Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019100.1 Corchorus olitorius cultivar O-4 contig19133, 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: 54590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:645 original size:329 final size:327
Alignment explanation
Indices: 1--1543 Score: 1553
Period size: 332 Copynumber: 4.7 Consensus size: 327
* * * * ** * * *
1 AAAACGCGTTCCGGGGCCCAGCTAAGTTTTGCATGATTTTTGGTATCAAAACTCTTTGAGATATC
1 AAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTCGTGCCAAGACTCCTTGAAATATC
* * * *
66 CATATTCATCTAATCAAATCTCAGCTACATTGGATTTAA-GAGTTTGATTTTAAGAGCATCTGAA
66 TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAA
* *
130 TCTTGTTTCGATATAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAACGTGAAA
130 TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAA
* *
195 AGTCCTCCAATCTTTTTGGCGTTAAATTATATATA--TTATGAGTA-TTTATGCCAAAAATTGAC
195 AGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTA-GCCAAAAATTGAG
* * * *
257 TAAAAATTTTTCGGGTC-ATTTTTACAAAATTTTAGCCGAAATCGTGTACTAATCATCACGGTTT
259 GAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCACGGTTT
321 TTGGCTA
321 TTGGCTA
* * *
328 AAAACGCGTTTCGGGATCCCGGCTTAGTTTTGCATGATTTTTCGCGCCAAGACTCCTTGAAATAT
1 AAAACGCGTTCCGGG-TCCCGGCTCAGTTTTGCATGATTTTTCGTGCCAAGACTCCTTGAAATAT
* * * ** *
393 CTATATTTATCTAATCATATCTTAGCCACATTCAATTGAAGGATTTGTTTTTACGAGCATCTGAA
65 CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
*
458 TCTTGTTTTGTATTTAATTATG-AATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT-A
130 TCTTGTTTCG-ATTTAATTA-GAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGA
* * * * * * *
521 AAGAGTCATCCAATCTTTTTGGCTTTTAAATTATATATATTCTATGAGTATTGTGGCTAAAAATG
193 AA-AGTCCTCCAATCTTTTTGGC-ATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATT
* * *
586 GAGGAAAAATATTTCGAGTCAATTTTTGGAAAATTTTAGCCGAAATCGTGT-ACCATCACGGTTT
256 GAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACGG-TT
650 TTTGGCTA
320 TTTGGCTA
* * * * * * *
658 AAAACGCGTTCTGGGCCCCAGG-TCAGTTTTGCATGATTTTTAGTGGCAACATTGCTTGAAATAT
1 AAAACGCGTTCCGGGTCCC-GGCTCAGTTTTGCATGATTTTTCGTGCCAAGACTCCTTGAAATAT
* * * * ** *
722 CTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGAATTTGTTTGTACGAGTTTCTAAA
65 CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * * * *
787 TCTTATTTCGATTTAATTAGAAATTAATTTTGAAATAAAATAAGAAAAACGATATTAGAAGCGTG
130 TCTTGTTTCGATTTAATTAGAAATTAA--TTCAGA-AAAATATGAAAAACGATATTAAAAGCGTG
* * * * * * * * * *
852 AAAAAGGCTTTCAATTTTTTTAGCATTGAATTATTTGTTTTTTATGAGTATTTTCA-CTAGAAAA
192 -AAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTT-AGCCA-AAAA
** *
916 -CAAGGAAAAATCTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCATGTACTAACCATCAC
254 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC--GT-GTAACCATCAC
*
979 GGTTTTCGGCTA
316 GGTTTTTGGCTA
*
991 AAAACGC-TTCCGCGGGT--CGGCTCAGTTTTGCATGA-TTTTCGGTGTCAAGACTCCTTGAAAT
1 AAAACGCGTT-C-CGGGTCCCGGCTCAGTTTTGCATGATTTTTC-GTGCCAAGACTCCTTGAAAT
* * * * * *
1052 ATTTATATTCATCT-ATCAAAATCTCAGCCACATTAGAATTAAGGATTTATTTTTACGGGCATTT
63 ATCTATATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * *
1116 GAATTTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACAATATTAGAAGCG
127 GAA-TCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCG
** * ** ** *
1181 CT-AAAAACCCTTCAATCTTTTTGATATCGAATTATATATTTTTTTATGAGTATTTTAGCCAAAA
190 -TGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATA-TATTTTATGAGTATTTTAGCCAAAA
* * * *
1245 ATTGAGGAAATATCTTTCGTGTCAATTTCTGCAAAATTTTAACCGAAATCGTGAACTAACCATCA
253 ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAACCATCA
1310 CGGTTTTTGGCTA
315 CGGTTTTTGGCTA
* * * * * *
1323 AAAACACGTTACAGGG-CCACGGCTCTGTTTTGCATGATTTTT-G-GCACTGAGACGCCTTAAAA
1 AAAACGCGTT-CCGGGTCC-CGGCTCAGTTTTGCATGATTTTTCGTGC-C-AAGACTCCTTGAAA
* * * * *
1385 TATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTATGTGCATCT
62 TATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * **
1450 GAATCTTGTTTCGATTTAATTAGAGAAATTAATTCATAAAAAGTATAAAAAACGATATTAACATT
127 GAATCTTGTTTCGATTTAATT--AGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGC
1515 GTGAAAAGTCCTCCAATCTTTTTTGGCAT
189 GTGAAAAGTCCTCCAATC-TTTTTGGCAT
1544 CTTTTCAAAA
Statistics
Matches: 1002, Mismatches: 162, Indels: 95
0.80 0.13 0.08
Matches are distributed among these distances:
327 15 0.01
328 118 0.12
329 177 0.18
330 91 0.09
331 164 0.16
332 182 0.18
333 97 0.10
334 104 0.10
335 46 0.05
336 8 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (327 bp):
AAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTCGTGCCAAGACTCCTTGAAATATC
TATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
GTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGA
AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCATCACGGTTTTTGGC
TA
Found at i:3848 original size:32 final size:32
Alignment explanation
Indices: 3807--3867 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3797 AAATATGTTT
*
3807 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
3839 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
3868 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:6647 original size:30 final size:31
Alignment explanation
Indices: 6611--6679 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
6601 TAGTTTATTT
**
6611 TTAGTATTCTGCCATTATTTT-TTA-TTTAGG
1 TTAGTATTAGGCCATTATTTTCTTATTTTA-G
**
6641 TTAGTATTAGGCTTTTATTTTCTTATTTTAG
1 TTAGTATTAGGCCATTATTTTCTTATTTTAG
6672 TTAGTATT
1 TTAGTATT
6680 GGGCTTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 12 0.36
32 4 0.12
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.59
Consensus pattern (31 bp):
TTAGTATTAGGCCATTATTTTCTTATTTTAG
Found at i:6688 original size:30 final size:30
Alignment explanation
Indices: 6625--6686 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
6615 TATTCTGCCA
6625 TTATTTTTTATTTAGGTTAGTATTAGGCTT
1 TTATTTTTTATTTAGGTTAGTATTAGGCTT
*
6655 TTATTTTCTTATTTTA-GTTAGTATTGGGCTT
1 TTATTTT-TTA-TTTAGGTTAGTATTAGGCTT
6686 T
1 T
6687 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTAGGTTAGTATTAGGCTT
Found at i:16072 original size:335 final size:327
Alignment explanation
Indices: 15267--16278 Score: 1045
Period size: 335 Copynumber: 3.0 Consensus size: 327
15257 TTTTTCCTCA
*
15267 ATATTTTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCAT-GTAAAAACAAAT
1 ATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGC-TCGTAAAAACAAAT
* * *
15331 CATTAAATCTAATGTGGCTGAGATTTAATTAGATGAATA-AAGATATTTTCAAGGAGCCGTGGTG
65 CCTTAAATC-AATGTGGCTGAGATTTAATTAGATGAATATAAGATA-TTTCAAGGAG-TGTGATG
* * * * *
15395 TCAAAAATCATGCAAAACAGAGCCGTGGCTCCGGAACGCGTTTTTAGCC-AAAACCGTGATGGTT
127 CCAAAAATCATGCAAAACTGA-CCGGGGCTCCGGAACGCGTTTTTAACCAAAAACCGTGATGATT
* * * * *
15459 AGTATACGATTTTGGCTAAAATTTTGCGAAAATTGACCCGAAAGATTTTTCCTCAATTTCTAGCG
191 AGTACACGATTTCGGCT-AAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT-TTGCT
* * * * * * *
15524 ACAATACTCATGAAAGATATATAATTCAACGCTAAAAAAATTCAAAGCCATTTTCACGCTTCTAA
254 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATT-GAAGGC-TTTTTACGCTTCTAA
15589 TATCA-TTTTTC
317 TAT-AGTTTTTC
** * * * *
15600 ATATTTTATTTCCAAATTAATTACTGATTAAATCGAAACAAGATTTAGATACTCGTGAAAACAAA
1 ATA-TTT-TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA
* * * ** * * * * *
15665 TTCTT-AATACAATATGGCTGAAATTTGGTTAAATGAATATAGATATATTTTAAGGAGTCTTAGT
64 TCCTTAAAT-CAATGTGGCTGAGATTTAATTAGATGAATATA-AGATATTTCAAGGAGTGTGA-T
* * *
15729 GCCAAAAATCTTGCAAAACTGACCCGGGGCTCTGGAATGCGTTTTTAACCAAAAACCGTGATTTC
126 GCCAAAAATCATGCAAAACTGA-CCGGGGCTCCGGAACGCGTTTTTAACCAAAAACCGTGA--T-
* * * * *
15794 GACTAACGTACACGATTTCGTCTAATATTTTGCAAAAATTAACCAGAAATATTTTTCCTCAATTT
187 GA-TTA-GTACACGATTTCGGCTAA-ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTT
* * * * *
15859 TTTCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTTACGCTT
249 TTGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGG-CTTTTTACGCTT
*
15924 TTAATATAGTTTTTC
313 CTAATATAGTTTTTC
* * *
15939 ATA-TTTTTCTGAATTAATTTTTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAATAAATC
1 ATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATC
16003 CTTAAATGCAATGTGGCTGAGATTTAATTAGATGAATATAA-ATATTTCAAGGAGTGTCGATGCC
66 CTTAAAT-CAATGTGGCTGAGATTTAATTAGATGAATATAAGATATTTCAAGGAGTGT-GATGCC
* ** * * * *
16067 AAAAATCATGTAAAACTGAGTGAGGG-TCCCGAAACGCGTTTCTAACAAAAAAAAAC-TG-TGAT
129 AAAAATCATGCAAAACTGACCG-GGGCT-CCGGAACGCGTTTTTAAC--CAAAAACCGTGATGAT
*
16129 TAGTACACGATTTCGGCTAAATTTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGC
190 TAGTACACGATTTCGGCTAAA-TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTT-GC
* * * * *
16194 TAAAATAATCACAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTACTCTTCTAAT
253 TAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGCTTTTTACGCTTCTAAT
*
16259 ATCGTTTTTC
318 ATAGTTTTTC
* *
16269 CTACTTTTTC
1 ATATTTTTTC
16279 CGAAAGGGAA
Statistics
Matches: 556, Mismatches: 98, Indels: 52
0.79 0.14 0.07
Matches are distributed among these distances:
329 1 0.00
330 78 0.14
331 51 0.09
332 2 0.00
333 4 0.01
334 34 0.06
335 157 0.28
336 70 0.13
337 38 0.07
338 2 0.00
339 28 0.05
340 43 0.08
341 48 0.09
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (327 bp):
ATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATC
CTTAAATCAATGTGGCTGAGATTTAATTAGATGAATATAAGATATTTCAAGGAGTGTGATGCCAA
AAATCATGCAAAACTGACCGGGGCTCCGGAACGCGTTTTTAACCAAAAACCGTGATGATTAGTAC
ACGATTTCGGCTAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTGCTAAAATAC
TCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGCTTTTTACGCTTCTAATATAGTTTT
TC
Found at i:19178 original size:5 final size:5
Alignment explanation
Indices: 19168--19213 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
19158 TATATAGTAG
19168 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
19214 GAAGGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:26609 original size:24 final size:24
Alignment explanation
Indices: 26596--26641 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
26586 TGCTGACGAA
**
26596 GACGAAGGTGAAGGTGAAGGTGCT
1 GACGAAGACGAAGGTGAAGGTGCT
26620 GACGAAGACGAAGGTGAAGGTG
1 GACGAAGACGAAGGTGAAGGTG
26642 ATGGAGAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.46, T:0.13
Consensus pattern (24 bp):
GACGAAGACGAAGGTGAAGGTGCT
Found at i:26613 original size:30 final size:30
Alignment explanation
Indices: 26578--26642 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
26568 TGGTGAAAAG
26578 GGTGAAGGTGCTGACGAAGACGAAGGTGAA
1 GGTGAAGGTGCTGACGAAGACGAAGGTGAA
26608 GGTGAAGGTGCTGACGAAGACGAAGGTGAA
1 GGTGAAGGTGCTGACGAAGACGAAGGTGAA
26638 GGTGA
1 GGTGA
26643 TGGAGAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.45, T:0.14
Consensus pattern (30 bp):
GGTGAAGGTGCTGACGAAGACGAAGGTGAA
Found at i:28345 original size:42 final size:42
Alignment explanation
Indices: 28285--28365 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
28275 AACTCACATT
*
28285 AAACCTGATTAATCCGGAATTGAATCATGTAGAATCTCAAAA
1 AAACCTGATTAATACGGAATTGAATCATGTAGAATCTCAAAA
28327 AAACCTGATTAATACGGAATTGAATCATGTAGAATCTCA
1 AAACCTGATTAATACGGAATTGAATCATGTAGAATCTCA
28366 GATGGGAGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (42 bp):
AAACCTGATTAATACGGAATTGAATCATGTAGAATCTCAAAA
Found at i:34874 original size:31 final size:32
Alignment explanation
Indices: 34831--34909 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
34821 CCTTGGTCTG
* *
34831 ACGTGGCCTTGCCATGTGGC-ATTTTGGTCCA
1 ACGTGGCATTGCCACGTGGCTATTTTGGTCCA
* *
34862 ACTTGGCATTGCCACGTGGCTTTTTTTGGTCCA
1 ACGTGGCATTGCCACGTGGC-TATTTTGGTCCA
*
34895 ACGTGGTATTGCCAC
1 ACGTGGCATTGCCAC
34910 ATCAACAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
31 17 0.43
33 23 0.57
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (32 bp):
ACGTGGCATTGCCACGTGGCTATTTTGGTCCA
Found at i:51086 original size:2 final size:2
Alignment explanation
Indices: 51079--51104 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51069 TTTATTGTTA
51079 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
51105 GACTCATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52067 original size:21 final size:21
Alignment explanation
Indices: 52026--52068 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
52016 CTTGTAATCT
*
52026 AAAGTTACTAAAAAGTTTATA
1 AAAGTTACTAAAAAGTCTATA
*
52047 AAAGTTATTAAAATAG-CTATA
1 AAAGTTACTAAAA-AGTCTATA
52068 A
1 A
52069 TGCTTTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAGTTACTAAAAAGTCTATA
Done.