Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018525.1 Corchorus olitorius cultivar O-4 contig18558, 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: 31915
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:2560 original size:15 final size:16
Alignment explanation
Indices: 2529--2563 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2519 TCACTTTGCT
2529 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
2545 TTGTTTTCT-TTTTAA
1 TTGTTTTCTAGTTTAA
2560 TTGT
1 TTGT
2564 GATTGTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:6460 original size:18 final size:18
Alignment explanation
Indices: 6426--6466 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
6416 TTAATGCTGA
*
6426 AATTATTAAATATATAAT
1 AATTATTAAATAAATAAT
6444 AATTATT--ATAAA-AAT
1 AATTATTAAATAAATAAT
6459 AATTATTA
1 AATTATTA
6467 TCTTTCCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
18 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTAAATAAATAAT
Found at i:10048 original size:85 final size:86
Alignment explanation
Indices: 9959--10126 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 86
9949 TAAAAATTCT
* * *
9959 AATATATATAAG-TTTTTAATTAAAATAGTAAAAT-AGTAAAAATTAATTAGTTATAAGGATATT
1 AATATATATAAGTTTTTTAATTAAAATAGTAAAATGA-TAAAAATAAAATAGGTATAAGGATATT
10022 AGATTGAATTAAATAAAAATAG
65 AGATTGAATTAAATAAAAATAG
*
10044 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTA
1 AATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTA
*
10109 GATTTAATTAAATAAAAA
66 GATTGAATTAAATAAAAA
10127 ATATAGTTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 11 0.14
86 64 0.84
87 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.36
Consensus pattern (86 bp):
AATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTA
GATTGAATTAAATAAAAATAG
Found at i:10202 original size:216 final size:216
Alignment explanation
Indices: 9828--10260 Score: 749
Period size: 216 Copynumber: 2.0 Consensus size: 216
9818 TGAAAATTCT
*
9828 AATATATCTAAGTTTTTTAATTAAAATAGTAATATAATAAAAATAAAATAGGTATAAGGATATCA
1 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATAATAAAAATAAAATAGGTATAAGGATATCA
* *
9893 GATTTAATTAAATAAAAAATAGAGTTTTTAATTAAGTAAGACTATAAAAGTATATTTAAAAATTC
66 GATTTAATTAAATAAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAAGTATATTGAAAAATTC
* * *
9958 TAATATATATAAGTTTTTAATTAAAATAGTAAAATAGTAAAAATTAATTAGTTATAAGGATATTA
131 TAATATATATAAGTTCTTAATTAAAATAGTAAAATAGTAAAAATTAAATAGTTATAAGGACATTA
*
10023 GATTGAATTAAATAAAAATAG
196 GATTAAATTAAATAAAAATAG
* *
10044 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTA
1 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATAATAAAAATAAAATAGGTATAAGGATATCA
* *
10109 GATTTAATTAAATAAAAAATATAGTTTTTAGTTAAGTAAAACTATAAAAGTATATTGAAAAATTC
66 GATTTAATTAAATAAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAAGTATATTGAAAAATTC
*
10174 TAATATATATAAGTTCTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGACATTA
131 TAATATATATAAGTTCTTAATTAAAATAGTAAAATAGTAAAAATTAAATAGTTATAAGGACATTA
*
10239 GATTAAATTAAATAACAATAG
196 GATTAAATTAAATAAAAATAG
10260 A
1 A
10261 GATTTTAGTT
Statistics
Matches: 204, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
216 204 1.00
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (216 bp):
AATATATCTAAGTTTTTTAATTAAAATAGTAAAATAATAAAAATAAAATAGGTATAAGGATATCA
GATTTAATTAAATAAAAAATAGAGTTTTTAATTAAGTAAAACTATAAAAGTATATTGAAAAATTC
TAATATATATAAGTTCTTAATTAAAATAGTAAAATAGTAAAAATTAAATAGTTATAAGGACATTA
GATTAAATTAAATAAAAATAG
Found at i:10223 original size:130 final size:130
Alignment explanation
Indices: 10044--10288 Score: 375
Period size: 130 Copynumber: 1.9 Consensus size: 130
10034 ATAAAAATAG
* * *
10044 AATATATCTAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTA
1 AATATATATAAGTTTCTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTA
* * *
10109 GATTTAATTAAATAAAAAATATAGTTTTTAGTTAAGTAAAACTATAAAAGTATATTGAAAAATTC
66 GATTAAATTAAAT-AAAAATAGAGATTTTAGTTAAGTAAAACTATAAAAGTATATTGAAAAATTC
10174 T
130 T
* * *
10175 AATATATATAAG-TTCTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGACATTA
1 AATATATATAAGTTTCTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTA
* *
10239 GATTAAATTAAATAACAATAGAGATTTTAGTTGAGTAAAACTATAAAAGT
66 GATTAAATTAAATAAAAATAGAGATTTTAGTTAAGTAAAACTATAAAAGT
10289 TTAAACAATA
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
129 33 0.32
130 59 0.57
131 11 0.11
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.35
Consensus pattern (130 bp):
AATATATATAAGTTTCTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTA
GATTAAATTAAATAAAAATAGAGATTTTAGTTAAGTAAAACTATAAAAGTATATTGAAAAATTCT
Found at i:10314 original size:130 final size:130
Alignment explanation
Indices: 10060--10314 Score: 343
Period size: 130 Copynumber: 2.0 Consensus size: 130
10050 TCTAAGTTTT
* *
10060 TTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAA
1 TTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTAGATTAAATTAAATAAA
* * *** * *
10125 AAATATAGTTTTTAGTTAAGTAAAACTATAAAAGTATATTGAAAAATTCTAATATATATAAGTTC
66 AAATAGAGATTTTAGTTAAGTAAAACTATAAAAGTATAAACAAAAATTCTAAGAAATATAAGTTC
* * *
10190 TTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGACATTAGATTAAATTAAAT-AA
1 TTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTAGATTAAATTAAATAAA
* * *
10254 CAATAGAGATTTTAGTTGAGTAAAACTATAAAAGTTTAAACAATAACATT-TAAGAAATATA
66 AAATAGAGATTTTAGTTAAGTAAAACTATAAAAGTATAAACAA-AA-ATTCTAAGAAATATA
10315 TTCGAAAATT
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 37 0.34
130 68 0.63
131 3 0.03
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (130 bp):
TTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGACATTAGATTAAATTAAATAAA
AAATAGAGATTTTAGTTAAGTAAAACTATAAAAGTATAAACAAAAATTCTAAGAAATATAAGTTC
Found at i:19973 original size:16 final size:16
Alignment explanation
Indices: 19952--19984 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19942 TGTACACAAT
*
19952 TAGGGATCTCTCTCTC
1 TAGGGATCTATCTCTC
19968 TAGGGATCTATCTCTC
1 TAGGGATCTATCTCTC
19984 T
1 T
19985 TTTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.39
Consensus pattern (16 bp):
TAGGGATCTATCTCTC
Found at i:24323 original size:31 final size:31
Alignment explanation
Indices: 24285--24348 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
24275 AAGCAATCAC
24285 AACAACATTCAAATATAAGATGCAACGATGA
1 AACAACATTCAAATATAAGATGCAACGATGA
24316 AACAACATTCAAATATAAGATGCAACGATGA
1 AACAACATTCAAATATAAGATGCAACGATGA
24347 AA
1 AA
24349 AGAGCTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (31 bp):
AACAACATTCAAATATAAGATGCAACGATGA
Found at i:30362 original size:20 final size:20
Alignment explanation
Indices: 30337--30406 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
30327 TTCTGCAAAG
30337 TTCAATAATGGAAGACAAGC
1 TTCAATAATGGAAGACAAGC
***
30357 TTCAATAATGCTCTG-CAAAG-
1 TTCAATAATG-GAAGAC-AAGC
30377 TTCAATAATGGAAGACAAGC
1 TTCAATAATGGAAGACAAGC
30397 TTCAATAATG
1 TTCAATAATG
30407 CTCTGCAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.10
20 32 0.80
21 4 0.10
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (20 bp):
TTCAATAATGGAAGACAAGC
Found at i:30372 original size:40 final size:40
Alignment explanation
Indices: 30328--30416 Score: 178
Period size: 40 Copynumber: 2.2 Consensus size: 40
30318 CAAGGGAATT
30328 TCTGCAAAGTTCAATAATGGAAGACAAGCTTCAATAATGC
1 TCTGCAAAGTTCAATAATGGAAGACAAGCTTCAATAATGC
30368 TCTGCAAAGTTCAATAATGGAAGACAAGCTTCAATAATGC
1 TCTGCAAAGTTCAATAATGGAAGACAAGCTTCAATAATGC
30408 TCTGCAAAG
1 TCTGCAAAG
30417 ATAGTTCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (40 bp):
TCTGCAAAGTTCAATAATGGAAGACAAGCTTCAATAATGC
Done.