Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010212.1 Corchorus olitorius cultivar O-4 contig10244, 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: 9500
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:356 original size:165 final size:160
Alignment explanation
Indices: 165--458 Score: 464
Period size: 165 Copynumber: 1.8 Consensus size: 160
155 CCGCGTTAGG
* *
165 TTTTTTTGATTTCTGCACAAAGAATTTTAATTTTAAGAAGGAAAACATGGCAT-AAGGTTTTTTA
1 TTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGAAGGAAAACATGACATAAAGG-TTTTTA
* *
229 ATTTGAAATGAGAGAAAACCTTGAATAAACAAATAGAGCTATTAATTCAAGTGAAAAATATTAAT
65 ATTTG---TG-GAGAAAACATTGAATAAACAAAGAGAGCTATTAATTCAAGTG-AAAATATTAAT
294 TGTAACTGGATATTATCCCTGCACATACGTGTCAGA
125 TGTAACTGGATATTATCCCTGCACATACGTGTCAGA
* *
330 TTTTTTTTATTTCCGCGCAAAGAATTTTAATTTTAAGAAGGAAAACATGACATAAAGGTTTTTAA
1 TTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGAAGGAAAACATGACATAAAGGTTTTTAA
*
395 TTTGTGGATAAAACATTGAATAAACAAAGAGAGCTATTAATTCAAGTGAAAATATTAATTGTAA
66 TTTGTGGAGAAAACATTGAATAAACAAAGAGAGCTATTAATTCAAGTGAAAATATTAATTGTAA
459 TACTATCTCA
Statistics
Matches: 121, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
160 16 0.13
161 39 0.32
162 2 0.02
165 60 0.50
166 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (160 bp):
TTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGAAGGAAAACATGACATAAAGGTTTTTAA
TTTGTGGAGAAAACATTGAATAAACAAAGAGAGCTATTAATTCAAGTGAAAATATTAATTGTAAC
TGGATATTATCCCTGCACATACGTGTCAGA
Found at i:1001 original size:39 final size:39
Alignment explanation
Indices: 934--1050 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
924 ACAATTTGAG
* *
934 GATAACTTCAATAGTAAGGTATAAATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
*
973 GATCACTTTAATAGTAAGGTATAGATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
1012 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
1051 TTGTAATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (39 bp):
GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
Found at i:1008 original size:23 final size:23
Alignment explanation
Indices: 982--1047 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
972 AGATCACTTT
982 AATAGTAAGGTATAGATAAATAA
1 AATAGTAAGGTATAGATAAATAA
*
1005 AATA-TAA-G-ATA-ACT---T-T
1 AATAGTAAGGTATAGA-TAAATAA
1021 AATAGTAAGGTATAGATAAATAA
1 AATAGTAAGGTATAGATAAATAA
1044 AATA
1 AATA
1048 TAATTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 18
0.62 0.04 0.35
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 1 0.03
19 5 0.16
20 5 0.16
21 1 0.03
22 4 0.12
23 8 0.25
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.29
Consensus pattern (23 bp):
AATAGTAAGGTATAGATAAATAA
Found at i:4497 original size:36 final size:36
Alignment explanation
Indices: 4457--4529 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4447 TGCGAGTTAT
4457 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
1 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
4493 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
1 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
4529 C
1 C
4530 ACTCCCACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
Found at i:9087 original size:27 final size:26
Alignment explanation
Indices: 9062--9207 Score: 177
Period size: 27 Copynumber: 5.3 Consensus size: 26
9052 TCAAGGTTAT
*
9062 ATCATATAGATTCAGGCCCAGCGTTAC
1 ATCATATAGATT-AGGCCCAGCATTAC
*
9089 ATCATATAGATTTAGGACCAGCATTAC
1 ATCATATAGA-TTAGGCCCAGCATTAC
*
9116 ATTATCATATA-ATCTTAGGCCTAGCATTAC
1 ---ATCATATAGA--TTAGGCCCAGCATTAC
9146 ATCATATAGACTTAGGCCCAGCATTAC
1 ATCATATAGA-TTAGGCCCAGCATTAC
9173 ATCATATAGACTTAGGCCCAGCATTAC
1 ATCATATAGA-TTAGGCCCAGCATTAC
9200 ATCATATA
1 ATCATATA
9208 CATCATATAA
Statistics
Matches: 107, Mismatches: 6, Indels: 12
0.86 0.05 0.10
Matches are distributed among these distances:
27 81 0.76
28 3 0.03
29 1 0.01
30 22 0.21
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (26 bp):
ATCATATAGATTAGGCCCAGCATTAC
Found at i:9136 original size:57 final size:56
Alignment explanation
Indices: 9061--9207 Score: 203
Period size: 57 Copynumber: 2.7 Consensus size: 56
9051 CTCAAGGTTA
* * *
9061 TATCATATAGAT-TCAGGCCCAGCGTTACATCATATAGATTTAGGACCAGCATTAC
1 TATCATATAGATCTTAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTAC
* *
9116 ATTATCATATA-ATCTTAGGCCTAGCATTACATCATATAGACTTAGGCCCAGCATTAC
1 --TATCATATAGATCTTAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTAC
9173 -ATCATATAGA-CTTAGGCCCAGCATTACATCATATA
1 TATCATATAGATCTTAGGCCCAGCATTACATCATATA
9208 CATCATATAA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
54 32 0.39
55 1 0.01
56 2 0.02
57 47 0.57
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (56 bp):
TATCATATAGATCTTAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTAC
Found at i:9163 original size:84 final size:88
Alignment explanation
Indices: 9062--9243 Score: 250
Period size: 84 Copynumber: 2.1 Consensus size: 88
9052 TCAAGGTTAT
* *
9062 ATCATATAGATTCAGGCCCAGCGTTACATCATATAGATTTAGGACCAGCATT-A-CAT-T-ATCA
1 ATCATATAGATTCAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTAATCATATAATCA
*
9123 TAT-AATCTTAGGCCTAGCATTAC
66 TATAAAT-TTAGGCCCAGCATTAC
*
9146 ATCATATAGACTT-AGGCCCAGCATTACATCATATAGACTTAGGCCCAGCATTACATCATATACA
1 ATCATATAGA-TTCAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTA-ATCATATA-A
9210 TCATATAAATTTAGGCCCAGCATTAC
63 TCATATAAATTTAGGCCCAGCATTAC
9236 ATCATATA
1 ATCATATA
9244 CATCATATAG
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
84 46 0.53
85 2 0.02
86 1 0.01
87 3 0.03
88 1 0.01
90 30 0.35
91 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (88 bp):
ATCATATAGATTCAGGCCCAGCATTACATCATATAGACTTAGGACCAGCATTAATCATATAATCA
TATAAATTTAGGCCCAGCATTAC
Found at i:9224 original size:36 final size:36
Alignment explanation
Indices: 9170--9258 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
9160 GGCCCAGCAT
*
9170 TACATCATATAGACTTAGGCCCAGCATTACATCATA
1 TACATCATATAGATTTAGGCCCAGCATTACATCATA
*
9206 TACATCATATAAATTTAGGCCCAGCATTACATCATA
1 TACATCATATAGATTTAGGCCCAGCATTACATCATA
9242 TACATCATATAGATTTA
1 TACATCATATAGATTTA
9259 ACATCATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.31
Consensus pattern (36 bp):
TACATCATATAGATTTAGGCCCAGCATTACATCATA
Found at i:9264 original size:16 final size:16
Alignment explanation
Indices: 9243--9274 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9233 TACATCATAT
*
9243 ACATCATATAGATTTA
1 ACATCATATAAATTTA
9259 ACATCATATAAATTTA
1 ACATCATATAAATTTA
9275 GGCCCAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (16 bp):
ACATCATATAAATTTA
Found at i:9366 original size:26 final size:27
Alignment explanation
Indices: 9320--9389 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
9310 GGAGTCACCT
* *
9320 GCATCATGTAGTTGCATATTCAATAGG
1 GCATCATATAGCTGCATATTCAATAGG
*
9347 GCATCATATAGCT-CATATTCAGTAGG
1 GCATCATATAGCTGCATATTCAATAGG
*
9373 G--TCATATAGTTGCATAT
1 GCATCATATAGCTGCATAT
9390 ATAGTTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.24
25 5 0.13
26 13 0.34
27 11 0.29
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (27 bp):
GCATCATATAGCTGCATATTCAATAGG
Found at i:9414 original size:63 final size:63
Alignment explanation
Indices: 9319--9452 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 63
9309 AGGAGTCACC
* *
9319 TGCATCATGTAGTTGCATATTCAATAGGGCATCATATAGCTCATATTCAGTAGGGTCATATAGT
1 TGCAT-ATATAGTTGCATATTCAATAGGGCATCATATAACTCATATTCAGTAGGGTCATATAGT
* *
9383 TGCATATATAGTTGTATATTCAATAGTGCATCATATAACTCATATTCAGTAGGGTCATATAGT
1 TGCATATATAGTTGCATATTCAATAGGGCATCATATAACTCATATTCAGTAGGGTCATATAGT
9446 TGCATAT
1 TGCATAT
9453 TCAGTAGGGA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 61 0.92
64 5 0.08
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (63 bp):
TGCATATATAGTTGCATATTCAATAGGGCATCATATAACTCATATTCAGTAGGGTCATATAGT
Found at i:9454 original size:25 final size:25
Alignment explanation
Indices: 9388--9461 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
9378 ATAGTTGCAT
* * *
9388 ATATAGTTGTATATTCAATAGTGCATC
1 ATATAGTTGCATATTCAGTAG-G-GTC
**
9415 ATATAACT-CATATTCAGTAGGGTC
1 ATATAGTTGCATATTCAGTAGGGTC
9439 ATATAGTTGCATATTCAGTAGGG
1 ATATAGTTGCATATTCAGTAGGG
9462 AACATCTGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.21
25 15 0.38
26 10 0.26
27 6 0.15
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (25 bp):
ATATAGTTGCATATTCAGTAGGGTC
Done.