Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013182.1 Corchorus capsularis cultivar CVL-1 contig13203, 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: 34836
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2116 original size:33 final size:33
Alignment explanation
Indices: 2074--2182 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 33
2064 GTGTTTTAGA
2074 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* * * * *
2107 TGTTGTTTGCAATGACACTAAATCT-GTTTTAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* *
2139 ATGTTGTCTACGATGATACTAAACCTAATTTGAG
1 -TGTTGTTTGCGATGATACTAAACCTAATTTGAG
2173 TGTTGTTTGC
1 TGTTGTTTGC
2183 AATAAAACTA
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 5 0.08
33 50 0.83
34 5 0.08
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (33 bp):
TGTTGTTTGCGATGATACTAAACCTAATTTGAG
Found at i:2171 original size:66 final size:66
Alignment explanation
Indices: 2065--2207 Score: 241
Period size: 66 Copynumber: 2.2 Consensus size: 66
2055 TTGAAAAGAG
* * * *
2065 TGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAAT
1 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
2130 C
66 C
2131 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
1 TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
2196 C
66 C
*
2197 TGTTTTGGATG
1 TGTTTTAGATG
2208 CTAATTGTGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (66 bp):
TGTTTTAGATGTTGTCTACGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAAT
C
Found at i:2257 original size:33 final size:33
Alignment explanation
Indices: 2220--2307 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
2210 AATTGTGATG
2220 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
** *
2253 AAAACAATTCTGTTTTGGTTGATTATAGCATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
* * *
2286 CAAATAATCCTGTTTTGGTTGA
1 AAAACAATTCTGTTTTGGTTGA
2308 TAGCATTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (33 bp):
AAAACAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:2313 original size:30 final size:31
Alignment explanation
Indices: 2218--2322 Score: 113
Period size: 33 Copynumber: 3.3 Consensus size: 31
2208 CTAATTGTGA
* *
2218 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTGTTTTGGTTG-A-ATAGCAT
* * *
2251 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGA--ATAGCAT
*
2284 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGAATAGCAT
2314 TGAAAATAA
1 TGAAAATAA
2323 ATCTGATTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
30 15 0.23
32 1 0.02
33 48 0.75
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (31 bp):
TGAAAATAATCCTGTTTTGGTTGAATAGCAT
Found at i:5325 original size:33 final size:32
Alignment explanation
Indices: 5283--5376 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 32
5273 AATCCGGCCA
*
5283 ACGCGACATGGAGATGCCCGCGCAACACCGGCT
1 ACGCAACATGGAGATGCCCG-GCAACACCGGCT
* *
5316 ATGCAACATGGAGATGCCCGGCCATCACCGGCT
1 ACGCAACATGGAGATGCCCGG-CAACACCGGCT
* ** *
5349 ACGCGACATGGCCATGCCCGGCTACACC
1 ACGCAACATGGAGATGCCCGGCAACACC
5377 CAGACACCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
32 6 0.12
33 45 0.88
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.12
Consensus pattern (32 bp):
ACGCAACATGGAGATGCCCGGCAACACCGGCT
Found at i:12598 original size:19 final size:18
Alignment explanation
Indices: 12574--12610 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12564 TTGAAGATTT
12574 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
12593 CTTGAAGATTATTGAAGA
1 CTTGAAGATAATTGAAGA
12611 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:13863 original size:22 final size:23
Alignment explanation
Indices: 13824--13866 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13814 ATTCACTGCT
*
13824 TTTTCTTTAATTGTTTTCTTAAA
1 TTTTCTTTAATTGCTTTCTTAAA
*
13847 TTTTC-TTGATTGCTTTCTTA
1 TTTTCTTTAATTGCTTTCTTA
13867 GTTAATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTCTTTAATTGCTTTCTTAAA
Found at i:20147 original size:21 final size:19
Alignment explanation
Indices: 20115--20162 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
20105 TAAAATTAGG
20115 GTTTTTAATTTAAGTTTAT
1 GTTTTTAATTTAAGTTTAT
* *
20134 GTTTTCTAGATTTAGGTTTTT
1 GTTTT-TA-ATTTAAGTTTAT
*
20155 CTTTTTAA
1 GTTTTTAA
20163 GCATCTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 14 0.58
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.62
Consensus pattern (19 bp):
GTTTTTAATTTAAGTTTAT
Found at i:22928 original size:22 final size:23
Alignment explanation
Indices: 22889--22931 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22879 ATTCACTGCT
*
22889 TTTTCTTTAATTGTTTTCTTAAA
1 TTTTCTTTAATTGCTTTCTTAAA
*
22912 TTTTC-TTGATTGCTTTCTTA
1 TTTTCTTTAATTGCTTTCTTA
22932 GTTAATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTCTTTAATTGCTTTCTTAAA
Found at i:23281 original size:73 final size:74
Alignment explanation
Indices: 23111--23388 Score: 370
Period size: 73 Copynumber: 3.8 Consensus size: 74
23101 CGATACGATC
* * * *
23111 AATGAGCGTCATTAAACATAATAAGACGAACATCTCCCTCGAGATTGTCTTATCAAAAAATAAAC
1 AATGAGTGTCATTAACCATAATAAGACGAACGTCTCCCTCGAGACTGTCTTATCAAAAAATAAAC
23176 GACAGCTCG
66 GACAGCTCG
* *
23185 AATGAGTGTCGTTAACCATAATAAGACGAACGTCTCCCTCGAGACTGTCTTA-CCAAAAATAAAC
1 AATGAGTGTCATTAACCATAATAAGACGAACGTCTCCCTCGAGACTGTCTTATCAAAAAATAAAC
23249 GACAGCTCG
66 GACAGCTCG
* *
23258 AATGAGTGTCATCAACCATAATAAGACGAACGTCTCCCTC-ATGACCGTCTTATCAAAAAAATAA
1 AATGAGTGTCATTAACCATAATAAGACGAACGTCTCCCTCGA-GACTGTCTTATC-AAAAAATAA
*
23322 GCGACAGCTCG
64 ACGACAGCTCG
* * * * *
23333 AAT-A---TCATTAACTATAATAAGACGAACGTCTCCCACGAGACCGTTTTATCTAAAAA
1 AATGAGTGTCATTAACCATAATAAGACGAACGTCTCCCTCGAGACTGTCTTATCAAAAAA
23389 CCAAACGATC
Statistics
Matches: 184, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
70 5 0.03
71 40 0.22
72 2 0.01
73 67 0.36
74 49 0.27
75 21 0.11
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (74 bp):
AATGAGTGTCATTAACCATAATAAGACGAACGTCTCCCTCGAGACTGTCTTATCAAAAAATAAAC
GACAGCTCG
Found at i:23437 original size:67 final size:66
Alignment explanation
Indices: 23347--23540 Score: 216
Period size: 65 Copynumber: 2.9 Consensus size: 66
23337 TCATTAACTA
* *
23347 TAATAAGACGAACGTCTCCCACGAGACCGTTTTATCTAAAAACCAAACGATCAAGCATCGTAATC
1 TAATAAGACGAATGTCTCCCACGAGACCGTTTTATCTAAAAA-TAAACGATCAAGCATCGTAATC
23412 AC
65 AC
* *
23414 TAATAAGACGAATGTCTCCCAC--GACCATTTTATCTAAAGAATAAACGATCAAGCATCGTAATT
1 TAATAAGACGAATGTCTCCCACGAGACCGTTTTATCTAAA-AATAAACGATCAAGCATCGTAATC
*
23477 TC
65 AC
* * * * * *
23479 TAAAAAGGCGGATGTC-CCATACGAAACCGTTTTATCTACAAAATTAAACGAT-AAACATCGTA
1 TAATAAGACGAATGTCTCC-CACGAGACCGTTTTATCTA-AAAA-TAAACGATCAAGCATCGTA
23541 GCTACAAACT
Statistics
Matches: 109, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
64 2 0.02
65 51 0.47
66 2 0.02
67 44 0.40
68 10 0.09
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (66 bp):
TAATAAGACGAATGTCTCCCACGAGACCGTTTTATCTAAAAATAAACGATCAAGCATCGTAATCA
C
Found at i:32282 original size:49 final size:49
Alignment explanation
Indices: 32223--32322 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
32213 ATTATTCAAT
32223 TTTAACTAAGGTTAAGATTAGGTTAAGATAATTAATAGTAAAAATTAAA
1 TTTAACTAAGGTTAAGATTAGGTTAAGATAATTAATAGTAAAAATTAAA
32272 TTTAACTAAGGTTAAGATTAGGTTAAGATAATTAATAGTAAAAATTAAA
1 TTTAACTAAGGTTAAGATTAGGTTAAGATAATTAATAGTAAAAATTAAA
32321 TT
1 TT
32323 AGGTGTGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (49 bp):
TTTAACTAAGGTTAAGATTAGGTTAAGATAATTAATAGTAAAAATTAAA
Found at i:32318 original size:27 final size:27
Alignment explanation
Indices: 32239--32318 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
32229 TAAGGTTAAG
32239 ATTAGGTTAAGATAATTAATAGTAAAA
1 ATTAGGTTAAGATAATTAATAGTAAAA
** * * * *
32266 ATTA----AATTTAACTAA-GGTTAAG
1 ATTAGGTTAAGATAATTAATAGTAAAA
32288 ATTAGGTTAAGATAATTAATAGTAAAA
1 ATTAGGTTAAGATAATTAATAGTAAAA
32315 ATTA
1 ATTA
32319 AATTAGGTGT
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
26 8 0.22
27 12 0.33
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (27 bp):
ATTAGGTTAAGATAATTAATAGTAAAA
Found at i:33039 original size:2 final size:2
Alignment explanation
Indices: 33026--33086 Score: 81
Period size: 2 Copynumber: 30.5 Consensus size: 2
33016 ACTGAAAATA
*
33026 AT AT AT AGT AT AT AT AT AT AT AT AT AT AC A- AGT -T AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
33068 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
33087 CAAGTTATAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
1 2 0.04
2 50 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33076 original size:33 final size:34
Alignment explanation
Indices: 33027--33096 Score: 133
Period size: 33 Copynumber: 2.1 Consensus size: 34
33017 CTGAAAATAA
33027 TATATAGTATATATATATATATATATACAAGTTA
1 TATATAGTATATATATATATATATATACAAGTTA
33061 TATATA-TATATATATATATATATATACAAGTTA
1 TATATAGTATATATATATATATATATACAAGTTA
33094 TAT
1 TAT
33097 TAGCCCGCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATAGTATATATATATATATATATACAAGTTA
Done.