Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010097.1 Corchorus capsularis cultivar CVL-1 contig10118, 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: 40475
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:663 original size:31 final size:30
Alignment explanation
Indices: 625--745 Score: 116
Period size: 31 Copynumber: 3.9 Consensus size: 30
615 AAGTCAATAA
625 TTGCAAAATCGGCTAAAATCAGTCCCTAACG
1 TTGCAAAATCGGCTAAAAT-AGTCCCTAACG
** *
656 TTGCAAAATCGGCTAAAATAGTCTTTAACA
1 TTGCAAAATCGGCTAAAATAGTCCCTAACG
* * *
686 TTGAAAAATCGGCTCAAATAAGTCACCTAGCG
1 TTGCAAAATCGGCTAAAAT-AGTC-CCTAACG
* ** *
718 TTGTAAAATAAGCTCAAATGAGTCCCTA
1 TTGCAAAATCGGCTAAAAT-AGTCCCTA
746 GTATGAATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
30 25 0.33
31 27 0.36
32 23 0.31
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (30 bp):
TTGCAAAATCGGCTAAAATAGTCCCTAACG
Found at i:696 original size:30 final size:30
Alignment explanation
Indices: 624--714 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 30
614 TAAGTCAATA
624 ATTGCAAAATCGGCTAAAATCAGTCCCTAAC
1 ATTGCAAAATCGGCTAAAAT-AGTCCCTAAC
* **
655 GTTGCAAAATCGGCTAAAATAGTCTTTAAC
1 ATTGCAAAATCGGCTAAAATAGTCCCTAAC
* *
685 ATTGAAAAATCGGCTCAAATAAGTCACCTA
1 ATTGCAAAATCGGCTAAAAT-AGTC-CCTA
715 GCGTTGTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 25 0.50
31 23 0.46
32 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (30 bp):
ATTGCAAAATCGGCTAAAATAGTCCCTAAC
Found at i:3851 original size:29 final size:30
Alignment explanation
Indices: 3808--3869 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
3798 TAAAACGCCT
* **
3808 AAAATTGAGAGTTTATGGGGGC-AAATGTCC
1 AAAATTGAAAGTTTAT-AAGGCAAAATGTCC
3838 AAAATT-AAAGTTTATAAGGCAAAATGTCC
1 AAAATTGAAAGTTTATAAGGCAAAATGTCC
3867 AAA
1 AAA
3870 CTGTACATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 19 0.68
30 6 0.21
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (30 bp):
AAAATTGAAAGTTTATAAGGCAAAATGTCC
Found at i:14055 original size:33 final size:33
Alignment explanation
Indices: 14013--14111 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
14003 TGCAGTCCAA
14013 AATTTACACCGCCGGTGTATCAAATAATTACCC
1 AATTTACACCGCCGGTGTATCAAATAATTACCC
* *
14046 AATTTACACCGCTGGTGTATCAAATAATTATCC
1 AATTTACACCGCCGGTGTATCAAATAATTACCC
* *
14079 AATTTACACCGCCGGTATATCAAACAATTACCC
1 AATTTACACCGCCGGTGTATCAAATAATTACCC
14112 TTACAATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (33 bp):
AATTTACACCGCCGGTGTATCAAATAATTACCC
Found at i:15208 original size:98 final size:98
Alignment explanation
Indices: 15039--15231 Score: 368
Period size: 98 Copynumber: 2.0 Consensus size: 98
15029 TAGTTAACAG
15039 ACTCATGGGCACTTGAGGCGCTTGGGCTCATAAATTACGGCACTTGGGGAATGACCTAAAATCTT
1 ACTCATGGGCACTTGAGGCGCTTGGGCTCATAAATTACGGCACTTGGGGAATGACCTAAAATCTT
15104 TATGCTAGACTAGTTTTAACCTTCACATGCAAC
66 TATGCTAGACTAGTTTTAACCTTCACATGCAAC
*
15137 ACTCATGGGCACTTGAGGCGCTTGGGCTCATAAATTACGGCACTTGGGGAATGACCTAGAATCTT
1 ACTCATGGGCACTTGAGGCGCTTGGGCTCATAAATTACGGCACTTGGGGAATGACCTAAAATCTT
*
15202 TATGCTAGACTAGTTTTCACCTTCACATGC
66 TATGCTAGACTAGTTTTAACCTTCACATGC
15232 GTTGCATGTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (98 bp):
ACTCATGGGCACTTGAGGCGCTTGGGCTCATAAATTACGGCACTTGGGGAATGACCTAAAATCTT
TATGCTAGACTAGTTTTAACCTTCACATGCAAC
Found at i:15642 original size:18 final size:18
Alignment explanation
Indices: 15619--15654 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15609 AAGGAAGCTT
15619 AGCCAAATCTGATTCCTC
1 AGCCAAATCTGATTCCTC
15637 AGCCAAATCTGATTCCTC
1 AGCCAAATCTGATTCCTC
15655 CATTAGCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (18 bp):
AGCCAAATCTGATTCCTC
Found at i:15847 original size:39 final size:41
Alignment explanation
Indices: 15793--15874 Score: 132
Period size: 39 Copynumber: 2.0 Consensus size: 41
15783 TTTAGTCTCG
*
15793 GTTCGTCCAATTTGAACATT-C-AAAAAAACATCAGTAATT
1 GTTCGTCCAATTTGAACATTCCAAAAAAAACATCAATAATT
15832 GTTCGTCCAATTTGAACATTCCAAAAAAAAACATCAATAATT
1 GTTCGTCCAATTTGAACATTCC-AAAAAAAACATCAATAATT
15874 G
1 G
15875 ATCAATTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 20 0.51
40 1 0.03
42 18 0.46
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (41 bp):
GTTCGTCCAATTTGAACATTCCAAAAAAAACATCAATAATT
Found at i:15886 original size:114 final size:110
Alignment explanation
Indices: 15721--15945 Score: 378
Period size: 114 Copynumber: 2.0 Consensus size: 110
15711 TGAAGTCTCG
* *
15721 GTTCATCCAATTTGAACATTAAAAAAAACATCAGTAATTGATTAATTATACCCAAGTCAATTTTT
1 GTTCATCCAATTTGAACATTAAAAAAAACATCAATAATTGATCAATTATACCCAAGTCAATTTTT
*
15786 AGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
66 AGTCTCGGTTCGTCCAATTTCAACATTC-AAAAAACATCAGTAATT
*
15832 GTTCGTCCAATTTGAACATTCCAAAAAAAAACATCAATAATTGATCAATTATACCCAAGTCAATT
1 GTTCATCCAATTTGAACATT---AAAAAAAACATCAATAATTGATCAATTATACCCAAGTCAATT
15897 TTTAGTCTCGGTTCGTCCAATTTCAACATTCAAAAAACATCAGTAATT
63 TTTAGTCTCGGTTCGTCCAATTTCAACATTCAAAAAACATCAGTAATT
15945 G
1 G
15946 ATCAATTATA
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
111 19 0.18
113 18 0.17
114 70 0.65
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (110 bp):
GTTCATCCAATTTGAACATTAAAAAAAACATCAATAATTGATCAATTATACCCAAGTCAATTTTT
AGTCTCGGTTCGTCCAATTTCAACATTCAAAAAACATCAGTAATT
Found at i:15953 original size:71 final size:71
Alignment explanation
Indices: 15832--16043 Score: 325
Period size: 73 Copynumber: 2.9 Consensus size: 71
15822 ATCAGTAATT
*
15832 GTTCGTCCAATTTGAACATTCCAAAAAAAAACATCAATAATTGATCAATTATACCCAAGTCAATT
1 GTTCGTCCAATTTGAACATT-C---AAAAAACATCAGTAATTGATCAATTATACCCAAGTCAATT
*
15897 TTTAGTCTCG
62 TTTAGCCTCG
* *
15907 GTTCGTCCAATTTCAACATTCAAAAAACATCAGTAATTGATCAATTATATCCAAGTCAATATTTT
1 GTTCGTCCAATTTGAACATTCAAAAAACATCAGTAATTGATCAATTATACCCAAGTC-A-ATTTT
15972 TAGCCTCG
64 TAGCCTCG
*
15980 GTTCGTCCAATTTGAACATTCAAAAAAAATCAGTAATTGATCAATTATACCCAAGTCAATTTTT
1 GTTCGTCCAATTTGAACATTCAAAAAACATCAGTAATTGATCAATTATACCCAAGTCAATTTTT
16044 GCAAAGATAA
Statistics
Matches: 128, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
71 40 0.31
72 2 0.02
73 66 0.52
74 1 0.01
75 19 0.15
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.33
Consensus pattern (71 bp):
GTTCGTCCAATTTGAACATTCAAAAAACATCAGTAATTGATCAATTATACCCAAGTCAATTTTTA
GCCTCG
Found at i:18921 original size:86 final size:86
Alignment explanation
Indices: 18823--18994 Score: 281
Period size: 86 Copynumber: 2.0 Consensus size: 86
18813 ATAGATAAAG
* * * *
18823 AGGCATTTTTTGAATGTGATAAAATGTTAAAAATTATATTTACAGTTTTTCAAGTTTAATAGATA
1 AGGCATTTTTTGAATGTAATAAAATGTTAAAAAATATATTTACAGTTTTCCAAGTTTAATAAATA
*
18888 ACTGTTGATGAATAGTTACCT
66 ACTGTTGATGAACAGTTACCT
* *
18909 AGGCATTTTTTGAATGTAATAAATTGTTAAAAAATGTATTTACAGTTTTCCAAGTTTAATAAATA
1 AGGCATTTTTTGAATGTAATAAAATGTTAAAAAATATATTTACAGTTTTCCAAGTTTAATAAATA
18974 ACTGTTGATGAACAGTTACCT
66 ACTGTTGATGAACAGTTACCT
18995 TGAAGAGATG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.41
Consensus pattern (86 bp):
AGGCATTTTTTGAATGTAATAAAATGTTAAAAAATATATTTACAGTTTTCCAAGTTTAATAAATA
ACTGTTGATGAACAGTTACCT
Found at i:24319 original size:13 final size:13
Alignment explanation
Indices: 24301--24328 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24291 CCACATAAAG
24301 AAAAATATTAACA
1 AAAAATATTAACA
24314 AAAAATATTAACA
1 AAAAATATTAACA
24327 AA
1 AA
24329 GTAAAATAGC
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:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATATTAACA
Found at i:24833 original size:98 final size:98
Alignment explanation
Indices: 24722--24921 Score: 382
Period size: 98 Copynumber: 2.0 Consensus size: 98
24712 GATATAATAG
24722 ACATTTCAAAAGTTAAATAAGGGTACAATAGGCGTTTCAAAAGTTTTACAAAACTCGTACTTTTA
1 ACATTTCAAAAGTTAAATAAGGGTACAATAGGCGTTTCAAAAGTTTTACAAAACTCGTACTTTTA
*
24787 TATATAGTATAGATTATAAATAAAATTTCTATA
66 TATATAGTATAGATTATAAATAAAATTTCTAAA
*
24820 ACATTTCAAAAGTTAAATAAGGGTACAATAGGTGTTTCAAAAGTTTTACAAAACTCGTACTTTTA
1 ACATTTCAAAAGTTAAATAAGGGTACAATAGGCGTTTCAAAAGTTTTACAAAACTCGTACTTTTA
24885 TATATAGTATAGATTATAAATAAAATTTCTAAA
66 TATATAGTATAGATTATAAATAAAATTTCTAAA
24918 ACAT
1 ACAT
24922 GGAGGCCATT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.35
Consensus pattern (98 bp):
ACATTTCAAAAGTTAAATAAGGGTACAATAGGCGTTTCAAAAGTTTTACAAAACTCGTACTTTTA
TATATAGTATAGATTATAAATAAAATTTCTAAA
Found at i:25410 original size:14 final size:14
Alignment explanation
Indices: 25393--25419 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25383 TCCTAATCCC
25393 TTGTTCCTTTTTAA
1 TTGTTCCTTTTTAA
25407 TTGTTCCTTTTTA
1 TTGTTCCTTTTTA
25420 TTAAAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.07, T:0.67
Consensus pattern (14 bp):
TTGTTCCTTTTTAA
Found at i:35909 original size:13 final size:13
Alignment explanation
Indices: 35891--35920 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35881 CTACATGACA
35891 CTCCAACTTGTCC
1 CTCCAACTTGTCC
*
35904 CTCCAATTTGTCC
1 CTCCAACTTGTCC
35917 CTCC
1 CTCC
35921 TGACGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.47, G:0.07, T:0.33
Consensus pattern (13 bp):
CTCCAACTTGTCC
Found at i:36078 original size:41 final size:41
Alignment explanation
Indices: 36021--36101 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
36011 TTTATAACTA
*
36021 GGGGCTAAACCTGGATTTAATTTCT-TACCTTAATTATTAGT
1 GGGGCTAAACCTGGATTTAATTTATGT-CCTTAATTATTAGT
36062 GGGGCTAAACCTGGATTTAATTTATGTCCTTAATTATTAG
1 GGGGCTAAACCTGGATTTAATTTATGTCCTTAATTATTAG
36102 GAGGGTCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (41 bp):
GGGGCTAAACCTGGATTTAATTTATGTCCTTAATTATTAGT
Found at i:36411 original size:63 final size:62
Alignment explanation
Indices: 36311--36431 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 62
36301 CAGTAATTAG
*
36311 TTTGATTTCACCCTTTATTTGCTTGATTGTTTTTTGCTATCCATTTCTCTTCTAAAAATTTA
1 TTTGATTTCACCCTTTATTTGCTTGATTGTTTCTTGCTATCCATTTCTCTTCTAAAAATTTA
* *
36373 TTTGATTTCACCCTTGTATTTGTTTGATTGTTTCTTGCTATCCATTTTTCTTCTAAAAA
1 TTTGATTTCACCCTT-TATTTGCTTGATTGTTTCTTGCTATCCATTTCTCTTCTAAAAA
36432 ACCATTACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 15 0.27
63 40 0.73
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (62 bp):
TTTGATTTCACCCTTTATTTGCTTGATTGTTTCTTGCTATCCATTTCTCTTCTAAAAATTTA
Found at i:39093 original size:6 final size:6
Alignment explanation
Indices: 39082--39114 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
39072 GTAATGATGT
39082 TTTTTC TTTTTC TTTTTC -TTTTC -TTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
39115 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:39115 original size:17 final size:17
Alignment explanation
Indices: 39083--39114 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39073 TAATGATGTT
39083 TTTTCTTTTTCTTTTTC
1 TTTTCTTTTTCTTTTTC
39100 TTTTC-TTTTCTTTTT
1 TTTTCTTTTTCTTTTT
39115 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTC
Found at i:39873 original size:56 final size:56
Alignment explanation
Indices: 39803--39957 Score: 240
Period size: 56 Copynumber: 2.8 Consensus size: 56
39793 CATTGTGTTA
* *
39803 GTCAACCAAATATAAACAAGGAAAGAAATTATCAAGGCAATCAATTGATAATCAAT
1 GTCAACCAACTATAAACAAGGAAAGAAATTATCAAGGCAATCAATCGATAATCAAT
* * *
39859 GTCAACCCACTATAAACAAGAAAAAAAATTATCAAGGCAATCAATCGATAATCAAT
1 GTCAACCAACTATAAACAAGGAAAGAAATTATCAAGGCAATCAATCGATAATCAAT
* *
39915 GTCAACCAACTACAAACAACGAAAGAAATTAT-AAGGCAATCAA
1 GTCAACCAACTATAAACAAGGAAAGAAATTATCAAGGCAATCAA
39958 CTACAATCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 11 0.12
56 78 0.88
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19
Consensus pattern (56 bp):
GTCAACCAACTATAAACAAGGAAAGAAATTATCAAGGCAATCAATCGATAATCAAT
Done.