Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009807.1 Corchorus olitorius cultivar O-4 contig09839, 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: 2382
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Found at i:72 original size:41 final size:40
Alignment explanation
Indices: 10--379 Score: 428
Period size: 41 Copynumber: 9.2 Consensus size: 40
1 TTGAGGGCC
10 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAATTTG
* *
51 AATGTGAATGAAGGCATGTTCAATGTCATTTGGG--A-TTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTG
*
89 AATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAA-TTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTG
* ** *
128 GATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTG
* * * *
168 GATGTGAATCAAGGCTAGTTCAATGTCAATT-GGAAAATTC
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTG
* * *
208 AGATGTGAATAAGGCAAGTTCAATGTTAATT-GGAAAATTC
1 A-ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTG
* *
248 AGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTG
1 A-ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTG
* *
289 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGTAAAGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTG
* ** * *
330 GATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTA
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAATTTG
371 AATGTGAAT
1 AATGTGAAT
380 GTGCCGCGTA
Statistics
Matches: 292, Mismatches: 29, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
37 23 0.08
38 12 0.04
39 36 0.12
40 86 0.29
41 135 0.46
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAATTTG
Found at i:231 original size:34 final size:34
Alignment explanation
Indices: 193--271 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 34
183 TAGTTCAATG
193 TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
1 TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
227 TCAATGTTAATTGGAAAATTCAGATGTGAATAAGGCAAGT
1 TC------AATTGGAAAATTCAGATGTGAATAAGGCAAGT
267 TCAAT
1 TCAAT
272 GTTAATTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
34 5 0.13
40 34 0.87
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (34 bp):
TCAATTGGAAAATTCAGATGTGAATAAGGCAAGT
Found at i:280 original size:121 final size:118
Alignment explanation
Indices: 11--379 Score: 483
Period size: 121 Copynumber: 3.1 Consensus size: 118
1 TTGAGGGCCA
* * *
11 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGAATGTGAATGAAGGCATGTTCAATG
1 ATGTGAA-TAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCA-GTTCAATG
* * * * * *
76 TCATTTGG--GATT-GAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTGG
64 TCAATTGGAAAATTAG-ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTAG
* *
129 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGGATGTGAATCAAGGCTAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGC-AGTTCAATGT
194 CAATTGGAAAATTCAGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTCAG
65 CAATTGGAAAATT-AGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATT-AG
250 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGC-AGTTCAATGT
* * * * *
315 CAATTGGTAAAGTTGGATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTAA
65 CAATTGG-AAAATTAGATGTGAAT-AAGGCAAGTTCAATGTTAATT-GGAAAATTAG
372 ATGTGAAT
1 ATGTGAAT
380 GTGCCGCGTA
Statistics
Matches: 223, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
117 57 0.26
118 8 0.04
119 3 0.01
120 34 0.15
121 80 0.36
122 34 0.15
123 7 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (118 bp):
ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAGTTCAATGTC
AATTGGAAAATTAGATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTAG
Found at i:1974 original size:337 final size:329
Alignment explanation
Indices: 1034--2379 Score: 1596
Period size: 337 Copynumber: 4.1 Consensus size: 329
1024 CTAAAAATGC
** * * * *
1034 GTTTCGATTTAATTAGAAATGTATT-GTGGCAAAATATGAAAAAACGATATTAGAAGCGTGAAAA
1 GTTTCGATTTAATTAGAAATAAATTCG-AGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** ** * *
1098 ACCCTAAAATAATTTTGGC-TCTGAATTATATAATTTTTCTGAGTATTATGGC-AAAAATTGGGG
65 ACATTAAAATTTTTTTTGCGT-TGAATTATATGATTTTTCTGAGTATTATGGCAAAAAATTGGGG
* * * **
1161 AAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCAAAATCGTGTACATCACGGTTTTTTGC
129 AAAA-ATTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTCTACATCACGGTTTTCGGC
* * *
1226 TGAAAACGCGTTTCGGGGCCCTAACTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTCGAAAT
193 TAAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAAT
* * * * * **
1291 ATTTGTATTCATCAAACCAAATCAT-AGCCACAATAGG-TTTA-AGGATTTATTTTTACTTGTAT
258 ATATGTATTCATCTAACCAAATCTTCAGCCA-TATTGGATTTACA-GATTTATTTTTACGAGTAT
1353 CTGAATCTT
321 CTGAATCTT
*
1362 GTTTCGATTTAATTAGAAATAAATTC-AGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAA
1 GTTTCGATTTAATTAGAAATAAATTCGAGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAA
* * * * ** *
1426 ACCCTT--CATTGTGTATTGATTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGG
65 A-CATTAAAATT-TTTTTTGCGTTGAATTATATGATTTTTCTGAGTATTATGGCAAAAAATTGGG
* *
1489 GAAAATATTTTCGGGTCAGTTTTTTGCAAAATTTTATCCGAAATCGTGT--A-CACGGTGTTT-G
128 GAAAA-ATTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTCTACATCACGGT-TTTCG
* * *
1550 GCTGAAAACGGGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGAATCCTCGAA
191 GCTAAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAA
* * * *
1615 ATATATGTTTTCATCTAACCAAAT-TTCAGCCATGTTGGATTTACAGATTTGTTTTTACGAGGAT
256 ATATATGTATTCATCTAACCAAATCTTCAGCCATATTGGATTTACAGATTTATTTTTACGAGTAT
1679 CTGAATCTT
321 CTGAATCTT
* *
1688 GTTTCCATTTAATTAGAAATAAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
1 GTTTCGATTTAATTAGAAATAAATTC-GAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* *
1753 ACATTAAAATTTTTTTTGCGTTGAATTATATGATTTTTCTGAGTGTTGTGGCAAAAAATTGGGGA
65 ACATTAAAATTTTTTTTGCGTTGAATTATATGATTTTTCTGAGTATTATGGCAAAAAATTGGGGA
*
1818 AAAACTTTTCGGGTCAGTTTTTTTTGCAAAATTTTAGCCGAAATCAAGTACTAACCATAACGGTT
130 AAAA-TTTTCGGGTCAG--TTTTTTGCAAAATTTTAGCCGAAATC--GT-CT-A-CATCACGGTT
* * *
1883 TTCGGTTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCTT
187 TTCGGCTAAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * * * *
1948 CGAAATATCTGTTTTCATCTAACCAAATC-TCAGCCATGTTGGATTTACGGATTTATTTTTACTA
252 CGAAATATATGTATTCATCTAACCAAATCTTCAGCCATATTGGATTTACAGATTTATTTTTACGA
*
2012 GTATTTGAATCTT
317 GTATCTGAATCTT
*
2025 GTTTCGATTTAATTAGAAATAAATT-GAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
1 GTTTCGATTTAATTAGAAATAAATTCGAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
* *
2089 CATTAAATTTTTTTTTTTGCGTTGAATTATATGATTTTTCTGAGTATTATGGCACAAAATTGGGG
66 CATTAAA--ATTTTTTTTGCGTTGAATTATATGATTTTTCTGAGTATTATGGCAAAAAATTGGGG
** *
2154 AAAAA-AATCGGGTCAGTTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGG-TTT
129 AAAAATTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATC--GT-CT-A-CATCACGGTTTT
* * ** * * *
2217 CTGGTTAAAAATGCGTTTCGGTTCCCTGACTCAGTTTTGCATTATTTTTGGAAGAAAGACTTCTC
189 C-GGCTAAAAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTC
* * * * * *
2282 GAAATATATAG-ATTAATGTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
253 GAAATATAT-GTATTCATCTAACCAAATCT-TCAGCCATATTGGATTTACAGATTTATTTTTACG
2346 AGTATCTGAATCTT
316 AGTATCTGAATCTT
*
2360 GTTTCGATTTCATTAGAAAT
1 GTTTCGATTTAATTAGAAAT
2380 GTA
Statistics
Matches: 894, Mismatches: 91, Indels: 59
0.86 0.09 0.06
Matches are distributed among these distances:
325 4 0.00
326 150 0.17
327 104 0.12
328 94 0.11
329 85 0.10
331 2 0.00
332 5 0.01
333 118 0.13
334 1 0.00
335 115 0.13
336 4 0.00
337 212 0.24
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (329 bp):
GTTTCGATTTAATTAGAAATAAATTCGAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
CATTAAAATTTTTTTTGCGTTGAATTATATGATTTTTCTGAGTATTATGGCAAAAAATTGGGGAA
AAATTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTCTACATCACGGTTTTCGGCTAA
AAACGCGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATA
TGTATTCATCTAACCAAATCTTCAGCCATATTGGATTTACAGATTTATTTTTACGAGTATCTGAA
TCTT
Done.