Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015535.1 Corchorus olitorius cultivar O-4 contig15568, 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: 124329
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1647 original size:28 final size:28
Alignment explanation
Indices: 1611--1666 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1601 CAAAAATATA
1611 ATTTTTATAATTTTTTTAAAATAAACTT
1 ATTTTTATAATTTTTTTAAAATAAACTT
1639 ATTTTTATAATTTTTTTAAAATAAACTT
1 ATTTTTATAATTTTTTTAAAATAAACTT
1667 TGGAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTTTATAATTTTTTTAAAATAAACTT
Found at i:4198 original size:27 final size:28
Alignment explanation
Indices: 4159--4213 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
4149 TAAATACTAC
*
4159 ATTTGTTATATTTATGTTATGTTTTTAT
1 ATTTGTTATATTTATATTATGTTTTTAT
4187 ATTT-TTATATTTATATTATGTTTTTAT
1 ATTTGTTATATTTATATTATGTTTTTAT
4214 TATATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (28 bp):
ATTTGTTATATTTATATTATGTTTTTAT
Found at i:17454 original size:14 final size:13
Alignment explanation
Indices: 17435--17473 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
17425 AAATTGTAAA
17435 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
17448 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
17462 ATTTAAAAAATT
1 ATTTAAAAAATT
17474 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:17691 original size:125 final size:127
Alignment explanation
Indices: 17459--17713 Score: 374
Period size: 125 Copynumber: 2.0 Consensus size: 127
17449 ATTTAAGAAA
17459 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAAT---A
* *
17524 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
17589 T
127 T
* * *
17590 TATATTTAAAAAATTTTAATATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-C
1 TATATTTAAAAAATTCT-A-ATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAC
*
17654 A-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAA
64 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
17714 GTTTAAACAA
Statistics
Matches: 116, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
125 53 0.46
126 2 0.02
127 2 0.02
129 1 0.01
131 16 0.14
132 1 0.01
133 41 0.35
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAT
Found at i:22813 original size:31 final size:31
Alignment explanation
Indices: 22766--22834 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
22756 GTGATTGAGG
* * *
22766 GTAATTTGGACTAAAATCAGTTTAATTTGAA
1 GTAATTCGGACCAAAATCAGTTCAATTTGAA
*
22797 GTAATTCGGACCAAAATCGGTTCAATTTGAA
1 GTAATTCGGACCAAAATCAGTTCAATTTGAA
22828 GTAATTC
1 GTAATTC
22835 ATCAAATAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (31 bp):
GTAATTCGGACCAAAATCAGTTCAATTTGAA
Found at i:32326 original size:13 final size:13
Alignment explanation
Indices: 32308--32333 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32298 AAGTTTGATA
32308 TCTATAACACTAG
1 TCTATAACACTAG
32321 TCTATAACACTAG
1 TCTATAACACTAG
32334 ATAAAAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TCTATAACACTAG
Found at i:38225 original size:79 final size:79
Alignment explanation
Indices: 38089--38251 Score: 308
Period size: 79 Copynumber: 2.1 Consensus size: 79
38079 CCGGTGCACA
*
38089 TGACTAATCGTGTTTAAATTAAAAGAAAAGTAAAATAATAATTGAAATTAATTATAAGTAAAACT
1 TGACCAATCGTGTTTAAATTAAAAGAAAAGTAAAATAATAATTGAAATTAATTATAAGTAAAACT
38154 ATCAAAATCTGATT
66 ATCAAAATCTGATT
38168 TGACCAATCGTGTTTAAATTAAAAGAAAAGTAAAATAATAATTGAAATTAATTATAAGTAAAACT
1 TGACCAATCGTGTTTAAATTAAAAGAAAAGTAAAATAATAATTGAAATTAATTATAAGTAAAACT
38233 ATCAAAATCTGATT
66 ATCAAAATCTGATT
*
38247 CGACC
1 TGACC
38252 TCGATAATCG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (79 bp):
TGACCAATCGTGTTTAAATTAAAAGAAAAGTAAAATAATAATTGAAATTAATTATAAGTAAAACT
ATCAAAATCTGATT
Found at i:40001 original size:716 final size:716
Alignment explanation
Indices: 38579--41406 Score: 4679
Period size: 716 Copynumber: 3.9 Consensus size: 716
38569 CCGCCTGACC
* *
38579 CTAAGTGATGATGAAGAGTACCAATTCAAAACACATTTGGAAGCACAGCCACAGCCACAACCACT
1 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTT-G--G-A-AG-CACAGCCACAACCACT
* ** *
38644 GGTGGAACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTAGTCAAAACCCC
60 AGTGGAACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCC
* *
38709 ATTCATTCCAACCTCCAGTGGCTCATCCACCAAATAATCACCTTGCACCTCAAGCACGTTCTCCT
125 ATTCATTCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCT
* * * * *
38774 CCACCTCCTCCAGTGACGATGAAGGGTGGAACAGAGGGTCTACCATATGCACAACAGCATCCCCA
190 CCACCTCCTCCGGTGACGATGGAGGGTGGAACAGGGGGTCTACCATACGCACAACAACATCCCCA
* * *
38839 CTTGGAACCACCCTGTTGAGGACATAGGTGAGCACATACCCCTCTGCCAAACTACCCTCAAATTG
255 CTTAGAACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTG
* * * * *
38904 AGCTGCGTACACTGGAAGAATGGAGTGGACCGCCGGGTAGTTGGTCGATTGGCGATCGATGAAGA
320 AGCTGCGTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAA
* * * * * *
38969 TGTCGGATGGAAAGCTGCCGACATATGAGGCCACAATGCCTTCACCAGAGGAAAACACCGGCTGC
385 TGTCGGAGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGC
* * * * * *
39034 ACAACCACCGGATAAGGTTGTCCCGTTGGAAGCAAACTCTCCAAGTGAAACTTCACCACAAACTC
450 ACAACCACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCC
* *
39099 ATTCTGGTGGTTGCCTTTGACGGTGGCTTTGTAGACAGGAACCACAAAATATGGTTTTGGAAAAG
515 ATTCTGGTGGTTGCCTCTGACGGTGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAG
* *
39164 CGTCGGAGTAGCCCCCAATAGTGATCGTTTCGGGGAAGTCACCACTCAATCCTTGCAAAAAGAAG
580 CGTCGGAGTAGCCCCCAACAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAG
**
39229 TTTGGGTTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTACCCCTTGATTAATTCTGATATA
645 TTTGGGTTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTCTGATATA
39294 CTAACTA
710 CTAACTA
39301 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAGCCACAACCACTAGTGGA
1 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAGCCACAACCACTAGTGGA
* * * *
39366 ACCGGAACACCTTCTTCCTCCTTATTCACAATCAGCCCTTCAAAATTACCCCAAAACCCATTCAT
66 ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCCATTCAT
** * *
39431 TCCAACCTCTGGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGTACGTTATCCTCCACCT
131 TCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
* * *
39496 CCTCCGGTGACGATGGAGGGTGAAACAGGGGGTCTACCATACGCAGAACAACATTCCCACTTAGA
196 CCTCCGGTGACGATGGAGGGTGGAACAGGGGGTCTACCATACGCACAACAACATCCCCACTTAGA
* *
39561 ACCACCCTGTTGAGGACATAGGTAAACACATACCCCTCTGTCAAATTACCCTCAAATTGAGCTGC
261 ACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTGAGCTGC
39626 GTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCGG
326 GTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCGG
39691 AGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAACC
391 AGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAACC
39756 ACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCTG
456 ACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCTG
**
39821 GTGGTTGCCTCTGACAATGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAGCGTCGG
521 GTGGTTGCCTCTGACGGTGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAGCGTCGG
39886 AGTAGCCCCCAACAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTGGG
586 AGTAGCCCCCAACAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTGGG
*
39951 TTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTTTGATATACTAACT
651 TTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTCTGATATACTAACT
40016 A
716 A
* *
40017 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAACCACAGCCACTAGTGGA
1 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAGCCACAACCACTAGTGGA
* *
40082 ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCATTCAAAATTACCCAAAAACGCATTCAT
66 ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCCATTCAT
*
40147 TCCAACCTCCAGTGGCTCATCCACCACAAAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
131 TCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
* * * *
40212 CCTCCGGTGACGATTGAGGGTGGAATAGGGGGTCTACCGTACGCACAACAACATCCCCACTTGGA
196 CCTCCGGTGACGATGGAGGGTGGAACAGGGGGTCTACCATACGCACAACAACATCCCCACTTAGA
*
40277 ACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTGAGTTGC
261 ACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTGAGCTGC
*
40342 GTACACCGGAAGAATGGAGTGGACTGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCGG
326 GTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCGG
40407 AGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAACC
391 AGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAACC
*
40472 ACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCGCAAACCCATTCTG
456 ACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCTG
* *
40537 GTGGTTGCCTCTAACGGTGGCTTTGTAGACAGGAACCACTAAATGTGGTTTTGGAAAAGCGTCGG
521 GTGGTTGCCTCTGACGGTGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAGCGTCGG
* *
40602 AGTAGCGCCCAATAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTGGG
586 AGTAGCCCCCAACAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTGGG
*
40667 TTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTCCGATATACTAACT
651 TTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTCTGATATACTAACT
40732 A
716 A
* * *
40733 CTAAGTGATGATGAAGAGTACCCATTCAAAATCCATTTGGAAGCACAGCCACAGCCACTAGTAGA
1 CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAGCCACAACCACTAGTGGA
40798 ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCCATTCAT
66 ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCCATTCAT
40863 TCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
131 TCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
* *
40928 CCTCCGGTGACGAT-GATGGGTGGAACAGGGGGTCTACCGTACGCACAACAGCATCCCCACTTAG
196 CCTCCGGTGACGATGGA-GGGTGGAACAGGGGGTCTACCATACGCACAACAACATCCCCACTTAG
* * *
40992 AACCACCCTGTTGAGGACATAGGTATGCACATATCCCTCTGCCAAATTACCCTCAAATTGAGTTG
260 AACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTGAGCTG
* * *
41057 CGTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGGCGACCAATGAAGATGTCG
325 CGTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCG
* * *
41122 GAGGGAAAGCTGTCGGCATTTGAGGCCACGGTGCCTTCACCAGAGGAAGACACCGGCTGCACAAC
390 GAGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAAC
* * *
41187 CACCGGAGAAGGCTATCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCT
455 CACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCT
* * * * * *
41252 GGTGGTTGCCTTTGACTGTGACTTTGTAGACCGGAACCACAAAATGTGGTTTTGGAAAAGCATCA
520 GGTGGTTGCCTCTGACGGTGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAGCGTCG
* * *
41317 GAGTAGCCCCCAATC-GTGATCGTTTAGGGGAAGTCACCACTCAATCCTTACAAAAAGAAGTTTG
585 GAGTAGCCCCCAA-CAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTG
*
41381 GGTTCTCCATCGGAGAAAGTAGACAA
649 GGTTCTCCATCGGAGAAAGAAGACAA
41407 TCAGAAGGTT
Statistics
Matches: 1980, Mismatches: 124, Indels: 10
0.94 0.06 0.00
Matches are distributed among these distances:
715 2 0.00
716 1937 0.98
717 2 0.00
718 1 0.00
719 1 0.00
721 1 0.00
722 36 0.02
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (716 bp):
CTAAGTGATGATGAAGAGTACCCATTCAAAACCCATTTGGAAGCACAGCCACAACCACTAGTGGA
ACTGGAACACCTTCTTCCTCCTCATTCACATTCAGCCCTTCAAAATTACCCAAAAACCCATTCAT
TCCAACCTCCAGTGGCTCATCCACCACATAACCACCTTGCACCTCAAGCACGTTCTCCTCCACCT
CCTCCGGTGACGATGGAGGGTGGAACAGGGGGTCTACCATACGCACAACAACATCCCCACTTAGA
ACCACCCTGTTGAGGACATAGGTAAGCACATACCCCTCTGCCAAATTACCCTCAAATTGAGCTGC
GTACACCGGAAGAATGGAGTGGACCGCCGGGTAGTCGGTCGATTGACGACCGATGAAAATGTCGG
AGGGAAAACTGCCGGCATTTGAGGCCACGATGCCTTCACCAGAGGAAGACACCGGCTGCACAACC
ACCGAAGAAGGTTGTCCCGTCGGATGCAAACTCTCCAAGTGATACTTCACCACAAACCCATTCTG
GTGGTTGCCTCTGACGGTGGCTTTGTAGACAGGAACCACAAAATGTGGTTTTGGAAAAGCGTCGG
AGTAGCCCCCAACAGTGATCGTTTCGGGAAAGTCACCACTCAATCCTTGCAAAAAGAAGTTTGGG
TTCTCCATCGGAGAAAGAAGACAACAAAACTAGACTAGTCCTTGATTAATTCTGATATACTAACT
A
Found at i:41687 original size:3 final size:3
Alignment explanation
Indices: 41681--41712 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
41671 ATTAAGTCCT
*
41681 TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
41713 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:41694 original size:9 final size:9
Alignment explanation
Indices: 41680--41717 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
41670 TATTAAGTCC
41680 TTTCTTCTT
1 TTTCTTCTT
41689 TTTCTTCTT
1 TTTCTTCTT
*
41698 CTTCTTCTT
1 TTTCTTCTT
*
41707 CTTCTT-TT
1 TTTCTTCTT
41715 TTT
1 TTT
41718 TTTATATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:42511 original size:47 final size:47
Alignment explanation
Indices: 42442--42535 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
42432 TATTTATTAC
42442 ATAAAAAGTGCTTTTTTGATTTCAGACTAATTATAACTTCTTGTTAA
1 ATAAAAAGTGCTTTTTTGATTTCAGACTAATTATAACTTCTTGTTAA
42489 ATAAAAAGTGCTTTTTTGATTTCAGACTAATTATAACTTCTTGTTAA
1 ATAAAAAGTGCTTTTTTGATTTCAGACTAATTATAACTTCTTGTTAA
42536 GAAAATTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (47 bp):
ATAAAAAGTGCTTTTTTGATTTCAGACTAATTATAACTTCTTGTTAA
Found at i:43431 original size:7 final size:7
Alignment explanation
Indices: 43407--43452 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
43397 TTGCTTAAGG
43407 ATATATA
1 ATATATA
*
43414 AT-CAT-
1 ATATATA
43419 ATATATA
1 ATATATA
43426 ATATATA
1 ATATATA
43433 ATATATA
1 ATATATA
43440 ATATAATA
1 ATAT-ATA
43448 ATATA
1 ATATA
43453 ATCATATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 4 0.12
7 21 0.62
8 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATATA
Found at i:43514 original size:13 final size:13
Alignment explanation
Indices: 43496--43528 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43486 CAACAGATTA
43496 ATTATATGATTGC
1 ATTATATGATTGC
43509 ATTATATGATTGC
1 ATTATATGATTGC
*
43522 AATATAT
1 ATTATAT
43529 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (13 bp):
ATTATATGATTGC
Found at i:43530 original size:2 final size:2
Alignment explanation
Indices: 43523--43552 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
43513 TATGATTGCA
43523 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43553 AGATAAGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51237 original size:45 final size:42
Alignment explanation
Indices: 51163--51258 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 42
51153 AAGGTGCATT
*
51163 ACCTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAA
1 ACCTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAA
51204 ACCTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAA
1 ACCTAATATTCTACT-C-C-ATCTCTAGATAATTCATCAAAATAA
*
51249 AGCTAATATT
1 ACCTAATATT
51259 AATTGTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 6 0.12
42 8 0.16
43 1 0.02
44 1 0.02
45 33 0.67
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (42 bp):
ACCTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAA
Found at i:52414 original size:217 final size:214
Alignment explanation
Indices: 51988--52421 Score: 717
Period size: 217 Copynumber: 2.0 Consensus size: 214
51978 AGTTGAACCG
51988 ATAAATCCTAATATCCACATACAATTAATATGTAATTAAAACACATTTAATCATAAATAAATATA
1 ATAAATCCTAATATCCACATACAATTAATATGTAATTAAAACACATTTAATCATAAATAAATATA
* * * *
52053 AAAATAGTAAATTACCAAAAATGGCAGTATGAAAAGTAAGAGAGGAAATTTATCGAGGATCTTTT
66 AAAATAGTAAATTACCAAAAAGGGCAGTAGGAAAAGCAAGAGAGGAAATTCATCGAGGATCTTTT
*
52118 TAGTCACTGAAAAGTGCGAAAAGATCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATT
131 TAGTCACTGAAAAGTGCGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATT
52183 TGCCCTTTAAGTAATTTCC
196 TGCCCTTTAAGTAATTTCC
*
52202 ATAAATCCTAATATCCACATACAATTAATATGTAATTATAACACATTTAATCATAAAATAAATAT
1 ATAAATCCTAATATCCACATACAATTAATATGTAATTAAAACACATTTAATCAT-AAATAAATAT
* *
52267 AAAAAATAGTAAATTACCAAAAAGGGCAGTAGGAAAAGCAAGGGAGGAAATTCATCGAGGGTCTT
65 -AAAAATAGTAAATTACCAAAAAGGGCAGTAGGAAAAGCAAGAGAGGAAATTCATCGAGGATCTT
* *
52332 TTTAGTCACT-AACTAAGTGCGAAAAGACCAAAAAAAGCTAAAAGGAGGCACCCCATTAATCCTC
129 TTTAGTCACTGAA--AAGTGCGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTC
* *
52396 TATTTGGCCTTTAAGTAATTTCC
192 AATTTGCCCTTTAAGTAATTTCC
52419 ATA
1 ATA
52422 GTCACTAAAA
Statistics
Matches: 204, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
214 53 0.26
215 12 0.06
216 68 0.33
217 71 0.35
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (214 bp):
ATAAATCCTAATATCCACATACAATTAATATGTAATTAAAACACATTTAATCATAAATAAATATA
AAAATAGTAAATTACCAAAAAGGGCAGTAGGAAAAGCAAGAGAGGAAATTCATCGAGGATCTTTT
TAGTCACTGAAAAGTGCGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACATTAATCCTCAATT
TGCCCTTTAAGTAATTTCC
Found at i:70685 original size:329 final size:330
Alignment explanation
Indices: 70060--70688 Score: 817
Period size: 331 Copynumber: 1.9 Consensus size: 330
70050 TTTCTTGCCA
* * * * *
70060 AAAATCGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAATTTACCCAAAAGAATTTT
1 AAAACCGTGATGGTTAGCACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGAATTTT
* ** * * ** *
70125 TCTCAATTTTTTGCCATGATAGTCATAAAAAATATATAATTCATTGTCAAAAAAATTGAAAGGCT
66 CCTCAATTTTTTGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAAATTGAAAGGCT
* * * * *
70190 TTTCACGTTTTCAATATCGGTTTTCTTATTTTTTTCCGAATTAAATTGTAATTAAATTGAAACAT
131 TCTCACGTTCTCAATATCGGTTTTCCTA-TTTTTTCCGAATTAAATTCTAATTAAATCGAAACAT
* * * *
70255 GATTCAGATGCTCGTAAAAACGAAACCTTAATCTGAAGTGGGTGAGATTTGGTTAGATGGATATA
195 GATTCAGATGCTCGTAAAAACGAAACCTTAATCTCAAGTGGCTGAGATTTCGTTAGATGAATATA
70320 AATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGCTGGGGCCCGGAACACGTTTT
260 AATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGCTGGGGCCCGGAACACGTTTT
70385 TAGTCC
325 TAGTCC
* * *
70391 AAAACCGTGATGGTTAGCATAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-CATTTC
1 AAAACCGTGATGGTTAGCACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGAATTT-
* *
70455 TCCTCAA-TTTTTGACCACAATACTCAT-AAAAATATATAACTCAACGCCAAAAAGATTGAAGGG
65 TCCTCAATTTTTTG-CCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAAATTGAAAGG
* * *
70518 CTTCTCACGCTTCT-AATATTGTTTTTCCTA-TTTTTCCGAATTAATTTCTAATTAAATCGAAAC
129 CTTCTCACG-TTCTCAATATCGGTTTTCCTATTTTTTCCGAATTAAATTCTAATTAAATCGAAA-
* *
70581 CA-GATTGAGATGCTCGTAAAAAC-AAATCCTTAAATC-CAATTTGGCTGAGATTTCGTTAGATG
192 CATGATTCAGATGCTCGTAAAAACGAAA-CCTT-AATCTCAA-GTGGCTGAGATTTCGTTAGATG
*
70643 AATATAAATATTTCAATGAGTCTT-AGCGCCAAAAATCATGCAAAAC
254 AATATAAATATTTCAATGAGACTTGA-CGCCAAAAATCATGCAAAAC
70689 TGAGTCGGGA
Statistics
Matches: 257, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
327 3 0.01
328 56 0.22
329 67 0.26
330 61 0.24
331 70 0.27
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
AAAACCGTGATGGTTAGCACAAGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGAATTTT
CCTCAATTTTTTGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAAAATTGAAAGGCT
TCTCACGTTCTCAATATCGGTTTTCCTATTTTTTCCGAATTAAATTCTAATTAAATCGAAACATG
ATTCAGATGCTCGTAAAAACGAAACCTTAATCTCAAGTGGCTGAGATTTCGTTAGATGAATATAA
ATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACAGAGCTGGGGCCCGGAACACGTTTTT
AGTCC
Found at i:70967 original size:21 final size:21
Alignment explanation
Indices: 70926--70969 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
70916 TATATCATTT
**
70926 AAAAAACTACCTATTTTAAAA
1 AAAAAACTACCTATTAAAAAA
70947 AAAAAACTATCC-ATTAAAAAA
1 AAAAAACTA-CCTATTAAAAAA
70968 AA
1 AA
70970 CTGTCACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAACTACCTATTAAAAAA
Found at i:74300 original size:26 final size:26
Alignment explanation
Indices: 74258--74312 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
74248 ATTAAAATTT
*
74258 TTTTTTTGGTAGAACTTTCAATTAAA
1 TTTTTTTGGCAGAACTTTCAATTAAA
74284 TTTTTTTGGCCAG-ACTTTCAATTAAA
1 TTTTTTTGG-CAGAACTTTCAATTAAA
74310 TTT
1 TTT
74313 AAAGTACTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (26 bp):
TTTTTTTGGCAGAACTTTCAATTAAA
Found at i:81263 original size:19 final size:20
Alignment explanation
Indices: 81215--81275 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
81205 ATCGCTACTC
*
81215 TAATAATCTCATCTGTACAG
1 TAATAATCTAATCTGTACAG
81235 TACATAATCTAATCTGTACAG
1 TA-ATAATCTAATCTGTACAG
* *
81256 T-GTAATCTTATCTGTACAG
1 TAATAATCTAATCTGTACAG
81275 T
1 T
81276 TGCCAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 18 0.49
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
TAATAATCTAATCTGTACAG
Found at i:84130 original size:12 final size:12
Alignment explanation
Indices: 84113--84137 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84103 CCGAGTTGAA
84113 TTTCCATTTCCG
1 TTTCCATTTCCG
84125 TTTCCATTTCCG
1 TTTCCATTTCCG
84137 T
1 T
84138 AACCTCCATG
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:0.32, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTCCATTTCCG
Found at i:85305 original size:19 final size:19
Alignment explanation
Indices: 85281--85338 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
85271 CTGTTTAGAT
85281 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* * *
85300 ACTGTACAGATTAAATTAGAT
1 ACTGTACAGATGAGATT--AC
*
85321 ACTATACAGATGAGATTA
1 ACTGTACAGATGAGATTA
85339 TTAGAGCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:98496 original size:17 final size:17
Alignment explanation
Indices: 98474--98512 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
98464 TAAGTTCTCT
* *
98474 CTTAACACCTTTCAAAA
1 CTTAACACCATTAAAAA
98491 CTTAACACCATTAAAAA
1 CTTAACACCATTAAAAA
98508 CTTAA
1 CTTAA
98513 AATGTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (17 bp):
CTTAACACCATTAAAAA
Found at i:99258 original size:29 final size:29
Alignment explanation
Indices: 99224--99285 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
99214 AGTTAATTGC
99224 TTGATTATGGAAATCGAACATATTGATTT
1 TTGATTATGGAAATCGAACATATTGATTT
*
99253 TTGATTATGGAAATTGAACATATTGATTT
1 TTGATTATGGAAATCGAACATATTGATTT
99282 TTGA
1 TTGA
99286 CTAAATTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (29 bp):
TTGATTATGGAAATCGAACATATTGATTT
Found at i:108123 original size:25 final size:25
Alignment explanation
Indices: 108094--108148 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
108084 TTTATTACTT
108094 TTAATATACTAGAATGA-ATTATTGG
1 TTAATATACTAGAATGATA-TATTGG
*
108119 TTAATATGCTAGAATGATATATTGG
1 TTAATATACTAGAATGATATATTGG
108144 TTAAT
1 TTAAT
108149 TTCGAGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (25 bp):
TTAATATACTAGAATGATATATTGG
Found at i:112183 original size:7 final size:6
Alignment explanation
Indices: 112149--112200 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
112139 ACACGTCAGA
* * * * *
112149 TATTCT TATTTT TGTTTT AATTTT TATTTT CTATTTT TCTTTT TGTTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT -TATTTT TATTTT TATTTT
112198 TAT
1 TAT
112201 AAAGTGAGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:113916 original size:42 final size:42
Alignment explanation
Indices: 113857--113938 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
113847 TAAGTCTTGA
113857 AAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATAG
1 AAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATAG
* * *
113899 AAAATTCTTTGTTAATTAAGAAATACTCAACTCAAATCAT
1 AAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCAT
113939 GATCCTTAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (42 bp):
AAAATTCTCTGTAAATTAAAAAATACTCAACTCAAATCATAG
Found at i:114072 original size:55 final size:56
Alignment explanation
Indices: 114002--114113 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
113992 TTTATTTTGT
114002 AGAATAATTAAGTAGAGATA-GGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
114057 AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
114113 A
1 A
114114 AGGAAACACA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 20 0.36
56 36 0.64
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATATGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:115247 original size:25 final size:26
Alignment explanation
Indices: 115195--115249 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
115185 TTTGACCATT
**
115195 AATTATTTTAAAAATATAATTTTTAA
1 AATTATTTTAAAAATATAATTTGGAA
115221 AATTATTTT-AAAATA-AACTTTGGAA
1 AATTATTTTAAAAATATAA-TTTGGAA
115246 AATT
1 AATT
115250 TAAAACTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
AATTATTTTAAAAATATAATTTGGAA
Found at i:121199 original size:31 final size:31
Alignment explanation
Indices: 121164--121225 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
121154 AAAGTTATTA
* *
121164 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
121195 ATGAATATTGTAAATATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
121226 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Found at i:124139 original size:31 final size:31
Alignment explanation
Indices: 124104--124165 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
124094 AAAGTTATTA
* *
124104 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
124135 ATGAATATTGTAAATATTCATGAATCAAGAG
1 ATGAATATTGTAAATATTCATGAATCAAGAG
124166 TTCTCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAGAG
Done.