Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019063.1 Corchorus olitorius cultivar O-4 contig19096, 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: 5673
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:1497 original size:648 final size:645
Alignment explanation
Indices: 244--1975 Score: 1861
Period size: 648 Copynumber: 2.6 Consensus size: 645
234 AGACTCCTTG
* * * * * * *
244 AAAAAATAGGAAAAACGATACTAGAAGCGTAAAAAAGCCCTTCAATATTTTTGGTATTGAATTAT
1 AAAAAATATGAAAAACGATATTAAAAGCGT-GAAAAGTCCTCCAATATTTTTGGCATTGAA-T-T
* * * * * *
309 ATATAATTTTTTATTGAGTATTTTAGCCAAGACTTGAG-GAAATATCTTTCTGGTCAATTTTTAC
63 ATAT-ATTTTTTA-TGAGTATTTTAGACAAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTAC
* * * * *
373 AAAGTTTA-AT--CATCACGGTTTTTTGCTAAAAACGTGTTCCAGGACCCCGGGTCAGTTTGGCA
126 AAAATTTAGCTGACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCCGGGTCAGTTT-GCA
** * * * * * *
435 TGATTTTTGACGCCAAGAGTCCTTGAGATATCCATATTTATCTAATCAAATCCCATCCACATTGT
190 TGATTTTTGGTGCCAAGACTCCTTGA-ATATCTATATTTATCTAAACAAATCTCAACCACATTGA
* *
500 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTTAGAA
254 ATTTAAGGATTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAA
* * *
565 AA-AATATGAAAAACGATATGAAAG-GTGTGAAAGTCC-TCTAATCTTTTTGGCGCTAAAAAAAT
319 AATAATA-GAAAAACGATATCAAAGCGTG-AAAAGTCCTTC-AATCTTTTTGGCG-T---TAAAT
* * * * * ** *
627 TATATATATTTCATGATTATTTTAGCCAAAAATTCA-GAGAAAACTTTCGAGTCAATTTTTGCAA
377 TATATATATTTTATGATTATTGTGGCTAAAAATTGAGGA-AAAACTTTCGAGGAAAATTTTGCAA
* * * *
691 AATTTTAATAGAAATTGTGTACTAAGCATCACAGTTATTTTGCTAAAAACGCGTTTCGAGGCCAC
441 AATATTAACAGAAATCGTGTAATAAGCATCACAGTTATTTTGCTAAAAACGCGTTTCGAGGCCAC
* * * * *
756 GACTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAATATCTATATTCATCTGACCAAAT
506 GACTAAGTTTTCCATGATTTTTGGCATCAAGACTTCTTGAAATATCTATATTCATCTAACCAAAT
* *
821 CTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTTGATTTAATTAG
571 CTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAG
886 AAATTAATTC
636 AAATTAATTC
896 AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGG-AGTTGAATTAT
1 AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCA-TTGAATTAT
*
960 ATATTTTTTATGAGTATTTTAGACAAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTGCAAAA
65 ATATTTTTTATGAGTATTTTAGACAAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTACAAAA
* * * * * **
1025 TATTAGCTGAAATCACGGTTTTTGGCTAAAAAAGCGTTTCGGGATCCCGGTTCAGTGTTATATGA
130 T-TTAGCTGACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCCGGGTCAGT-TTGCATGA
* * * * *
1090 TTTTTGGTGCCGAGACTCCTTGAACTATCTATATTTATCTAAACAAAACTCAGCTACATTGGATT
193 TTTTTGGTGCCAAGACTCCTTGAA-TATCTATATTTATCTAAACAAATCTCAACCACATTGAATT
* * * * * * *
1155 TAAGGA-TTGGTAAAACAATCATCTGAATCATGTTTCGATTTAATTAGAAATTAA-TTCGCAAAA
257 TAAGGATTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAG-AAAA
* * ** * *
1218 TAATAGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATCCTTTTGGCGTTGAATTATATA-
321 TAATA-GAAAAACGATATCA-AAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATATAT
*
1282 ATTTTTATGATTATTGTGGCTATAAATTGAGGAAATAACTTTCG-GGAAAATTTTGCAAAATATT
384 A-TTTTATGATTATTGTGGCTAAAAATTGAGGAAA-AACTTTCGAGGAAAATTTTGCAAAATATT
* * * * * * *
1346 AGCCGAAATCGTGTAAT-AGTCATCAC-GGT-TTTTGTTTAAAAACGCGTTTTGTGGCCCCTG-C
447 AACAGAAATCGTGTAATAAG-CATCACAGTTATTTTG-CTAAAAACGCGTTTCGAGGCCAC-GAC
* *
1407 TAAGTTTTCCATGATTTTTGGCATCAAGAC-TCTTTGAGATATCTATATTCATCTAATCAAATCT
509 TAAGTTTTCCATGATTTTTGGCATCAAGACTTC-TTGAAATATCTATATTCATCTAACCAAATCT
** * *
1471 CAGCTTCATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAA
573 CAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAA
1536 ATTAATTC
638 ATTAATTC
* *
1544 AGAAAATATGAAAGAACGATATTAAAAGCGTGAAAAGTCCTCCAAT-TTTTTGGCATTCAATTAT
1 AAAAAATATGAAA-AACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTGAATTAT
* * * ** *
1608 ATATATTTTATGAGTATTGT-GGCTAAAAATTGAGAAAAAAATATTTCAAGTCAACTTTTACAAA
65 ATATTTTTTATGAGTATTTTAGAC-AAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTACAAA
* *
1672 ATTTTAGCCGAAATCCTGTACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGGGTC
129 A-TTTA---G-----CTG-A-CATCACGG-TTTTTGGCTAAAAACGCGTTCCGGGACCCCGGGTC
* * ** * * * * *
1737 AGTTTTGCAAGATTTTCGGTGGTAAAACGCCTTGTAATACCTATATTCATCTAACCAAATCTCAA
182 AG-TTTGCATGATTTTTGGTGCCAAGACTCCTTG-AATATCTATATTTATCTAAACAAATCTCAA
* * * *
1802 CCACATTGAATTTAAGGATTTGTTTCTATGAGCATCTAAATCTTTTTTCGATTTAATTAGAAATT
245 CCACATTGAATTTAAGGATTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* *
1867 AATTTAGAAAAT-AT-GAAAAACGATATCAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTC
310 AATTTAGAAAATAATAGAAAAACGATATC-AAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTA
*
1930 AATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAA
374 AATTATATATATTTTATGATTATTGTGGCTAAAAATTGAGGAAAAA
1976 TATTTCAGGT
Statistics
Matches: 900, Mismatches: 139, Indels: 78
0.81 0.12 0.07
Matches are distributed among these distances:
647 30 0.03
648 265 0.29
649 110 0.12
650 16 0.02
651 71 0.08
652 145 0.16
653 22 0.02
654 4 0.00
656 5 0.01
657 81 0.09
658 9 0.01
659 93 0.10
660 46 0.05
661 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (645 bp):
AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTGAATTATA
TATTTTTTATGAGTATTTTAGACAAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTACAAAAT
TTAGCTGACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCCGGGTCAGTTTGCATGATTT
TTGGTGCCAAGACTCCTTGAATATCTATATTTATCTAAACAAATCTCAACCACATTGAATTTAAG
GATTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAATAATA
GAAAAACGATATCAAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTAAATTATATATATTTTAT
GATTATTGTGGCTAAAAATTGAGGAAAAACTTTCGAGGAAAATTTTGCAAAATATTAACAGAAAT
CGTGTAATAAGCATCACAGTTATTTTGCTAAAAACGCGTTTCGAGGCCACGACTAAGTTTTCCAT
GATTTTTGGCATCAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCA
TTTAAGAATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTC
Found at i:1825 original size:328 final size:324
Alignment explanation
Indices: 383--2024 Score: 1519
Period size: 328 Copynumber: 5.0 Consensus size: 324
373 AAAGTTTAAT
* * ** * * *
383 CATCACGGTTTTTT-GCTAAAAACGTGTTCCAGGACCCCGGGTCAGTTTGGCATGATTTTTGACG
1 CATCACGGTTTTTTGGCTAAAAACGCGTTTC-GGGGCCCGGCTCAGTTTTGCATGATTTTTG-GG
* * * * * * * *
447 CCAAGAGTCCTTGAGATATCCATATTTATCTAATCAAATCCCATCCACATTGTATTTAAGGATTT
64 CTAAGACTCCTTGA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
* * *
512 GTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTTAGAAAAAATATGAAAA
128 GTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAG--AAAATATGAAAA
* * * * *** *
577 ACGATATGAAAGGTGTG-AAAGTCCTCTAATCTTTTTGGCGCTAAAAAAATTATATATATTTCAT
191 ACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTT-G-GC--ATTCAATTATATATATTTTAT
* * * * * * * * ***
641 GATTATTTTAGCCAAAAATTCAGAGAAAA-CTTTC-GAGTCAATTTTTGCAAAATTTTAATAGAA
252 GAGTATTGTGGCTAAAAATTGAGAAAAAATATTTCAG-GTCAACTTTTGCAAAATTTTAGCCGAA
*
704 ATTGTGTAC
316 ATCGTGTAC
* * *
713 TAAGCATCACAGTTATTTT-GCTAAAAACGCGTTTCGAGGCCACGACTCAGTTTTGCATGATTTT
1 ----CATCACGGTT-TTTTGGCTAAAAACGCGTTTCGGGGCC-CGGCTCAGTTTTGCATGATTTT
* * * *
777 T-GGCGTCGAGACTTCTTGAAATATCTATATTCATCTGACCAAATCTCAGCCACATTGCATTTAA
60 TGGGC-T-AAGACTCCTTG-AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
* *
841 GGATTTGTTTTTACGAGCATCTGAATTTTGTTTTGATTTAATTAGAAATTAATTCAAAAAATATG
122 GGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATG
* * *
906 AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGG-AGTTGAATTATATATTTTTTA
187 AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCA-TTCAATTATATATATTTTA
* * * * *
970 TGAGTATTTTAGAC-AAAAATTGAGAAAAAAATATTTCTGGTCAATTTTTGCAAAATATTA---G
251 TGAGTATTGT-GGCTAAAAATTGAG-AAAAAATATTTCAGGTCAACTTTTGCAAAATTTTAGCCG
1031 ----C-TG-A-
314 AAATCGTGTAC
* * * * * **
1035 AATCACGG-TTTTTGGCTAAAAAAGCGTTTCGGGATCCCGGTTCAGTGTTATATGATTTTTGGTG
1 CATCACGGTTTTTTGGCTAAAAACGCGTTTCGGG-GCCCGGCTCAGTTTTGCATGATTTTTGG-G
** * * * *
1099 CCGAGACTCCTTGAACTATCTATATTTATCTAAACAAAACTCAGCTACATTGGATTTAAGGA-TT
64 CTAAGACTCCTTGAA-TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
* *** * * **
1163 GGTAAAACAATCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTC-GCAAAATAATAGGAA
128 GTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAT-AT--GAA
* * ** * * * *
1227 AAACGATATTAGAAGCATGAAAAACCCTTCAATCCTTTTGGCGTTGAATTATATA-ATTTTTATG
189 AAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTCAATTATATATA-TTTTATG
* * * * ** * *
1291 ATTATTGTGGCTATAAATTGAGGAAATAA-CTTTC-GGGAAAATTTTGCAAAATATTAGCCGAAA
253 AGTATTGTGGCTAAAAATTGA-GAAAAAATATTTCAGGTCAACTTTTGCAAAATTTTAGCCGAAA
*
1354 TCGTGTAATAGT
317 TCGTG---TA-C
** * * * * *
1366 CATCACGG-TTTTTGTTTAAAAACGCGTTTTGTGGCCCCTGCTAAGTTTTCCATGATTTTT-GGC
1 CATCACGGTTTTTTGGCTAAAAACGCGTTTCG-GGGCCCGGCTCAGTTTTGCATGATTTTTGGGC
* * ** *
1429 ATCAAGACTCTTTGAGATATCTATATTCATCTAATCAAATCTCAGCTTCATTGGATTTAAGAATT
65 -T-AAGACTCCTTGA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATT
*
1494 TGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAAGA
127 TGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAA-A
1559 ACGATATTAAAAGCGTGAAAAGTCCTCCAAT-TTTTTGGCATTCAATTATATATATTTTATGAGT
191 ACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTCAATTATATATATTTTATGAGT
* * *
1623 ATTGTGGCTAAAAATTGAGAAAAAAATATTTCAAGTCAACTTTTACAAAATTTTAGCCGAAATCC
256 ATTGTGGCTAAAAATTGAG-AAAAAATATTTCAGGTCAACTTTTGCAAAATTTTAGCCGAAATCG
1688 TGTAC
320 TGTAC
* * * *
1693 CATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGGGTCAGTTTTGCAAGATTTTCGGTG
1 CATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCC-GGCTCAGTTTTGCATGATTTTTGG-G
* * * * * *
1758 GTAAAACGCCTTGTAATACCTATATTCATCTAACCAAATCTCAACCACATTGAATTTAAGGATTT
64 CTAAGACTCCTTG-AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
* * * *
1823 GTTTCTATGAGCATCTAAATCTTT-TTTCGATTTAATTAGAAATTAATTTAGAAAATATGAAAAA
128 GTTTTTACGAGCATCTGAAT-TTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAA
* *
1887 CGATATCAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTCAATTATATATATTTTATGAGTA
192 CGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTCAATTATATATATTTTATGAGTA
* *
1952 TTGTGGCTAAAAATTGAGGAAAAATATTTCAGGTCAACTTTTACAAAATTTTAGCC---ATCGTG
257 TTGTGGCTAAAAATTGAGAAAAAATATTTCAGGTCAACTTTTGCAAAATTTTAGCCGAAATCGTG
2014 TAC
322 TAC
2017 CATCACGG
1 CATCACGG
2025 CTGCCAAGTC
Statistics
Matches: 1081, Mismatches: 171, Indels: 122
0.79 0.12 0.09
Matches are distributed among these distances:
316 53 0.05
317 107 0.10
318 15 0.01
319 77 0.07
320 2 0.00
323 1 0.00
324 19 0.02
325 2 0.00
327 80 0.07
328 193 0.18
329 64 0.06
330 66 0.06
331 131 0.12
332 75 0.07
333 31 0.03
334 29 0.03
335 135 0.12
336 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (324 bp):
CATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGGCT
AAGACTCCTTGAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
TTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCAGAAAATATGAAAAACGAT
ATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTCAATTATATATATTTTATGAGTATTGT
GGCTAAAAATTGAGAAAAAATATTTCAGGTCAACTTTTGCAAAATTTTAGCCGAAATCGTGTAC
Found at i:5019 original size:13 final size:13
Alignment explanation
Indices: 5001--5040 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
4991 ATATTATTGC
5001 ATATATCTATATA
1 ATATATCTATATA
5014 ATATATCTATAT-
1 ATATATCTATATA
*
5026 CTATATACTATATA
1 ATATAT-CTATATA
5040 A
1 A
5041 GTCTAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATCTATATA
Found at i:5026 original size:19 final size:19
Alignment explanation
Indices: 5002--5038 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4992 TATTATTGCA
5002 TATATCTATATAATATATC
1 TATATCTATATAATATATC
*
5021 TATATCTATATACTATAT
1 TATATCTATATAATATAT
5039 AAGTCTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATCTATATAATATATC
Done.