAATCTTC
**
3501 AGAAATATTTAATA-TTAATTTAT
1 AGAAATATAAAATAGTT-ATTTAT
3524 AGAAATATAAAATAGTTATTTA
1 AGAAATATAAAATAGTTATTTA
3546 ATTAGTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
AGAAATATAAAATAGTTATTTAT
Found at i:4279 original size:33 final size:31
Alignment explanation
Indices: 4226--4286 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
4216 CCCCGTCAAT
** *
4226 TATATTTTTAATTATTAATAATATACAAAAAAA
1 TATATTTTTAAAAATAAATAA-ATA-AAAAAAA
4259 TATATTTTTAAAAATAAATAAATAAAAA
1 TATATTTTTAAAAATAAATAAATAAAAA
4287 TTTATCAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 3 0.12
33 18 0.72
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TATATTTTTAAAAATAAATAAATAAAAAAAA
Found at i:22187 original size:24 final size:24
Alignment explanation
Indices: 22133--22189 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
22123 TCCGGTTCAA
*
22133 TCTCCGATTTAGCCTCTTGTTTGG
1 TCTCCGGTTTAGCCTCTTGTTTGG
*
22157 TATCCGGTTTAGCCTCTTGTTTGG
1 TCTCCGGTTTAGCCTCTTGTTTGG
22181 TCTCCGGTT
1 TCTCCGGTT
22190 CCGGCATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (24 bp):
TCTCCGGTTTAGCCTCTTGTTTGG
Found at i:27615 original size:23 final size:27
Alignment explanation
Indices: 27589--27654 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 27
27579 ATTAATTGCT
27589 ATATTAATTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTAATATTAAATTATAG
*
27612 ATATTAATTTTTAATATTATATTATAG
1 ATATTAATTTTTAATATTAAATTATAG
27639 ATATTAA-TTTTAATAT
1 ATATTAATTTTTAATAT
27655 AATTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 14 0.37
24 1 0.03
25 6 0.16
26 10 0.26
27 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATATTAATTTTTAATATTAAATTATAG
Found at i:27635 original size:62 final size:60
Alignment explanation
Indices: 27559--27708 Score: 223
Period size: 62 Copynumber: 2.5 Consensus size: 60
27549 AGGTTTTATA
*
27559 TTTAATTTTATATTATAGATATTAATTGCT-ATATTAA-TTTTTAAATAAATTAAATATTAATT
1 TTTAATATTATATTATAGATATTAATT-CTAATA-TAATTTTTTAAATAAATT-AATA-TAATT
*
27621 TTTAATATTATATTATAGATATTAATTTTAATATAATTTTTTAAATAAATTAATATAATT
1 TTTAATATTATATTATAGATATTAATTCTAATATAATTTTTTAAATAAATTAATATAATT
27681 TTTAATATTATATTATAGATATTTAATT
1 TTTAATATTATATTATAGATA-TTAATT
27709 TTATATCATA
Statistics
Matches: 83, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
60 26 0.31
61 14 0.17
62 43 0.52
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (60 bp):
TTTAATATTATATTATAGATATTAATTCTAATATAATTTTTTAAATAAATTAATATAATT
Found at i:27661 original size:12 final size:12
Alignment explanation
Indices: 27593--27688 Score: 60
Period size: 12 Copynumber: 8.1 Consensus size: 12
27583 ATTGCTATAT
27593 TAATTTTTAA-A
1 TAATTTTTAATA
* *
27604 TAA-ATTAAATA
1 TAATTTTTAATA
27615 TTAATTTTTAATA
1 -TAATTTTTAATA
* *
27628 TTATATTATAGATA
1 TAAT-TTTTA-ATA
27642 TTAA-TTTTAATA
1 -TAATTTTTAATA
27654 TAATTTTTTAA-A
1 TAA-TTTTTAATA
*
27666 TAA--ATTAATA
1 TAATTTTTAATA
27676 TAATTTTTAATA
1 TAATTTTTAATA
27688 T
1 T
27689 TATATTATAG
Statistics
Matches: 64, Mismatches: 10, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
9 4 0.06
10 8 0.12
11 7 0.11
12 20 0.31
13 20 0.31
14 3 0.05
15 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (12 bp):
TAATTTTTAATA
Found at i:27749 original size:60 final size:58
Alignment explanation
Indices: 27559--27744 Score: 171
Period size: 62 Copynumber: 3.0 Consensus size: 58
27549 AGGTTTTATA
* * *
27559 TTTAATTTTATATTATAGATATTAATTGCT-ATATTAATT-TTTAAATAAATTAAATATTAATT
1 TTTAATATTATATTATAGATATTAATT-TTAATA-TAATTATTT-AATAAATT-AATA-CAA-T
* *
27621 TTTAATATTATATTATAGATATTAATTTTAATATAATTTTTTAAATAAATTAATATAATT
1 TTTAATATTATATTATAGATATTAATTTTAATATAATTATTT-AATAAATTAATACAA-T
* *
27681 TTTAATATTATATTATAGATATTTAATTTTATATCATATAATTATTT-ATATATTATTACAAT
1 TTTAATATTATATTATAGATA-TTAA-TTT-TA--ATATAATTATTTAATAAATTAATACAAT
27743 TT
1 TT
27745 ATATTTATTT
Statistics
Matches: 111, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
60 26 0.23
61 14 0.13
62 47 0.42
63 13 0.12
65 11 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (58 bp):
TTTAATATTATATTATAGATATTAATTTTAATATAATTATTTAATAAATTAATACAAT
Found at i:28424 original size:31 final size:31
Alignment explanation
Indices: 28366--28425 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28356 TAGTTGTATG
* **
28366 AATTATTTAAATTTCAGTATTGGAAAACTAA
1 AATTATTTAAATATCAGTATTACAAAACTAA
28397 AATTATTTAAATATCAGTATTACAAAACT
1 AATTATTTAAATATCAGTATTACAAAACT
28426 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
AATTATTTAAATATCAGTATTACAAAACTAA
Found at i:28696 original size:159 final size:160
Alignment explanation
Indices: 28406--28724 Score: 631
Period size: 159 Copynumber: 2.0 Consensus size: 160
28396 AAATTATTTA
28406 AATATCAGTATTACAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAGTTTATTTT
1 AATATCAGTATTACAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAGTTTATTTT
28471 AGCAGTCTGCAGACGTTAAAAAACAAACAGTCTTCTTCTTGCATACTGCAAACTTTTGGTCCACC
66 AGCAGTCTGCAGACGTTAAAAAACAAACAGTCTTCTTCTTGCATACTGCAAACTTTTGGTCCACC
28536 TCTTCTGCTGCAGATGTATGCGGATGTGAT
131 TCTTCTGCTGCAGATGTATGCGGATGTGAT
28566 AATATCAGTATTACAAAACTCTTTTAAGTTT-AAAAATCAGTTTATTTATATTTCAGTTTATTTT
1 AATATCAGTATTACAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAGTTTATTTT
28630 AGCAGTCTGCAGACGTTAAAAAACAAACAGTCTTCTTCTTGCATACTGCAAACTTTTGGTCCACC
66 AGCAGTCTGCAGACGTTAAAAAACAAACAGTCTTCTTCTTGCATACTGCAAACTTTTGGTCCACC
28695 TCTTCTGCTGCAGATGTATGCGGATGTGAT
131 TCTTCTGCTGCAGATGTATGCGGATGTGAT
28725 CCGCAGACTG
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
159 128 0.81
160 31 0.19
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (160 bp):
AATATCAGTATTACAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAGTTTATTTT
AGCAGTCTGCAGACGTTAAAAAACAAACAGTCTTCTTCTTGCATACTGCAAACTTTTGGTCCACC
TCTTCTGCTGCAGATGTATGCGGATGTGAT
Found at i:33519 original size:19 final size:19
Alignment explanation
Indices: 33459--33512 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
33449 TTTTGTACAC
33459 AAAGTTTCGAAACTCTGAG
1 AAAGTTTCGAAACTCTGAG
33478 AAAGTTTCGAAACTCTGAG
1 AAAGTTTCGAAACTCTGAG
*
33497 AAAGTTTCAAAACTCT
1 AAAGTTTCGAAACTCT
33513 TCGAAAGAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (19 bp):
AAAGTTTCGAAACTCTGAG
Found at i:33671 original size:20 final size:22
Alignment explanation
Indices: 33641--33681 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
33631 TTCTGTCTTG
33641 GAAAGTTTCGAAAC-TCTTGTA
1 GAAAGTTTCGAAACTTCTTGTA
33662 GAAA-TTTCGAAACTTCTTGT
1 GAAAGTTTCGAAACTTCTTGT
33682 CAAAGCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
GAAAGTTTCGAAACTTCTTGTA
Found at i:34491 original size:43 final size:43
Alignment explanation
Indices: 34411--34509 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
34401 TTTAAAGGTT
* *
34411 AAAAGTGAGATTGAAAAAAATTAGGGGCCTAAATTATACAAGTA
1 AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATA-AAGTA
* * * *
34455 AAAAATGAGATTG-AAAAAATTAGAGGCTTCAGTTATAAAGTT
1 AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATAAAGTA
34497 AAAAATAGAGATT
1 AAAAAT-GAGATT
34510 AGGGGTGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 10 0.21
43 26 0.54
44 12 0.25
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (43 bp):
AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATAAAGTA
Found at i:34570 original size:41 final size:42
Alignment explanation
Indices: 34517--34698 Score: 151
Period size: 43 Copynumber: 4.3 Consensus size: 42
34507 ATTAGGGGTG
*
34517 TCAATTGA-AAAGGTAGAAAGTGAGATTGAAAAATT-AGGAGC-
1 TCAATT-ATAAAGGTAAAAAGTGAGATTGAAAAATTAAGG-GCA
* * *
34558 TCAATTATAAAGGTACAAAGTGGGATTGAAAAACTTAAGGTCA
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAA-TTAAGGGCA
* *
34601 TCAATTATAAATGTACAAAAGTGGGATTGAAAAAAATTAAGGG--
1 TCAATTATAAAGGTA-AAAAGTGAGATTG--AAAAATTAAGGGCA
* * * * *
34644 TCAATTATAAAGATAAAAATTAAGATTACAAAAATT-AGGGACT
1 TCAATTATAAAGGTAAAAAGTGAGATT-GAAAAATTAAGGG-CA
34687 TCAATTATAAAG
1 TCAATTATAAAG
34699 ACAAAAATAT
Statistics
Matches: 118, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
40 5 0.04
41 36 0.31
42 12 0.10
43 42 0.36
44 12 0.10
45 6 0.05
46 5 0.04
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAGGTAAAAAGTGAGATTGAAAAATTAAGGGCA
Found at i:35908 original size:22 final size:21
Alignment explanation
Indices: 35862--35924 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
35852 ATGGCTCGTT
35862 TGTTC-ATTTATGTTCGTGAA
1 TGTTCGATTTATGTTCGTGAA
* **
35882 CGTTCGATTATATGTTCGTTTA
1 TGTTCGATT-TATGTTCGTGAA
35904 TGTTCGTTCATTTATGTTCGT
1 TGTTCG---ATTTATGTTCGT
35925 TCATTTATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 15 0.44
24 9 0.26
25 3 0.09
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (21 bp):
TGTTCGATTTATGTTCGTGAA
Found at i:35917 original size:14 final size:14
Alignment explanation
Indices: 35895--35961 Score: 97
Period size: 14 Copynumber: 5.1 Consensus size: 14
35885 TCGATTATAT
*
35895 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
35909 GTTCATTTATGTTC
1 GTTCATTTATGTTC
35923 GTTCATTTA---T-
1 GTTCATTTATGTTC
35933 GTTCATTTATGTTC
1 GTTCATTTATGTTC
35947 GTTCATTTATGTTC
1 GTTCATTTATGTTC
35961 G
1 G
35962 AACAAAGGGC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.19
11 1 0.02
13 1 0.02
14 37 0.77
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:35924 original size:24 final size:24
Alignment explanation
Indices: 35881--35960 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
35871 ATGTTCGTGA
*
35881 ACGTTCGATTATATGTTCGTTTATGTT
1 ACGTTC-ATT-TATGTTCGTTCAT-TT
35908 -CGTTCATTTATGTTCGTTCATTT
1 ACGTTCATTTATGTTCGTTCATTT
*
35931 ATGTTCATTTATGTTCGTTCATTT
1 ACGTTCATTTATGTTCGTTCATTT
*
35955 ATGTTC
1 ACGTTC
35961 GAACAAAGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
23 2 0.04
24 40 0.80
25 3 0.06
26 5 0.10
ACGTcount: A:0.16, C:0.14, G:0.15, T:0.55
Consensus pattern (24 bp):
ACGTTCATTTATGTTCGTTCATTT
Found at i:35960 original size:10 final size:10
Alignment explanation
Indices: 35862--35946 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 10
35852 ATGGCTCGTT
35862 TGTTCATTTA
1 TGTTCATTTA
* **
35872 TGTTCGTGAA
1 TGTTCATTTA
*
35882 CGTTCGATTATA
1 TGTTC-ATT-TA
*
35894 TGTTCGTTTA
1 TGTTCATTTA
* *
35904 TGTTCGTTCA
1 TGTTCATTTA
35914 T-TT-ATGTT-
1 TGTTCAT-TTA
*
35922 CGTTCATTTA
1 TGTTCATTTA
35932 TGTTCATTTA
1 TGTTCATTTA
35942 TGTTC
1 TGTTC
35947 GTTCATTTAT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
8 1 0.02
9 7 0.13
10 39 0.71
11 3 0.05
12 5 0.09
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.54
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:36282 original size:14 final size:14
Alignment explanation
Indices: 36229--36284 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
36219 GTGTTGTTCG
*
36229 TTTATGTTCATTTA
1 TTTATGTTCGTTTA
**
36243 -TTATGTTCGTTCG
1 TTTATGTTCGTTTA
*
36256 TTTTTGTTCGTTTA
1 TTTATGTTCGTTTA
*
36270 TTTGTGTTCGTTTA
1 TTTATGTTCGTTTA
36284 T
1 T
36285 GTTCCTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 10 0.29
14 24 0.71
ACGTcount: A:0.11, C:0.09, G:0.16, T:0.64
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:36349 original size:61 final size:61
Alignment explanation
Indices: 36284--36447 Score: 179
Period size: 71 Copynumber: 2.5 Consensus size: 61
36274 TGTTCGTTTA
36284 TGTTCCTTTATTATTTAAATGAACG-ACAATGAACAAAATTTTTTTTGTTCATTTATGTTCG
1 TGTTCCTTTATTATTTAAATGAACGAAC-ATGAACAAAATTTTTTTTGTTCATTTATGTTCG
*
36345 TGTTCATTTATGTTCGTTTATTATTTAAATAAACGAACATGAACAAAATTTTTTTTGTTCATTTA
1 TGTTC---------C-TTTATTATTTAAATGAACGAACATGAACAAAATTTTTTTTGTTCATTTA
36410 TGTTCG
56 TGTTCG
* *
36416 TGTTCGTTTATT-TATTAAATGAATGAACATGA
1 TGTTCCTTTATTAT-TTAAATGAACGAACATGA
36448 CATACCTCCA
Statistics
Matches: 87, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
60 1 0.01
61 27 0.31
70 1 0.01
71 56 0.64
72 2 0.02
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (61 bp):
TGTTCCTTTATTATTTAAATGAACGAACATGAACAAAATTTTTTTTGTTCATTTATGTTCG
Found at i:36350 original size:16 final size:16
Alignment explanation
Indices: 36329--36361 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
36319 AAATTTTTTT
36329 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
36345 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
36361 T
1 T
36362 TTATTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:36369 original size:71 final size:71
Alignment explanation
Indices: 36256--36426 Score: 276
Period size: 71 Copynumber: 2.4 Consensus size: 71
36246 TGTTCGTTCG
* *
36256 TTTTTGTTCGTTTAT-TT-GTGTTCGTTTATGTTCCTTTATTATTTAAATGAACG-ACAATGAAC
1 TTTTTGTTCATTTATGTTCGTGTTCGTTTATGTTCCTTTATTATTTAAATAAACGAAC-ATGAAC
36318 AAAATTT
65 AAAATTT
* *
36325 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTATTTAAATAAACGAACATGAACA
1 TTTTTGTTCATTTATGTTCGTGTTCGTTTATGTTCCTTTATTATTTAAATAAACGAACATGAACA
36390 AAATTT
66 AAATTT
36396 TTTTTGTTCATTTATGTTCGTGTTCGTTTAT
1 TTTTTGTTCATTTATGTTCGTGTTCGTTTAT
36427 TTATTAAATG
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
69 14 0.15
70 2 0.02
71 76 0.81
72 2 0.02
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.53
Consensus pattern (71 bp):
TTTTTGTTCATTTATGTTCGTGTTCGTTTATGTTCCTTTATTATTTAAATAAACGAACATGAACA
AAATTT
Found at i:42194 original size:24 final size:24
Alignment explanation
Indices: 42162--42215 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
42152 ACTGAAAATT
42162 GACCCACACCCATCCCTATAAACC
1 GACCCACACCCATCCCTATAAACC
42186 GACCCACACCCATCCCTATAAACC
1 GACCCACACCCATCCCTATAAACC
42210 GACCCA
1 GACCCA
42216 AAACGACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.06, T:0.11
Consensus pattern (24 bp):
GACCCACACCCATCCCTATAAACC
Found at i:43671 original size:72 final size:72
Alignment explanation
Indices: 43527--43771 Score: 225
Period size: 74 Copynumber: 3.3 Consensus size: 72
43517 TGTTTTTTGT
* * *
43527 ATTAA-AAAATTTAAAAAATATAAAATATATTGTAAATAGTAGTT--TAGAGATAAAAATT-AAG
1 ATTAACAAAA-TTAAAATATATAAAA-ATGTTGTAAATA-TAGTTAATA-AG-T-AAAATTAAAA
*
43588 AATTATTTCTTCC
60 AAATATTTCTTCC
43601 ATTAA-AAAATTAAAATATATAAAAATGTTGTAAACTATAGTTAATAAGTAAAATTAAAAAAATA
1 ATTAACAAAATTAAAATATATAAAAATGTTGTAAA-TATAGTTAATAAGTAAAATTAAAAAAATA
*
43665 TCTCTTCC
65 TTTCTTCC
* * * * * * *
43673 ATTAATAATAATAAAAATACATAAAAATGTTATAAATTAAAGTTAATAAATAAAA--ATAAAAAT
1 ATTAACAA-AATTAAAATATATAAAAATGTTGTAAA-TATAGTTAATAAGTAAAATTAAAAAAAT
43736 CATTTCTTCC
64 -ATTTCTTCC
43746 ATTAACAAAATTAAAAATATTATAAA
1 ATTAACAAAATT-AAAATA-TATAAA
43772 TATTATAAAT
Statistics
Matches: 146, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
71 6 0.04
72 43 0.29
73 41 0.28
74 56 0.38
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.34
Consensus pattern (72 bp):
ATTAACAAAATTAAAATATATAAAAATGTTGTAAATATAGTTAATAAGTAAAATTAAAAAAATAT
TTCTTCC
Found at i:44958 original size:42 final size:43
Alignment explanation
Indices: 44880--44960 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
44870 TAGTGACTCT
* * *
44880 TTTTTTCTAATACTTGTTATTATGGATCCACCCTTAAATTTTA
1 TTTTTTCTAACACTTGTTATTATGGATCAACACTTAAATTTTA
*
44923 TTTTTT-TAACACTTGTTATTAT-GATCAATTACTTAAAT
1 TTTTTTCTAACACTTGTTATTATGGATCAA-CACTTAAAT
44961 AAACGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.15
42 22 0.67
43 6 0.18
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (43 bp):
TTTTTTCTAACACTTGTTATTATGGATCAACACTTAAATTTTA
Found at i:46127 original size:32 final size:33
Alignment explanation
Indices: 46066--46131 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
46056 TAAGCTAAAA
* *
46066 TTTTGTTCCATGGGATTACCCAGCGTCTTTAGT
1 TTTTGCTCCATGGGATTACCCAGCATCTTTAGT
* *
46099 TTTTGCTCCAT-GGATTACTCGGCATCTTTAGT
1 TTTTGCTCCATGGGATTACCCAGCATCTTTAGT
46131 T
1 T
46132 AAATTCTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
TTTTGCTCCATGGGATTACCCAGCATCTTTAGT
Found at i:47053 original size:23 final size:24
Alignment explanation
Indices: 47026--47072 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
47016 TAACCCCGAA
47026 ATATTTTGA-ATAGATTAA-ATTTT
1 ATATTTTGACATA-ATTAACATTTT
47049 ATATTTTGACATAATTAACATTTT
1 ATATTTTGACATAATTAACATTTT
47073 GTTTTGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
ATATTTTGACATAATTAACATTTT
Found at i:51084 original size:46 final size:46
Alignment explanation
Indices: 51031--51270 Score: 118
Period size: 51 Copynumber: 4.9 Consensus size: 46
51021 AAGATGTACA
* *
51031 TACTTACATCGGCGTAAGCATAT-G-TTAGGTGCTACACTTTTTTATT
1 TACTTACACCGGCGTAAG--TATGGATTAAGTGCTACACTTTTTTATT
** *
51077 TACTTACACCGTTGTAAGTATGGATTAAGTGTTACACTTTTTTATTTTAT
1 TACTTACACCGGCGTAAGTATGGATTAAGTGCTACACTTTTTTA---T-T
* *
51127 TCACTTACACC-G-GTATAGTATGTG-TTAAGTGTTACATTTTTTTATTTTAT
1 T-ACTTACACCGGCGTA-AGTATG-GATTAAGTGCTACACTTTTTTA---T-T
* * * *
51177 TCACTTACACCGGTGTAAGTGTGTATTAAGTACTACA-TTTATTTATTTTAT
1 T-ACTTACACCGGCGTAAGTATGGATTAAGTGCTACACTTT-TTTA---T-T
* *
51228 TCACTTACACCGGTGTAAGTATGTG-TTAAATGCTACA-TTTTTT
1 T-ACTTACACCGGCGTAAGTATG-GATTAAGTGCTACACTTTTTT
51271 GTAGTATAAA
Statistics
Matches: 165, Mismatches: 15, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 33 0.20
49 4 0.02
50 50 0.30
51 71 0.43
52 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (46 bp):
TACTTACACCGGCGTAAGTATGGATTAAGTGCTACACTTTTTTATT
Found at i:51169 original size:51 final size:51
Alignment explanation
Indices: 51070--51270 Score: 262
Period size: 51 Copynumber: 4.0 Consensus size: 51
51060 TGCTACACTT
* * * * *
51070 TTTTATTTACTTACACCGTTGTAAGTATG-GATTAAGTGTTACACTTTTTTA
1 TTTTATTCACTTACACCGGTATAAGTATGTG-TTAAGTGCTACATTTTTTTA
*
51121 TTTTATTCACTTACACCGGTAT-AGTATGTGTTAAGTGTTACATTTTTTTA
1 TTTTATTCACTTACACCGGTATAAGTATGTGTTAAGTGCTACATTTTTTTA
* * * * *
51171 TTTTATTCACTTACACCGGTGTAAGTGTGTATTAAGTACTACATTTATTTA
1 TTTTATTCACTTACACCGGTATAAGTATGTGTTAAGTGCTACATTTTTTTA
* *
51222 TTTTATTCACTTACACCGGTGTAAGTATGTGTTAAATGCTACATTTTTT
1 TTTTATTCACTTACACCGGTATAAGTATGTGTTAAGTGCTACATTTTTT
51271 GTAGTATAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
50 46 0.35
51 87 0.65
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (51 bp):
TTTTATTCACTTACACCGGTATAAGTATGTGTTAAGTGCTACATTTTTTTA
Found at i:51205 original size:101 final size:102
Alignment explanation
Indices: 51070--51270 Score: 298
Period size: 101 Copynumber: 2.0 Consensus size: 102
51060 TGCTACACTT
* * **
51070 TTTTATTTACTTACACCGTTGTAAGTATGGATTAAGTGTTACACTTT-TTTATTTTATTCACTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTACTACA-TTTATTTATTTTATTCACTTA
* *
51134 CACCGGTAT-AGTATGTGTTAAGTGTTACATTTTTTTA
65 CACCGGTATAAGTATGTGTTAAATGCTACATTTTTTTA
* *
51171 TTTTATTCACTTACACCGGTGTAAGTGTGTATTAAGTACTACATTTATTTATTTTATTCACTTAC
1 TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTACTACATTTATTTATTTTATTCACTTAC
*
51236 ACCGGTGTAAGTATGTGTTAAATGCTACATTTTTT
66 ACCGGTATAAGTATGTGTTAAATGCTACATTTTTT
51271 GTAGTATAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 3 0.03
101 62 0.70
102 24 0.27
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (102 bp):
TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTACTACATTTATTTATTTTATTCACTTAC
ACCGGTATAAGTATGTGTTAAATGCTACATTTTTTTA
Found at i:53638 original size:21 final size:21
Alignment explanation
Indices: 53614--53653 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
53604 AAGACTTTAT
53614 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
53635 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
53654 AAATAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:57507 original size:21 final size:22
Alignment explanation
Indices: 57460--57539 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
57450 ACACTACCTA
57460 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * *
57483 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
57504 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
57527 GTGCATCGATGCA
1 GTGCATCGATGCA
57540 CTCTGCTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 17 0.36
23 30 0.64
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:59438 original size:26 final size:25
Alignment explanation
Indices: 59400--59465 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
59390 GAAACCGGTT
*
59400 TTGACCGGTTTGACCAGTCACGACCCG
1 TTGACC-G-TTGACCAGACACGACCCG
* * *
59427 TTTACCCGTTGACCCGACCCGACCCG
1 TTGA-CCGTTGACCAGACACGACCCG
59453 TTGACCGTTGACC
1 TTGACCGTTGACC
59466 GGTGCTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 9 0.27
26 18 0.55
27 4 0.12
28 2 0.06
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (25 bp):
TTGACCGTTGACCAGACACGACCCG
Found at i:59527 original size:29 final size:29
Alignment explanation
Indices: 59466--59624 Score: 159
Period size: 29 Copynumber: 5.7 Consensus size: 29
59456 ACCGTTGACC
*** *
59466 GGTGCTATTTTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* *
59495 GGTGATATTTTGGGAATTAATTTGAAATA
1 GGTGCTATTTTGGGAATTAATTCGAAATA
*
59524 GGTGCTATTTTGGTAATT--TT-GAAA-A
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * * *
59549 AGTGATATTATGGGAATTAATTCGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAATA
59578 GGTGCTATTTTGGGAATTAA-TCGAAA-A
1 GGTGCTATTTTGGGAATTAATTCGAAATA
*
59605 GGGTGCTATTTTGGTAATTA
1 -GGTGCTATTTTGGGAATTA
59625 TTTTAAAAAG
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
25 15 0.14
26 4 0.04
27 4 0.04
28 28 0.26
29 56 0.52
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATA
Found at i:59632 original size:28 final size:27
Alignment explanation
Indices: 59495--59632 Score: 118
Period size: 28 Copynumber: 5.0 Consensus size: 27
59485 ATTCGGTTTT
*
59495 GGTGATATTTTGGGAATTAATTTGAAATA
1 GGTGCTATTTTGGGAATT-ATTTGAAA-A
*
59524 GGTGCTATTTTGGTAA-T-TTTGAAAA
1 GGTGCTATTTTGGGAATTATTTGAAAA
* * * * *
59549 AGTGATATTATGGGAATTAATTCGAAATT
1 GGTGCTATTTTGGGAATT-ATTTGAAA-A
* *
59578 GGTGCTATTTTGGGAATTAATCGAAAA
1 GGTGCTATTTTGGGAATTATTTGAAAA
* *
59605 GGGTGCTATTTTGGTAATTATTTTAAAA
1 -GGTGCTATTTTGGGAATTATTTGAAAA
59633 AGGGTACTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 11
0.76 0.15 0.10
Matches are distributed among these distances:
25 13 0.15
26 8 0.09
28 37 0.43
29 29 0.33
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.41
Consensus pattern (27 bp):
GGTGCTATTTTGGGAATTATTTGAAAA
Found at i:66790 original size:18 final size:18
Alignment explanation
Indices: 66748--66811 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
66738 CGACCCGTTT
*
66748 ACCCGTTGATCCGACCCG
1 ACCCGTTGACCCGACCCG
66766 A-CCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
*
66783 ACCCGTTGACTCGACCCG
1 ACCCGTTGACCCGACCCG
66801 ACCCGTTGACC
1 ACCCGTTGACC
66812 GTTGACCGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
17 16 0.38
18 26 0.62
ACGTcount: A:0.17, C:0.45, G:0.22, T:0.16
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:66880 original size:29 final size:29
Alignment explanation
Indices: 66819--66997 Score: 172
Period size: 29 Copynumber: 6.3 Consensus size: 29
66809 ACCGTTGACC
*** *
66819 GGTGCTATTTTGGGAATTAATTCGGTTTT
1 GGTGCTATTTTGGGAATTAATTCGAAATA
*
66848 GGTGCTATTTTGGGAATTAATTTGAAATA
1 GGTGCTATTTTGGGAATTAATTCGAAATA
*
66877 GGTGCTATTTTGGTAATT--TTCGAAA-A
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * * *
66903 AGTGATATTATGGGAATTAATTCGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAATA
*
66932 GGTGCTATTTTAGGAATTAA-TCGAAA-A
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * *
66959 GGGTGCTATTTTGGTAATT-ATTCTAAAAA
1 -GGTGCTATTTTGGGAATTAATTCGAAATA
*
66988 GGTACTATTT
1 GGTGCTATTT
66998 ATGTAAAATG
Statistics
Matches: 123, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
26 15 0.12
27 7 0.06
28 43 0.35
29 58 0.47
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATA
Found at i:66959 original size:55 final size:55
Alignment explanation
Indices: 66853--66958 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
66843 GTTTTGGTGC
* * *
66853 TATTTTGGGAATTAATTTGAAATAGGTGCTATTTTGGTAATTTTCGAAAAAGTGA
1 TATTATGGGAATTAATTCGAAATAGGTGCTATTTTGGTAATTATCGAAAAAGTGA
*
66908 TATTATGGGAATTAATTCGAAATTGGTGCTATTTTAGG-AATTAATCGAAAA
1 TATTATGGGAATTAATTCGAAATAGGTGCTATTTT-GGTAATT-ATCGAAAA
66959 GGGTGCTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 36 0.80
56 9 0.20
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (55 bp):
TATTATGGGAATTAATTCGAAATAGGTGCTATTTTGGTAATTATCGAAAAAGTGA
Found at i:66987 original size:84 final size:84
Alignment explanation
Indices: 66824--66988 Score: 235
Period size: 84 Copynumber: 2.0 Consensus size: 84
66814 TGACCGGTGC
* *** * *
66824 TATTTTGGGAATTAATTCGGTTTTGGTGCTATTTTGGGAATTAATTTGAAATAGGTGCTATTTTG
1 TATTATGGGAATTAATTCGAAATTGGTGCTATTTTAGGAATTAATTCGAAATAGGTGCTATTTTG
66889 GTAATTTTCGAAAAAGTGA
66 GTAATTTTCGAAAAAGTGA
66908 TATTATGGGAATTAATTCGAAATTGGTGCTATTTTAGGAATTAA-TCGAAA-AGGGTGCTATTTT
1 TATTATGGGAATTAATTCGAAATTGGTGCTATTTTAGGAATTAATTCGAAATA-GGTGCTATTTT
*
66971 GGTAATTATTCTAAAAAG
65 GGTAATT-TTCGAAAAAG
66989 GTACTATTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 1 0.01
83 23 0.32
84 48 0.67
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.41
Consensus pattern (84 bp):
TATTATGGGAATTAATTCGAAATTGGTGCTATTTTAGGAATTAATTCGAAATAGGTGCTATTTTG
GTAATTTTCGAAAAAGTGA
Found at i:67003 original size:28 final size:28
Alignment explanation
Indices: 66852--66997 Score: 102
Period size: 28 Copynumber: 5.2 Consensus size: 28
66842 GGTTTTGGTG
* * * *
66852 CTATTTTGGGAATTAATTTGAAATAGGTG
1 CTATTTTGGTAATTAA-TCGAAAAAGGTA
*
66881 CTATTTTGGTAATT-TTCGAAAAA-GTGA
1 CTATTTTGGTAATTAATCGAAAAAGGT-A
* * ** *
66908 -TATTATGGGAATTAATTCGAAATTGGTG
1 CTATTTTGGTAATTAA-TCGAAAAAGGTA
* *
66936 CTATTTTAGG-AATTAATCGAAAAGGGTG
1 CTATTTT-GGTAATTAATCGAAAAAGGTA
* *
66964 CTATTTTGGTAATTATTCTAAAAAGGTA
1 CTATTTTGGTAATTAATCGAAAAAGGTA
66992 CTATTT
1 CTATTT
66998 ATGTAAAATG
Statistics
Matches: 92, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
26 13 0.14
27 8 0.09
28 43 0.47
29 26 0.28
30 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (28 bp):
CTATTTTGGTAATTAATCGAAAAAGGTA
Found at i:68910 original size:18 final size:18
Alignment explanation
Indices: 68887--68923 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
68877 GCACAGCAAG
68887 AGGAACAAATGCCTCCAT
1 AGGAACAAATGCCTCCAT
68905 AGGAACAAATGCCTCCAT
1 AGGAACAAATGCCTCCAT
68923 A
1 A
68924 TTTTCGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (18 bp):
AGGAACAAATGCCTCCAT
Found at i:70884 original size:16 final size:17
Alignment explanation
Indices: 70863--70900 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
70853 TGAACGGATT
* *
70863 TAAATTTATAT-TTTCA
1 TAAATTTAAATATTTAA
70879 TAAATTTAAATATTTAA
1 TAAATTTAAATATTTAA
70896 TAAAT
1 TAAAT
70901 AATAATATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATATTTAA
Found at i:72558 original size:21 final size:22
Alignment explanation
Indices: 72514--72561 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
72504 AATTAATAAG
72514 TTATATTTTATAATTTAAAAATT
1 TTATATTTTATAATTT-AAAATT
*
72537 TTATATTTTGTAATTT-AAATT
1 TTATATTTTATAATTTAAAATT
72558 TTAT
1 TTAT
72562 TTTAGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATTTTATAATTTAAAATT
Found at i:72585 original size:25 final size:26
Alignment explanation
Indices: 72534--72585 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
72524 TAATTTAAAA
* * *
72534 ATTTTATATTTTGTAATTTAAATTTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
72560 ATTTTAGATTTT-TAAGTTAAAATTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
72585 A
1 A
72586 CAAAATTACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATTTTAGATTTTGTAAGTTAAAATTT
Found at i:72941 original size:19 final size:19
Alignment explanation
Indices: 72917--72957 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
72907 CTACAATTAA
72917 TTATAAAAGTTTAAT-AAAT
1 TTATAAAA-TTTAATAAAAT
*
72936 TTATAATATTTAATAAAAT
1 TTATAAAATTTAATAAAAT
72955 TTA
1 TTA
72958 ATGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTATAAAATTTAATAAAAT
Found at i:72956 original size:10 final size:10
Alignment explanation
Indices: 72919--72959 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
72909 ACAATTAATT
72919 ATAAAAGTTTA
1 ATAAAA-TTTA
72930 AT-AAATTT-
1 ATAAAATTTA
*
72938 ATAATATTTA
1 ATAAAATTTA
72948 ATAAAATTTA
1 ATAAAATTTA
72958 AT
1 AT
72960 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 2 0.08
9 8 0.31
10 14 0.54
11 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
ATAAAATTTA
Found at i:73282 original size:23 final size:22
Alignment explanation
Indices: 73256--73299 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
73246 TTGTAAATTT
73256 ATAATATTT-TAATAAATTTAATG
1 ATAAT-TTTATAAT-AATTTAATG
73279 ATAATTTTATAATAATTTAAT
1 ATAATTTTATAATAATTTAAT
73300 AATTATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTTTATAATAATTTAATG
Found at i:73284 original size:11 final size:11
Alignment explanation
Indices: 73251--73302 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
73241 AATTTTTGTA
73251 AATTT-ATAAT
1 AATTTAATAAT
*
73261 ATTTTAAT-A-
1 AATTTAATAAT
*
73270 AATTTAATGAT
1 AATTTAATAAT
*
73281 AATTTTATAAT
1 AATTTAATAAT
73292 AATTTAATAAT
1 AATTTAATAAT
73303 TATAACGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.21
10 6 0.18
11 21 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AATTTAATAAT
Done.