Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012723.1 Corchorus olitorius cultivar O-4 contig12756, 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: 71721
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:272 original size:21 final size:21
Alignment explanation
Indices: 225--265 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
215 AAAAAATCTT
225 TATTTTAAATAAATAATTTTA
1 TATTTTAAATAAATAATTTTA
246 TATTTTAAA-AAATACATTTT
1 TATTTTAAATAAATA-ATTTT
266 TGATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTTAAATAAATAATTTTA
Found at i:2148 original size:2 final size:2
Alignment explanation
Indices: 2141--2177 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2131 TTGGATCATA
*
2141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2178 ATAGTTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6709 original size:31 final size:30
Alignment explanation
Indices: 6674--6870 Score: 190
Period size: 31 Copynumber: 6.5 Consensus size: 30
6664 CTCGGCTAAT
6674 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CTAAAA
6705 TGCTCAAATAAGGGCCTAACGTTTGCTAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CTAAAA
* *
6736 TGCTCAAATAAGGGCCCAATC-TTT-TAAAT
1 TGCTCAAATAAGGGCCTAA-CGTTTCTAAAA
*
6765 TCGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCTAAAA
* * * **
6796 TGCTCAAATAAGCGTCCGATC-TTT-TAATT
1 TGCTCAAATAAG-GGCCTAACGTTTCTAAAA
* *
6825 TGGC-CAAATAAGGGCCTAAAGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TCTAAAA
6856 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
6871 TTGGCGTCAG
Statistics
Matches: 136, Mismatches: 18, Indels: 24
0.76 0.10 0.13
Matches are distributed among these distances:
28 5 0.04
29 34 0.25
30 11 0.08
31 80 0.59
32 6 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCTAAAA
Found at i:6784 original size:60 final size:59
Alignment explanation
Indices: 6674--6870 Score: 245
Period size: 60 Copynumber: 3.3 Consensus size: 59
6664 CTCGGCTAAT
* * *
6674 TGCTCAAATAAGGGCCTAA-CGTTTGCTAAAATGCTCAAATAAGGGCCTAACGTT-TGCTAAAA
1 TGCTCAAATAAGGGCCCAATC-TTT--TAAATTGC-CAAATAAGGGCCTAACGTTAT-CGAAAA
6736 TGCTCAAATAAGGGCCCAATCTTTTAAATTCGCCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCCAATCTTTTAAATT-GCCAAATAAGGGCCTAACGTTATCGAAAA
* * * * *
6796 TGCTCAAATAAGCGTCCGATCTTTTAATTTGGCCAAATAAGGGCCTAAAGTTATCGAAAA
1 TGCTCAAATAAGGGCCCAATCTTTTAAATT-GCCAAATAAGGGCCTAACGTTATCGAAAA
6856 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
6871 TTGGCGTCAG
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
60 96 0.79
61 3 0.02
62 21 0.17
63 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (59 bp):
TGCTCAAATAAGGGCCCAATCTTTTAAATTGCCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:7009 original size:60 final size:59
Alignment explanation
Indices: 6910--7074 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 59
6900 TTTTCGACGT
* *
6910 CAGGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGCCCAAATTAAAAGAC
1 CAGGCCCTTATTTGAGCATTTTGGA-AACGTTAGGCCCTTATTTGCCCAAATTAAAAGAC
* * * * ** *
6970 CGGGCCCTCATTTGAGCATTTTGGCAAATGTTAGGCCCTTACTTGGTCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGG-AAACGTTAGGCCCTTATTTGCCCAAATTAAAAGAC
* *
7030 CAGCCCCTTATTTGAGCATTTTGGTAAACGTTAGGCTCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGG-AAACGTTAGGCCCTTATTTG
7075 AATAATTAGC
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 87 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (59 bp):
CAGGCCCTTATTTGAGCATTTTGGAAACGTTAGGCCCTTATTTGCCCAAATTAAAAGAC
Found at i:7315 original size:95 final size:98
Alignment explanation
Indices: 7210--7388 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 98
7200 AAAGGCCACT
* ** *
7210 AAAATTACTAATG-ATA-AAAGGTTACTAAATTTGTTGATAGTATTATAAC-ATTTT-A-ACTTT
1 AAAAATACTAA-GAATATAAAGGTTACT-AATTTCATGATAGTATTATAACAATTTTGATACTCT
* * *
7270 TATAGCTTTTTTAGTAAACTTAAATAATAACCCTA
64 TATAACCTTTTAAGTAAACTTAAATAATAACCCTA
* *
7305 AAAAATACTAAGAATATAAAGTTTACTTATTTCATGATAGTATTATAACAATTTTGATACTCTTA
1 AAAAATACTAAGAATATAAAGGTTACTAATTTCATGATAGTATTATAACAATTTTGATACTCTTA
7370 TAACCTTTTAAGTAAACTT
66 TAACCTTTTAAGTAAACTT
7389 TGATAAGAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
94 1 0.01
95 32 0.46
96 14 0.20
97 1 0.01
98 22 0.31
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (98 bp):
AAAAATACTAAGAATATAAAGGTTACTAATTTCATGATAGTATTATAACAATTTTGATACTCTTA
TAACCTTTTAAGTAAACTTAAATAATAACCCTA
Found at i:7576 original size:107 final size:111
Alignment explanation
Indices: 7455--7677 Score: 294
Period size: 115 Copynumber: 2.0 Consensus size: 111
7445 ATAATGATAC
* * * *
7455 ACCTTTTTGGATAACCACTGCAGTTTTTTAGTGATTTTAGATCAGATAATTGGTAATTTT-C-A-
1 ACCTTTTTGGATAACCACTACA-TTTTTTAGTAATTTTAAATAAGATAATTGGTAATTTTACTAC
*
7517 T-T-ACTTAAGTTGCTATGGATTTAAAGTTACTTAATTTTTGTCGAT
65 TATAACTTAAGTTGCTATGAATTTAAAGTTACTTAATTTTTGTCGAT
*
7562 ACCTTTTTGGATAACCACTACATTTTTTATTAATTTTAAATAAGATAATTGGTAATTTTCACTAC
1 ACCTTTTTGGATAACCACTACATTTTTTAGTAATTTTAAATAAGATAATTGGTAATTTT-ACTAC
* *
7627 TAATGCAACTTAAGTTGCTATGAATTTAAAGTTCCTTAATTTTTGTTGAT
65 T-AT--AACTTAAGTTGCTATGAATTTAAAGTTACTTAATTTTTGTCGAT
7677 A
1 A
7678 GCATCATATA
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
106 33 0.33
107 21 0.21
108 1 0.01
109 1 0.01
110 1 0.01
112 1 0.01
115 41 0.41
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (111 bp):
ACCTTTTTGGATAACCACTACATTTTTTAGTAATTTTAAATAAGATAATTGGTAATTTTACTACT
ATAACTTAAGTTGCTATGAATTTAAAGTTACTTAATTTTTGTCGAT
Found at i:10452 original size:24 final size:23
Alignment explanation
Indices: 10420--10476 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
10410 GCCTTATACA
**
10420 CAAACTAATGATATGTTTAGGATT
1 CAAACTAATGATATGTACA-GATT
10444 CAAACTAATG---TGTACAGATT
1 CAAACTAATGATATGTACAGATT
10464 CAAACTAATGATA
1 CAAACTAATGATA
10477 AACAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
24 10 0.36
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (23 bp):
CAAACTAATGATATGTACAGATT
Found at i:16071 original size:2 final size:2
Alignment explanation
Indices: 16020--16063 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
16010 GAGAGTTTGA
* * *
16020 AG AG AG TG AG AC AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16062 AG
1 AG
16064 TCGAGAGAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.48, C:0.02, G:0.45, T:0.05
Consensus pattern (2 bp):
AG
Found at i:23015 original size:6 final size:6
Alignment explanation
Indices: 22999--23031 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
22989 TCTTGGAAGT
22999 TATTT- TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
23032 ATACATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATTTA
Found at i:36520 original size:23 final size:22
Alignment explanation
Indices: 36478--36525 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
36468 GTCAATCATC
*
36478 TAAAATCAAATTCAAACTAAAA
1 TAAAATAAAATTCAAACTAAAA
*
36500 TAAAATAACAATT-AAACCTAATA
1 TAAAATAA-AATTCAAA-CTAAAA
36523 TAA
1 TAA
36526 CCATAGAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAAATAAAATTCAAACTAAAA
Found at i:40441 original size:16 final size:16
Alignment explanation
Indices: 40402--40439 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40392 AAAGCAAAAT
40402 AAAT-AAATAAATGTA
1 AAATGAAATAAATGTA
*
40417 AAATGAAATAAATG-G
1 AAATGAAATAAATGTA
40432 AAATGAAA
1 AAATGAAA
40440 ATTTTATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (16 bp):
AAATGAAATAAATGTA
Found at i:43520 original size:42 final size:43
Alignment explanation
Indices: 43469--43562 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
43459 AGTGCATTAC
*
43469 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
43510 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
43555 CTAATATT
1 CTAATATT
43563 AATTATTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:44515 original size:49 final size:49
Alignment explanation
Indices: 44443--44542 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
44433 GAGGCACCGC
44443 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
1 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
44492 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
1 ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
44541 AT
1 AT
44543 ATATAGTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (49 bp):
ATTAATCCTCAATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATA
Found at i:51989 original size:14 final size:14
Alignment explanation
Indices: 51970--52014 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
51960 TGATTCAATG
*
51970 CTAACTCCTAAGTT
1 CTAACTCCTAAGTC
*
51984 CTAACTCCTAAATC
1 CTAACTCCTAAGTC
*
51998 CTAA-TCCTAAGGC
1 CTAACTCCTAAGTC
52011 CTAA
1 CTAA
52015 GCTATAAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (14 bp):
CTAACTCCTAAGTC
Found at i:53328 original size:27 final size:28
Alignment explanation
Indices: 53298--53358 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
53288 AGAATTACTG
53298 AATTACAAAAACAGAATTG-AAAAACAA
1 AATTACAAAAACAGAATTGAAAAAACAA
* * *
53325 AATTTCAATAACAGAATTGAAAAAACAG
1 AATTACAAAAACAGAATTGAAAAAACAA
53353 AATTAC
1 AATTAC
53359 TACAGAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.20
Consensus pattern (28 bp):
AATTACAAAAACAGAATTGAAAAAACAA
Found at i:53397 original size:14 final size:14
Alignment explanation
Indices: 53297--53397 Score: 69
Period size: 14 Copynumber: 7.0 Consensus size: 14
53287 CAGAATTACT
*
53297 GAATTACAAAAACA
1 GAATTAAAAAAACA
*
53311 GAATT-GAAAAACA
1 GAATTAAAAAAACA
* ** *
53324 AAATTTCAATAACA
1 GAATTAAAAAAACA
*
53338 GAATTGAAAAAACA
1 GAATTAAAAAAACA
* *
53352 GAATTACTACAGAAATA
1 GAATTA--A-AAAAACA
*
53369 GAGTTAAACAAAACA
1 GAATTAAA-AAAACA
53384 GAATTAAAAAAACA
1 GAATTAAAAAAACA
53398 AAAATATAGA
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
13 11 0.16
14 33 0.49
15 12 0.18
16 1 0.01
17 10 0.15
ACGTcount: A:0.61, C:0.11, G:0.10, T:0.18
Consensus pattern (14 bp):
GAATTAAAAAAACA
Done.