Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010450.1 Corchorus capsularis cultivar CVL-1 contig10471, 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: 24354
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:1004 original size:223 final size:222
Alignment explanation
Indices: 613--1044 Score: 731
Period size: 223 Copynumber: 1.9 Consensus size: 222
603 AATTGTCCGA
*
613 TGTCAACTAGTTAGCTTACTATATCAACTAGTTTACCTTGATAACAGTTATTAGTTATCAACTTG
1 TGTCAACAAGTTAGCTTACTATATCAACTAGTTTACCTTGATAACAG-T-TTAGTTATCAACTTG
*
678 TTAGCTTTTTTTGGTAGAAGTCAACTAGTTAGCTATACTCTATCAACTATTTAACCTTAATTGAT
64 TTAGCTTTTTTTGGTAGAAGTCAACTAGTTAGCTATACTCTATCAACTATTTAACCTTAACTGAT
* *
743 AAGAGTTAGTTGTTAACTAGTTAGCTTTACTCTATCAACTAGTTAACCTTAATTGATAAGAGTTT
129 AAGAGTTAGTTGTTAACTAGCTAGCTTTACTCTATCAACTAGTTAACCTTAATTGAT-AG-GTGT
808 TTTTTTTTTTGCTACACATACATGTGGTAAT
192 TTTTTTTTTTGCTACACATACATGTGGTAAT
* * * *
839 TGTCAACAAGTTATCTTACTCTATCAACTAGTTTATCTTGATAACAG-TTAGTTGTCAACTTGTT
1 TGTCAACAAGTTAGCTTACTATATCAACTAGTTTACCTTGATAACAGTTTAGTTATCAACTTGTT
* *
903 AGCTTTTTTTGGTAGAAGTCAACTAGTTAGCTTTACTCTATCAACTATTTAACCTTAACTGGTAA
66 AGCTTTTTTTGGTAGAAGTCAACTAGTTAGCTATACTCTATCAACTATTTAACCTTAACTGATAA
968 GAGTTAGTTGTTAACTAGCTAGCTTTACTCTATCAACTAGTTAACCTTAATTGATAGGTGTTTTT
131 GAGTTAGTTGTTAACTAGCTAGCTTTACTCTATCAACTAGTTAACCTTAATTGATAGGTGTTTTT
1033 TTTTTTGCTACA
196 TTTTTTGCTACA
1045 TGTGGTTTGA
Statistics
Matches: 196, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
221 19 0.10
222 2 0.01
223 132 0.67
226 43 0.22
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (222 bp):
TGTCAACAAGTTAGCTTACTATATCAACTAGTTTACCTTGATAACAGTTTAGTTATCAACTTGTT
AGCTTTTTTTGGTAGAAGTCAACTAGTTAGCTATACTCTATCAACTATTTAACCTTAACTGATAA
GAGTTAGTTGTTAACTAGCTAGCTTTACTCTATCAACTAGTTAACCTTAATTGATAGGTGTTTTT
TTTTTTGCTACACATACATGTGGTAAT
Found at i:8357 original size:23 final size:23
Alignment explanation
Indices: 8327--8397 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
8317 TGCTTGGCGC
8327 CCGACCACTTCCAAGGCCAGCGT
1 CCGACCACTTCCAAGGCCAGCGT
** *
8350 CCGACCACTTGTGAA--CCTAGCGA
1 CCGACCACTT-CCAAGGCC-AGCGT
*
8373 CCGACCACTTCCAAGGTCAGCGT
1 CCGACCACTTCCAAGGCCAGCGT
8396 CC
1 CC
8398 AACTACCTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
22 4 0.11
23 30 0.81
24 3 0.08
ACGTcount: A:0.23, C:0.41, G:0.21, T:0.15
Consensus pattern (23 bp):
CCGACCACTTCCAAGGCCAGCGT
Found at i:8541 original size:51 final size:52
Alignment explanation
Indices: 8485--8597 Score: 149
Period size: 53 Copynumber: 2.2 Consensus size: 52
8475 GCTAGCTAGC
* * *
8485 ACTCCACACATGACCTCC-ACGTACGACC-CCACACGTGATCTCCGAAGTACA
1 ACTCCACACATGACCTCCAACGGA-GACCTCAACACGTGACCTCCGAAGTACA
* *
8536 ACTCCACACGTGACCTCCAACGGATACCTTCAACACGTGACCTCCGAAGTACA
1 ACTCCACACATGACCTCCAACGGAGACC-TCAACACGTGACCTCCGAAGTACA
8589 ACTCCACAC
1 ACTCCACAC
8598 GTGATCTCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 20 0.37
52 4 0.07
53 30 0.56
ACGTcount: A:0.30, C:0.41, G:0.13, T:0.16
Consensus pattern (52 bp):
ACTCCACACATGACCTCCAACGGAGACCTCAACACGTGACCTCCGAAGTACA
Found at i:8542 original size:26 final size:25
Alignment explanation
Indices: 8485--8601 Score: 117
Period size: 26 Copynumber: 4.5 Consensus size: 25
8475 GCTAGCTAGC
* * *
8485 ACTCCACACATGACCTCCACGTACG
1 ACTCCACACGTGACCTCCAAGTACA
* *
8510 ACCCCACACGTGATCTCCGAAGTACA
1 ACTCCACACGTGACCTCC-AAGTACA
* *
8536 ACTCCACACGTGACCTCCAACGGATA
1 ACTCCACACGTGACCTCCAA-GTACA
* *
8562 CCTTCAACACGTGACCTCCGAAGTACA
1 AC-TCCACACGTGACCTCC-AAGTACA
8589 ACTCCACACGTGA
1 ACTCCACACGTGA
8602 TCTCACGTGT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
25 17 0.23
26 35 0.48
27 19 0.26
28 2 0.03
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.16
Consensus pattern (25 bp):
ACTCCACACGTGACCTCCAAGTACA
Found at i:9478 original size:9 final size:9
Alignment explanation
Indices: 9464--9493 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9454 TGAGAGGGTT
9464 TAATCAGGC
1 TAATCAGGC
*
9473 TAATCAGCC
1 TAATCAGGC
9482 TAATCAGGC
1 TAATCAGGC
9491 TAA
1 TAA
9494 ACATTTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (9 bp):
TAATCAGGC
Found at i:11728 original size:30 final size:30
Alignment explanation
Indices: 11692--11838 Score: 177
Period size: 30 Copynumber: 4.8 Consensus size: 30
11682 GCACCTCTCG
* * *
11692 TGGTTGCTGCTGCGCCACCTCCTCCGCTGC
1 TGGTTGCGGCGGCGCCACCTCCCCCGCTGC
* *
11722 TGGTTGCGGCGGCGCCACCTCCCCCTCTGG
1 TGGTTGCGGCGGCGCCACCTCCCCCGCTGC
* *
11752 TGGTTGCGGCGGCGCCTCCTCCCCCTCTGC
1 TGGTTGCGGCGGCGCCACCTCCCCCGCTGC
*
11782 TGGTTGCGGCGGCGCCACCTCCCCCGCTGG
1 TGGTTGCGGCGGCGCCACCTCCCCCGCTGC
* *
11812 TGGATCTTGCTGCGGCGCCACGTCCCC
1 TGG---TTGCGGCGGCGCCACCTCCCC
11839 TGGTGGATGT
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
30 83 0.81
33 19 0.19
ACGTcount: A:0.03, C:0.44, G:0.31, T:0.22
Consensus pattern (30 bp):
TGGTTGCGGCGGCGCCACCTCCCCCGCTGC
Found at i:11782 original size:60 final size:60
Alignment explanation
Indices: 11685--11838 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 60
11675 AACGCCGGCA
* * * *
11685 CCTCTCGTGGTTGCTGCTGCGCCACCTCCTCCGCTGCTGGTTGCGGCGGCGCCACCTCCC
1 CCTCTGGTGGTTGCGGCGGCGCCACCTCCCCCGCTGCTGGTTGCGGCGGCGCCACCTCCC
* *
11745 CCTCTGGTGGTTGCGGCGGCGCCTCCTCCCCCTCTGCTGGTTGCGGCGGCGCCACCTCCC
1 CCTCTGGTGGTTGCGGCGGCGCCACCTCCCCCGCTGCTGGTTGCGGCGGCGCCACCTCCC
* * *
11805 CCGCTGGTGGATCTTGCTGCGGCGCCACGTCCCC
1 CCTCTGGTGG---TTGCGGCGGCGCCACCTCCCC
11839 TGGTGGATGT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 63 0.78
63 18 0.22
ACGTcount: A:0.03, C:0.44, G:0.31, T:0.22
Consensus pattern (60 bp):
CCTCTGGTGGTTGCGGCGGCGCCACCTCCCCCGCTGCTGGTTGCGGCGGCGCCACCTCCC
Found at i:11844 original size:30 final size:30
Alignment explanation
Indices: 11785--11881 Score: 140
Period size: 30 Copynumber: 3.1 Consensus size: 30
11775 CCTCTGCTGG
* *
11785 TTGCGGCGGCGCCACCTCCCCCGCTGGTGGATC
1 TTGCTGCGGCGCCACGT--CCC-CTGGTGGATC
*
11818 TTGCTGCGGCGCCACGTCCCCTGGTGGATG
1 TTGCTGCGGCGCCACGTCCCCTGGTGGATC
11848 TTGCTGCGGCGCCACGTCCCCTGGTGGATC
1 TTGCTGCGGCGCCACGTCCCCTGGTGGATC
11878 TTGC
1 TTGC
11882 GGCCCCGCCT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
30 42 0.70
31 3 0.05
33 15 0.25
ACGTcount: A:0.06, C:0.37, G:0.34, T:0.23
Consensus pattern (30 bp):
TTGCTGCGGCGCCACGTCCCCTGGTGGATC
Found at i:11903 original size:30 final size:30
Alignment explanation
Indices: 11869--11962 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
11859 CCACGTCCCC
*
11869 TGGTGGATCTTGCGGCCCCGCCTCCCCTGG
1 TGGTGGATCTTGCGGCCCCGCCGCCCCTGG
*
11899 TGGTGGATCTTGCGGCTCCGCCGCCCCTGG
1 TGGTGGATCTTGCGGCCCCGCCGCCCCTGG
* * *
11929 TGGTGGATTTTGCAGCCCCGCCGCCTCTGG
1 TGGTGGATCTTGCGGCCCCGCCGCCCCTGG
11959 TGGT
1 TGGT
11963 TGCTCCGGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.04, C:0.35, G:0.35, T:0.26
Consensus pattern (30 bp):
TGGTGGATCTTGCGGCCCCGCCGCCCCTGG
Found at i:12375 original size:2 final size:2
Alignment explanation
Indices: 12363--12394 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12353 GCTATATGAA
12363 AT AT AT A- 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 AT A
12395 ATGAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15530 original size:31 final size:31
Alignment explanation
Indices: 15462--15526 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
15452 TGACAATTTA
* *
15462 GAAATATGTTTTTTAAAAAAGGGTAGAATCG
1 GAAATATGTTTTTAAAAAAAGGGTACAATCG
**
15493 GAAATATG-TTTTAAAAAAATTGTACAATCG
1 GAAATATGTTTTTAAAAAAAGGGTACAATCG
15523 GAAA
1 GAAA
15527 ATATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTTAAAAAAAGGGTACAATCG
Found at i:19359 original size:19 final size:20
Alignment explanation
Indices: 19335--19373 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19325 TTAAATTAAA
19335 TGAAAATT-AAAATAATTAT
1 TGAAAATTGAAAATAATTAT
*
19354 TGAAAATTGAAATTAATTAT
1 TGAAAATTGAAAATAATTAT
19374 ATATATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
TGAAAATTGAAAATAATTAT
Found at i:21592 original size:31 final size:31
Alignment explanation
Indices: 21554--21612 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
21544 TATGTTAGAC
* *
21554 AAATAAGGATATAATTGGCGTTTCAAAAATT
1 AAATAAGGACATAATAGGCGTTTCAAAAATT
21585 AAATAAGGACATAATAGGCGTTTCAAAA
1 AAATAAGGACATAATAGGCGTTTCAAAA
21613 GTTTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.27
Consensus pattern (31 bp):
AAATAAGGACATAATAGGCGTTTCAAAAATT
Found at i:22598 original size:2 final size:2
Alignment explanation
Indices: 22591--22680 Score: 108
Period size: 2 Copynumber: 41.0 Consensus size: 2
22581 CTCGTACTTT
22591 TA TA TA TA GTA TA GTA TA GTA TA GTA TA TA TA TA TA GTA TA TA CTA
1 TA TA TA TA -TA TA -TA TA -TA TA -TA TA TA TA TA TA -TA TA TA -TA
22637 TA GTA TA TA TA TA TA TA TA TA CTA 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
22681 CTAGTTTTAG
Statistics
Matches: 80, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
2 64 0.80
3 16 0.20
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (2 bp):
TA
Found at i:22605 original size:5 final size:5
Alignment explanation
Indices: 22591--22631 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
22581 CTCGTACTTT
22591 TATA- TATAG TATAG TATAG TATAG TATA- TATA- TATAG TATA
1 TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATA
22632 TACTATAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 12 0.34
5 23 0.66
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (5 bp):
TATAG
Found at i:22630 original size:23 final size:21
Alignment explanation
Indices: 22591--22678 Score: 106
Period size: 23 Copynumber: 4.0 Consensus size: 21
22581 CTCGTACTTT
22591 TATATATAGTATAGTATAGTATAG
1 TATATATA-TATA-TATA-TATAG
22615 TATATATATATAGTATATACTA-
1 TATATATATATA-TATATA-TAG
*
22637 TAGTATATATATATATATATAC
1 TA-TATATATATATATATATAG
22659 TATATATATATATATATATA
1 TATATATATATATATATATA
22679 TACTAGTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.33
22 12 0.20
23 21 0.34
24 8 0.13
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
TATATATATATATATATATAG
Found at i:22679 original size:23 final size:24
Alignment explanation
Indices: 22591--22683 Score: 143
Period size: 25 Copynumber: 3.8 Consensus size: 24
22581 CTCGTACTTT
*
22591 TATATATAGTATAGTATAGTATAGTA
1 TATATATA-TATA-TATACTATAGTA
22617 TATATATATAGTATATACTATAGTA
1 TATATATATA-TATATACTATAGTA
22642 TATATATATATATATACTATA-TA
1 TATATATATATATATACTATAGTA
22665 TATATATATATATATACTA
1 TATATATATATATATACTA
22684 GTTTTAGCTT
Statistics
Matches: 65, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
23 21 0.32
24 11 0.17
25 23 0.35
26 10 0.15
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (24 bp):
TATATATATATATATACTATAGTA
Found at i:22826 original size:22 final size:22
Alignment explanation
Indices: 22801--23323 Score: 207
Period size: 22 Copynumber: 23.6 Consensus size: 22
22791 ATGATCCCAT
22801 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * * *
22823 TATGAAATTTTAATAACGATACTA
1 TATGAAATTTTGATAAC-CTTC-C
* * * **
22847 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
22869 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* *
22891 TATGAAATTTGGTTAACC-TCTC
1 TATGAAATTTTGATAACCTTC-C
* * **
22913 TAAGGAATTTTGA-ATACCTTAA
1 TATGAAATTTTGATA-ACCTTCC
**
22935 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
22958 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
22979 ATATGATATATTGATAACC-ACA
1 -TATGAAATTTTGATAACCTTCC
* * *
23001 TCATGAAAATTTAAAAACC-TCC
1 T-ATGAAATTTTGATAACCTTCC
* *
23023 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
23046 TCTGAAAATTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
23068 TATGAAATTGTGATAATC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
23090 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
23113 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
23136 TATAAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
** **
23158 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTTCC
* * *
23180 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
23202 TATGAAGTTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
*
23224 TATGAAATTTTGATAATCC-TCT
1 TATGAAATTTTGATAA-CCTTCC
* * **
23246 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
23268 TATAAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
23290 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
23311 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
23324 TACTCCATAA
Statistics
Matches: 375, Mismatches: 99, Indels: 56
0.71 0.19 0.11
Matches are distributed among these distances:
20 13 0.03
21 19 0.05
22 250 0.67
23 78 0.21
24 15 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:23454 original size:22 final size:22
Alignment explanation
Indices: 23429--23598 Score: 96
Period size: 22 Copynumber: 7.8 Consensus size: 22
23419 AATCACATTT
23429 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
23451 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
23473 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
23495 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* * *
23517 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
* ** **
23539 TGAAATTTTGATAACAACACTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
23561 TGAAATTTTGATAATCACTCTA
1 TGAAAATTTGATAACCTCTTTA
*
23583 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
23599 TCTATCAAAT
Statistics
Matches: 114, Mismatches: 28, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
21 16 0.14
22 92 0.81
23 6 0.05
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:23497 original size:44 final size:44
Alignment explanation
Indices: 23404--23597 Score: 142
Period size: 44 Copynumber: 4.4 Consensus size: 44
23394 AAAAATACCA
* * * *
23404 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAACCACATTAT-AAAATTTTGATAACCCCG
* * * * * *
23448 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * ** *
23492 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
* * * * * * *
23536 CTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCACT
1 CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
*
23580 CTATGAGA-TTTGATAACC
1 CTATGAAATTTTGATAACC
23598 TTCTATCAAA
Statistics
Matches: 117, Mismatches: 31, Indels: 5
0.76 0.20 0.03
Matches are distributed among these distances:
43 18 0.15
44 99 0.85
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACATTATAAAATTTTGATAACCCCG
Found at i:23518 original size:66 final size:64
Alignment explanation
Indices: 23448--23629 Score: 174
Period size: 66 Copynumber: 2.8 Consensus size: 64
23438 GATAACCTCT
* *
23448 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGAT-ACACCTCTATGAAATTCTGATAATCAC
* * * * * *
23513 ATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 -TTATGAAATTTTGATAACCTC-TTTATAAAATTTTGAT-ACACCTCTATGAAATTCTGATAATC
23577 AC
63 AC
* * * * *
23579 TCTATGAGA-TTTGATAACCT-TCTATCAAATTTTGGTACTCCT-TATGAAATT
1 T-TATGAAATTTTGATAACCTCTTTATAAAATTTTGATACACCTCTATGAAATT
23630 GAGACTTTTA
Statistics
Matches: 95, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
62 9 0.09
63 4 0.04
64 10 0.11
65 12 0.13
66 58 0.61
67 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (64 bp):
TTATGAAATTTTGATAACCTCTTTATAAAATTTTGATACACCTCTATGAAATTCTGATAATCAC
Found at i:23567 original size:88 final size:88
Alignment explanation
Indices: 23404--23570 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
23394 AAAAATACCA
* * * **
23404 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
23469 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
23492 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
23555 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
23571 ATAATCACTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 61 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:23676 original size:22 final size:22
Alignment explanation
Indices: 23651--23708 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
23641 AACCTTCATT
23651 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* *
23673 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCACACTA
*
23695 TGACATTTTGATAA
1 TGAAATTTTGATAA
23709 TCTCTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:23776 original size:22 final size:22
Alignment explanation
Indices: 23744--23883 Score: 122
Period size: 22 Copynumber: 6.3 Consensus size: 22
23734 TTGTGATAAT
* *
23744 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* * *
23766 TAACCAACCTAAGAGATTTTAA
1 TAACCATCCTATGAAATTTTAA
**
23788 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTAA
**
23812 TAACCA-CACTATGAAATTTTGG
1 TAACCATC-CTATGAAATTTTAA
*
23834 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTAA
* *
23856 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
23878 TAACCA
1 TAACCA
23884 CATAGAGACA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.03
22 74 0.76
23 3 0.03
24 17 0.18
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:24080 original size:19 final size:20
Alignment explanation
Indices: 24049--24086 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
24039 TATTGATATT
24049 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
24068 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
24087 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Done.