Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010569.1 Corchorus capsularis cultivar CVL-1 contig10590, 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: 170092
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:964 original size:2 final size:2
Alignment explanation
Indices: 959--987 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
949 TAACTATAAC
959 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
988 AGAAAGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19711 original size:5 final size:5
Alignment explanation
Indices: 19701--19730 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
19691 AGCCCCCCCA
19701 AAAAG AAAAG AAAAG AAAAG AAAATG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AAAA
19731 AGGAACTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:35218 original size:31 final size:31
Alignment explanation
Indices: 35159--35218 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
35149 TTTCAAATCT
** *
35159 AGTTAGAAGGTTACAATATTGAACAAAAAAA
1 AGTTAGAAGGTTACAATATAAAAAAAAAAAA
35190 AGTTAGAAGGTTACAAT-TAAAAAAAAAAA
1 AGTTAGAAGGTTACAATATAAAAAAAAAAA
35219 TACTAGATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (31 bp):
AGTTAGAAGGTTACAATATAAAAAAAAAAAA
Found at i:40765 original size:15 final size:15
Alignment explanation
Indices: 40745--40778 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40735 TCCATCTCTT
*
40745 AACTTAATTTAATTC
1 AACTTAACTTAATTC
*
40760 AACTTAACTTAATTT
1 AACTTAACTTAATTC
40775 AACT
1 AACT
40779 GCAAGTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (15 bp):
AACTTAACTTAATTC
Found at i:50298 original size:25 final size:25
Alignment explanation
Indices: 50264--50311 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
50254 CTAGATAGGA
50264 AATACTCCCTTTGTCCCTTTTTATG
1 AATACTCCCTTTGTCCCTTTTTATG
*
50289 AATACTCCCTTTGTCCTTTTTTA
1 AATACTCCCTTTGTCCCTTTTTA
50312 CAAGTCCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50
Consensus pattern (25 bp):
AATACTCCCTTTGTCCCTTTTTATG
Found at i:50911 original size:17 final size:17
Alignment explanation
Indices: 50889--50921 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
50879 CAATCAAGGA
50889 GGCATGTCCTCTATCCG
1 GGCATGTCCTCTATCCG
50906 GGCATGTCCTCTATCC
1 GGCATGTCCTCTATCC
50922 AAACAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.36, G:0.21, T:0.30
Consensus pattern (17 bp):
GGCATGTCCTCTATCCG
Found at i:51403 original size:91 final size:92
Alignment explanation
Indices: 51236--51412 Score: 203
Period size: 91 Copynumber: 1.9 Consensus size: 92
51226 AACCTTCAAC
* *
51236 TTTCTTAACATTTTCTATGTAATTTTACATGGTGTCCACCCTTACACGGTCCTAGATGCCCATCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGTCCACCCTTACACGGTCCTAAATGCCCACCC
51301 TAAATTAATTAACTCGTCAAATGTCCA
66 TAAATTAATTAACTCGTCAAATGTCCA
* * * * * *** **
51328 TTTCTT-ATATTTTGTATGTAATTTTATATGGTGTTCATCCTTATTTGGTCCTAAATGTTCACCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGTCCACCCTTACACGGTCCTAAATGCCCACCC
* * * *
51392 TCAATTGATTAATTTGTCAAA
66 TAAATTAATTAACTCGTCAAA
51413 ATATCTTTGA
Statistics
Matches: 69, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
91 63 0.91
92 6 0.09
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (92 bp):
TTTCTTAACATTTTCTATGTAATTTTACATGGTGTCCACCCTTACACGGTCCTAAATGCCCACCC
TAAATTAATTAACTCGTCAAATGTCCA
Found at i:56986 original size:20 final size:20
Alignment explanation
Indices: 56961--57000 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56951 TGGTCGTGGG
56961 GTTGGATTAAATGGCTTGTT
1 GTTGGATTAAATGGCTTGTT
56981 GTTGGATTAAATGGCTTGTT
1 GTTGGATTAAATGGCTTGTT
57001 TTAGTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (20 bp):
GTTGGATTAAATGGCTTGTT
Found at i:57106 original size:13 final size:13
Alignment explanation
Indices: 57088--57115 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57078 ATCGATTTTT
57088 ATCTAGAGCAAAA
1 ATCTAGAGCAAAA
57101 ATCTAGAGCAAAA
1 ATCTAGAGCAAAA
57114 AT
1 AT
57116 TTGGATACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (13 bp):
ATCTAGAGCAAAA
Found at i:61863 original size:25 final size:25
Alignment explanation
Indices: 61829--61879 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
61819 GAAAGTCCAA
61829 TGGGTCCGTAAATCCCAAAAATGGG
1 TGGGTCCGTAAATCCCAAAAATGGG
61854 TGGGTCCGTAAATCCCAAAAATGGG
1 TGGGTCCGTAAATCCCAAAAATGGG
61879 T
1 T
61880 CGGCGGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (25 bp):
TGGGTCCGTAAATCCCAAAAATGGG
Found at i:68706 original size:7 final size:7
Alignment explanation
Indices: 68694--68720 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
68684 AAAACTCAGG
68694 AGAGGGA
1 AGAGGGA
68701 AGAGGGA
1 AGAGGGA
68708 AGAGGGA
1 AGAGGGA
68715 AGAGGG
1 AGAGGG
68721 CTTAAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (7 bp):
AGAGGGA
Found at i:69987 original size:15 final size:15
Alignment explanation
Indices: 69963--69994 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
69953 GAAAGAAGCG
69963 AAACCAAGATAAGGA
1 AAACCAAGATAAGGA
*
69978 AAACCCAGATAAGGA
1 AAACCAAGATAAGGA
69993 AA
1 AA
69995 CGGGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.16, G:0.19, T:0.06
Consensus pattern (15 bp):
AAACCAAGATAAGGA
Found at i:77686 original size:20 final size:20
Alignment explanation
Indices: 77643--77686 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
77633 TTTTACAAGG
*
77643 TTTTTTTGGTGAATTAACTT
1 TTTTTTTGGTGAATTAACTC
77663 TTTTTTTGGTGAA-TAATCTC
1 TTTTTTTGGTGAATTAA-CTC
77683 TTTT
1 TTTT
77687 ACAAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (20 bp):
TTTTTTTGGTGAATTAACTC
Found at i:83506 original size:2 final size:2
Alignment explanation
Indices: 83499--83524 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83489 ACATGATTTA
83499 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
83525 AGTTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:87641 original size:18 final size:18
Alignment explanation
Indices: 87618--87656 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
87608 AGAGTTCAAT
87618 TTGGCTTTCCTAATCTTG
1 TTGGCTTTCCTAATCTTG
87636 TTGGCTTTCCTAATCTTG
1 TTGGCTTTCCTAATCTTG
87654 TTG
1 TTG
87657 AAGAAACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.18, T:0.51
Consensus pattern (18 bp):
TTGGCTTTCCTAATCTTG
Found at i:92820 original size:109 final size:109
Alignment explanation
Indices: 92629--92838 Score: 393
Period size: 109 Copynumber: 1.9 Consensus size: 109
92619 TAAATTATTA
* *
92629 TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGTACACATACCAAACAATACAAAGTGC
1 TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAAGACAAAGTGC
92694 AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTTTTG
66 AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTTTTG
*
92738 TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACTAAACAAGACAAAGTGC
1 TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAAGACAAAGTGC
92803 AATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AATGAACTATTGGATTTAAAGAAAAATACAAGCACC
92839 AAAATGACTA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (109 bp):
TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAAGACAAAGTGC
AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTTTTG
Found at i:104451 original size:2 final size:2
Alignment explanation
Indices: 104444--104506 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
104434 TAATTTCTAC
104444 TA TA TA TA TA TA TA TA T- TCA TA T- TA GTA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA
*
104484 T- TA -A T- TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
104507 GTTATCAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
1 7 0.14
2 40 0.80
3 3 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122683 original size:6 final size:6
Alignment explanation
Indices: 122667--122703 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
122657 GCTAGAGAGA
* *
122667 GGCTTT AGCTTT TGCTTT GGCTTT GGCTTT GGCTTT G
1 GGCTTT GGCTTT GGCTTT GGCTTT GGCTTT GGCTTT G
122704 AAATGAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.16, G:0.30, T:0.51
Consensus pattern (6 bp):
GGCTTT
Found at i:131808 original size:2 final size:2
Alignment explanation
Indices: 131801--131828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
131791 TTAATTACCC
131801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131829 TCTTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157407 original size:15 final size:15
Alignment explanation
Indices: 157387--157417 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
157377 TGTTGTTTAT
*
157387 TCTTTTTTGCTTTTC
1 TCTTTTTTCCTTTTC
157402 TCTTTTTTCCTTTTC
1 TCTTTTTTCCTTTTC
157417 T
1 T
157418 TGACCCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (15 bp):
TCTTTTTTCCTTTTC
Found at i:169172 original size:334 final size:334
Alignment explanation
Indices: 168573--169707 Score: 1601
Period size: 336 Copynumber: 3.4 Consensus size: 334
168563 CGAATCATGA
* * * * * *
168573 TTCGTTTTAATTAAAAATTAATTCGTGAAAAAATAGGGAAAACAATATTAAAAGCGTGAAAAGCA
1 TTCGATTTAATTAAAAATTAATTC-AGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* ** * * * ** *
168638 ATTCAATCTTTTTGGTTTTGAAGTATATATTTTGTATGAGTATTGTGGCTAAAAATTGAGTTAAA
65 ATTCAATATTTTTGGCGTTGAATTATACATTTTATATGAGTATTGTGGCTAAAAATTGAGGGAGA
* * * ** *
168703 ATTTTTCTGGTCATTTTTTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACGATCACGGTTTTA
130 ATTTTTCTGG---TTATTTTTTGCAAAGTTTTAGCCGAAATCGTGTACTAATTATCACGGTTTTT
* * * **
168768 TGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGGTTTTTGACGCTGACACTCCTTGA
192 TGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGGTTTTGGGCACCAACACTCCTTGA
* *
168833 AATATCTATATTTATCTAGTAAAAGCATAGCCACATTGCAATCAAGGATTTGTTTTTACGATCAT
257 AATATCTATATTTATCTAGTAAAAGCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGATCAT
*
168898 CTAAATCTTCTTT
322 CTAAATCTTGTTT
**
168911 TTCGATTTAATTCGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
1 TTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
*
168976 TTCAAT-TGTTTTGGCGTTGAATTATACATTTTATATGAGTATTGTGGTTAAAAATTGAGGGAGA
66 TTCAATAT-TTTTGGCGTTGAATTATACATTTTATATGAGTATTGTGGCTAAAAATTGAGGGAGA
*
169040 ATTTTTCTGGTTATTTTTTGCAAAGTTTTAGCTGAAATCGTGTACTAATTATCACGGTTTTTTGC
130 ATTTTTCTGGTTATTTTTTGCAAAGTTTTAGCCGAAATCGTGTACTAATTATCACGGTTTTTTGC
* * *
169105 TAAAAACACGTTTCGGGGCCTCGACTCAGTTTTGCATGGTTTTGGGCACCAACACTCGTTGAAAT
195 TAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGGTTTTGGGCACCAACACTCCTTGAAAT
169170 ATCTATATTTATCTAGTAAAAGCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGATCATCTA
260 ATCTATATTTATCTAGTAAAAGCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGATCATCTA
169235 AATCTTGTTTTTT
325 AATCTTG---TTT
** ** *
169248 TTTTATTTCCTTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
1 TTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
* * * *
169312 TTCAATTTTTTTTGCGTTGAATTATACATTTTGTATGAGTATTGTGGCTAAAAATTGAGGGAGAT
66 TTCAATATTTTTGGCGTTGAATTATACATTTTATATGAGTATTGTGGCTAAAAATTGAGGGAGAA
* *
169377 TTTTTCTGGTCATTTTTTGCAAAGTTTTAGCCGAAATCGTTTACTAATTATCACGGTTTTTTGCT
131 TTTTTCTGGTTATTTTTTGCAAAGTTTTAGCCGAAATCGTGTACTAATTATCACGGTTTTTTGCT
* * * *
169442 AAAAACGCGTTTCGTGTCCCCGGCTCAGTTTTGCATGGTTTTGGGCGA-GAACACTCCTTGAAAT
196 AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGGTTTTGGGC-ACCAACACTCCTTGAAAT
* *
169506 ATCTATATTTATCTAGTAAAATCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGAGCATCTA
260 ATCTATATTTATCTAGTAAAAGCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGATCATCTA
169571 AATCTTGTTT
325 AATCTTGTTT
* * * *
169581 TTCGAATTAATTAAAAATTAATTCAGAAAAAATATGAAGAACGATAGTAAAAGCGTGAAAAGCCC
1 TTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
* * * *
169646 TTCAATATTTTTGGCGTTGAATTACATATATATATTATGAGTATTATGGCTAAAAATTGAGG
66 TTCAATATTTTTGGCGTTGAATTATACAT-TTTA-TATGAGTATTGTGGCTAAAAATTGAGG
169708 AAATCCCTTT
Statistics
Matches: 716, Mismatches: 72, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
333 23 0.03
334 234 0.33
335 2 0.00
336 311 0.43
337 125 0.17
338 21 0.03
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (334 bp):
TTCGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCA
TTCAATATTTTTGGCGTTGAATTATACATTTTATATGAGTATTGTGGCTAAAAATTGAGGGAGAA
TTTTTCTGGTTATTTTTTGCAAAGTTTTAGCCGAAATCGTGTACTAATTATCACGGTTTTTTGCT
AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGGTTTTGGGCACCAACACTCCTTGAAATA
TCTATATTTATCTAGTAAAAGCTTAGCCACATTGCAATTAAGGATTTGTTTTTACGATCATCTAA
ATCTTGTTT
Done.