Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006893.1 Corchorus capsularis cultivar CVL-1 contig06914, 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: 59063
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2993 original size:17 final size:17
Alignment explanation
Indices: 2971--3005 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2961 AAAACGCAAG
*
2971 AAACAATTAGCCTTCAA
1 AAACAATTAACCTTCAA
2988 AAACAATTAACCTTCAA
1 AAACAATTAACCTTCAA
3005 A
1 A
3006 GGATAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (17 bp):
AAACAATTAACCTTCAA
Found at i:11859 original size:15 final size:15
Alignment explanation
Indices: 11839--11868 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11829 GAACTTTAAA
11839 ATCTTATGGGTATTT
1 ATCTTATGGGTATTT
11854 ATCTTATGGGTATTT
1 ATCTTATGGGTATTT
11869 CTTTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
ATCTTATGGGTATTT
Found at i:12758 original size:2 final size:2
Alignment explanation
Indices: 12751--12784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12741 GCATAAGGAA
12751 AT AT AT 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 AT AT AT
12785 CATGTTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18411 original size:66 final size:66
Alignment explanation
Indices: 18305--18438 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
18295 CTAACTCCAA
** *
18305 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTTAATTAAGAAATGAC
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGCCAATTAACAAATGAC
18370 C
66 C
*
18371 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGCCAATTGACAAATGAC
1 AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGCCAATTAACAAATGAC
18436 C
66 C
18437 AA
1 AA
18439 AAAGTCTAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (66 bp):
AAGCAAGCCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGCCAATTAACAAATGAC
C
Found at i:21175 original size:69 final size:69
Alignment explanation
Indices: 21045--21183 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
21035 TTGCTTGAAA
*
21045 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATAAATGGTGATCCTACCATTTTTTCC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATAAATGGTGATCCCACCATTTTTTCC
21110 TTAG
66 TTAG
* * * *
21114 TGCATTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATGTTGTTCCCACCTTTTTTTC
1 TGCATTGTCTTTATATGTAATTTTAGCATTTG-GATGTAATAAATGGTGATCCCACCATTTTTTC
21178 CTTAG
65 CTTAG
21183 T
1 T
21184 TGTTAGTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 3 0.05
69 61 0.95
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (69 bp):
TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATAAATGGTGATCCCACCATTTTTTCC
TTAG
Found at i:22217 original size:170 final size:169
Alignment explanation
Indices: 21909--22230 Score: 466
Period size: 170 Copynumber: 1.9 Consensus size: 169
21899 AAAAAGCTCA
* * *
21909 TAGTTATAGCCCAAACAACATTTTTTAATGTAACCACCATGCAGTCTAAGTTCAACTATCTGAAT
1 TAGTTATAGCCCAAACAACATTTTTTAATGAAACCACCATGCAATCTAAGTTCAACCATCTGAAT
** *
21974 TCTAAAGTCCAAAATAAAAATCGTAGCCATGAAAATGCATGTTAAATTTGCCAACATCTTGAAAA
66 TCTAAAAACCAAAATAAAAATCGTAGCCATAAAAATGCATGTTAAATTTGCCAACATCTTGAAAA
* *
22039 AATGTTTTTGTGGAAAGGGACAAGTAAGTGCAAAACAGG
131 AATGTTTTTATGGAAAAGGACAAGTAAGTGCAAAACAGG
* *
22078 TAGTT-TAGCCGAAACAACATTTTTTTTAATGAAACCATCATGCAATCTAAGTTCAACCATCTGA
1 TAGTTATAGCCCAAACAACA--TTTTTTAATGAAACCACCATGCAATCTAAGTTCAACCATCTGA
* * ** * *
22142 ATTCTAAAAACCAAATTAGAAATCGTCTCCATAAAAATGCATGTTAAATTTGTCAACATTTTGAA
64 ATTCTAAAAACCAAAATAAAAATCGTAGCCATAAAAATGCATGTTAAATTTGCCAACATCTTGAA
*
22207 AAACTGTTTTTATGGAAAAGGACA
129 AAAATGTTTTTATGGAAAAGGACA
22231 TGTAGGAGCA
Statistics
Matches: 134, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
168 13 0.10
169 5 0.04
170 116 0.87
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (169 bp):
TAGTTATAGCCCAAACAACATTTTTTAATGAAACCACCATGCAATCTAAGTTCAACCATCTGAAT
TCTAAAAACCAAAATAAAAATCGTAGCCATAAAAATGCATGTTAAATTTGCCAACATCTTGAAAA
AATGTTTTTATGGAAAAGGACAAGTAAGTGCAAAACAGG
Found at i:23096 original size:42 final size:42
Alignment explanation
Indices: 23049--23137 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
23039 AATGGTCGGT
*
23049 TGTGCCCGGTCATATGCGATTGCCCCATGCAATGGCCGGTCA
1 TGTGCCCGATCATATGCGATTGCCCCATGCAATGGCCGGTCA
* * * *
23091 TGTGCCCGATCTTGTGCGATTGCTCCATGCAATGGCCGGTTA
1 TGTGCCCGATCATATGCGATTGCCCCATGCAATGGCCGGTCA
23133 TGTGC
1 TGTGC
23138 GATCCCTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.15, C:0.28, G:0.29, T:0.28
Consensus pattern (42 bp):
TGTGCCCGATCATATGCGATTGCCCCATGCAATGGCCGGTCA
Found at i:26012 original size:23 final size:23
Alignment explanation
Indices: 25986--26029 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
25976 TGGGTGGTTT
25986 CAATTTCTT-TTTATTTTTTTTCC
1 CAATTT-TTATTTATTTTTTTTCC
26009 CAATTTTTATTTATTTTTTTT
1 CAATTTTTATTTATTTTTTTT
26030 TTTACCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (23 bp):
CAATTTTTATTTATTTTTTTTCC
Found at i:27070 original size:133 final size:134
Alignment explanation
Indices: 26831--27090 Score: 423
Period size: 133 Copynumber: 1.9 Consensus size: 134
26821 CTGTCAGTCT
*
26831 CTCTCTCAATCTCTCTCTAACAGTATTTTAGGGCTTCCATCGACAAATCTTCGAACAATGGAAGG
1 CTCTCTC-ATCTCTCTATAACAGTATTTTAGGGCTTCCATCGACAAATCTTCGAACAATGGAAGG
** * * * *
26896 TATATCTTATCCACTTTTATTTTCATTATTTTCTTTGTTGTTTGTTAAATGTTTTTATTAGACTC
65 TATATCCGATCAACTTTTATTCTCACTATTTTCTTTGTTGTTTATTAAATGTTTTTATTAGACTC
26961 TCTCC
130 TCTCC
*
26966 CTCTCTC-TCTCTCTATAACAGTATTTTAGGGCTTCCATCGACAAATCTTTGAACAATGGAAGGT
1 CTCTCTCATCTCTCTATAACAGTATTTTAGGGCTTCCATCGACAAATCTTCGAACAATGGAAGGT
*
27030 ATATCCGATCAACTTTTATTCTGACTATTTTCTTTGTTGTTTATTAAATGTTTTTATTAGA
66 ATATCCGATCAACTTTTATTCTCACTATTTTCTTTGTTGTTTATTAAATGTTTTTATTAGA
27091 GCATGAGTGC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
133 109 0.94
135 7 0.06
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (134 bp):
CTCTCTCATCTCTCTATAACAGTATTTTAGGGCTTCCATCGACAAATCTTCGAACAATGGAAGGT
ATATCCGATCAACTTTTATTCTCACTATTTTCTTTGTTGTTTATTAAATGTTTTTATTAGACTCT
CTCC
Found at i:27486 original size:16 final size:16
Alignment explanation
Indices: 27467--27594 Score: 84
Period size: 16 Copynumber: 7.9 Consensus size: 16
27457 CCGATCCGAG
27467 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGTA
*
27483 ACCC-AGATGACCTG-A
1 ACCCGA-ATGACCCGTA
*
27498 GACCCGAATGACCTGTA
1 -ACCCGAATGACCCGTA
* **
27515 ATCC-AGATGACCCAAA
1 ACCCGA-ATGACCCGTA
27531 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGTA
* *
27547 ACCCGAGTGATCCG-A
1 ACCCGAATGACCCGTA
* **
27562 GACCCGTATGACTTGAATA
1 -ACCCGAATGACCCG--TA
27581 ACCCGAATGACCCG
1 ACCCGAATGACCCG
27595 AAAATATTAT
Statistics
Matches: 84, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
15 4 0.05
16 65 0.77
17 3 0.04
18 11 0.13
19 1 0.01
ACGTcount: A:0.32, C:0.33, G:0.20, T:0.15
Consensus pattern (16 bp):
ACCCGAATGACCCGTA
Found at i:27500 original size:32 final size:31
Alignment explanation
Indices: 27462--27573 Score: 136
Period size: 32 Copynumber: 3.5 Consensus size: 31
27452 CCCGCCCGAT
27462 CCGAGACCCGAATGACCCGTAACCCAGATGA
1 CCGAGACCCGAATGACCCGTAACCCAGATGA
* *
27493 CCTGAGACCCGAATGACCTGTAATCCAGATGA
1 CC-GAGACCCGAATGACCCGTAACCCAGATGA
* *
27525 CCCAAAACCCGAATGACCCGTAACCC-GAGTGA
1 -CCGAGACCCGAATGACCCGTAACCCAGA-TGA
*
27557 TCCGAGACCCGTATGAC
1 -CCGAGACCCGAATGAC
27574 TTGAATAACC
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.06
32 62 0.91
33 2 0.03
ACGTcount: A:0.31, C:0.34, G:0.21, T:0.13
Consensus pattern (31 bp):
CCGAGACCCGAATGACCCGTAACCCAGATGA
Found at i:28172 original size:42 final size:42
Alignment explanation
Indices: 28108--28189 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
28098 TGTTGATACA
*
28108 TACCGCACCTGATAATTAATTATGTATTTAATATTCAAAACC
1 TACCGCACCTGATAATCAATTATGTATTTAATATTCAAAACC
*
28150 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAA
1 TACCGCACCTGATAATCAATTATGTATTTAATATTCAAAA
28190 TTAATATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (42 bp):
TACCGCACCTGATAATCAATTATGTATTTAATATTCAAAACC
Found at i:28441 original size:23 final size:22
Alignment explanation
Indices: 28414--28514 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 22
28404 AACCCGCCCA
*
28414 ACCCGAGACCTGGTAGACCCGAG
1 ACCCGAAACC-GGTAGACCCGAG
**
28437 ACCCGAATGACC-CAAGACCCGAATG
1 ACCCGAA--ACCGGTAGACCCG-A-G
* *
28462 ACCCGAAACCTGATTGACCCGAG
1 ACCCGAAACC-GGTAGACCCGAG
* *
28485 ACCCGAAACCCGTATGACCCAAG
1 ACCCGAAACCGGTA-GACCCGAG
28508 ACCCGAA
1 ACCCGAA
28515 TGATCTGAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.02
23 41 0.67
24 2 0.03
25 17 0.28
ACGTcount: A:0.33, C:0.37, G:0.22, T:0.09
Consensus pattern (22 bp):
ACCCGAAACCGGTAGACCCGAG
Found at i:28448 original size:16 final size:16
Alignment explanation
Indices: 28429--28571 Score: 110
Period size: 16 Copynumber: 8.6 Consensus size: 16
28419 AGACCTGGTA
28429 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
28445 GACCCAAGACCCGAAT
1 GACCCGAGACCCGAAT
* * *
28461 GACCCGAAACCTGATT
1 GACCCGAGACCCGAAT
28477 GACCCGAGACCCGAAACCCGTAT
1 GACCCGAGACCCG--A-----AT
*
28500 GACCCAAGACCCGAAT
1 GACCCGAGACCCGAAT
* * *
28516 GATCTGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
28532 AACCCGA-ACCC-AGAT
1 GACCCGAGACCCGA-AT
*
28547 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
28563 GACCCGAGA
1 GACCCGAGA
28572 AAACTACCTG
Statistics
Matches: 99, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.01
15 12 0.12
16 70 0.71
17 1 0.01
18 1 0.01
21 1 0.01
23 13 0.13
ACGTcount: A:0.35, C:0.36, G:0.20, T:0.09
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:28465 original size:32 final size:32
Alignment explanation
Indices: 28429--28567 Score: 120
Period size: 31 Copynumber: 4.7 Consensus size: 32
28419 AGACCTGGTA
*
28429 GACCCGAGACCCGAATGACCCAAGACCCGAAT
1 GACCCGAAACCCGAATGACCCAAGACCCGAAT
**
28461 GACCCGAAA-CC---TGA---TTGACCCG-A-
1 GACCCGAAACCCGAATGACCCAAGACCCGAAT
*
28484 GACCCGAAACCCGTATGACCCAAGACCCGAAT
1 GACCCGAAACCCGAATGACCCAAGACCCGAAT
* * * *
28516 GATCTGAAACCCGAATAACCCGA-ACCC-AGAT
1 GACCCGAAACCCGAATGACCCAAGACCCGA-AT
28547 GACCCGAAACCCGAATGACCC
1 GACCCGAAACCCGAATGACCC
28568 GAGAAAACTA
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
23 9 0.11
24 3 0.04
25 6 0.07
27 3 0.04
28 3 0.04
30 7 0.08
31 27 0.32
32 26 0.31
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCAAGACCCGAAT
Found at i:28537 original size:55 final size:55
Alignment explanation
Indices: 28428--28542 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
28418 GAGACCTGGT
* * * *
28428 AGACCCGAGACCCGAATGACCCAAGACCCGAATGACCCGAAACCTGATTGACCCG
1 AGACCCGAAACCCGAATGACCCAAGACCCGAATGACCCGAAACCCGAATAACCCG
* * *
28483 AGACCCGAAACCCGTATGACCCAAGACCCGAATGATCTGAAACCCGAATAACCCG
1 AGACCCGAAACCCGAATGACCCAAGACCCGAATGACCCGAAACCCGAATAACCCG
28538 A-ACCC
1 AGACCC
28543 AGATGACCCG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 4 0.08
55 49 0.92
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.10
Consensus pattern (55 bp):
AGACCCGAAACCCGAATGACCCAAGACCCGAATGACCCGAAACCCGAATAACCCG
Found at i:29676 original size:2 final size:2
Alignment explanation
Indices: 29669--29695 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29659 AACATCAAAC
29669 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29696 GTGGTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30966 original size:31 final size:31
Alignment explanation
Indices: 30928--30989 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
30918 TATGTTAGAC
*
30928 AAATAAGGATATAATAGACATTTCAAAAGTT
1 AAATAAGGATACAATAGACATTTCAAAAGTT
* * *
30959 AAATAAGGGTACAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGACATTTCAAAAGTT
30990 TTACAAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (31 bp):
AAATAAGGATACAATAGACATTTCAAAAGTT
Found at i:33854 original size:21 final size:21
Alignment explanation
Indices: 33830--33873 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
33820 CTTTGAGGAG
33830 GAACATCATTAAGTTTAAAGA
1 GAACATCATTAAGTTTAAAGA
*
33851 GAACATTATTAAGTTTAAAGA
1 GAACATCATTAAGTTTAAAGA
33872 GA
1 GA
33874 CTAAGGCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.30
Consensus pattern (21 bp):
GAACATCATTAAGTTTAAAGA
Found at i:34236 original size:2 final size:2
Alignment explanation
Indices: 34229--34259 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34219 TTATAACTAC
34229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34260 GATAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35779 original size:20 final size:22
Alignment explanation
Indices: 35740--35779 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
35730 CAAATTATGC
*
35740 ATATTTTTATGGCTATTTTTCT
1 ATATTTTTATGGCTACTTTTCT
35762 ATATTTTT-T-GCTACTTTT
1 ATATTTTTATGGCTACTTTT
35780 ATATGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (22 bp):
ATATTTTTATGGCTACTTTTCT
Found at i:50696 original size:29 final size:29
Alignment explanation
Indices: 50660--50717 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
50650 TCTCGTTTTT
*
50660 AAAAGTTATGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
*
50689 AAAAGTTAAGGGGCCAATTTGTCTCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
50718 TGGATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Done.