Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010334.1 Corchorus capsularis cultivar CVL-1 contig10355, 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: 74032
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:693 original size:331 final size:327
Alignment explanation
Indices: 26--896 Score: 958
Period size: 331 Copynumber: 2.6 Consensus size: 327
16 AAGAAAACTC
* * *
26 CTTGAAATATCTATATTCATTTAACCAA-ATCTCAGCCATATTGAAATTAAGGATTTGTTTTTAC
1 CTTGAAATATCTATATTCATCTAACCAATAT-T-AGCCACATTGATA-TAAGGATTTGTTTTTAC
* * * * * *
90 GAGTATTTGAATCTTGTTTCGATTTAGTTAAAAATAAATTCGG-GAAAAATGGAAAAACGAAATT
63 GAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATT
* * * * * * *
154 AGAAGCATGAAAAAACCCT-TCATTTTTTTTTGCGTTGAATTATATATTTTTTCTGACTATTGTG
128 AAAAGCGTG--AAAAGCCTGTCAATCTTTTTAGCGTTGAATTATATATTTTTT-TGAGTATTGTG
*** * **
218 GCAAAAAATTGAGGAAAAATTTTTCCGGTCTGTATTTACAAAATGTTAGCCGAAATCGTGTAATA
190 G-AAAAAATTGA-GAAAAAAAATTCCGATCAATATTTACAAAATGTTAGCCGAAATCGTGTAATA
* * *
283 ACCATCACGGTCTTTTGCTAAAAACGCATTCCGAAGCCCCGGCTCAGTTTTGCATGATTTTTGGT
253 ACCATCACGGTCTTTGGCTAAAAACGCATTCCGAAGCCCCGGCTCAGTTTTGCATGATTGTTGGG
348 GTAAAGAGTT
318 GTAAAGAGTT
*
358 CTTGAAATATCTATATTCATCGAACCAAGTATTAGCCACATTGGATATAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCTAACCAA-TATTAGCCACATT-GATATAAGGATTTGTTTTTACG
* *
423 AGCATCTGAATCTGGTTTCGATTTAATTAAAAATTAATTTGGAAAAAAGAT-GAAAAATCGATAT
64 AGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAA-ATGGAAAAA-CGATAT
*
487 TAAAAGCGTGAAAAGCCTGTCAATCTTTTTAGCGTTAGAATTATATA-TTTATTGAGTATTGTGG
127 TAAAAGCGTGAAAAGCCTGTCAATCTTTTTAGCGTT-GAATTATATATTTTTTTGAGTATTGTGG
* * * * * *
551 AAAAGAATGGAGAAAAAAAATT-CGAATCAATTTTTGCAAAATTTTATCCGAAATCGTGTATTAA
191 AAAA-AATTGAGAAAAAAAATTCCG-ATCAATATTTACAAAATGTTAGCCGAAATCGTGTAATAA
* ** ** *
615 CCATCACGGT-TTATGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTTTGGATGATTGTTGGG
254 CCATCACGGTCTT-TGGCTAAAAACGCATTCCGAAGCCCCGGCTCAGTTTTGCATGATTGTTGGG
*
679 GTAAAGATTT
318 GTAAAGAGTT
* * * **
689 CTTGAAATATCTATATTCGTCTAACCAA-A-T-CCCGGC-TCAAT-TAAGGATTTGTTTTTACGA
1 CTTGAAATATCTATATTCATCTAACCAATATTAGCC-ACATTGATATAAGGATTTGTTTTTACGA
* * *
749 GCATCTTAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAGAAAAAAAATGGAAAAACGATAT
65 GCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTC-G-G-AAAAAAATGGAAAAACGATAT
* * * * *
814 TAGAAA-CGTGAAGAGCCCGTCAATCTTCTTGGCGTTGAATTATATATTTTTTTGAGTATTATGG
127 TA-AAAGCGTGAAAAGCCTGTCAATCTTTTTAGCGTTGAATTATATATTTTTTTGAGTATTGTGG
*
878 CAAAAATTGAGAAAAAAAA
191 AAAAAATTGAGAAAAAAAA
897 ACTTTTCAGA
Statistics
Matches: 460, Mismatches: 61, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
325 53 0.12
326 27 0.06
327 58 0.13
328 17 0.04
329 1 0.00
330 4 0.01
331 130 0.28
332 111 0.24
333 32 0.07
334 27 0.06
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (327 bp):
CTTGAAATATCTATATTCATCTAACCAATATTAGCCACATTGATATAAGGATTTGTTTTTACGAG
CATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAAA
AGCGTGAAAAGCCTGTCAATCTTTTTAGCGTTGAATTATATATTTTTTTGAGTATTGTGGAAAAA
ATTGAGAAAAAAAATTCCGATCAATATTTACAAAATGTTAGCCGAAATCGTGTAATAACCATCAC
GGTCTTTGGCTAAAAACGCATTCCGAAGCCCCGGCTCAGTTTTGCATGATTGTTGGGGTAAAGAG
TT
Found at i:16950 original size:32 final size:32
Alignment explanation
Indices: 16889--16959 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
16879 CCTGGCAAGA
* *
16889 TATGCACCTGACATGGTCTGCACAGAATATGT
1 TATGCACCTGACATGGTCGGCACAGAATATAT
*
16921 TATGCACCTGACATGGTGCGGCATA-AATATAT
1 TATGCACCTGACATGGT-CGGCACAGAATATAT
*
16953 TCTGCAC
1 TATGCAC
16960 AGAAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (32 bp):
TATGCACCTGACATGGTCGGCACAGAATATAT
Found at i:17364 original size:125 final size:127
Alignment explanation
Indices: 17220--17473 Score: 476
Period size: 129 Copynumber: 2.0 Consensus size: 127
17210 TCATTAGGGC
17220 TTAATCACCTTGTCATGGCGTTATTACCTTGGCTC-A-TATACTATATACAAAAGTACAAATAAG
1 TTAATCACCTTGTCATGGCGTTATTACCTTGGCTCAACTATACTATATACAAAAGTACAAATAAG
17283 GGAAACTTTATATTTTCCAATTGTATCCTTTTTTTAATATATTTCTAAATTGTCATTATTAA
66 GGAAACTTTATATTTTCCAATTGTATCCTTTTTTTAATATATTTCTAAATTGTCATTATTAA
17345 TTAATCACCTTGTCATGGCGTTATTACCTTGGCTCATATCTATACTATATACAAAAGTACAAATA
1 TTAATCACCTTGTCATGGCGTTATTACCTTGGCTCA-A-CTATACTATATACAAAAGTACAAATA
17410 AGGGAAACTTTATATTTTCCAATTGTATCCTTTTTTTAATATATTTCTAAATTGTCATTATTAA
64 AGGGAAACTTTATATTTTCCAATTGTATCCTTTTTTTAATATATTTCTAAATTGTCATTATTAA
17474 AAAAATATTT
Statistics
Matches: 125, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
125 35 0.28
127 1 0.01
129 89 0.71
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (127 bp):
TTAATCACCTTGTCATGGCGTTATTACCTTGGCTCAACTATACTATATACAAAAGTACAAATAAG
GGAAACTTTATATTTTCCAATTGTATCCTTTTTTTAATATATTTCTAAATTGTCATTATTAA
Found at i:18436 original size:21 final size:22
Alignment explanation
Indices: 18408--18461 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
18398 GAGGTTTATA
18408 AAAATTTCATAGTGA-GGT-ATC
1 AAAATTTCATAGT-ATGGTAATC
* *
18429 ACAATTTCATGGTATGGTAATC
1 AAAATTTCATAGTATGGTAATC
18451 AAAATTTCATA
1 AAAATTTCATA
18462 ATGTAATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 12 0.44
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTATGGTAATC
Found at i:18598 original size:22 final size:21
Alignment explanation
Indices: 18193--18663 Score: 186
Period size: 22 Copynumber: 21.5 Consensus size: 21
18183 TTATGAAATT
* *
18193 AAATTTCATTGGGGGTTATCA
1 AAATTTCATAGGTGGTTATCA
* * ** *
18214 AAATTTAATAGTTTTCTTATAA
1 AAATTTCATAG-GTGGTTATCA
* * *
18236 AAATTTCCTAGGAGGTTAACA
1 AAATTTCATAGGTGGTTATCA
* *
18257 AAATCTT-ATAAGGAGGTTATAA
1 AAAT-TTCAT-AGGTGGTTATCA
*
18279 AACATTT-ATAGAGAT-GTTTTCA
1 AA-ATTTCATAG-G-TGGTTATCA
* *
18301 AAATTTCATAAGATGATTATCA
1 AAATTTCAT-AGGTGGTTATCA
*
18323 AAATTTCATGAGGTGGTTTTCA
1 AAATTTCAT-AGGTGGTTATCA
* *
18345 AAATTCCAT--GAGGTTATCA
1 AAATTTCATAGGTGGTTATCA
* *
18364 AAATTTCAAAAGCAT-GTTATCA
1 AAATTTC-ATAG-GTGGTTATCA
* * *
18386 AAATTTTATAGGGAGGTTTATAA
1 AAATTTCATA-GGTGG-TTATCA
*
18409 AAATTTCATA-GTGAGGTATCA
1 AAATTTCATAGGTG-GTTATCA
* *
18430 CAATTTCAT-GGTATGGTAATCA
1 AAATTTCATAGG--TGGTTATCA
* ** *
18452 AAATTTCATAATGTAATTACCA
1 AAATTTCAT-AGGTGGTTATCA
* * **
18474 ATATTTTATATGAAGGTTATCA
1 AAATTTCATA-GGTGGTTATCA
* *
18496 AAATTTCATAATGTGCGCTTACCA
1 AAATTTCAT-AGGTG-G-TTATCA
* * *
18520 ACATTTCATTGGGAGGTTATCA
1 AAATTTCA-TAGGTGGTTATCA
18542 AAATTTCATAGGGTGGTTATCA
1 AAATTTCATA-GGTGGTTATCA
*
18564 AAATTTCATTAGGTGGTTATTA
1 AAATTTCA-TAGGTGGTTATCA
* *
18586 AAATTTTTATAGG-GAGTGTAACA
1 AAA-TTTCATAGGTG-GT-TATCA
* ** *
18609 AAATTTTATAAGGAAGTTAACA
1 AAATTTCAT-AGGTGGTTATCA
* *
18631 AAATTTCATATGGTGGTTCTCG
1 AAATTTCATA-GGTGGTTATCA
*
18653 AAATTTTATAG
1 AAATTTCATAG
18664 TATCATCATA
Statistics
Matches: 328, Mismatches: 87, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
19 14 0.04
20 1 0.00
21 47 0.14
22 210 0.64
23 40 0.12
24 15 0.05
25 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
AAATTTCATAGGTGGTTATCA
Found at i:18699 original size:22 final size:23
Alignment explanation
Indices: 18674--18731 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
18664 TATCATCATA
* *
18674 AAAACTTTATATTGTA-ATTATC
1 AAAATTTTATATTGGAGATTATC
*
18696 AAAATTTTATA-TGGAGGTTATC
1 AAAATTTTATATTGGAGATTATC
18718 AAAATTTTATATTG
1 AAAATTTTATATTG
18732 ATTATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (23 bp):
AAAATTTTATATTGGAGATTATC
Found at i:18727 original size:44 final size:44
Alignment explanation
Indices: 18354--18743 Score: 192
Period size: 44 Copynumber: 8.9 Consensus size: 44
18344 AAAATTCCAT
** * *
18354 GAGGTTATCAAAATTTCA-AAAGCATGTTATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATATTGTA-GTTATCAAAATTTTATATG
* * * * *
18398 GAGGTTTATAAAAATTTCATAGTG-AGGTATCACAA-TTT-CATG
1 GAGG-TTATCAAAATTTCATATTGTAGTTATCAAAATTTTATATG
* * * * *
18440 GTATGGTAATCAAAATTTCATAATGTAATTACCAATATTTTATATG
1 G-A-GGTTATCAAAATTTCATATTGTAGTTATCAAAATTTTATATG
* * * * * *
18486 AAGGTTATCAAAATTTCATAATGTGCGCTTACCAACATTTCAT-TGG
1 GAGGTTATCAAAATTTCATATTGT-AG-TTATCAAAATTTTATAT-G
** * *
18532 GAGGTTATCAAAATTTCATAGGGTGGTTATCAAAATTTCAT-TAG
1 GAGGTTATCAAAATTTCATATTGTAGTTATCAAAATTTTATAT-G
* * * * * * *
18576 GTGGTTATTAAAATTT-TTATAGGGAGTGTAACAAAATTTTATAAG
1 GAGGTTATCAAAATTTCATAT-TGTAGT-TATCAAAATTTTATATG
* * * * * *
18621 GAAGTTAACAAAATTTCATATGGTGGTTCTCGAAATTTTATA-G
1 GAGGTTATCAAAATTTCATATTGTAGTTATCAAAATTTTATATG
* ** * * *
18664 TATCATCATAAAAACTTT-ATATTGTAATTATCAAAATTTTATATG
1 GA-GGTTATCAAAA-TTTCATATTGTAGTTATCAAAATTTTATATG
*
18709 GAGGTTATCAAAATTTTATATTG-A-TTAT-AAAATTT
1 GAGGTTATCAAAATTTCATATTGTAGTTATCAAAATTT
18744 CATAAAAATA
Statistics
Matches: 264, Mismatches: 64, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
41 7 0.03
42 7 0.03
43 28 0.11
44 125 0.47
45 54 0.20
46 43 0.16
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATATTGTAGTTATCAAAATTTTATATG
Found at i:19207 original size:29 final size:29
Alignment explanation
Indices: 19171--19226 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
19161 AGCCTTATTT
**
19171 AAATCACAAAGCCAACTTTTTTTTGGCCA
1 AAATCACAAAGCCAACTTGATTTTGGCCA
19200 AAATCACAAAGCCAACTTGATTTTGGC
1 AAATCACAAAGCCAACTTGATTTTGGC
19227 TTCTGGAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (29 bp):
AAATCACAAAGCCAACTTGATTTTGGCCA
Found at i:19270 original size:16 final size:17
Alignment explanation
Indices: 19249--19281 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19239 TCGGCTCCCC
*
19249 TCCAATACTAT-CAATA
1 TCCAATAATATCCAATA
19265 TCCAATAATATCCAATA
1 TCCAATAATATCCAATA
19282 CACATCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (17 bp):
TCCAATAATATCCAATA
Found at i:33976 original size:20 final size:21
Alignment explanation
Indices: 33948--33987 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33938 ATGTAAAGTT
33948 CCTGATTTT-TGTAAAATTAC
1 CCTGATTTTATGTAAAATTAC
* *
33968 CCTGCTTTTATGTAACATTA
1 CCTGATTTTATGTAAAATTA
33988 TCAGTCATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
CCTGATTTTATGTAAAATTAC
Found at i:71035 original size:77 final size:79
Alignment explanation
Indices: 70942--71093 Score: 263
Period size: 78 Copynumber: 1.9 Consensus size: 79
70932 ACTTCATATA
*
70942 TAAATATAATCTCATATTACAAACAT-ATAATAAGTAATTAATGACTAGATCTCAACAAAATTTA
1 TAAATATAATCTCATATTACAAACATAATAATAAGTAATTAATGACTAAATCTCAACAAAATTTA
71006 AAGAATAATAGTAC
66 AAGAATAATAGTAC
* *
71020 TAAA-ATAATCTCATATTACAAACATAATAATAATTAATTTATGACTAAATCTCAACAAAATTTA
1 TAAATATAATCTCATATTACAAACATAATAATAAGTAATTAATGACTAAATCTCAACAAAATTTA
71084 AAGAATAATA
66 AAGAATAATA
71094 ATATTATAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 21 0.30
78 49 0.70
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (79 bp):
TAAATATAATCTCATATTACAAACATAATAATAAGTAATTAATGACTAAATCTCAACAAAATTTA
AAGAATAATAGTAC
Done.