Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009705.1 Corchorus capsularis cultivar CVL-1 contig09726, 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: 47874
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:678 original size:22 final size:22
Alignment explanation
Indices: 653--709 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
643 ATTTTAAAAT
653 TGATAAATTATATTTGTTTTAG
1 TGATAAATTATATTTGTTTTAG
*
675 TGATAAATTATATTTTTTTTAG
1 TGATAAATTATATTTGTTTTAG
697 TGATAAATTATAT
1 TGATAAATTATAT
710 CGTCACAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (22 bp):
TGATAAATTATATTTGTTTTAG
Found at i:3567 original size:47 final size:45
Alignment explanation
Indices: 3470--3555 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3460 AAGACTCTTA
* *
3470 AAATTCAATGTGTAATGAAAAGCTACCAAAATATAATAATAGAAG
1 AAATTGAAAGTGTAATGAAAAGCTACCAAAATATAATAATAGAAG
*
3515 AAATTGAAAGTGTAATGAAAAGCTACCAAAAAAT-ATAATAG
1 AAATTGAAAGTGTAATGAAAAGCTACCAAAATATAATAATAG
3556 GTGTTGCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 7 0.18
45 31 0.82
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.23
Consensus pattern (45 bp):
AAATTGAAAGTGTAATGAAAAGCTACCAAAATATAATAATAGAAG
Found at i:23963 original size:12 final size:12
Alignment explanation
Indices: 23946--23977 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
23936 GCTGTAAGGA
23946 AGAGCAAAGGCG
1 AGAGCAAAGGCG
23958 AGAGCAAAGGCG
1 AGAGCAAAGGCG
*
23970 ACAGCAAA
1 AGAGCAAA
23978 AGAGAACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.19, G:0.34, T:0.00
Consensus pattern (12 bp):
AGAGCAAAGGCG
Found at i:31207 original size:757 final size:756
Alignment explanation
Indices: 29754--32027 Score: 4035
Period size: 757 Copynumber: 3.0 Consensus size: 756
29744 TTTTCAAAAA
* * * *
29754 ACCCTTTACTAAGTTAAAGTAAGTATTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTAT
1 ACCCTTTAATAGGTTAAAGTAAGTACTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTGT
29819 TGACATTGGAACTCAGGCTCAAATTCGCATTCTTTCATTTGTGTAACATTGACATTTCTTTTTTA
66 TGACATTGGAACTCAGGCTCAAATTCGCATTCTTTCATTTGTGTAACATTGACATTTCTTTTTTA
* *
29884 AAAATTGTTACAATGGTCACTCTTACTTGTGGGAAAAATCATTTCTCAAATAGGCCAATAAAGCC
131 AAAATTGTTACAATGGCCACTCTTACTTCTGGGAAAAATCATTTCTCAAATAGGCCAATAAAGCC
29949 TAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTAT
196 TAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTAT
* * *
30014 TTTTTCAAATTGTTGGATTCACTCATATCGACGAGAAGAGAGTTGTTGAGACAGTATCAATCCTT
261 TTTTTCAGATTGTTGGATTCACTCATATCGACGAGAAGAGAGTTGCTGAGACAGTATCCATCCTT
* *
30079 GTCTATTGGAGGCTTGTTACGGATTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGTCT
326 GTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGTCT
* *
30144 TCTATCCAATAGTTCGATATTATCCTAAACTACACCTTCAACTCCATGTTTTCTGTTCTGATGAT
391 TCTATCCAATAGTTCAATATTATCCTAAACTACACCTTCAACTCCGTGTTTTCTGTTCTGATGAT
*
30209 CATGGCCAACGGTTCTATACATATTGACATAATTAATGTTTGGTATGCTCTGTTGGGATAGATGG
456 CATGGCCAACGGTTCTATACATATTGACATAATTAATGTTTGGTATGCTCTGTTGGGATTGATGG
30274 GCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGGATCTAA
521 GCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGGATCTAA
*
30339 ACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAGTTTGCAAAACAA
586 ACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAATTTGCAAAACAA
* *
30404 ATGAGACTATTCAATATTACACAATTTTTAACGTAATTTATCTGATTTCTATGTCGTTATCTTTT
651 ATGAGACTATTCAATATTACACAATTTCTAACGCAATTTATCTGATTTCTATGTCGTTATCTTTT
* *
30469 ATCTTGGTTTATTTTTTATCTTGTATCAAAGCTCAGGTGTT
716 ATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
30510 ACCCTTTAATAGGTTAAAGTAAGTACTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTGT
1 ACCCTTTAATAGGTTAAAGTAAGTACTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTGT
* *
30575 TGACATTGGAACTCAGGCTCAAATTCACATTCTTTCATTTGTGTAACATTGACAATTTCTTTTTC
66 TGACATTGGAACTCAGGCTCAAATTCGCATTCTTTCATTTGTGTAACATTGAC-ATTTCTTTTTT
*
30640 AAAAATTGTTACAATGGCCACTCTTACTTCTGGTAAAAATCATTTCTCAAATAGGCCAATAAAGC
130 AAAAATTGTTACAATGGCCACTCTTACTTCTGGGAAAAATCATTTCTCAAATAGGCCAATAAAGC
30705 CTAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTA
195 CTAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTA
* *
30770 TTTTTTCAGATTGTTGGATTCACTCATATCGGCGAGAAGAGAGTTGCTGAGACATTATCCATCCT
260 TTTTTTCAGATTGTTGGATTCACTCATATCGACGAGAAGAGAGTTGCTGAGACAGTATCCATCCT
30835 TGTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGTC
325 TGTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGTC
* *
30900 TTCTATCCAATAGTTCAATATTTTCCTAAACTACACCTTCAACTCCGTGTTTTCAGTTCTGATGA
390 TTCTATCCAATAGTTCAATATTATCCTAAACTACACCTTCAACTCCGTGTTTTCTGTTCTGATGA
** * *
30965 TCATGGCCAACAATTCTATACATATTGACATGATTAATGTTTGGTATGCTCTGTTGGGATTGATA
455 TCATGGCCAACGGTTCTATACATATTGACATAATTAATGTTTGGTATGCTCTGTTGGGATTGATG
*
31030 GGCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAACTTAACATTTAGATTTTGGATCTA
520 GGCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGGATCTA
* *
31095 AACAGTGTGCGATGGGGGATACGATTCTATATTTAATAATCTCAGGGCTTATAATTTGCAAAACA
585 AACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAATTTGCAAAACA
* *
31160 AATGAGACTATTCAATATTACACAACTTCTAACGCAATTTATCTGATTTCGATGTCGTTATCTTT
650 AATGAGACTATTCAATATTACACAATTTCTAACGCAATTTATCTGATTTCTATGTCGTTATCTTT
31225 TATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
715 TATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
** *
31267 ACCCTTTAATAGGTTAAAGTAACAACTGTTGGAATGGATGTTTAGAAAAAACCAGCTTTGGTTGT
1 ACCCTTTAATAGGTTAAAGTAAGTACTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTGT
* * *
31332 TGACATTGGAACTCAGACTCAAATTTGCATTCTTTCATTTCTGTAACATTGACATTTCTTTTTTA
66 TGACATTGGAACTCAGGCTCAAATTCGCATTCTTTCATTTGTGTAACATTGACATTTCTTTTTTA
*
31397 AAAATTGTTACAATGGCCACTCTTACTTCTGGGAAAAATCATTTCTCAAATAGGCCAGTAAAGCC
131 AAAATTGTTACAATGGCCACTCTTACTTCTGGGAAAAATCATTTCTCAAATAGGCCAATAAAGCC
* *
31462 TAGCTTGATTTTTTAGGGTGTTAGTATTGTCAAAAATACAATCTGTAGATTAGTTTGTAAATTAT
196 TAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTAT
* * * *
31527 TTTTTCAGATTGTTGGATTCACTCATGTCCACGAGAAGAGAGTTGCGGAGACAGTACCCATCCTT
261 TTTTTCAGATTGTTGGATTCACTCATATCGACGAGAAGAGAGTTGCTGAGACAGTATCCATCCTT
31592 GTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGATC
326 GTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGG-TC
* *
31657 TTCTATGCAATAGTTCAATATTATCCTAAACTACACCATCAACTCCGTGTTTTCTGTTCTGATGA
390 TTCTATCCAATAGTTCAATATTATCCTAAACTACACCTTCAACTCCGTGTTTTCTGTTCTGATGA
* *
31722 TCCTGGCCAACGGTTCTATACATATTGGCATAATTAATGTTTGGTATGCTCTGTTGGGATTGATG
455 TCATGGCCAACGGTTCTATACATATTGACATAATTAATGTTTGGTATGCTCTGTTGGGATTGATG
*
31787 GGCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGAATCTA
520 GGCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGGATCTA
*
31852 AACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAATTTTCAAAACA
585 AACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAATTTGCAAAACA
*
31917 AATGAGACCATTCAATATTACACAATTTCTAACGCAATTTATCTGATTTCTATGTCGTTATCTTT
650 AATGAGACTATTCAATATTACACAATTTCTAACGCAATTTATCTGATTTCTATGTCGTTATCTTT
31982 TATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
715 TATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
32024 ACCC
1 ACCC
32028 CATGCTACCT
Statistics
Matches: 1445, Mismatches: 71, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
756 371 0.26
757 1074 0.74
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (756 bp):
ACCCTTTAATAGGTTAAAGTAAGTACTGTTGGAATGGATGCTTAGAAAAAACCAGCTTTGGTTGT
TGACATTGGAACTCAGGCTCAAATTCGCATTCTTTCATTTGTGTAACATTGACATTTCTTTTTTA
AAAATTGTTACAATGGCCACTCTTACTTCTGGGAAAAATCATTTCTCAAATAGGCCAATAAAGCC
TAGCTTGATTTTTTAGGGTGTTAGTATTGTCAACAATACAATCTGTAGATTAGTTCGTAAATTAT
TTTTTCAGATTGTTGGATTCACTCATATCGACGAGAAGAGAGTTGCTGAGACAGTATCCATCCTT
GTCTATTGGAGCCTTGTTACGGAGTTGAAAGCTCTTCTGCGTCCGGTAAGCCCATGTAGGGGTCT
TCTATCCAATAGTTCAATATTATCCTAAACTACACCTTCAACTCCGTGTTTTCTGTTCTGATGAT
CATGGCCAACGGTTCTATACATATTGACATAATTAATGTTTGGTATGCTCTGTTGGGATTGATGG
GCACTGTAATTACGGTTGGATTGGGGATAATATTTTCCAGCTTAACATTTAGATTTTGGATCTAA
ACGGTGTGCGATGGGGGATACGATTCTATATTTAATAATTTCAGGGCTTATAATTTGCAAAACAA
ATGAGACTATTCAATATTACACAATTTCTAACGCAATTTATCTGATTTCTATGTCGTTATCTTTT
ATCTTGGTTTATTTTTTATCTTGTATCAGAGCTCAGGTTTT
Found at i:34822 original size:29 final size:29
Alignment explanation
Indices: 34785--34885 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
34775 CCAAAATGCT
34785 CAAATAAGGGCCCGGTCTTTGAATTTGGC
1 CAAATAAGGGCCCGGTCTTTGAATTTGGC
** **
34814 CAAATAAGGG-CCGAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCCCGGTC-TTTG--AATTTGGC
* *
34844 TCATATAAGGGCCCAGTCTTTGAATTTGGC
1 -CAAATAAGGGCCCGGTCTTTGAATTTGGC
34874 CAAATAAGGGCC
1 CAAATAAGGGCC
34886 TAATGTTTGC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 28 0.51
30 4 0.07
31 16 0.29
32 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (29 bp):
CAAATAAGGGCCCGGTCTTTGAATTTGGC
Found at i:34894 original size:29 final size:30
Alignment explanation
Indices: 34693--34918 Score: 140
Period size: 31 Copynumber: 7.5 Consensus size: 30
34683 GGCTAATTGT
*
34693 TCAAATAAGGGCCTAAGGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTG-CAAAATGC
* * * * **
34724 TCAAATAAGGGCATGATCTTT-TAATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCAAAAT-GC
* *
34754 -CACATAAGGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTG-CAAAATGC
*** * **
34784 TCAAATAAGGGCCCGGTCTTTG-AATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCAAAAT-GC
* *
34814 -CAAATAAGGGCCGAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTG-CAAAATGC
* * * * **
34844 TCATATAAGGGCCCAGTCTTTG-AATTTGGC
1 TCAAATAAGGGCCTAATGTTTGCAAAAT-GC
34874 -CAAATAAGGGCCTAATGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAATGTTTG-CAAAATGC
34904 TCAAATAAGGGCCTA
1 TCAAATAAGGGCCTA
34919 TCTCATATGT
Statistics
Matches: 140, Mismatches: 43, Indels: 24
0.68 0.21 0.12
Matches are distributed among these distances:
29 57 0.41
30 12 0.09
31 71 0.51
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (30 bp):
TCAAATAAGGGCCTAATGTTTGCAAAATGC
Found at i:34916 original size:60 final size:60
Alignment explanation
Indices: 34694--34916 Score: 351
Period size: 60 Copynumber: 3.7 Consensus size: 60
34684 GCTAATTGTT
* *
34694 CAAATAAGGGCCTAAGGTTTGCCAAAATGCTCAAATAAGGG--CATGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCA-G-TCTTTGAATTTGGC
* *
34754 CACATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAGTCTTTGAATTTGGC
* *
34814 CAAATAAGGGCCGAACGTTTGCCAAAATGCTCATATAAGGGCCCAGTCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAGTCTTTGAATTTGGC
*
34874 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
34917 TATCTCATAT
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
60 148 0.99
61 1 0.01
62 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAGTCTTTGAATTTGGC
Found at i:34983 original size:31 final size:30
Alignment explanation
Indices: 34945--35143 Score: 140
Period size: 31 Copynumber: 6.6 Consensus size: 30
34935 AACTAAAACC
34945 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
*
34976 AGGCCCTTATTTGAGCATTTTCAATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
** * *
35007 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* *
35036 GGGCCCTTCTTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
* * ** * *
35067 AGGCCATTGTTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* * *
35096 AGACCCTTATTTTAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTCG-AAACGTT
35127 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
35144 ATTAGCCCCA
Statistics
Matches: 128, Mismatches: 28, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
28 6 0.05
29 32 0.25
30 4 0.03
31 79 0.62
32 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTCGAAACGTT
Found at i:35050 original size:60 final size:59
Alignment explanation
Indices: 34976--35139 Score: 231
Period size: 60 Copynumber: 2.7 Consensus size: 59
34966 CGATAACGTT
34976 AGGCCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* * * *
35036 GGGCCCTTCTTTGAGCATTTTCGATAACGTTAGGCCATTGTTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTC-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* *
35096 AGACCCTTATTTTAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTT--CATAACGTTAGGCCCTTATTTG
35140 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 89 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTCATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:35924 original size:21 final size:21
Alignment explanation
Indices: 35900--35946 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
35890 CGCGAGTCAA
35900 AGACCAATTTTTTAGCCACAT
1 AGACCAATTTTTTAGCCACAT
*
35921 AGACCATTTTTTTAGCCACAT
1 AGACCAATTTTTTAGCCACAT
35942 AGACC
1 AGACC
35947 TGATATAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (21 bp):
AGACCAATTTTTTAGCCACAT
Done.