Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022381.1 Corchorus olitorius cultivar O-4 contig22414, 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: 46887
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1306 original size:18 final size:18
Alignment explanation
Indices: 1269--1306 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1259 CTAGCCCTAA
**
1269 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAAAAG
1287 AACTAGAAGAAAAAAAAG
1 AACTAGAAGAAAAAAAAG
1305 AA
1 AA
1307 GAGAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (18 bp):
AACTAGAAGAAAAAAAAG
Found at i:6053 original size:20 final size:21
Alignment explanation
Indices: 6019--6060 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6009 CATAAACAAT
*
6019 ATTTTTTTTTC-AAAAACGCA
1 ATTTTTTTTACAAAAAACGCA
*
6039 ATTTTTTTTAGAAAAAACGCA
1 ATTTTTTTTACAAAAAACGCA
6060 A
1 A
6061 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTTTTTTTACAAAAAACGCA
Found at i:13246 original size:44 final size:44
Alignment explanation
Indices: 13190--13334 Score: 150
Period size: 44 Copynumber: 3.3 Consensus size: 44
13180 CTCGAATGTA
* * *
13190 GAAATATTGATAACCACATTTTGAAAATTTGATAACCTCA-TTAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTT-T
* * * * *
13234 GAAATTTCGATAACCTCCCTATGAAAAATTGATAACCACACTTT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTTT
* * * *
13278 GAAATTTTGGTAACCACACTATG-AAATTTCGATAATCTTAGTTT
1 GAAATTTTGATAACCACACTATGAAAATTT-GATAACCTCACTTT
13322 GAAATTTTGATAA
1 GAAATTTTGATAA
13335 TCTGCCTATA
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
43 5 0.06
44 74 0.91
45 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (44 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCTCACTTT
Found at i:13761 original size:21 final size:22
Alignment explanation
Indices: 13211--13766 Score: 127
Period size: 22 Copynumber: 25.5 Consensus size: 22
13201 AACCACATTT
*
13211 TGAAAATTTGATAACCTCAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* *
13233 TGAAATTTCGATAACCTCCCTA
1 TGAAATTTTGATAACCTCTCTA
** * * *
13255 TGAAAAATTGATAACCACACTT
1 TGAAATTTTGATAACCTCTCTA
* * *
13277 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
13299 TGAAATTTCGATAATCT-TAGTT
1 TGAAATTTTGATAACCTCT-CTA
*
13321 TGAAATTTTGATAATCTGC-CTA
1 TGAAATTTTGATAACCT-CTCTA
* * * **
13343 TAAAATTTTAATAAACACACTAAA
1 TGAAATTTTGAT-AAC-CTCTCTA
* * * *
13367 T-AAA-ATTGGTAACCGCACTA
1 TGAAATTTTGATAACCTCTCTA
*
13387 AGAAAATTTTGATAA-C-CTC-A
1 TG-AAATTTTGATAACCTCTCTA
* ** * *
13407 TAAAATTTTGATAACAACACCA
1 TGAAATTTTGATAACCTCTCTA
* * *
13429 TAAAATTTCGATAACCTC-CAAA
1 TGAAATTTTGATAACCTCTC-TA
* *
13451 TGAGAATGACTGTGATATCCTCTCTA
1 TGA-AAT---TTTGATAACCTCTCTA
* * *
13477 TG-TATTTTCAATAACCTCTCCA
1 TGAAATTTT-GATAACCTCTCTA
* ** *
13499 TAAAATTTCCATAACCTCCCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
13521 T-AGAATTTTGTTAACCGCCCTA
1 TGA-AATTTTGATAACCTCTCTA
* * *
13543 GGAAATTTCGATAA----GC-A
1 TGAAATTTTGATAACCTCTCTA
* *
13560 -CAAATTTTGGTAACCTCCCTCCCTA
1 TGAAATTTTGATAACCT--CT--CTA
* *
13585 TGAAA-TTTCA-AA-CTTTCATA
1 TGAAATTTTGATAACCTCTC-TA
* *
13605 TGAAATTTT-ATTAACATCCCTA
1 TGAAATTTTGA-TAACCTCTCTA
* * * *
13627 AGAAATTTTGGTAACCTTTTTA
1 TGAAATTTTGATAACCTCTCTA
* *
13649 TGAAATTTTGGTAACCTCTGTA
1 TGAAATTTTGATAACCTCTCTA
*
13671 TGAAATTTTGATAA-CTACACTA
1 TGAAATTTTGATAACCT-CTCTA
** *
13693 T-AAAGTTTTGATAAATTCTATA
1 TGAAA-TTTTGATAACCTCTCTA
* *
13715 TGAAATTTTG-TAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
13736 CGAAA-TTTGATAATCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
13757 TGAAATTTTG
1 TGAAATTTTG
13767 GTTTGATTGT
Statistics
Matches: 381, Mismatches: 108, Indels: 90
0.66 0.19 0.16
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
18 1 0.00
19 13 0.03
20 16 0.04
21 42 0.11
22 242 0.64
23 28 0.07
24 8 0.02
25 4 0.01
26 15 0.04
27 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:15776 original size:13 final size:13
Alignment explanation
Indices: 15758--15784 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15748 AGATATCTAG
15758 AGCTAACTAAAAT
1 AGCTAACTAAAAT
15771 AGCTAACTAAAAT
1 AGCTAACTAAAAT
15784 A
1 A
15785 AATGAAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
AGCTAACTAAAAT
Found at i:21605 original size:29 final size:30
Alignment explanation
Indices: 21555--21632 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
21545 CCTGATTTTA
* *
21555 CAAA-TTCAGGGGGTAAAGTGG-CACAATTT
1 CAAAGTTCAGGGGGCAAACTGGCCA-AATTT
*
21584 -AAAGTTCAGGGGGCAATCTGGCCTAAATTT
1 CAAAGTTCAGGGGGCAAACTGGCC-AAATTT
21614 GCAAAGTTCAGGGGGCAAA
1 -CAAAGTTCAGGGGGCAAA
21633 GGGGCTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 3 0.08
29 14 0.35
30 6 0.15
31 1 0.03
32 16 0.40
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (30 bp):
CAAAGTTCAGGGGGCAAACTGGCCAAATTT
Found at i:23335 original size:168 final size:168
Alignment explanation
Indices: 23057--23397 Score: 682
Period size: 168 Copynumber: 2.0 Consensus size: 168
23047 ATAAGAGCAC
23057 TTGGAGGAGTAAGGAGTTAAAGTTTGGATTCTTGGGTAAGTTGATTTTTGAATCTTGATGTTGAG
1 TTGGAGGAGTAAGGAGTTAAAGTTTGGATTCTTGGGTAAGTTGATTTTTGAATCTTGATGTTGAG
23122 TTTTGTTGGAATTGATGATCAAAATGTTGTTTTGGAGATGATTATTGTTTGGGCTTGCAATTAGA
66 TTTTGTTGGAATTGATGATCAAAATGTTGTTTTGGAGATGATTATTGTTTGGGCTTGCAATTAGA
23187 ATTGTTTGGGAGTGTTTTGAAGTGAATTTGGGAAGTTA
131 ATTGTTTGGGAGTGTTTTGAAGTGAATTTGGGAAGTTA
23225 TTGGAGGAGTAAGGAGTTAAAGTTTGGATTCTTGGGTAAGTTGATTTTTGAATCTTGATGTTGAG
1 TTGGAGGAGTAAGGAGTTAAAGTTTGGATTCTTGGGTAAGTTGATTTTTGAATCTTGATGTTGAG
23290 TTTTGTTGGAATTGATGATCAAAATGTTGTTTTGGAGATGATTATTGTTTGGGCTTGCAATTAGA
66 TTTTGTTGGAATTGATGATCAAAATGTTGTTTTGGAGATGATTATTGTTTGGGCTTGCAATTAGA
23355 ATTGTTTGGGAGTGTTTTGAAGTGAATTTGGGAAGTTA
131 ATTGTTTGGGAGTGTTTTGAAGTGAATTTGGGAAGTTA
23393 TTGGA
1 TTGGA
23398 TAAATAAATA
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 173 1.00
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.42
Consensus pattern (168 bp):
TTGGAGGAGTAAGGAGTTAAAGTTTGGATTCTTGGGTAAGTTGATTTTTGAATCTTGATGTTGAG
TTTTGTTGGAATTGATGATCAAAATGTTGTTTTGGAGATGATTATTGTTTGGGCTTGCAATTAGA
ATTGTTTGGGAGTGTTTTGAAGTGAATTTGGGAAGTTA
Found at i:23498 original size:3 final size:3
Alignment explanation
Indices: 23480--23520 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
23470 GGCAACCAGG
* *
23480 AGA AGA CGA GGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA A
23521 AAAAGGGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:23651 original size:7 final size:7
Alignment explanation
Indices: 23622--23677 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
23612 CACCAGGCCC
23622 AAGGAGAA
1 AAGGA-AA
23630 AAGG-AA
1 AAGGAAA
*
23636 AA-TAAA
1 AAGGAAA
23642 AAGGAAA
1 AAGGAAA
23649 AAGGAAA
1 AAGGAAA
23656 AAGGAAGA
1 AAGGAA-A
*
23664 AAAGAAA
1 AAGGAAA
23671 AAGGAAA
1 AAGGAAA
23678 GGAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
6 8 0.20
7 23 0.56
8 10 0.24
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (7 bp):
AAGGAAA
Found at i:23686 original size:15 final size:15
Alignment explanation
Indices: 23633--23676 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
23623 AGGAGAAAAG
*
23633 GAAAATAAAAAGGAA
1 GAAAAGAAAAAGGAA
*
23648 -AAAGGAAAAAGGAA
1 GAAAAGAAAAAGGAA
23662 GAAAAGAAAAAGGAA
1 GAAAAGAAAAAGGAA
23677 AGGAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (15 bp):
GAAAAGAAAAAGGAA
Found at i:28788 original size:16 final size:15
Alignment explanation
Indices: 28750--28791 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
28740 ACAGAGGTTG
* *
28750 ACAGAAAGCAATTAA
1 ACAGAAAACAATGAA
28765 ACAGAAAACAATGAA
1 ACAGAAAACAATGAA
28780 ACTAGAAAACAA
1 AC-AGAAAACAA
28792 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (15 bp):
ACAGAAAACAATGAA
Found at i:30366 original size:35 final size:35
Alignment explanation
Indices: 30287--30353 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
30277 CAAAATAGCT
30287 ACAAAAATAGTGAAAAATAACAATTTCTCAATTTC
1 ACAAAAATAGTGAAAAATAACAATTTCTCAATTTC
30322 ACAAAAATAGTGAAAAATAACAATTTCTCAAT
1 ACAAAAATAGTGAAAAATAACAATTTCTCAAT
30354 ATTAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (35 bp):
ACAAAAATAGTGAAAAATAACAATTTCTCAATTTC
Found at i:32796 original size:32 final size:32
Alignment explanation
Indices: 32750--32825 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
32740 GAGTTCGAGT
*
32750 CGAGCTCGAGTTCATCTCGCTACGAACTCAAA
1 CGAGTTCGAGTTCATCTCGCTACGAACTCAAA
* * *
32782 CGAGTTCGAGTTCATCTCGCTGCGAACTCGAG
1 CGAGTTCGAGTTCATCTCGCTACGAACTCAAA
32814 CGAGTTCGAGTT
1 CGAGTTCGAGTT
32826 GGCTCGCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (32 bp):
CGAGTTCGAGTTCATCTCGCTACGAACTCAAA
Found at i:39426 original size:194 final size:195
Alignment explanation
Indices: 39195--39625 Score: 643
Period size: 194 Copynumber: 2.2 Consensus size: 195
39185 TATGTTTAGT
* * * * **
39195 CACAAAAAGAACCATTCCCGCCATATGCATGTTGGCGCCAAAATGGCTAACATTTTTGTGACGAT
1 CACAAAAAGTATCATTCCCGCCATATACATATTGGCGCCAAAATAACTAACATTTTTGTGACGAT
* *
39260 ATTCCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAA-CTTGTCGTCACAAAA-GTTACACA
66 ATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACA-AACCGTGTCGTCACAAAATGTTACACA
39323 CAAAAGTGACGAGGTAAATTTTCGTCACAGAA-AAATGAAACTTGTAGTGACCAATATAGGTTTG
130 CAAAAGTGACGAGGTAAATTTTCGTCACA-AACAAATGAAACTTGTAGTGACCAATATAGGTTTG
39387 GC
194 GC
* *
39389 CACAAAAAGTATCATTCCCGCCATATCCATATTGGCGCCAAAATAACTAACGTTTTTGTGACGAT
1 CACAAAAAGTATCATTCCCGCCATATACATATTGGCGCCAAAATAACTAACATTTTTGTGACGAT
**
39454 ATTGTGTAGCCACTAATTAATTGAATTGTTAGTGACAAACCGTGTCGTCACAAAATGTTACACAC
66 ATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACAAACCGTGTCGTCACAAAATGTTACACAC
* ** * *
39519 AAATGTGACGAGGTACTTTTTCGTCACAAACCAATGAAACTTGTAGTGACCAATATAGGTTTTGC
131 AAAAGTGACGAGGTAAATTTTCGTCACAAACAAATGAAACTTGTAGTGACCAATATAGGTTTGGC
* * *
39584 CACAAAAAGTATCATTCCCGCCAAATACGTAGTGGCGCCAAA
1 CACAAAAAGTATCATTCCCGCCATATACATATTGGCGCCAAA
39626 TTGATTAAGC
Statistics
Matches: 214, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
193 2 0.01
194 108 0.50
195 104 0.49
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (195 bp):
CACAAAAAGTATCATTCCCGCCATATACATATTGGCGCCAAAATAACTAACATTTTTGTGACGAT
ATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACAAACCGTGTCGTCACAAAATGTTACACAC
AAAAGTGACGAGGTAAATTTTCGTCACAAACAAATGAAACTTGTAGTGACCAATATAGGTTTGGC
Found at i:39647 original size:195 final size:194
Alignment explanation
Indices: 39195--39647 Score: 572
Period size: 195 Copynumber: 2.3 Consensus size: 194
39185 TATGTTTAGT
* * * * ** * * **
39195 CACAAAAAGAACCATTCCCGCCATATGCAT-GTTGGCGCCAAAATGGCTAACATTTTTGTGACGA
1 CACAAAAAGTATCATTCCCGCCAAATACATAG-TGGCGCCAAAATAACTAACGTATCAGTGACGA
* *
39259 TATTCCGTAGCCACTAATTAGTTGAATTGTTAGTGACACAACTTGTCGTCACAAAAGTTACACAC
65 TATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACAACGTGTCGTCACAAAAGTTACACAC
39324 AAAAGTGACGAGGTAAATTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGC
130 AAAAGTGACGAGGTAAATTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGC
* * * * **
39389 CACAAAAAGTATCATTCCCGCCATATCCATATTGGCGCCAAAATAACTAACGTTTTTGTGACGAT
1 CACAAAAAGTATCATTCCCGCCAAATACATAGTGGCGCCAAAATAACTAACGTATCAGTGACGAT
**
39454 ATTGTGTAGCCACTAATTAATTGAATTGTTAGTGACA-AACCGTGTCGTCACAAAATGTTACACA
66 ATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACAA-CGTGTCGTCACAAAA-GTTACACA
* ** * *
39518 CAAATGTGACGAGGTACTTTTTCGTCACA-AACCAATGAAACTTGTAGTGACCAATATAGGTTTT
129 CAAAAGTGACGAGGTAAATTTTCGTCACAGAA-AAATGAAACTTGTAGTGACCAATATAGGTTTG
39582 GC
193 GC
* * * *
39584 CACAAAAAGTATCATTCCCGCCAAATACGTAGTGGCGCCAAATTGATTAA-GCTATCAGTGACGA
1 CACAAAAAGTATCATTCCCGCCAAATACATAGTGGCGCCAAAATAACTAACG-TATCAGTGACGA
39648 ATTTTTAATG
Statistics
Matches: 228, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
193 2 0.01
194 108 0.47
195 118 0.52
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (194 bp):
CACAAAAAGTATCATTCCCGCCAAATACATAGTGGCGCCAAAATAACTAACGTATCAGTGACGAT
ATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACAACGTGTCGTCACAAAAGTTACACACA
AAAGTGACGAGGTAAATTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGC
Found at i:43974 original size:439 final size:443
Alignment explanation
Indices: 43198--44456 Score: 1875
Period size: 439 Copynumber: 2.8 Consensus size: 443
43188 GAAACCTGTA
* * * * * * ** * * * **
43198 AATCAAATTCAGCTTTCGGATCCTTCATGAAAGTCTTAAATCATGCAATGACCTTTTAGCCGACA
1 AATCAAATTTAGCTTTCAGACCCTTAATGAAAGTCGTAGATCACACAATAAACGTTTAATCGACA
* * * *
43263 CTTAAACAACCTTAATCGGACAAGTGGACCGAAAATTATACGGTATTAAATAGACCGGCAATCGA
66 CTTGAACAACCTCAATC-GACAAGTGGACCGAAAATTATACGATATTAGATAGACCGGCAATCGA
* * * * *
43328 AATCACAAAATTTCAGAAGTATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTGTTTAT
130 GACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCAT
* * * *
43393 GAAAGTTGTAGATTATGAAATCACCTTTTAATAGACACCTAAATAACCTTAATCGGACAAATAGA
195 GAAAGTTGTAGATTATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGA
* * * *
43458 ACAAAATATACAAAAATAAAAGCCAACGCGTTAAATCGTCCAATCCATAATTGTAAAGGATTAAA
260 ACAAAAAATACAACAATAAAAGCGAA-GCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAA
43523 TAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAAC-AAAAAA-A-TG-AT-T
324 TAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAAGATTGAATAT
43583 TTTT-ATGGAGACGAAACATAAAAATCCCCTCTTGAACCCACCACGAAACTCATT
389 TTTTGATGGAGACGAAACATAAAAATCCCCTCTTGAACCCACCACGAAACTCATT
* * *
43637 AATCAAATTTAGCTTTCAGACCCTTAATGAAAGTCGTAGATCACAGAATAAACTTTTAATCGATA
1 AATCAAATTTAGCTTTCAGACCCTTAATGAAAGTCGTAGATCACACAATAAACGTTTAATCGACA
* * **
43702 GTTGAACAACCTCAATCAGACAAGTGGACCGAAAATTATACGATATTAGATAGATCAACAATCGA
66 CTTGAACAACCTCAATC-GACAAGTGGACCGAAAATTATACGATATTAGATAGACCGGCAATCGA
43767 GACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCAT
130 GACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCAT
43832 GAAAGTTGTAGATTATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGA
195 GAAAGTTGTAGATTATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGA
43897 ACAAAAAATACAACAATAAAAGTCGAAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAA
260 ACAAAAAATACAACAATAAAAG-CGAAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAA
* * *
43962 TAGCATAAAGCATAAAAAGTATGAGGATCAATTGATAGATAATCTAACAAAAAAATGATTTGTTA
324 TAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAA-GA-TTG---
* *
44027 AAAATGATTTTTGATGGAGACGAAACATAAAAGTCCCCTCTTGAACCCTCCACGAAACTCATT
384 --AAT-ATTTTTGATGGAGACGAAACATAAAAATCCCCTCTTGAACCCACCACGAAACTCATT
* *
44090 AATCAAATTTTGCTTTCAGACCCTTAATGAAAGTCGTAGATCACACAGTAAACGTTTAATCGACA
1 AATCAAATTTAGCTTTCAGACCCTTAATGAAAGTCGTAGATCACACAATAAACGTTTAATCGACA
*
44155 CTTGAACAACCTCAATCGAACAAGTGGACCAAAAATTATACGATATTAGATAGACCGGCAATCGA
66 CTTGAACAACCTCAATCG-ACAAGTGGACCGAAAATTATACGATATTAGATAGACCGGCAATCGA
44220 GACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCAT
130 GACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCAT
* *
44285 GAAAGTTGTATATCATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGA
195 GAAAGTTGTAGATTATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGA
* *
44350 ACAAAAAAATACAACAATAAAAGCTGATGCGTTAAATCGTCCAACCCATAATTGTAAAGGACTAA
260 AC-AAAAAATACAACAATAAAAGC-GAAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAA
* *
44415 ATAGCATAAAGAAT-AAAAGTATGAGGATCATTCGATAAATAA
323 ATAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAA
44457 CTGGAAAAAA
Statistics
Matches: 743, Mismatches: 59, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
439 330 0.44
440 9 0.01
442 1 0.00
444 2 0.00
450 2 0.00
452 6 0.01
453 322 0.43
454 71 0.10
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (443 bp):
AATCAAATTTAGCTTTCAGACCCTTAATGAAAGTCGTAGATCACACAATAAACGTTTAATCGACA
CTTGAACAACCTCAATCGACAAGTGGACCGAAAATTATACGATATTAGATAGACCGGCAATCGAG
ACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTTCATG
AAAGTTGTAGATTATGAAATCACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGAA
CAAAAAATACAACAATAAAAGCGAAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATA
GCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAACAAAAAAAGATTGAATATTT
TTGATGGAGACGAAACATAAAAATCCCCTCTTGAACCCACCACGAAACTCATT
Found at i:45438 original size:2 final size:2
Alignment explanation
Indices: 45431--45456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45421 CCTATTTTTG
45431 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
45457 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:45461 original size:2 final size:2
Alignment explanation
Indices: 45456--45550 Score: 181
Period size: 2 Copynumber: 47.5 Consensus size: 2
45446 TCTCTCTCTC
45456 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
45498 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
45540 TG TG TT TG TG T
1 TG TG TG TG TG T
45551 TGTTGTTTGG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.