Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014034.1 Corchorus capsularis cultivar CVL-1 contig14055, 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: 40791
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:212 original size:11 final size:12
Alignment explanation
Indices: 187--225 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
177 AGAAAATCTC
187 TTTTTATTTTAT
1 TTTTTATTTTAT
199 TTTTTATTTT-T
1 TTTTTATTTTAT
* *
210 TTTTCATTTTGT
1 TTTTTATTTTAT
222 TTTT
1 TTTT
226 CCTCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:226 original size:12 final size:11
Alignment explanation
Indices: 187--237 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
177 AGAAAATCTC
187 TTTTT-ATTTT
1 TTTTTCATTTT
*
197 ATTTTTTATTTT
1 -TTTTTCATTTT
209 TTTTTCATTTT
1 TTTTTCATTTT
*
220 GTTTTTCCTCTTT
1 -TTTTTCAT-TTT
233 TTTTT
1 TTTTT
238 ACTTAAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 15 0.43
12 17 0.49
13 3 0.09
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:5968 original size:73 final size:76
Alignment explanation
Indices: 5877--6072 Score: 258
Period size: 75 Copynumber: 2.6 Consensus size: 76
5867 TTCAGTCACC
* * * * *
5877 TAGTAAGTTTGACACATCTTAATCTCTCTTCTAAATCA-TT-T-TGGCTCTTTCTTATCTTCCTC
1 TAGTAAGTCTGACGCATCTTGATCTCTCTTCTAAATCACTTCTCTGGCTCTATCTCATCTTCCTC
5939 TTTTAGTCAGT
66 TTTTAGTCAGT
* * * *
5950 TAGTGAGTCTGACGCATCTTGATCTCTCTTCT-AATTACTTCTCTGGCTCTATCTCATCTTCGTT
1 TAGTAAGTCTGACGCATCTTGATCTCTCTTCTAAATCACTTCTCTGGCTCTATCTCATCTTCCTC
6014 TTTTAGTCAGT
66 TTTTAGTCAGT
* *
6025 TAGTAAGACTGACGCATCTTGATCTCTCTTCT-AATCAATTCTCTGGCT
1 TAGTAAGTCTGACGCATCTTGATCTCTCTTCTAAATCACTTCTCTGGCT
6073 TAATCCCATC
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
72 4 0.04
73 30 0.28
74 1 0.01
75 72 0.67
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.44
Consensus pattern (76 bp):
TAGTAAGTCTGACGCATCTTGATCTCTCTTCTAAATCACTTCTCTGGCTCTATCTCATCTTCCTC
TTTTAGTCAGT
Found at i:6019 original size:75 final size:75
Alignment explanation
Indices: 5845--6072 Score: 255
Period size: 75 Copynumber: 3.1 Consensus size: 75
5835 ACTATCTCTA
** * * ** * * *
5845 TGGCTCTATCTCATCGGCGGATTTCAGTCACCTAGTAAGTTTGACACATCTTAATCTCTCTTCTA
1 TGGCTCTATCTCATCTTCGTATTTTAGTCAGTTAGTAAGTCTGACGCATCTTGATCTCTCTTCTA
*
5910 AAT-CATT-T-
66 ATTAC-TTCTC
* * * * *
5918 TGGCTCTTTCTTATCTTCCTCTTTTAGTCAGTTAGTGAGTCTGACGCATCTTGATCTCTCTTCTA
1 TGGCTCTATCTCATCTTCGTATTTTAGTCAGTTAGTAAGTCTGACGCATCTTGATCTCTCTTCTA
5983 ATTACTTCTC
66 ATTACTTCTC
* *
5993 TGGCTCTATCTCATCTTCGTTTTTTAGTCAGTTAGTAAGACTGACGCATCTTGATCTCTCTTCTA
1 TGGCTCTATCTCATCTTCGTATTTTAGTCAGTTAGTAAGTCTGACGCATCTTGATCTCTCTTCTA
* *
6058 ATCAATTCTC
66 ATTACTTCTC
6068 TGGCT
1 TGGCT
6073 TAATCCCATC
Statistics
Matches: 129, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
73 55 0.43
74 2 0.02
75 72 0.56
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.43
Consensus pattern (75 bp):
TGGCTCTATCTCATCTTCGTATTTTAGTCAGTTAGTAAGTCTGACGCATCTTGATCTCTCTTCTA
ATTACTTCTC
Found at i:6091 original size:41 final size:40
Alignment explanation
Indices: 6046--6174 Score: 105
Period size: 41 Copynumber: 3.4 Consensus size: 40
6036 ACGCATCTTG
6046 ATCTCTCTTCTAATCAATTCTCTGGCTTAATCCCATCTGAA
1 ATCTCTCTTCT-ATCAATTCTCTGGCTTAATCCCATCTGAA
* ** *
6087 ATCTCTCTTCTACCAA--AACTGG-TT--TCAC-T-TG--
1 ATCTCTCTTCTATCAATTCTCTGGCTTAATCCCATCTGAA
* * * *
6118 ATCTCTCTTTTAATTATTTCTCTGGCTCAATCCCATCTGAA
1 ATCTCTCTTCT-ATCAATTCTCTGGCTTAATCCCATCTGAA
6159 ATCTCTCTTCTATCAA
1 ATCTCTCTTCTATCAA
6175 AACTGGTTTC
Statistics
Matches: 63, Mismatches: 15, Indels: 21
0.64 0.15 0.21
Matches are distributed among these distances:
31 10 0.16
32 2 0.03
33 2 0.03
34 5 0.08
35 4 0.06
37 5 0.08
38 5 0.08
39 2 0.03
40 7 0.11
41 21 0.33
ACGTcount: A:0.23, C:0.29, G:0.07, T:0.41
Consensus pattern (40 bp):
ATCTCTCTTCTATCAATTCTCTGGCTTAATCCCATCTGAA
Found at i:6139 original size:72 final size:72
Alignment explanation
Indices: 6042--6193 Score: 259
Period size: 72 Copynumber: 2.1 Consensus size: 72
6032 ACTGACGCAT
*
6042 CTTGATCTCTCTTCTAATCAATTCTCTGGCTTAATCCCATCTGAAATCTCTCTTCTACCAAAACT
1 CTTGATCTCTCTTCTAATCAATTCTCTGGCTCAATCCCATCTGAAATCTCTCTTCTACCAAAACT
6107 GGTTTCA
66 GGTTTCA
* * * *
6114 CTTGATCTCTCTTTTAATTATTTCTCTGGCTCAATCCCATCTGAAATCTCTCTTCTATCAAAACT
1 CTTGATCTCTCTTCTAATCAATTCTCTGGCTCAATCCCATCTGAAATCTCTCTTCTACCAAAACT
6179 GGTTTCA
66 GGTTTCA
6186 CTTGATCT
1 CTTGATCT
6194 TTCTAACAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.22, C:0.28, G:0.09, T:0.41
Consensus pattern (72 bp):
CTTGATCTCTCTTCTAATCAATTCTCTGGCTCAATCCCATCTGAAATCTCTCTTCTACCAAAACT
GGTTTCA
Found at i:30422 original size:31 final size:32
Alignment explanation
Indices: 30377--30444 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
30367 TTGAGTAATG
* * *
30377 ACAATTTAGAAATATAATTTTTAGAA-AAGGGT
1 ACAATTGAGAAATAT-ATTTTAAAAATAAGGGT
*
30409 ACAATTGA-AAATATGTTTTAAAAATAAGGGT
1 ACAATTGAGAAATATATTTTAAAAATAAGGGT
30440 ACAAT
1 ACAAT
30445 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 7 0.23
31 17 0.55
32 7 0.23
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (32 bp):
ACAATTGAGAAATATATTTTAAAAATAAGGGT
Found at i:31378 original size:116 final size:114
Alignment explanation
Indices: 31244--31469 Score: 314
Period size: 115 Copynumber: 2.0 Consensus size: 114
31234 TTAATAATAA
** * *
31244 TAAAAAACAATAAGATTAGAAAGTGAAA-A-TTAAAAAAAAAAACGACGTAAAGATTTTAGCTCA
1 TAAAAAACAATAAGATTAGAAA---AAATACCAAAAAAAAAAAACAACCTAAAGATTTTAGCTCA
31307 TTAAATTGCTTAATATTCAATT-AGGTTTTTCCGTCATTTCAAATCTTGGTTTT
63 TTAAATTGCTTAATATTCAATTGA-GTTTTTCCGTCATTTC-AATCTTGGTTTT
31360 TAAAAAACAATAAGATTAGAAAAAATACCAAAAAAAAAAAACAACCTAAAGATTTTAGCTCATTA
1 TAAAAAACAATAAGATTAGAAAAAATACCAAAAAAAAAAAACAACCTAAAGATTTTAGCTCATTA
* * **
31425 ATTTGCTTAATATTCAGTTGAGTTTTTTTGTCATTTCAATCTTGG
66 AATTGCTTAATATTCAATTGAGTTTTTCCGTCATTTCAATCTTGG
31470 GGTTTTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
113 3 0.03
114 9 0.09
115 64 0.65
116 23 0.23
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (114 bp):
TAAAAAACAATAAGATTAGAAAAAATACCAAAAAAAAAAAACAACCTAAAGATTTTAGCTCATTA
AATTGCTTAATATTCAATTGAGTTTTTCCGTCATTTCAATCTTGGTTTT
Found at i:33903 original size:177 final size:179
Alignment explanation
Indices: 33606--33951 Score: 502
Period size: 177 Copynumber: 1.9 Consensus size: 179
33596 CCAACTCACG
*
33606 ACGTGGTTGGGCTTCAAAATCTACAAAGCCTTGACTTATCCGGTAACCTAATAAGTGGTGCAGTA
1 ACGTGGTTGGGCCTCAAAATCTACAAAGCCTTGACTTATCCGGTAACCTAATAAGTGGTGCAGTA
* *
33671 CCATCTTGGTTGTTTGCTCTGCCATCTTTGGAAACCTTGGATCTTAGCAACAACAAATTACTCT-
66 CCATCTTGGTTGTTTGCTCTGCCATCTTTGGAAAACTTGAATCTTAGCAACAACAAATTACTCTC
33735 CC-CTTCCAACTGATGACCAAATTCAAAACCCTAGTTCCCTTCCAACTC
131 CCACTTCCAACTGATGACCAAATTCAAAACCCTAGTTCCCTTCCAACTC
* * *
33783 ACGTGGTTGGGCCTCAAAGTCTAGAAATCCTTGACTTATCTC-GTAACCTAATAAGTGGTGCAGT
1 ACGTGGTTGGGCCTCAAAATCTACAAAGCCTTGACTTATC-CGGTAACCTAATAAGTGGTGCAGT
* * * * * * *
33847 ACCATCTTGGTTGTTTGGTTTGGCATCTTT-GACAAATTTGAATCTTGGCTACAACAATTTACTC
65 ACCATCTTGGTTGTTTGCTCTGCCATCTTTGGA-AAACTTGAATCTTAGCAACAACAAATTACTC
* *
33911 TCCCAGCTTCCAACTGATGTCCAATTTCAAAACCCTAGTTC
129 TCCCA-CTTCCAACTGATGACCAAATTCAAAACCCTAGTTC
33952 ACTCCAAGAG
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
176 2 0.01
177 111 0.74
178 3 0.02
180 33 0.22
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (179 bp):
ACGTGGTTGGGCCTCAAAATCTACAAAGCCTTGACTTATCCGGTAACCTAATAAGTGGTGCAGTA
CCATCTTGGTTGTTTGCTCTGCCATCTTTGGAAAACTTGAATCTTAGCAACAACAAATTACTCTC
CCACTTCCAACTGATGACCAAATTCAAAACCCTAGTTCCCTTCCAACTC
Found at i:35530 original size:1 final size:1
Alignment explanation
Indices: 35524--35560 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
35514 CAATACCAAG
35524 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35561 GTGATCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.