Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014298.1 Corchorus olitorius cultivar O-4 contig14331, 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: 11431
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Found at i:1147 original size:327 final size:327
Alignment explanation
Indices: 399--1853 Score: 1481
Period size: 332 Copynumber: 4.4 Consensus size: 327
389 TGCAGACTCC
* * * *
399 TTGGCGCCAAGACTCCTTGGAATATCTATTTTGATCTAACCAAATCTCAGAA-ATGATGGACTTA
1 TTGGCGTCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGAACAT--TGGATTTA
* * * * *
463 AGGATTTGTTTTTACGAGCATCTGAATGTTGTGTCGATTTAATTTAGAAAATAATTAAGAAAAAA
64 AGGATTTGTTTTTACGAGAATCTGAATATTGTTTCGATTTAA-TTAGAAATTAATTCAGAAAAAA
* * * *
528 TAGAAAAACGATATTAGAAACGTTAAAAGCCCTCAAATCTTTTTGGCGTTGAATTATATATTTTT
128 TGGAAAAACGATATTAGAAGCGTGAAAAGCCCTCAAATCATTTTGGCGTTGAATTATATATTTTT
* *
593 TTGAGTATTCTGGGAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGA
193 ATGAGTATTCTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGA
* * **
658 AATCGTGTACTAACCCTCACGATTTTTTGGCTAAAAACGCGTTCCTAGGCCCCGGCAAAGTTTTG
258 AATCGTG-A-TAACCATCACGA-TTTTTGGCTAAAAACGCGTTCCTAGGCCCCGACTCAGTTTTG
723 CATGATTT
320 CATGATTT
** * * * *
731 TTGGCGTCAAGACTCCTTGAAAT-TCCTATAATAATCTAA-CATAATCTCAACAAAATTTGATTT
1 TTGGCGTCAAGACTCCTTGAAATAT-CTATTTTCATCTAACCA-AATCTC-AGAACATTGGATTT
* * * *
794 AAGGATTTGTTTTTACGATAATCTGAATATTGTTTTGATTTTATTAGAAATTAATTCCGAAAAAA
63 AAGGATTTGTTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA
* ** * * * *
859 TGGAAAAACGATACTAGAAGTTTGAAAAGCCCTCCAATCATTTTGGCGTTGAAATGTATACCTTT
128 TGGAAAAACGATATTAGAAGCGTGAAAAGCCCTCAAATCATTTTGGCGTTGAATTATATA-TTTT
* * * * *
924 TATGAGTATTGTGGCTAAAAATTGAGGAAAAATCTGTCGAGTCAATTTTTGCAAAATTTTAG-CG
192 TATGAGTATTCTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCG
* *
988 AAAATCGTG-T-ACCATCACGATTTTTGGCTAAAAACGCGTTCCTAGGCCACAACTCAGTTTTGC
257 -AAATCGTGATAACCATCACGATTTTTGGCTAAAAACGCGTTCCTAGGCCCCGACTCAGTTTTGC
1051 ATG-TTAT
321 ATGATT-T
* * * * *
1058 TTGACGTCAAGACTCATTGAAATATCCATATTCATATAACCAAATCTCAGCAACATTGGATTTAA
1 TTGGCGTCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAG-AACATTGGATTTAA
* * *
1123 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTAGAAATTAATTTAGAAAAAA-
65 GGATTTGTTTTTACGAGAATCTGAATATTGTTTCGATTTAA-TTAGAAATTAATTCAGAAAAAAT
*
1187 GAAAAAAGAACAACGATATTAGAAGCGTGAAAAGCCCTTCAACGAT-ATTTTGGCGTTGAATTAT
129 G------GAAAAACGATATTAGAAGCGTGAAAAGCCC-TCAA--ATCATTTTGGCGTTGAATTAT
* * * * * * *
1251 ATATTTTTTTGAGTATTCTGGGAAAAAATTCAGGAAAAGTTTTTCGGGTCTATTTTTGCAAAATT
185 ATATTTTTATGAGTATTCTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATT
* * **** * * * * * *
1316 TTATCCGAAATCGTGTTCGTTATCACCAATTTTGGTTAAAAACGCGTT-TTGGGGGCCCGACTCA
250 TTAGCCGAAATCGTGATAACCATCACGATTTTTGGCTAAAAACGCGTTCCT-AGGCCCCGACTCA
* *
1380 ATTCTGCATGATTT
314 GTTTTGCATGATTT
* * * *
1394 TTTGCGCCAAG-GTCCTTGAAATATCTATTTTCATCTAACAAAATCTCAG-ACGTATTGGATTTA
1 TTGGCGTCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGAAC--ATTGGATTTA
*
1457 AGGATTTGTTTTTACGAGAATCT-AAGTATTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAA
64 AGGATTTGTTTTTACGAGAATCTGAA-TATTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAA
* * * *
1521 AT--AAAAACGATAATAGAAGCGTGAAAATCCCTCAAAAT-TTTTTGACGTTGAATTATATATTT
127 ATGGAAAAACGATATTAGAAGCGTGAAAAGCCCTC-AAATCATTTTGGCGTTGAATTATATA-TT
* * * * *
1583 TTTATGAGTATTTTGGCCAAAAATTGAGGAAAAA-CTATTCTGGTTAATTTTCGTAAAATTTTAG
190 TTTATGAGTATTCTGGCAAAAAATTGAGGAAAAATCT-TTCGGGTCAATTTTCGCAAAATTTTAG
* * * * * *
1647 TCAAAATCGTGTACTAATAACCATCACGGTTTTTGACTAAAAACGCATTTC-AGGGCCCCTG-CT
254 CCGAAATCGTG-----ATAACCATCACGATTTTTGGCTAAAAACGCGTTCCTA-GGCCCC-GACT
1710 CAGTTTTGCATGATTT
312 CAGTTTTGCATGATTT
* * * * * *
1726 TTGGTGGCAAGACTTCTTGAAATATCTATTTTCATCTGACCAAATCTCAAACACATTCGATTTAA
1 TTGGCGTCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGA-ACATTGGATTTAA
* * * * * *
1791 GGATTTATTTTTACGAGTATCCGAATATTGTTTCTATTTAATTAGAAATTAATTTAAAAAAAA
65 GGATTTGTTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA
1854 ATCACATCAA
Statistics
Matches: 924, Mismatches: 154, Indels: 90
0.79 0.13 0.08
Matches are distributed among these distances:
326 25 0.03
327 190 0.21
328 60 0.06
329 1 0.00
331 74 0.08
332 203 0.22
333 122 0.13
334 85 0.09
335 110 0.12
336 52 0.06
337 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (327 bp):
TTGGCGTCAAGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTCAGAACATTGGATTTAAG
GATTTGTTTTTACGAGAATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATGG
AAAAACGATATTAGAAGCGTGAAAAGCCCTCAAATCATTTTGGCGTTGAATTATATATTTTTATG
AGTATTCTGGCAAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTAGCCGAAAT
CGTGATAACCATCACGATTTTTGGCTAAAAACGCGTTCCTAGGCCCCGACTCAGTTTTGCATGAT
TT
Found at i:2084 original size:29 final size:29
Alignment explanation
Indices: 2004--2084 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
1994 TTTTCTAGAT
* * *
2004 GAAAAGCTCAAATAGGGGCCTGACTTTTAG
1 GAAAAGGTCAAATA-GGGCCTAAATTTTAG
**
2034 TGAAAAGGTCATTTAAGGGCCTAAATTTTA-
1 -GAAAAGGTCAAAT-AGGGCCTAAATTTTAG
2064 GAAAAGGTCAAATAGGTGCCT
1 GAAAAGGTCAAATAGG-GCCT
2085 TACCTTTTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 3 0.07
29 15 0.37
31 22 0.54
32 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (29 bp):
GAAAAGGTCAAATAGGGCCTAAATTTTAG
Found at i:4776 original size:22 final size:22
Alignment explanation
Indices: 4745--4796 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4735 CTTTGCAAGT
*
4745 GGACAAATAGGATTGTCGCCAC
1 GGACAAATAGGATTGTCCCCAC
* *
4767 GGACAGATAGGATTGTCCCCAT
1 GGACAAATAGGATTGTCCCCAC
4789 GGACAAAT
1 GGACAAAT
4797 GAACTATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (22 bp):
GGACAAATAGGATTGTCCCCAC
Found at i:4865 original size:31 final size:31
Alignment explanation
Indices: 4818--5495 Score: 969
Period size: 31 Copynumber: 22.4 Consensus size: 31
4808 ATAGACCTAA
* * *
4818 AACTATATGCATTAACGATAGACTTA-AACTG
1 AACTATATGCAATAACGATGGACCTAGAA-TG
* *
4849 AA-TAATATGCAATAACGATAGACCTAAAATG
1 AACT-ATATGCAATAACGATGGACCTAGAATG
* *
4880 AACCATATGCAATAACGATGGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
*
4911 AACCATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
* *
4942 AACCATATGCAATAACGATGGACCTACAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
*
4973 AACTATATGCAATAACGATGGACCTACAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5004 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5035 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5066 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5097 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5128 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
*
5159 AACTATATGCAATAACGATAGACCT---A-G
1 AACTATATGCAATAACGATGGACCTAGAATG
*
5186 AACTATATGCAATAACGATAGACCT---A-G
1 AACTATATGCAATAACGATGGACCTAGAATG
*
5213 AACTATATGCAATAACGATAGACCT---A-G
1 AACTATATGCAATAACGATGGACCTAGAATG
*
5240 AACTATATGCAATAACGATAGACCT---A-G
1 AACTATATGCAATAACGATGGACCTAGAATG
** *
5267 AACTATATGCAATAACGATAAACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
*
5298 AACTATATGCAATAACGATGGACCTAGAATA
1 AACTATATGCAATAACGATGGACCTAGAATG
5329 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5360 AACTATATGCAATAACGATGGACCTAGAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
* * *
5391 AACTATAAGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
* *
5422 AACTATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
** *
5453 AACTATATGCAATAACGATAAACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAGAATG
5484 AACTATATGCAA
1 AACTATATGCAA
5496 CAACCACACT
Statistics
Matches: 620, Mismatches: 20, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
27 106 0.17
28 1 0.00
30 2 0.00
31 509 0.82
32 2 0.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (31 bp):
AACTATATGCAATAACGATGGACCTAGAATG
Found at i:8965 original size:16 final size:16
Alignment explanation
Indices: 8944--8977 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8934 GAATAAAACC
8944 CCCAAAATACTTTCTT
1 CCCAAAATACTTTCTT
8960 CCCAAAATACTTTCTT
1 CCCAAAATACTTTCTT
8976 CC
1 CC
8978 TGGCTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (16 bp):
CCCAAAATACTTTCTT
Found at i:10406 original size:13 final size:13
Alignment explanation
Indices: 10374--10407 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
10364 ATAGAGTGCA
10374 TGCAAGATTGATT
1 TGCAAGATTGATT
*
10387 TGAAAGATTGATT
1 TGCAAGATTGATT
*
10400 TTCAAGAT
1 TGCAAGAT
10408 CATGATGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (13 bp):
TGCAAGATTGATT
Done.