Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014739.1 Corchorus capsularis cultivar CVL-1 contig14760, 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: 17181
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Found at i:87 original size:50 final size:51
Alignment explanation
Indices: 5--289 Score: 317
Period size: 50 Copynumber: 5.6 Consensus size: 51
1 TACT
* * *
5 AATTACTCTAAAGATTCAATCTTTTACCCAAAGACGACATTTTTATTTACC
1 AATTACTCTAAAAATTCAATCTTTTATCCAAAGATGACATTTTTATTTACC
* * * * * *
56 AATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACT
1 AATTACTCTAAAAATTCAATCTTTTATCCAAAGATGACATTTTTATTTACC
* * * **
106 AATTACTCTAAAGATTCAATCTTTTACCCAAATATGACATTTTTGCTTACC
1 AATTACTCTAAAAATTCAATCTTTTATCCAAAGATGACATTTTTATTTACC
* * * * * *
157 AATTACT-TAAAAATTCAATCTTTTATTCAAAGCTTAAAATTTTATTTACT
1 AATTACTCTAAAAATTCAATCTTTTATCCAAAGATGACATTTTTATTTACC
* * *
207 AATCACTCTAAAAATTCAATCTTTTA-CCGAAAGATGACATTTTTAGTTATC
1 AATTACTCTAAAAATTCAATCTTTTATCC-AAAGATGACATTTTTATTTACC
*
258 AATTACT-TAAAAATTCAATCTTTTATTCAAAG
1 AATTACTCTAAAAATTCAATCTTTTATCCAAAG
290 GTTACATCTT
Statistics
Matches: 188, Mismatches: 42, Indels: 9
0.79 0.18 0.04
Matches are distributed among these distances:
50 102 0.54
51 86 0.46
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (51 bp):
AATTACTCTAAAAATTCAATCTTTTATCCAAAGATGACATTTTTATTTACC
Found at i:176 original size:101 final size:100
Alignment explanation
Indices: 1--300 Score: 476
Period size: 101 Copynumber: 3.0 Consensus size: 100
* *
1 TACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGACGACATTTTTATTTACCAATTACTTAA
1 TACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTT-GTTACCAATTACTTAA
66 AAATTCAATCTTTTATTCAAAGGTTAAATCTTTATT
65 AAATTCAATCTTTTATTCAAAGGTTAAATCTTTATT
*
102 TACTAATTACTCTAAAGATTCAATCTTTTACCCAAATATGACATTTTTGCTTACCAATTACTTAA
1 TACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTTG-TTACCAATTACTTAA
*
167 AAATTCAATCTTTTATTCAAAGCTTAAAAT-TTTATT
65 AAATTCAATCTTTTATTCAAAGGTT-AAATCTTTATT
* * * *
203 TACTAATCACTCTAAAAATTCAATCTTTTACCGAAAGATGACATTTTTAGTTATCAATTACTTAA
1 TACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTT-GTTACCAATTACTTAA
*
268 AAATTCAATCTTTTATTCAAAGGTTACATCTTT
65 AAATTCAATCTTTTATTCAAAGGTTAAATCTTT
301 TAGCCAAGTA
Statistics
Matches: 184, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
100 3 0.02
101 176 0.96
102 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.42
Consensus pattern (100 bp):
TACTAATTACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTTGTTACCAATTACTTAAA
AATTCAATCTTTTATTCAAAGGTTAAATCTTTATT
Found at i:2769 original size:27 final size:27
Alignment explanation
Indices: 2733--2800 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
2723 CCACCGATTT
* *
2733 ACCAAGATG-CCCTCAGGTGCGAAAATG
1 ACCAAAATGCCCCT-AGGTGCAAAAATG
*
2760 ACCAAAATGCCCCTGGGTGCAAAAATG
1 ACCAAAATGCCCCTAGGTGCAAAAATG
*
2787 AGCAAAATGCCCCT
1 ACCAAAATGCCCCT
2801 GGGCGACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 32 0.89
28 4 0.11
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (27 bp):
ACCAAAATGCCCCTAGGTGCAAAAATG
Found at i:2801 original size:27 final size:27
Alignment explanation
Indices: 2748--2803 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2738 GATGCCCTCA
*
2748 GGTGCGAAAATGACCAAAATGCCCCTG
1 GGTGCAAAAATGACCAAAATGCCCCTG
*
2775 GGTGCAAAAATGAGCAAAATGCCCCTG
1 GGTGCAAAAATGACCAAAATGCCCCTG
2802 GG
1 GG
2804 CGACCCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.29, T:0.14
Consensus pattern (27 bp):
GGTGCAAAAATGACCAAAATGCCCCTG
Found at i:3979 original size:17 final size:17
Alignment explanation
Indices: 3959--4022 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
3949 GATCTCTTTC
3959 TTTTTTAGGCCCAGTTT
1 TTTTTTAGGCCCAGTTT
* **
3976 TTTTTTTGGCGACCTCTTT
1 TTTTTTAGGC--CCAGTTT
*
3995 CTTTTTTTGGCCCAGTTT
1 -TTTTTTAGGCCCAGTTT
4013 TTTTTTAGGC
1 TTTTTTAGGC
4023 ATAATATTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 18 0.47
18 5 0.13
19 5 0.13
20 10 0.26
ACGTcount: A:0.08, C:0.19, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTTTTAGGCCCAGTTT
Found at i:3993 original size:37 final size:36
Alignment explanation
Indices: 3935--4018 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 36
3925 CTTATATTTC
*
3935 GTTTTTCTTTTTGCGATCTCTTTCTTTTTTAGGCCCA
1 GTTTTT-TTTTTGCGACCTCTTTCTTTTTTAGGCCCA
*
3972 GTTTTTTTTTTGGCGACCTCTTTCTTTTTTTGGCCCA
1 GTTTTTTTTTT-GCGACCTCTTTCTTTTTTAGGCCCA
4009 GTTTTTTTTT
1 GTTTTTTTTT
4019 AGGCATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
36 5 0.11
37 39 0.89
ACGTcount: A:0.06, C:0.19, G:0.14, T:0.61
Consensus pattern (36 bp):
GTTTTTTTTTTGCGACCTCTTTCTTTTTTAGGCCCA
Found at i:3999 original size:20 final size:20
Alignment explanation
Indices: 3942--4005 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
3932 TTCGTTTTTC
*
3942 TTTTT-GCGATCTCTTTCTT
1 TTTTTGGCGACCTCTTTCTT
* **
3961 TTTTAGGC--CCAGTTT-TT
1 TTTTTGGCGACCTCTTTCTT
3978 TTTTTGGCGACCTCTTTCTT
1 TTTTTGGCGACCTCTTTCTT
3998 TTTTTGGC
1 TTTTTGGC
4006 CCAGTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
17 9 0.26
18 4 0.12
19 9 0.26
20 12 0.35
ACGTcount: A:0.06, C:0.20, G:0.16, T:0.58
Consensus pattern (20 bp):
TTTTTGGCGACCTCTTTCTT
Found at i:4033 original size:37 final size:37
Alignment explanation
Indices: 3955--4034 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
3945 TTGCGATCTC
* ** *
3955 TTTCTTTTTTAGGCCCAGTTTTTTTTTTGGCGACCTC
1 TTTCTTTTTTAGGCCCAGTTTTTTTTTAGGCGAAATA
*
3992 TTTCTTTTTTTGGCCCAGTTTTTTTTTAGGC-ATAATA
1 TTTCTTTTTTAGGCCCAGTTTTTTTTTAGGCGA-AATA
4029 TTTCTT
1 TTTCTT
4035 GACTGTGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.57
Consensus pattern (37 bp):
TTTCTTTTTTAGGCCCAGTTTTTTTTTAGGCGAAATA
Found at i:11747 original size:63 final size:63
Alignment explanation
Indices: 11676--11875 Score: 197
Period size: 63 Copynumber: 3.2 Consensus size: 63
11666 CACATCATAC
* * * *
11676 ACTGCTGAATAATATCATAAATTCCGAGTACAAAATTAAACACATAGTCTGAAAATAGCATCT
1 ACTGCTGAATAATACCATAAACTCCGAGTACAAAATTAAACACATAGTCTGAAAATACCATCA
* * * * *** * * *
11739 ACTGCTGAATAATACCATGAACTACAAGCATTGAA-TAATA-ACATAGTCTGGAAACACCATCC
1 ACTGCTGAATAATACCATAAACTCCGAGTACAAAATTAA-ACACATAGTCTGAAAATACCATCA
* * * * *
11801 CCTGCCGAATAATACCATAAACTCCGAGTACATAATTAAACATATAGTCTGAAAATACCACCA
1 ACTGCTGAATAATACCATAAACTCCGAGTACAAAATTAAACACATAGTCTGAAAATACCATCA
*
11864 ACTACTGAATAA
1 ACTGCTGAATAA
11876 CACATTGTCT
Statistics
Matches: 104, Mismatches: 30, Indels: 6
0.74 0.21 0.04
Matches are distributed among these distances:
62 48 0.46
63 56 0.54
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (63 bp):
ACTGCTGAATAATACCATAAACTCCGAGTACAAAATTAAACACATAGTCTGAAAATACCATCA
Found at i:15499 original size:15 final size:15
Alignment explanation
Indices: 15481--15536 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
15471 AAATACCATT
15481 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
15496 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
15509 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
15524 TTACTCTTTTACT
1 TTACTCTTTTACT
15537 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:15539 original size:21 final size:20
Alignment explanation
Indices: 15515--15750 Score: 179
Period size: 21 Copynumber: 11.0 Consensus size: 20
15505 TCTGCTCCTT
15515 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTAC-CTTTTAC
* *
15536 TTTTTACTGATTGCCTTTTGC
1 -TTTTACTGATTACCTTTTAC
15557 TTTTTACTGATTACC-TTTAC
1 -TTTTACTGATTACCTTTTAC
*
15577 TTCTTACTGATTAGCCTTTTAT
1 TT-TTACTGATTA-CCTTTTAC
* *
15599 TCTTTGCTGATCACCTTTTGAC
1 T-TTTACTGATTACCTTTT-AC
*
15621 TTCTTACTGATTACTATTTTAC
1 TT-TTACTGATTAC-CTTTTAC
*
15643 TCTTACTGATTA-CTATTTAC
1 TTTTACTGATTACCT-TTTAC
* *
15663 TTTTTACTGACTACTATTTTAC
1 -TTTTACTGATTAC-CTTTTAC
* **
15685 TCTTGTTGATTACCTTCTTAC
1 TTTTACTGATTACCTT-TTAC
*
15706 TTTTTACTGATTACTATTTTACTC
1 -TTTTACTGATTAC-CTTTTA--C
15730 TTTTACTGATTACCATTTTAC
1 TTTTACTGATTACC-TTTTAC
15751 CCTTTCAGAT
Statistics
Matches: 171, Mismatches: 26, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.02
20 21 0.12
21 63 0.37
22 57 0.33
23 26 0.15
24 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTTACTGATTACCTTTTAC
Found at i:15649 original size:85 final size:85
Alignment explanation
Indices: 15532--15743 Score: 234
Period size: 85 Copynumber: 2.5 Consensus size: 85
15522 GATTACTCTT
* * * * * * *
15532 TTACTTTTTACTGATTGC-CTTTTGCTTTTTACTGATTACCTTTACTTCTTACTGATTAGC-CTT
1 TTACTTCTTACTGATTACTATTTTACTCTTTACTGATTACCTTTACTTCTTACTGACTA-CTATT
*
15595 TTATTCTTTGCTGATCACCTT-
65 TTACTC-TTGCTGATCACCTTC
* *
15616 TTGACTTCTTACTGATTACTATTTTACTC-TTACTGATTACTATTTACTTTTTACTGACTACTAT
1 TT-ACTTCTTACTGATTACTATTTTACTCTTTACTGATTAC-CTTTACTTCTTACTGACTACTAT
* *
15680 TTTACTCTTGTTGATTACCTTC
64 TTTACTCTTGCTGATCACCTTC
*
15702 TTACTTTTTACTGATTACTATTTTACTCTTTTACTGATTACC
1 TTACTTCTTACTGATTACTATTTTACTC-TTTACTGATTACC
15744 ATTTTACCCT
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
84 2 0.02
85 63 0.59
86 31 0.29
87 11 0.10
ACGTcount: A:0.19, C:0.20, G:0.08, T:0.53
Consensus pattern (85 bp):
TTACTTCTTACTGATTACTATTTTACTCTTTACTGATTACCTTTACTTCTTACTGACTACTATTT
TACTCTTGCTGATCACCTTC
Found at i:16110 original size:55 final size:55
Alignment explanation
Indices: 16041--16387 Score: 584
Period size: 55 Copynumber: 6.5 Consensus size: 55
16031 CTAATTACTA
* *
16041 TCTTTTTACCTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
16096 TCTTTTTACTTAATTACTGA-TTAC----TAC---TACTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
*
16143 TCTTTTTACTTAATTACTGATTCACTGATTACTATTACTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
16198 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
*
16253 TTTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
**
16308 TCTTTTTACTTAATTACTGATTTACTGATTACTATTGTTTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
16363 TCTTTTTACTTAATTACTGATTTAC
1 TCTTTTTACTTAATTACTGATTTAC
16388 CCCTTTTACT
Statistics
Matches: 276, Mismatches: 8, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
47 39 0.14
48 3 0.01
50 3 0.01
52 3 0.01
54 4 0.01
55 224 0.81
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (55 bp):
TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATC
Found at i:17149 original size:2 final size:2
Alignment explanation
Indices: 17144--17175 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17134 ATTAACACAC
17144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17176 GTAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.