Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011046.1 Corchorus capsularis cultivar CVL-1 contig11067, 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: 69055
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Found at i:1443 original size:334 final size:333
Alignment explanation
Indices: 819--1446 Score: 877
Period size: 335 Copynumber: 1.9 Consensus size: 333
809 GTTTTGCATG
* *
819 TATATATTTTCATGGGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGGGTCAGTTTTTGCAAA
1 TATATATTTTCATGAGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAA
**
884 ATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTCGGCTAAAAACGCGGTCCGGGGCCCAGC
66 ATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTCGGCTAAAAACGCGGTCCGGAACCCAGC
* * * * *
949 TTAGTTTTGCATGATTTTTTGTGACAAGACTCCTTGAAATATCTATATACATCTAACCAAATATC
131 TCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATATATATATACATCTAACCAAATATC
* *
1014 AGCCACATTGGATTTTAGGATTTGTTTTTACGAGTATATAAATCTTATTTCGATTTAATCAGAAA
196 AGCCACATTGGATTTAAAGATTTGTTTTTACGAGTATATAAATCTTATTTCGATTTAATCAGAAA
* *
1079 TTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAACGTTAAAAAGCCCTTCAATATTTTTGG
261 TTAAATTAGAAATAAAATAGGAAAAACGATATTAGAAACGTTAAAAAGCCCTTCAATATTTTTGG
1144 CGTTGAAT
326 CGTTGAAT
* * *
1152 TATATATTTTTTATGAGTATTTTCGTTAGAAATTGAGGAAATATCTTTGGGGTCAATTTTTGCAA
1 TATATA-TTTTCATGAGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGGGTCAATTTTTGC--
* * * * **
1217 AAAATTTTAGCCGAAATCGTGTACTTAACTATCATGGTTTTCGGCTAAAAACGCGTTTTGGAACC
63 AAAATTTTAGCCGAAATCGTATAC-TAACCATCACGGTTTTCGGCTAAAAACGCGGTCCGGAACC
* * * * *
1282 CAGCTCAATTTTGCATGATTTTTGGCGCCGAGACTTCTTGAAATATAT-TTTA-ATCTAATCAAA
127 CAGCTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATATATATATACATCTAACCAAA
* * * * * *
1345 TCTCAGCCACATTGGATTTAAAGATTTGTTTTTGCGTGTATCTTAATCTTGTTTCGATTTAATTC
192 TATCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGTATATAAATCTTATTTCGATTTAA-TC
*
1410 -GAAATTAAATTAGAAA-AAAATATGAAAAACGATATTA
256 AGAAATTAAATTAGAAATAAAATAGGAAAAACGATATTA
1447 AAAGCGTGAA
Statistics
Matches: 256, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
333 6 0.02
334 71 0.28
335 78 0.30
336 28 0.11
337 73 0.29
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (333 bp):
TATATATTTTCATGAGTATTTTCGCTAGAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAA
ATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTCGGCTAAAAACGCGGTCCGGAACCCAGC
TCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATATATATATACATCTAACCAAATATC
AGCCACATTGGATTTAAAGATTTGTTTTTACGAGTATATAAATCTTATTTCGATTTAATCAGAAA
TTAAATTAGAAATAAAATAGGAAAAACGATATTAGAAACGTTAAAAAGCCCTTCAATATTTTTGG
CGTTGAAT
Found at i:1736 original size:12 final size:12
Alignment explanation
Indices: 1719--1761 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1709 ATTCAATTAG
1719 AAATTAATTCAA
1 AAATTAATTCAA
*
1731 AAATTATGATT-AG
1 AAATTA--ATTCAA
1744 AAATTAATTCAA
1 AAATTAATTCAA
1756 AAATTA
1 AAATTA
1762 TGAGACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 7 0.27
14 3 0.12
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (12 bp):
AAATTAATTCAA
Found at i:1742 original size:25 final size:25
Alignment explanation
Indices: 1714--1764 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1704 TTTCGATTCA
1714 ATTAGAAATTAATTCAAAAATTATG
1 ATTAGAAATTAATTCAAAAATTATG
1739 ATTAGAAATTAATTCAAAAATTATG
1 ATTAGAAATTAATTCAAAAATTATG
1764 A
1 A
1765 GACAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (25 bp):
ATTAGAAATTAATTCAAAAATTATG
Found at i:3182 original size:38 final size:38
Alignment explanation
Indices: 3140--3219 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
3130 GAGAACATTT
3140 TCAATTTGGTTAATTGGTTGGAAGGAGAAATAAACATG
1 TCAATTTGGTTAATTGGTTGGAAGGAGAAATAAACATG
3178 TCAATTTGGTTAATTGGTTGGAAGGAGAAATAAACATG
1 TCAATTTGGTTAATTGGTTGGAAGGAGAAATAAACATG
3216 TCAA
1 TCAA
3220 CAGGTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (38 bp):
TCAATTTGGTTAATTGGTTGGAAGGAGAAATAAACATG
Found at i:51046 original size:2 final size:2
Alignment explanation
Indices: 51039--51068 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51029 TTTATATGGA
51039 AT AT 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 AT AT
51069 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52468 original size:14 final size:14
Alignment explanation
Indices: 52449--52481 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52439 TAGCCGCTCT
*
52449 CTCTCCCTTTCTCC
1 CTCTCCCCTTCTCC
52463 CTCTCCCCTTCTCC
1 CTCTCCCCTTCTCC
52477 CTCTC
1 CTCTC
52482 TAGTTCTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCTCCCCTTCTCC
Found at i:53508 original size:13 final size:13
Alignment explanation
Indices: 53490--53518 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53480 GTAAAAGTAC
53490 AAAATTGGTCTCT
1 AAAATTGGTCTCT
53503 AAAATTGGTCTCT
1 AAAATTGGTCTCT
53516 AAA
1 AAA
53519 GTGGAGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (13 bp):
AAAATTGGTCTCT
Found at i:55902 original size:18 final size:18
Alignment explanation
Indices: 55879--55913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
55869 GACCCGCCTG
55879 TTTTTCT-TCTTCTTCTTC
1 TTTTTCTCTC-TCTTCTTC
55897 TTTTTCTCTCTCTTCTT
1 TTTTTCTCTCTCTTCTT
55914 TAAACGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCTCTCTCTTCTTC
Found at i:60218 original size:2 final size:2
Alignment explanation
Indices: 60213--60239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60203 TTTTTTTAAT
60213 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60240 TGACTGAAGA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68991 original size:2 final size:2
Alignment explanation
Indices: 68984--69055 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
68974 CGCCTAATAT
68984 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
69026 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.