Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012572.1 Corchorus olitorius cultivar O-4 contig12605, 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: 8724
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:510 original size:25 final size:25
Alignment explanation
Indices: 482--535 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
472 GATACTAACC
482 TAAGGGACTAATTAGATATGCAAAG
1 TAAGGGACTAATTAGATATGCAAAG
507 TAAGGGACTAATTAGATATGCAAAG
1 TAAGGGACTAATTAGATATGCAAAG
532 TAAG
1 TAAG
536 AAAGTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (25 bp):
TAAGGGACTAATTAGATATGCAAAG
Found at i:1285 original size:40 final size:40
Alignment explanation
Indices: 1237--1796 Score: 831
Period size: 40 Copynumber: 14.1 Consensus size: 40
1227 CCTGAATAAA
* * * * **
1237 ATTTTGAAATTGATCTGATAAAGAAAAGATCCTGAATAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
* * *
1277 ATTCTGAAATTCATTTGATAAAGCAATGATCCTGAGTAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1317 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
* *
1357 GTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1397 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1437 ATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1477 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1517 GTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1557 GTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1597 GTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
*
1637 GTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
* * *
1677 ATTCTGAAATTAATTTGATAAA-AAGATAATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGG
* * * * *
1717 ATTCTGAAATTCACTTAATAAAGCAATGACCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
* * *
1757 ATTCTG--ATTAA-CTGGTAAAGCAATGATCCTGAGCAGG
1 ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
1794 ATT
1 ATT
1797 AAAACCCATA
Statistics
Matches: 485, Mismatches: 33, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
37 25 0.05
38 4 0.01
39 1 0.00
40 454 0.94
41 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (40 bp):
ATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGG
Found at i:1336 original size:80 final size:80
Alignment explanation
Indices: 1102--1796 Score: 846
Period size: 80 Copynumber: 8.8 Consensus size: 80
1092 ACTGGCAAAA
* * * ** * *
1102 CAATGACCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAAGGATCCTGAATAGGCTTCTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
**** *
1167 ATT-GGCGGATAAAA
66 ATTAATTTGATAAAG
* ** * * * ** * * ** **
1181 CAATAATCCTGAATAGGATTCTAAAAATGA-CCGATGAAG-ACATTATCCTGAATAAAATTTTGA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGATTTTGA
* *
1244 AATTGATCTGATAAAG
65 AATTAATTTGATAAAG
* * ** * *
1260 AAAAGATCCTGAATAGGATTCTGAAATTCATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1325 ATTAATTTGATAAAG
66 ATTAATTTGATAAAG
* * *
1340 CAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1405 ATTAATTTGATAAAG
66 ATTAATTTGATAAAG
1420 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1485 ATTAATTTGATAAAG
66 ATTAATTTGATAAAG
* * * *
1500 CAATGATCCTGAGTAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1565 ATTAATTTGATAAAG
66 ATTAATTTGATAAAG
* * *
1580 CAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
1645 ATTAATTTGATAAAG
66 ATTAATTTGATAAAG
* * *
1660 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAA-AAGATAATCCTGAGCAGGATTCTGA
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGATTTTGA
* * *
1724 AATTCACTTAATAAAG
65 AATTAATTTGATAAAG
* * *
1740 CAATGACCCTGAGCAGGATTCTG--ATTAA-CTGGTAAAGCAATGATCCTGAGCAGGATT
1 CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATT
1797 AAAACCCATA
Statistics
Matches: 547, Mismatches: 63, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
77 24 0.04
78 32 0.06
79 56 0.10
80 434 0.79
81 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (80 bp):
CAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAA
ATTAATTTGATAAAG
Found at i:1377 original size:120 final size:120
Alignment explanation
Indices: 1102--1796 Score: 846
Period size: 120 Copynumber: 5.8 Consensus size: 120
1092 ACTGGCAAAA
* * * * * * *
1102 CAATGACCCTGAACAGGATTCTGAAATTAATTTGATAAAGCAAGGATCCTGAATAGGCTTCTGAA
1 CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
**** * * ** * * * ** *
1167 ATT-GGCGGATAAAACAATAATCCTGAATAGGATTCTAAAAATGA-CCGATGAAG
66 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
* ** ** * * * * * *
1220 -ACATTATCCTGAATAAAATTTTGAAATTGATCTGATAAAGAAAAGATCCTGAATAGGATTCTGA
1 CA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGA
* * *
1284 AATTCATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAAATTAATTTGATAAAG
65 AATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
*
1340 CAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
1 CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
1405 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
66 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
*
1460 CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGGTTTTGAA
1 CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
* *
1525 ATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAG
66 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
* * *
1580 CAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGGTTTTGAA
1 CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
1645 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAA-
66 ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
* * * * * * * * *
1699 AAGATAATCCTGAGCAGGATTCTGAAATTCACTTAATAAAGCAATGACCCTGAGCAGGATTCTG-
1 CA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGA
* *
1763 -ATTAA-CTGGTAAAGCAATGATCCTGAGCAGGATT
65 AATTAATTTGATAAAGCAATGATCCTGAGCAGGATT
1797 AAAACCCATA
Statistics
Matches: 512, Mismatches: 60, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
117 28 0.05
118 60 0.12
119 31 0.06
120 392 0.77
121 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (120 bp):
CAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGTAGGATTTTGAA
ATTAATTTGATAAAGCAATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAG
Found at i:2165 original size:145 final size:140
Alignment explanation
Indices: 1846--2263 Score: 512
Period size: 145 Copynumber: 2.9 Consensus size: 140
1836 ATATAGAATG
* * *
1846 CCCGGAGGACTTGTCAGAATTAATACCCGGAGGTTTCTGAAATTGTGACCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* * * * * *
1911 GCAAAAATTGGCCTTGGGCAAGGTTTATTAAAATTTAAACACAACTTTGCTGAAAATTTGATGAA
66 GC-AAACTTGACCTTGAGCAAGGTTTATTAAAACTTAAACACAACTTTGCTAAAAACTTGATGAA
1976 ATGAAATGATA
130 ATGAAATGATA
*
1987 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGGAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* * * ** * *
2052 GCCAACTTGACCTTGAGTAAGGTTTTGATTTTGAAACTTAAATGCAGCTTTGATTAAAAACTTGA
66 GCAAACTTGACCTTGAGCAAGG-TTT-A--TTAAAACTTAAACACAACTTTG-CTAAAAACTTGA
2117 TGAAATGAAATGATA
126 TGAAATGAAATGATA
* *
2132 CCCGGAGGATTTATCAGAATTGATACCCGGAGGTTTTTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* *
2197 GCAAACTTGACCTAGAGACCTTGAGCAAGGTTTATTGAAATTTAAACACAACTTTGCTGAAAAAC
66 GCAAAC-T----T---GACCTTGAGCAAGGTTTATTAAAACTTAAACACAACTTTGCT-AAAAAC
2262 TT
122 TT
2264 ACCAAAATGG
Statistics
Matches: 236, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
140 15 0.06
141 66 0.28
142 1 0.00
144 17 0.07
145 91 0.39
146 1 0.00
148 1 0.00
149 26 0.11
150 1 0.00
151 1 0.00
152 3 0.01
153 13 0.06
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (140 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
GCAAACTTGACCTTGAGCAAGGTTTATTAAAACTTAAACACAACTTTGCTAAAAACTTGATGAAA
TGAAATGATA
Found at i:3487 original size:7 final size:7
Alignment explanation
Indices: 3475--3500 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3465 TCTTATGCTT
3475 TTTTCAA
1 TTTTCAA
3482 TTTTCAA
1 TTTTCAA
3489 TTTTCAA
1 TTTTCAA
3496 TTTTC
1 TTTTC
3501 GCATTCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAA
Found at i:3540 original size:16 final size:17
Alignment explanation
Indices: 3516--3578 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
3506 CACTTTCAAT
3516 TTTTACTTCTTTTTTCG-
1 TTTT-CTTCTTTTTTCGA
*
3533 TTTTCTTCATTTTTT-GT
1 TTTTCTTC-TTTTTTCGA
* *
3550 TTTTGTTTTTTTTTCGA
1 TTTTCTTCTTTTTTCGA
3567 TTTT-TT-TTTTTT
1 TTTTCTTCTTTTTT
3579 TTTGCAGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.15
16 13 0.32
17 21 0.52
ACGTcount: A:0.05, C:0.10, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTTTTCGA
Found at i:3560 original size:24 final size:23
Alignment explanation
Indices: 3533--3581 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
3523 TCTTTTTTCG
3533 TTTTCTTC-ATTTTTTGTTTTTGTT
1 TTTTCTTCGATTTTTT-TTTTT-TT
*
3557 TTTTTTTCGATTTTTTTTTTTTT
1 TTTTCTTCGATTTTTTTTTTTTT
3580 TT
1 TT
3582 GCAGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.04, C:0.06, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTCTTCGATTTTTTTTTTTTT
Done.