Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006333.1 Corchorus capsularis cultivar CVL-1 contig06354, 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: 13663
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:619 original size:5 final size:5
Alignment explanation
Indices: 609--650 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
599 TAAATAGATA
609 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT A
651 ATTGGCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:1116 original size:262 final size:263
Alignment explanation
Indices: 651--1174 Score: 1005
Period size: 262 Copynumber: 2.0 Consensus size: 263
641 AATAATAATA
* *
651 ATTGGCTAAACGGTGCACAAGGCATGTTAGCCGAACTCAATAACAAAAAAAATCTTCTCATTTCG
1 ATTGGCTAAACGGTGCACAAGACATGTTAGCCAAACTCAATAACAAAAAAAATCTTCTCATTTCG
*
716 GCCCAAAGGTCCTAAAACATTTGATTGGAGAAGGCCTTTCCTGAATGGTGGTCCACTGCCATCAA
66 GCCCAAAGGTCCTAAAACATTTGATTGGAGAAGGCCTTACCTGAATGGTGGTCCACTGCCATCAA
781 AATTTTAGAGGCCAATTAGAAGGCCCAATAACCTGATTATTTGTCCACATTGTCCTACGTATAAA
131 AATTTTAGAGGCCAATTAGAAGGCCCAATAACCTGATTATTTGTCCACATTGTCCTACGTATAAA
846 TAATTTTTCATAATTCTGGCCAAAAAAATAATAA-TTTTTATTATGGAATTATGGACTCTACACT
196 TAATTTTTCATAATTCTGGCCAAAAAAATAATAATTTTTTATTATGGAATTATGGACTCTACACT
910 ATT
261 ATT
*
913 ATTGGCTAAACGGTGCACAAGACATGTTAGCCAAACTCAATAACAAAAAAATTCTTCTCATTTCG
1 ATTGGCTAAACGGTGCACAAGACATGTTAGCCAAACTCAATAACAAAAAAAATCTTCTCATTTCG
978 GCCCAAAGGTCCTAAAACATTTGATTGGAGAAGGCCTTACCTGAATGGTGGTCCACTGCCATCAA
66 GCCCAAAGGTCCTAAAACATTTGATTGGAGAAGGCCTTACCTGAATGGTGGTCCACTGCCATCAA
1043 AATTTTAGAGGCCAATTAGAAGGCCCAATAACCTGATTATTTGTCCACATTGTCCTACGTATAAA
131 AATTTTAGAGGCCAATTAGAAGGCCCAATAACCTGATTATTTGTCCACATTGTCCTACGTATAAA
1108 TAATTTTTCATAATTCTGGCCAAAAAAATAATAATTTTTTATTATGGAATTATGGACTCTACACT
196 TAATTTTTCATAATTCTGGCCAAAAAAATAATAATTTTTTATTATGGAATTATGGACTCTACACT
1173 AT
261 AT
1175 ACTAAGTCCA
Statistics
Matches: 257, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
262 225 0.88
263 32 0.12
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (263 bp):
ATTGGCTAAACGGTGCACAAGACATGTTAGCCAAACTCAATAACAAAAAAAATCTTCTCATTTCG
GCCCAAAGGTCCTAAAACATTTGATTGGAGAAGGCCTTACCTGAATGGTGGTCCACTGCCATCAA
AATTTTAGAGGCCAATTAGAAGGCCCAATAACCTGATTATTTGTCCACATTGTCCTACGTATAAA
TAATTTTTCATAATTCTGGCCAAAAAAATAATAATTTTTTATTATGGAATTATGGACTCTACACT
ATT
Found at i:2340 original size:30 final size:30
Alignment explanation
Indices: 2280--2451 Score: 236
Period size: 30 Copynumber: 5.7 Consensus size: 30
2270 TTAAATCTCC
* *
2280 ATTGACACCAGAAGTTGTCAATGGTGTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
*
2311 ATTGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * *
2341 AATGACACTAGAAGTTGTCATGATTTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
2371 ATTGACACTAGAAGTTGTCAATAATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
2402 AATGACACCAGAAGTTGTCATGATTTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
2432 ATTGACACCAGAAGTTGTCA
1 ATTGACACCAGAAGTTGTCA
2452 ACAGTCCTAT
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
30 82 0.65
31 45 0.35
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:2399 original size:61 final size:61
Alignment explanation
Indices: 2250--2756 Score: 281
Period size: 61 Copynumber: 8.3 Consensus size: 61
2240 AGTCTCCAAA
* * * *
2250 TGACACCAGAAGTTGTCATATTAAATC-T-CCATTGACACCAGAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTCA-A-T-AATCTTACAAATGACACCAGAAGTTGTC-ATGATTTTACAAT
** *
2313 TGACACCAGAAGTTGTC-ATGGTCTTACAAATGACACTAGAAGTTGTCATGATTTTACAAT
1 TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
*
2373 TGACACTAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
1 TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
* * * ** * * * * * *
2434 TGACACCAGAAGTTGTCAACAGTC---C-TATGAACAATAGAA-TGGGTGACCGTATAGTGATAA
1 TGACACCAGAAGTTGTCAATAATCTTACAAATG-ACACCAGAAGT-TGTCA-TG-AT-TTTACAA
2494 TGT
61 --T
** * **** * * **
2497 TTTC-TC-TTTCTTAG-C--GAATCTTATAAATGACACCAGAAGTTGTCATGATTTTTGTAAT
1 TGACACCAGAAGTT-GTCAATAATCTTACAAATGACACCAGAAGTTGTCATGA-TTTTACAAT
* * * * * *
2555 TGACACCAGAAGTTGTC-ATGATTTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAGT
1 TGACACCAGAAGTTGTCAAT-AATCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
* * * * * *
2616 TGACACCAAAAGTTGTC-ATAATTTTTGCAATTGACATCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCAATAA-TCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
** * * * * * ** *
2677 TGACACTTGAAGATGTC-ATGATTTTGCAATTGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTA--CAAT
2739 TGACACCAGAAGTTGTCA
1 TGACACCAGAAGTTGTCA
2757 TATACACCTT
Statistics
Matches: 344, Mismatches: 74, Indels: 52
0.73 0.16 0.11
Matches are distributed among these distances:
57 4 0.01
58 14 0.04
59 8 0.02
60 70 0.20
61 167 0.49
62 57 0.17
63 24 0.07
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (61 bp):
TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTACAAT
Found at i:2408 original size:91 final size:91
Alignment explanation
Indices: 2246--2451 Score: 272
Period size: 91 Copynumber: 2.2 Consensus size: 91
2236 TCAAAGTCTC
* ** *
2246 CAAATGACACCAGAAGTTGTCATATTAAATCTCCATTGACACCAGAAGTTGTCAATGGTGTTACA
1 CAAATGACACCAGAAGTTGTCATATT--ATCTCAATTGACACCAGAAGTTGTCAATAATCTTACA
* *
2311 ATTGACACCAGAAGTTGTCATGGTCTTA
64 AATGACACCAGAAGTTGTCATGATCTTA
* *
2339 CAAATGACACTAGAAGTTGTCATGATT-T-TACAATTGACACTAGAAGTTGTCAATAATCTTACA
1 CAAATGACACCAGAAGTTGTCAT-ATTATCT-CAATTGACACCAGAAGTTGTCAATAATCTTACA
*
2402 AATGACACCAGAAGTTGTCATGATTTTA
64 AATGACACCAGAAGTTGTCATGATCTTA
*
2430 CAATTGACACCAGAAGTTGTCA
1 CAAATGACACCAGAAGTTGTCA
2452 ACAGTCCTAT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 74 0.74
93 22 0.22
94 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (91 bp):
CAAATGACACCAGAAGTTGTCATATTATCTCAATTGACACCAGAAGTTGTCAATAATCTTACAAA
TGACACCAGAAGTTGTCATGATCTTA
Found at i:2613 original size:30 final size:31
Alignment explanation
Indices: 2524--2757 Score: 330
Period size: 30 Copynumber: 7.6 Consensus size: 31
2514 ATCTTATAAA
*
2524 TGACACCAGAAGTTGTCATGATTTTTGTAAT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
2555 TGACACCAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
*
2586 TGACACCAGAAGTTGTCATGA-TTTTGCAGT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
* *
2616 TGACACCAAAAGTTGTCATAATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
*
2647 TGACATCAGAAGTTGTCATGA-TTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
** *
2677 TGACACTTGAAGATGTCATGA-TTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTTGCAAT
** * *
2707 TGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATTTT-TGCAAT
2739 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
2758 ATACACCTTG
Statistics
Matches: 184, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
30 83 0.45
31 80 0.43
32 21 0.11
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (31 bp):
TGACACCAGAAGTTGTCATGATTTTTGCAAT
Found at i:4111 original size:179 final size:179
Alignment explanation
Indices: 3887--4245 Score: 718
Period size: 179 Copynumber: 2.0 Consensus size: 179
3877 AAGTGAGATG
3887 CTAATTACACGCGTAATTTTATATGGGCTATTATAGAAGCCATCATTATGGGTCGTTATGGAGGC
1 CTAATTACACGCGTAATTTTATATGGGCTATTATAGAAGCCATCATTATGGGTCGTTATGGAGGC
3952 TAGTATCATGAGCCATAGCAAAGGCCATGAACATATTTATTATGGGCCATTATAGAGGCCATGAT
66 TAGTATCATGAGCCATAGCAAAGGCCATGAACATATTTATTATGGGCCATTATAGAGGCCATGAT
4017 CATGCTTATTATGCCCTTGTTAAGGCTTTGAGCATATACATATTGTTCT
131 CATGCTTATTATGCCCTTGTTAAGGCTTTGAGCATATACATATTGTTCT
4066 CTAATTACACGCGTAATTTTATATGGGCTATTATAGAAGCCATCATTATGGGTCGTTATGGAGGC
1 CTAATTACACGCGTAATTTTATATGGGCTATTATAGAAGCCATCATTATGGGTCGTTATGGAGGC
4131 TAGTATCATGAGCCATAGCAAAGGCCATGAACATATTTATTATGGGCCATTATAGAGGCCATGAT
66 TAGTATCATGAGCCATAGCAAAGGCCATGAACATATTTATTATGGGCCATTATAGAGGCCATGAT
4196 CATGCTTATTATGCCCTTGTTAAGGCTTTGAGCATATACATATTGTTCT
131 CATGCTTATTATGCCCTTGTTAAGGCTTTGAGCATATACATATTGTTCT
4245 C
1 C
4246 ATGAGAATGA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (179 bp):
CTAATTACACGCGTAATTTTATATGGGCTATTATAGAAGCCATCATTATGGGTCGTTATGGAGGC
TAGTATCATGAGCCATAGCAAAGGCCATGAACATATTTATTATGGGCCATTATAGAGGCCATGAT
CATGCTTATTATGCCCTTGTTAAGGCTTTGAGCATATACATATTGTTCT
Found at i:7513 original size:3 final size:3
Alignment explanation
Indices: 7505--7539 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
7495 AACATTTTTC
7505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7540 GATTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11933 original size:28 final size:26
Alignment explanation
Indices: 11902--11962 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
11892 TTATTTTAGA
11902 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
11930 CAAACTC--ACAATTTTAATCTCAAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
11954 CAACCTCTT
1 CAAACTCTT
11963 CAAGATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
28 7 0.23
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:12068 original size:34 final size:34
Alignment explanation
Indices: 12028--12136 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 34
12018 ATATCCACTT
*
12028 AACCCGTAATATATAATTGGAATTGGACTAAGAA
1 AACCCGTAATATATAATTGGAATTGGACTAAAAA
*
12062 AACCCGTAATATATAATTTGAATTGGACTAATAAAA
1 AACCCGTAATATATAATTGGAATTGGACT-A-AAAA
12098 TTCAACCCGTAATATATAATTGGAATTGGACTAAAAA
1 ---AACCCGTAATATATAATTGGAATTGGACTAAAAA
12135 AA
1 AA
12137 TTCAATTTGA
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 30 0.45
35 1 0.01
36 3 0.04
37 4 0.06
38 1 0.01
39 28 0.42
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (34 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAA
Found at i:12107 original size:39 final size:38
Alignment explanation
Indices: 12028--12141 Score: 164
Period size: 39 Copynumber: 3.1 Consensus size: 38
12018 ATATCCACTT
*
12028 AACCCGTAATATATAATTGGAATTGGACT-AAGAA---
1 AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
*
12062 AACCCGTAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACTAA-AAAATTC
12101 AACCCGTAATATATAATTGGAATTGGACTAAAAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACT-AAAAAATTC
12140 AA
1 AA
12142 TTTGATTACT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 28 0.39
35 1 0.01
36 3 0.04
39 37 0.52
40 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (38 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
Done.