Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019276.1 Corchorus olitorius cultivar O-4 contig19309, 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: 43137
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1358 original size:18 final size:19
Alignment explanation
Indices: 1335--1374 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1325 TCCTTCATTT
1335 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
1353 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
1372 AAT
1 AAT
1375 AAGTCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:2230 original size:17 final size:18
Alignment explanation
Indices: 2205--2238 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2195 CTCTTTCATG
2205 AAAACACTTCTTTTTAAT
1 AAAACACTTCTTTTTAAT
*
2223 AAAA-ACTTTTTTTTAA
1 AAAACACTTCTTTTTAA
2239 ATGGTCCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAACACTTCTTTTTAAT
Found at i:2678 original size:17 final size:17
Alignment explanation
Indices: 2645--2677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2635 ATGACTCAAT
2645 TATCAAGCATTCACCCC
1 TATCAAGCATTCACCCC
*
2662 TATCAAGTATTC-CCCC
1 TATCAAGCATTCACCCC
2678 CCCCCCCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.39, G:0.06, T:0.27
Consensus pattern (17 bp):
TATCAAGCATTCACCCC
Found at i:3008 original size:18 final size:20
Alignment explanation
Indices: 2972--3014 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
2962 ACATAAAACC
**
2972 CTAAAGCTAAAATTTTAAAT
1 CTAAAGCTAAAATCCTAAAT
2992 -TAAA-CTAAAATCCTAAAT
1 CTAAAGCTAAAATCCTAAAT
3010 CTAAA
1 CTAAA
3015 TAGGTTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (20 bp):
CTAAAGCTAAAATCCTAAAT
Found at i:4873 original size:334 final size:334
Alignment explanation
Indices: 4261--4928 Score: 1282
Period size: 334 Copynumber: 2.0 Consensus size: 334
4251 CTTTGTCAAA
*
4261 GTTGAGATTGCATTGCTTTACTGCCCACCATGCTTTGTACTCTAACTCCACAAGTAGATGACATG
1 GTTGAGACTGCATTGCTTTACTGCCCACCATGCTTTGTACTCTAACTCCACAAGTAGATGACATG
4326 GCTTACCAAACACAATTCTGTATGGAGACATACCAAGTGGTGTTTTGTAAGCTGTACGATAGGCC
66 GCTTACCAAACACAATTCTGTATGGAGACATACCAAGTGGTGTTTTGTAAGCTGTACGATAGGCC
4391 CATAAAGCATCTCCTAATCACATACTCCAATCTTTTCTCTGAACATTAACCGTCTTCTCCAGAAT
131 CATAAAGCATCTCCTAATCACATACTCCAATCTTTTCTCTGAACATTAACCGTCTTCTCCAGAAT
4456 TAGCTTCACTTGTCGATTTGAAACTTCAGCTTGACCACTGGTTTGAGGATGATATGAAGTAGATA
196 TAGCTTCACTTGTCGATTTGAAACTTCAGCTTGACCACTGGTTTGAGGATGATATGAAGTAGATA
* * *
4521 CCCTATGGTAGGCTCCATATTTTTCAACCAATGATTGCACAATCTTGTTGCTGAAGTGAGTACCT
261 CCCTATGGTAGACTCCATATTTTTCAACCAATGATTGCACAATCTTATTGCAGAAGTGAGTACCT
4586 CGATCACTG
326 CGATCACTG
* *
4595 GTTGAGACTGCATTGTTTTACTGCCCACCATGCTTTGTACTCTAACTCCACAAGTAGATGACTTG
1 GTTGAGACTGCATTGCTTTACTGCCCACCATGCTTTGTACTCTAACTCCACAAGTAGATGACATG
4660 GCTTACCAAACACAATTCTGTATGGAGACATACCAAGTGGTGTTTTGTAAGCTGTACGATAGGCC
66 GCTTACCAAACACAATTCTGTATGGAGACATACCAAGTGGTGTTTTGTAAGCTGTACGATAGGCC
4725 CATAAAGCATCTCCTAATCACATACTCCAATCTTTTCTCTGAACATTAACCGTCTTCTCCAGAAT
131 CATAAAGCATCTCCTAATCACATACTCCAATCTTTTCTCTGAACATTAACCGTCTTCTCCAGAAT
4790 TAGCTTCACTTGTCGATTTGAAACTTCAGCTTGACCACTGGTTTGAGGATGATATGAAGTAGATA
196 TAGCTTCACTTGTCGATTTGAAACTTCAGCTTGACCACTGGTTTGAGGATGATATGAAGTAGATA
4855 CCCTATGGTAGACTCCATATTTTTCAACCAATGATTGCACAATCTTATTGCAGAAGTGAGTACCT
261 CCCTATGGTAGACTCCATATTTTTCAACCAATGATTGCACAATCTTATTGCAGAAGTGAGTACCT
4920 CGATCACTG
326 CGATCACTG
4929 ATAAAAGCTC
Statistics
Matches: 328, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
334 328 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (334 bp):
GTTGAGACTGCATTGCTTTACTGCCCACCATGCTTTGTACTCTAACTCCACAAGTAGATGACATG
GCTTACCAAACACAATTCTGTATGGAGACATACCAAGTGGTGTTTTGTAAGCTGTACGATAGGCC
CATAAAGCATCTCCTAATCACATACTCCAATCTTTTCTCTGAACATTAACCGTCTTCTCCAGAAT
TAGCTTCACTTGTCGATTTGAAACTTCAGCTTGACCACTGGTTTGAGGATGATATGAAGTAGATA
CCCTATGGTAGACTCCATATTTTTCAACCAATGATTGCACAATCTTATTGCAGAAGTGAGTACCT
CGATCACTG
Found at i:13821 original size:32 final size:33
Alignment explanation
Indices: 13785--13849 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
13775 TCTGAGAGAT
13785 CAGATTGAAGAAAG-AATTAA-A-GCAGAACAAAA
1 CAGATTGAAG-AAGCAATTAATAGGCAG-ACAAAA
13817 CAGATTGAAGAAGCAATTAATAGGCAGACAAAA
1 CAGATTGAAGAAGCAATTAATAGGCAGACAAAA
13850 TGGGGAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 3 0.10
32 16 0.53
33 7 0.23
34 4 0.13
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.14
Consensus pattern (33 bp):
CAGATTGAAGAAGCAATTAATAGGCAGACAAAA
Found at i:17442 original size:15 final size:16
Alignment explanation
Indices: 17412--17451 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
17402 TTTCTTTGCT
*
17412 TTGTTTCCTAGTTTAA
1 TTGTTTTCTAGTTTAA
17428 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
17443 TTGTTTTCT
1 TTGTTTTCT
17452 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:23393 original size:15 final size:16
Alignment explanation
Indices: 23363--23402 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
23353 TTGCTTTGCT
*
23363 TTGTTTCCTAGTTTAA
1 TTGTTTTCTAGTTTAA
23379 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
23394 TTGTTTTCT
1 TTGTTTTCT
23403 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:24238 original size:18 final size:17
Alignment explanation
Indices: 24211--24245 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
24201 CCTTCCCCAG
*
24211 TAAACATAACCATAGTT
1 TAAACATAACAATAGTT
24228 TAAATCATAACAATAGTT
1 TAAA-CATAACAATAGTT
24246 GGATTGGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAACATAACAATAGTT
Found at i:26479 original size:19 final size:18
Alignment explanation
Indices: 26446--26511 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 18
26436 TGGAAATTAT
*
26446 TCTTCAATGGTCTTCAAA
1 TCTTCAATTGTCTTCAAA
26464 TCTTCAAATTGTCTTC-AA
1 TCTTC-AATTGTCTTCAAA
26482 ---T-AA--GTCTTCAAA
1 TCTTCAATTGTCTTCAAA
26494 TCTTCAAATTGTCTTCAA
1 TCTTC-AATTGTCTTCAA
26512 TAAGTCTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 17
0.68 0.02 0.30
Matches are distributed among these distances:
11 6 0.16
12 2 0.05
13 2 0.05
15 2 0.05
17 2 0.05
18 7 0.18
19 17 0.45
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATTGTCTTCAAA
Found at i:26489 original size:30 final size:30
Alignment explanation
Indices: 26446--26523 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
26436 TGGAAATTAT
*
26446 TCTTCAAT-GGTCTTCAAATCTTCAAATTG
1 TCTTCAATAAGTCTTCAAATCTTCAAATTG
26475 TCTTCAATAAGTCTTCAAATCTTCAAATTG
1 TCTTCAATAAGTCTTCAAATCTTCAAATTG
26505 TCTTCAATAAGTCTTCAAA
1 TCTTCAATAAGTCTTCAAA
26524 CACGAACTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 8 0.17
30 39 0.83
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (30 bp):
TCTTCAATAAGTCTTCAAATCTTCAAATTG
Found at i:26518 original size:11 final size:10
Alignment explanation
Indices: 26455--26523 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 10
26445 TTCTTCAATG
26455 GTCTTC-AAA
1 GTCTTCAAAA
*
26464 -TCTTCAAATT
1 GTCTTCAAA-A
26474 GTCTTCAATAA
1 GTCTTCAA-AA
26485 GTCTTC-AAA
1 GTCTTCAAAA
*
26494 -TCTTCAAATT
1 GTCTTCAAA-A
26504 GTCTTCAATAA
1 GTCTTCAA-AA
26515 GTCTTCAAA
1 GTCTTCAAA
26524 CACGAACTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 10 0.21
9 6 0.12
10 2 0.04
11 28 0.58
12 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (10 bp):
GTCTTCAAAA
Found at i:31606 original size:18 final size:18
Alignment explanation
Indices: 31583--31618 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31573 CTTTCTGAAG
31583 GACAAGAAAATTTTCCAA
1 GACAAGAAAATTTTCCAA
* *
31601 GACAAGGACATTTTCCAA
1 GACAAGAAAATTTTCCAA
31619 AGGCAAGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (18 bp):
GACAAGAAAATTTTCCAA
Found at i:32889 original size:17 final size:17
Alignment explanation
Indices: 32869--32902 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32859 GGTAGTTTAA
*
32869 AAAAAAATTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
*
32886 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
32903 GCAAGAGGAG
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:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAAAAGTGTTTTCAT
Found at i:40678 original size:19 final size:18
Alignment explanation
Indices: 40654--40689 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40644 TGAAGATTTA
40654 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
40673 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
40690 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.