Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017305.1 Corchorus olitorius cultivar O-4 contig17338, 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: 93088
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1394 original size:25 final size:24
Alignment explanation
Indices: 1349--1425 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 24
1339 CTTTAGGTGA
1349 CATGTTAGGGTTT-GCCTTTCATGT
1 CATGTTAGGGTTTAGCC-TTCATGT
*
1373 CATGATTAGGGTTTAGCCTTCATCT
1 CATG-TTAGGGTTTAGCCTTCATGT
*
1398 CAT-TTAGGGTTTGAG-TTTCATGT
1 CATGTTAGGGTTT-AGCCTTCATGT
1421 CATGT
1 CATGT
1426 CATTTTTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 18 0.39
24 7 0.15
25 18 0.39
26 3 0.07
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (24 bp):
CATGTTAGGGTTTAGCCTTCATGT
Found at i:1408 original size:23 final size:24
Alignment explanation
Indices: 1353--1410 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
1343 AGGTGACATG
*
1353 TTAGGGTTTGCCTTTCATGTCATGA
1 TTAGGGTTTGCCTTTCATCTCAT-A
1378 TTAGGGTTTAGCC-TTCATCTCAT-
1 TTAGGGTTT-GCCTTTCATCTCATA
1401 TTAGGGTTTG
1 TTAGGGTTTG
1411 AGTTTCATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
25 18 0.58
26 3 0.10
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (24 bp):
TTAGGGTTTGCCTTTCATCTCATA
Found at i:13585 original size:29 final size:29
Alignment explanation
Indices: 13544--13612 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
13534 CTATCTTTCA
*
13544 ATTG-TTGATTTGAAGTGCTA-TATTTTGCT
1 ATTGATTGA-TTGAAGTGCAATTA-TTTGCT
* *
13573 ATTGATTGATTGAATTGCAATTATTTGTT
1 ATTGATTGATTGAAGTGCAATTATTTGCT
13602 AGTTGATTGAT
1 A-TTGATTGAT
13613 AGATTGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (29 bp):
ATTGATTGATTGAAGTGCAATTATTTGCT
Found at i:26117 original size:15 final size:16
Alignment explanation
Indices: 26084--26123 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
26074 TTACTTTGCT
26084 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
26100 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
26115 TTGCTTTCT
1 TTGTTTTCT
26124 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:26683 original size:21 final size:21
Alignment explanation
Indices: 26644--26692 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
26634 TCAATGCTTT
**
26644 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
26666 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
26687 A-GAAGC
1 AGGAAGC
26693 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:29170 original size:21 final size:21
Alignment explanation
Indices: 29146--29186 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29136 CTATAAATAC
* *
29146 CTCCATCACCCATCTTCAATT
1 CTCCAACACCCATCTCCAATT
29167 CTCCAACACCCATCTCCAAT
1 CTCCAACACCCATCTCCAAT
29187 CCAAAACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (21 bp):
CTCCAACACCCATCTCCAATT
Found at i:29362 original size:17 final size:16
Alignment explanation
Indices: 29340--29373 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29330 ACCTTTTCCA
29340 TCAAATTCCTCAAGTTT
1 TCAAATT-CTCAAGTTT
*
29357 TCAAATTTTCAAGTTT
1 TCAAATTCTCAAGTTT
29373 T
1 T
29374 GGAGAAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (16 bp):
TCAAATTCTCAAGTTT
Found at i:31719 original size:28 final size:27
Alignment explanation
Indices: 31673--31725 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
31663 TGTCCCTCTG
*
31673 AAAAAAAAAAAGAGTGTTAATAACCTC
1 AAAAAAAAAAAGAGAGTTAATAACCTC
* *
31700 AAAAGAAAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAAAGAGAGTTAATAACC
31726 CCTAAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.58, C:0.09, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAAAAAAAAAGAGAGTTAATAACCTC
Found at i:44607 original size:15 final size:16
Alignment explanation
Indices: 44587--44622 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
44577 TATCTCAAAT
44587 AAATACCCAAATAC-C
1 AAATACCCAAATACTC
*
44602 AAATACTCAAATACTC
1 AAATACCCAAATACTC
44618 AAATA
1 AAATA
44623 GCCATAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATACCCAAATACTC
Found at i:48646 original size:17 final size:19
Alignment explanation
Indices: 48616--48655 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
48606 AGAGAAAAAG
48616 AAGAGAAAGGGAATA-AGAA
1 AAGAGAAA-GGAATAGAGAA
48635 AAGAGAAA-GAATAGAGAA
1 AAGAGAAAGGAATAGAGAA
48653 AAG
1 AAG
48656 GGGGCTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 7 0.35
19 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (19 bp):
AAGAGAAAGGAATAGAGAA
Found at i:49440 original size:41 final size:41
Alignment explanation
Indices: 49281--49432 Score: 169
Period size: 41 Copynumber: 3.7 Consensus size: 41
49271 CTGTCTTTCT
* * * **
49281 AAAGTCCTCAAGCACATTTATAACACAGAGGCATATATATC
1 AAAGTCCCCAAGCACAATTATAACACAAAGGCATCCATATC
* * * * * *
49322 AAAGTCCCCAAACACAATTATAACACAAGGGCAATTCTTCCTA
1 AAAGTCCCCAAGCACAATTATAACACAAAGGC-ATCCAT-ATC
* *
49365 AAAGTCCTCAAGCACATTTATAACACAAAGGCATCCATATC
1 AAAGTCCCCAAGCACAATTATAACACAAAGGCATCCATATC
49406 AAAGTCCCCAAGCACAATTATAACACA
1 AAAGTCCCCAAGCACAATTATAACACA
49433 GGGGCATCTC
Statistics
Matches: 89, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
41 53 0.60
42 7 0.08
43 29 0.33
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.21
Consensus pattern (41 bp):
AAAGTCCCCAAGCACAATTATAACACAAAGGCATCCATATC
Found at i:49485 original size:88 final size:84
Alignment explanation
Indices: 49239--49534 Score: 359
Period size: 84 Copynumber: 3.5 Consensus size: 84
49229 CAATAACCAT
* * *
49239 AGTCCCTAAACACATTTATAACACAGGGGAAACTGTCTT-TCTAAAGTCCTCAAGCACATTTATA
1 AGTCCCCAAACACAATTATAACACAGGGG-CACT-TCTTCTCTAAAGTCCTCAAGCACATTTATA
*
49303 ACACAGAGGCATATATATCAA
64 ACACAGAGGCATCTATATCAA
* *
49324 AGTCCCCAAACACAATTATAACACAAGGGCAATTCTTC-CTAAAAGTCCTCAAGCACATTTATAA
1 AGTCCCCAAACACAATTATAACACAGGGGCACTTCTTCTCT-AAAGTCCTCAAGCACATTTATAA
* *
49388 CACAAAGGCATCCATATCAA
65 CACAGAGGCATCTATATCAA
* **
49408 AGTCCCCAAGCACAATTATAACACAGGGGCATCTCTCTCTCTCTCAAAGTCCTCAAGCGTATTTA
1 AGTCCCCAAACACAATTATAACACAGGGGCA-CT-TCT-TCTCT-AAAGTCCTCAAGCACATTTA
49473 TAACACAGAGGCATCTATATCAA
62 TAACACAGAGGCATCTATATCAA
* * * *
49496 AGTCCCTAAACAC-A-TGTAACACAAGGGCAATT-TTCTCTA
1 AGTCCCCAAACACAATTATAACACAGGGGCACTTCTTCTCTA
49535 CATGGCAAAG
Statistics
Matches: 184, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
81 1 0.01
82 5 0.03
83 7 0.04
84 72 0.39
85 28 0.15
86 16 0.09
87 3 0.02
88 52 0.28
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (84 bp):
AGTCCCCAAACACAATTATAACACAGGGGCACTTCTTCTCTAAAGTCCTCAAGCACATTTATAAC
ACAGAGGCATCTATATCAA
Found at i:61552 original size:21 final size:21
Alignment explanation
Indices: 61526--61596 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
61516 TGCTAGGAGT
61526 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
61547 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
61568 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
61589 TCATTGGA
1 TCATTGGA
61597 ATTACCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:68547 original size:19 final size:19
Alignment explanation
Indices: 68523--68594 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 19
68513 AATCCTAAAG
68523 CCCAAAGCAAAAATCTAGA
1 CCCAAAGCAAAAATCTAGA
* *
68542 CCCAAATG-AATAGTCTAGA
1 CCCAAA-GCAAAAATCTAGA
68561 GCCC-AAGTCAAAGAAT-TAGAA
1 -CCCAAAG-CAAA-AATCTAG-A
*
68582 CCCAAATCAAAAA
1 CCCAAAGCAAAAA
68595 ACCCAAGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 1 0.02
19 19 0.46
20 16 0.39
21 5 0.12
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.14
Consensus pattern (19 bp):
CCCAAAGCAAAAATCTAGA
Found at i:68547 original size:39 final size:40
Alignment explanation
Indices: 68503--68588 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
68493 AATCCAAAAG
68503 CCCAAAT-AATAATCCTAAAGCCCAAAG-CAAA-AATCTAG-A
1 CCCAAATGAATAAT-CTAAAGCCC-AAGTCAAAGAAT-TAGAA
* *
68542 CCCAAATGAATAGTCTAGAGCCCAAGTCAAAGAATTAGAA
1 CCCAAATGAATAATCTAAAGCCCAAGTCAAAGAATTAGAA
68582 CCCAAAT
1 CCCAAAT
68589 CAAAAAACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 3 0.07
39 22 0.54
40 16 0.39
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (40 bp):
CCCAAATGAATAATCTAAAGCCCAAGTCAAAGAATTAGAA
Found at i:69391 original size:25 final size:27
Alignment explanation
Indices: 69348--69399 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
69338 GCTCCCTGTT
69348 TTGTTGTTTGTTTCATTTTTTGTTTTTG
1 TTGTTGTTTGTTT-ATTTTTTGTTTTTG
*
69376 TTGTT-TTTGTTT-TTTTTTTTTTTT
1 TTGTTGTTTGTTTATTTTTTGTTTTT
69400 AATTCTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
27 7 0.30
28 5 0.22
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (27 bp):
TTGTTGTTTGTTTATTTTTTGTTTTTG
Found at i:69398 original size:15 final size:15
Alignment explanation
Indices: 69363--69397 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
69353 GTTTGTTTCA
69363 TTTTTTGTTTTTGTT
1 TTTTTTGTTTTTGTT
*
69378 GTTTTTGTTTTT-TT
1 TTTTTTGTTTTTGTT
69392 TTTTTT
1 TTTTTT
69398 TTAATTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTTTGTTTTTGTT
Found at i:76436 original size:27 final size:27
Alignment explanation
Indices: 76371--76447 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
76361 ATTAGGGTCA
* * * *
76371 TCCAGGGGCACTTTGATCATTTTGCATG
1 TCCAGGGGCATTTTGGTCA-TTTACACG
*
76399 TCCAAGGGCATTTTGGTCATTTACACG
1 TCCAGGGGCATTTTGGTCATTTACACG
*
76426 TCCAGGGGCATTTTAGTCATTT
1 TCCAGGGGCATTTTGGTCATTT
76448 CAAGTACACT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTACACG
Found at i:78347 original size:14 final size:14
Alignment explanation
Indices: 78328--78354 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
78318 CAGTCACCCT
78328 GCCAGCTCACCAAG
1 GCCAGCTCACCAAG
78342 GCCAGCTCACCAA
1 GCCAGCTCACCAA
78355 CCTCCTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.44, G:0.19, T:0.07
Consensus pattern (14 bp):
GCCAGCTCACCAAG
Found at i:80384 original size:16 final size:15
Alignment explanation
Indices: 80359--80388 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
80349 CTTTAAGAAC
80359 AAAAATTATTTCGAA
1 AAAAATTATTTCGAA
80374 AAAAGATTATTTCGA
1 AAAA-ATTATTTCGA
80389 GCGAAAGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAAATTATTTCGAA
Found at i:80828 original size:14 final size:14
Alignment explanation
Indices: 80809--80835 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80799 GATCAGGAGG
80809 TTGGTGAGCTGGCC
1 TTGGTGAGCTGGCC
80823 TTGGTGAGCTGGC
1 TTGGTGAGCTGGC
80836 AGGGTGACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.44, T:0.30
Consensus pattern (14 bp):
TTGGTGAGCTGGCC
Done.