Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011592.1 Corchorus olitorius cultivar O-4 contig11625, 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: 4666
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Found at i:719 original size:154 final size:154
Alignment explanation
Indices: 439--1324 Score: 1479
Period size: 154 Copynumber: 5.8 Consensus size: 154
429 GATTCGTATC
*
439 ACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
504 CAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
*
569 AATGAGCTAAAAAGTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
593 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
658 CAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* **
723 AATCAGCTAAAAACTTCACAGTAA
131 AATGAGCTAAAAACTTCACAGTGG
747 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * ** * * *
812 TAAATCGAAGACGATACAGTACGTCACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTATTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
877 AATGAGCTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
901 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
966 CAAATCGAAGACTATTCAAAACGG-ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* **
1030 AATCAGCTAAAAACTTCACAGTAA
131 AATGAGCTAAAAACTTCACAGTGG
1054 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * *
1119 CAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
1184 AATGAGCTAAAAACTCCACGGTGG
131 AATGAGCTAAAAACTTCACAGTGG
1208 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATT-AGGTTTG
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTTG
* * * *
1272 CCGAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
65 CCAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAAT
1325 CCAAAATGAT
Statistics
Matches: 684, Mismatches: 46, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
153 143 0.21
154 537 0.79
155 4 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGG
Found at i:1144 original size:307 final size:307
Alignment explanation
Indices: 439--1324 Score: 1560
Period size: 307 Copynumber: 2.9 Consensus size: 307
429 GATTCGTATC
*
439 ACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
504 CAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
66 CAAATCGAAGACGATTCAATAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC
*
568 AAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
130 AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
633 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGA
195 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG-ACTAATGAGCCCCGA
698 TAGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAA
259 TAGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAA
747 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* * * * *
812 TAAATCGAAGACGATACAGTACGTCACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTATTCCA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
877 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
131 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
942 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACTATTCAAAACGGACTAATGAGCCCCGATA
196 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACTAATGAGCCCCGATA
1007 GGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAA
261 GGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAA
1054 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
*
1119 CAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
1184 AATGAGCTAAAAACTCCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
131 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * *
1249 GGAAAGAAAAGACATT-AGGTTTGCCGAATCGAAGACGATTCAAAACGTCACTAATGGGCCTCAA
196 GGAAAGAAAAG-CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG-GACTAATGAGCCCCGA
1313 TAGGCCCAAAAT
259 TAGGCCCAAAAT
1325 CCAAAATGAT
Statistics
Matches: 551, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
307 292 0.53
308 259 0.47
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (307 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
CAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGACTAATGAGCCCCGATA
GGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAA
Found at i:1318 original size:461 final size:462
Alignment explanation
Indices: 439--1324 Score: 1515
Period size: 461 Copynumber: 1.9 Consensus size: 462
429 GATTCGTATC
*
439 ACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
*
504 CAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACAGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* * **
569 AATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
131 AATCAGCTAAAAACTTCACAGTAAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
634 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGAT
196 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGAGCCCCGAT
*
699 AGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTTCACAGTAAACTAATCTCACCAAAAT
261 AGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTCCACAGTAAACTAATCTCACCAAAAT
*
764 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATAC
326 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATAC
** * *
829 AGTACGTCACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTC
391 AAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTC
894 ACAGTGG
456 ACAGTGG
901 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
* *
966 CAAATCGAAGACTATTCAAAAC-GGACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACAGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
1030 AATCAGCTAAAAACTTCACAGTAAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
131 AATCAGCTAAAAACTTCACAGTAAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* ** *
1095 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAATACGTCACTAATGGGCCCCGAT
196 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGAGCCCCGAT
* * **
1160 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTCCACGGTGGACTAATCTCACCAAAAT
261 AGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTCCACAGTAAACTAATCTCACCAAAAT
* *
1225 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATT-AGGTTTGCCGAATCGAAGACGATT
326 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGGTTTGCCAAATCGAAGACGATA
*
1289 CAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
390 CAAAACGTCACTAATGGGCCCCAATAGGCCCAAAAT
1325 CCAAAATGAT
Statistics
Matches: 397, Mismatches: 26, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
461 308 0.78
462 89 0.22
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (462 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
CAAATCGAAGACGATTCAAAACAGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
AATCAGCTAAAAACTTCACAGTAAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGAGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCAAATCAGCTAAAAACTCCACAGTAAACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATAC
AAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTC
ACAGTGG
Found at i:1404 original size:107 final size:107
Alignment explanation
Indices: 1218--1431 Score: 340
Period size: 107 Copynumber: 2.0 Consensus size: 107
1208 ACTAATCTCA
* *
1218 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGACATTAGGTTTGCCGAATCGAAG
1 CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGACATTAGGTTTGCCGAATCGAAG
1283 ACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
66 ACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
** * *
1325 CCAAAATGATTATAGTTAGTTAATAAGCAATGAAAAGAAAAG-CATTAGCGTTTGCCGAATTGAA
1 CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGACATTAG-GTTTGCCGAATCGAA
* *
1389 GACGATTCAAAACGTCACTAATGGGTCTCGATAGGCCCAAAAT
65 GACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
1432 AACAAGTGTT
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 6 0.06
107 92 0.94
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (107 bp):
CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGACATTAGGTTTGCCGAATCGAAG
ACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAAT
Found at i:1532 original size:261 final size:261
Alignment explanation
Indices: 1064--1586 Score: 800
Period size: 261 Copynumber: 2.0 Consensus size: 261
1054 ACTAATCTCA
* *
1064 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
1129 AAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
66 AAGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * * * **
1194 AAACTCCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
131 AAACTCCACAGTGAACTAATCTAAACAAAATGAGAATAGTTAGGCCATAAACAATGGAAAGAAAA
*
1259 GACATTAGGTTTGCCGAATCGAAGACGATTCAAAACGTCACTAATGGGCCTC-AATAGGCCCAAA
196 GACATTAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC-CAAATAGGCCCAAA
1323 AT
260 AT
** * * *
1325 CCAAAATGATTATAGTTAGTTAATAAGCAATGAAAAGAAAAGCATT-AGCGTTTGCCGAATTGAA
1 CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGCATTGAG-GTTTGCCAAATCGAA
* * *
1389 GACGATTCAAAACGTCACTAATGGGTCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
65 GAAGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
*
1454 AAAACTTCACAGTGAACTAATCTAAACAAAATGAGAATAGTTAGGCCATAAACAATGGAAAGAAA
130 AAAACTCCACAGTGAACTAATCTAAACAAAATGAGAATAGTTAGGCCATAAACAATGGAAAGAAA
* *
1519 AG-CATTGAGGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCGAAATAGGCCCA
195 AGACATT-AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC-AAATAGGCCCA
1583 AAAT
258 AAAT
1587 AACAAGTGTT
Statistics
Matches: 237, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
260 7 0.03
261 216 0.91
262 14 0.06
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.21
Consensus pattern (261 bp):
CCAAAATGATTATAGTTAGGCAATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
AAGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AAACTCCACAGTGAACTAATCTAAACAAAATGAGAATAGTTAGGCCATAAACAATGGAAAGAAAA
GACATTAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCAAATAGGCCCAAAA
T
Found at i:1641 original size:155 final size:154
Alignment explanation
Indices: 1347--1686 Score: 504
Period size: 155 Copynumber: 2.2 Consensus size: 154
1337 TAGTTAGTTA
* * * *
1347 ATAAGCAATGAAAAGAAAAGCATT-AGCGTTTGCCGAATTGAAGACGATTCAAAACGTCACTAAT
1 ATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT
*
1411 GGGTCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATC
65 GGGTCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATC
1476 TAAACAAAATGAGAATAGTTAGGCC
130 TAAACAAAATGAGAATAGTTAGGCC
* *
1501 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATG
1 ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATG
* *
1566 GG-CCCGAAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAAT
66 GGTCCCG--ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAAT
* * **
1630 CTCACCAAAATGATTATAGTTAGGCC
129 CTAAACAAAATGAGAATAGTTAGGCC
**
1656 ATAAACGGTGGAAAGAAAAGCATTGAGGTTT
1 ATAAACAATGGAAAGAAAAGCATTGAGGTTT
1687 ACAAGAGTTA
Statistics
Matches: 168, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
153 3 0.02
154 58 0.35
155 107 0.64
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (154 bp):
ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATG
GGTCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCT
AAACAAAATGAGAATAGTTAGGCC
Done.