Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007485.1 Corchorus capsularis cultivar CVL-1 contig07506, 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: 17113
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1996 original size:329 final size:329
Alignment explanation
Indices: 889--3450 Score: 2844
Period size: 329 Copynumber: 7.8 Consensus size: 329
879 GAAAGATTTG
* * * *
889 TACCCACATTAGATTTAAAGATTTGTATTTACAACAATCTCAATCCAGTTTCAATTTAATTAAAA
1 TACCCACATTA-ATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
* * * * *
954 ATTAATTCGGGAAAAA-A-GAAAAATGATATTAGAAGCATGAGAAACTCGTT-AATTTTTTTGGC
65 ATTAATTC-GGAAAAATATGAAAAATGATATTAGAAACGTGAG-AAGTCCTTCAATATTTTTGGC
* * * *
1016 GTTGAGTTATATATATATTTTAGGATTATTGTGGCCAAAAATTGAGGAGAAATGTTTCTGATCAA
128 GTTGACTTATATAT-T-TTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAA
* * * *
1081 TTTTGGCAAAATTTTACCCGAAATCATGTGCTAACCATCACAATTTTGGACCAAAAATGCGTTCC
191 TTTTGGCAAAATTTTACCCGAAATCGTGTGCT-ACCATCACAGTTTTTGACCAAAAATGCATTCC
* * *
1146 GGAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGACTAGTCTCTCTGAAATATCTATATCCATCT
255 GGAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCT
1211 GACAAAATCT
320 GACAAAATCT
* ** **
1221 TACCCACATTAGATTTAAAGATTTTTATTTACGAGAATCTCAATTTGGTTTCGATTTAATTAAAA
1 TACCCACATTA-ATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
* * * * *
1286 ATTAATTCGGGAAAAA-A-GAAAAAAGGATATTAGAAGCGTGAGAAATCCGTCAATCTTTTTGTG
65 ATTAATTC-GGAAAAATATG-AAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTG-G
* * * * ** *
1349 -TTTGAATTATATATATTTTTTATGAGTATTGTAGCTAAAAATTGAGCTGAAATGTTTCGGGTCA
127 CGTTG-ACT-TATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCA
* * * * * * * * *
1413 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGGTTCTGGCTAAAAACGCATTC
190 ATTTTGGCAAAATTTTACCCGAAATCGTGTGCT-ACCATCACAGTTTTTGACCAAAAATGCATTC
* * * ** * * * * * **
1478 CGGGGCCTCGGTTCAATTTTGCATGATTTTTGACGCCAAGACTCATTGAAATATTTATGTAAATC
254 CGGAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATC
*
1543 TTA-AGAAATCT
319 TGACA-AAATCT
* * * * *
1554 TACCCACATTAA--T---GA-TTGTTTTTTACAAGCATCTTAGTCCGGGTTTCGATTTAATTAAA
1 TACCCACATTAATTTAAAGATTTG-TATTTACGACCATCTCAATCC-GGTTTCGATTTAATTAAA
* ** *
1613 AATTAATTTGGAAAAATATGAAAAACAATATTAGAAACGTGATAAGTCCTTCAATATTTTTGGCG
64 AATTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGCG
* * * *
1678 TTGACTTGTATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAAGAAATGTTTTGGGTCAATTT
129 TTGACTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAATTT
* * * *
1743 TGGCAAAATTTTACCCGAAAGCATGTGC-ACCATCACGGTTTTTGACCAAAAATGCAATCCGGAG
194 TGGCAAAATTTTACCCGAAATCGTGTGCTACCATCACAGTTTTTGACCAAAAATGCATTCCGGAG
* * * * * *
1807 CCCTGGCT-TGGTTTTACATAATTTTTGGCGCCATGTCTCTTTGAAATATATATATCTATCTGAC
259 CCCCGGCTCT-GTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGAC
*
1871 CAAATCT
323 AAAATCT
* * * * *
1878 TACCCACATTTAATTTAAAGATTTGTATTTACGACTATTTCAATCCAGTTTTGATTTAATTAGAA
1 TACCCACA-TTAATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
1943 ATTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGATG-AGTCCTTCAATATTTTTGGCG
65 ATTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGA-GAAGTCCTTCAATATTTTTGGCG
* * *
2007 TTGACTTGTATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAAGAAATGTTTCGGTTCAATTT
129 TTGACTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAATTT
* * *
2072 TGGCAAAATTTTACCCGAAATCATGTGC-ACCATCACGGTTTTTGACCAAAAATGCAATCCGGAG
194 TGGCAAAATTTTACCCGAAATCGTGTGCTACCATCACAGTTTTTGACCAAAAATGCATTCCGGAG
* * * * * *
2136 CCCTGGCT-TGGTTATACATAATTTTTGGCGCCATGTCTCTTTGAAATATCTATATCCATCTAAC
259 CCCCGGCTCT-GTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGAC
*
2200 CAAATCT
323 AAAATCT
* * **
2207 TACCCACATTAAATTTAAAGATTTGTATTTACGACCATCTCAATCCAGTTTTGATTTAATTTGAA
1 TACCCACATT-AATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
* * * *
2272 ATTAATTCAGAAAAATATGAAAAATGATATTAAAAACGTGATATGTCCTTCAATATTTTTGGCGT
65 ATTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGCGT
* * * *
2337 TGACTTTTATATTTTTTATGAGTATTGTGGCAAAAAACTGAGGAGAAATGTTTTGGATCAATTTT
130 TGACTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAATTTT
* * **
2402 GGCAAAATTTTACCTGAAATCGTGTGCTAACCATCACAGTTTTTGACCAAAAATGCGTTCCATAG
195 GGCAAAATTTTACCCGAAATCGTGTGCT-ACCATCACAGTTTTTGACCAAAAATGCATTCCGGAG
* * * * *
2467 CCCCGACTCTGTTTTGCATGATTTGTGGCGTCAAGTCTCTTTGAAATATCTAAATCAATCTGACA
259 CCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGACA
*
2532 AAATAT
324 AAATCT
* *
2538 TACCCTCATTAGATTTAAAGATTTGAATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
1 TACCCACATTA-ATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
* * * ** * *
2603 ATTAATTCGGGAAAAAAAAGAAAAATGATATTAGAAGCGTGAGAAACCCGTCAATTTTTTTGGCG
65 ATTAATTC-GGAAAAATATGAAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGCG
* *
2668 TTGAGTTATATATATTTTTTATGATTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAAT
129 TTGA-CT-TATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAAT
* * * **
2733 TTTGGCAAAATTTTACCCGAAATCGTATGCTAACCATCAAAGTTTTGGAAAAAAAAATGCATTCC
192 TTTGGCAAAATTTTACCCGAAATCGTGTGCT-ACCATCACAGTTTTTG-ACCAAAAATGCATTCC
* *
2798 GGAGCCCCGGCTCTGTTTTGCATGATTTTTTGG-GTCAAGTTTCTTTGAAATATCTATATCCATC
255 GGAGCCCCGGCTCTGTTTTGCATGA-TTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATC
2862 TGACAAAATCT
319 TGACAAAATCT
* * ** **
2873 TAACCACATTAGATTTAAAGATTTTTATTTACGAGAATCTCAATTTGGTTTCGATTTAATTAAAA
1 TACCCACATTA-ATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAA
* * *
2938 ATTAATTCGGTAAAAA-A-GAAAAAAGAATATTAGAAGCGTGAGAAATCCTTCAATATTTTTGGC
65 ATTAATTCGG-AAAAATATGAAAAATG-ATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGC
* * * *
3001 GTTGAATTATATATATTTTCTATGAGTATTGTGGCTAAAAATTGAGGTGAAATGTTTCGGGTCAA
128 GTTGACTTATATAT-TTTT-TATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAA
* * * * * ** *
3066 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGGTTTTGGCTTAAAACGCATTCC
191 TTTTGGCAAAATTTTACCCGAAATCGTGTGCT-ACCATCACAGTTTTTGACCAAAAATGCATTCC
* * ** * * * * * **
3131 GGGGCCCCGGTTCAATTTTGCATGATTTTTTGCGCCGAGACTCATTGAAATATTTATATAAATCT
255 GGAGCCCCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCT
*
3196 TA-AGAAATCT
320 GACA-AAATCT
* * * * *
3206 TACCCACATTAA--T---GA-TTGTTTTTTACAAGCATCTTAATCCGGGTTTTGATTTAATTAAA
1 TACCCACATTAATTTAAAGATTTG-TATTTACGACCATCTCAATCC-GGTTTCGATTTAATTAAA
* ** *
3265 AATTAATTTGGAAAAATATGAAAAACAATATTAGAAACGTGATAAGTCCTTCAATATTTTTGGCG
64 AATTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGCG
* * *
3330 TTGACTTGTATATTTTTTATGAGTATTGTGGCCAAAAAAATTAAGAAGAAATGTTTCAGG-TCAA
129 TTGACTTATATATTTTTTATGAGTATTGTGGCC--AAAAATTGAGGAGAAATGTTTC-GGATCAA
* * *
3394 TTTTGGCAAAATTTTACCCGAAATCATGTG-GACCATCACGGTTTTTGACCAAAAATG
191 TTTTGGCAAAATTTTACCCGAAATCGTGTGCTACCATCACAGTTTTTGACCAAAAATG
3451 TAAAGGGGTT
Statistics
Matches: 1911, Mismatches: 274, Indels: 96
0.84 0.12 0.04
Matches are distributed among these distances:
324 87 0.05
325 4 0.00
326 115 0.06
327 53 0.03
328 190 0.10
329 480 0.25
330 19 0.01
331 155 0.08
332 148 0.08
333 279 0.15
334 225 0.12
335 150 0.08
336 6 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (329 bp):
TACCCACATTAATTTAAAGATTTGTATTTACGACCATCTCAATCCGGTTTCGATTTAATTAAAAA
TTAATTCGGAAAAATATGAAAAATGATATTAGAAACGTGAGAAGTCCTTCAATATTTTTGGCGTT
GACTTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGGAGAAATGTTTCGGATCAATTTTG
GCAAAATTTTACCCGAAATCGTGTGCTACCATCACAGTTTTTGACCAAAAATGCATTCCGGAGCC
CCGGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCTTTGAAATATCTATATCCATCTGACAAA
ATCT
Found at i:3483 original size:21 final size:22
Alignment explanation
Indices: 3459--3503 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3449 TGTAAAGGGG
3459 TTGCTAAAT-ACCGCCCC-CTTT
1 TTGCT-AATCACCGCCCCACTTT
*
3480 TTGCTATTCACCGCCCCACTTT
1 TTGCTAATCACCGCCCCACTTT
3502 TT
1 TT
3504 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.16, C:0.38, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCACTTT
Found at i:9585 original size:2 final size:2
Alignment explanation
Indices: 9531--9576 Score: 51
Period size: 2 Copynumber: 22.5 Consensus size: 2
9521 CTTAATATCT
9531 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA GT- TCA TA TA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA
9572 TA TA T
1 TA TA T
9577 TTTTATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 2 0.05
2 33 0.85
3 4 0.10
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10315 original size:17 final size:17
Alignment explanation
Indices: 10284--10317 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10274 AAAAAAACTG
**
10284 GAATTCAGTTCACTAAT
1 GAATTCAGTAAACTAAT
10301 GAATTCAGTAAACTAAT
1 GAATTCAGTAAACTAAT
10318 TAAAAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (17 bp):
GAATTCAGTAAACTAAT
Found at i:12091 original size:2 final size:2
Alignment explanation
Indices: 12084--12110 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12074 TGGTTTTGAT
12084 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
12111 CTTATTTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13104 original size:35 final size:38
Alignment explanation
Indices: 13032--13109 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 38
13022 TTATTGCGTC
13032 AATTATATTATGTTAAAAAATGCAATAATAAAGATGCAAT
1 AATTATATTATGTTAAAAAATG--ATAATAAAGATGCAAT
*
13072 AATTATATTATGTTAAAAAA-G-TACTAAA-ATGCAAT
1 AATTATATTATGTTAAAAAATGATAATAAAGATGCAAT
13107 AAT
1 AAT
13110 CCCAATTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 10 0.27
36 6 0.16
39 1 0.03
40 20 0.54
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (38 bp):
AATTATATTATGTTAAAAAATGATAATAAAGATGCAAT
Done.