Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019374.1 Corchorus olitorius cultivar O-4 contig19407, 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: 20015
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:178 original size:22 final size:22
Alignment explanation
Indices: 161--217 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
151 CTGTAGTATC
*
161 GTTATTAAAATTTCGTAGGAAT
1 GTTATCAAAATTTCGTAGGAAT
* *
183 GTTATCAAAATTTCATAGGGA-
1 GTTATCAAAATTTCGTAGGAAT
204 GATTATCAAAATTT
1 G-TTATCAAAATTT
218 TATAAGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCGTAGGAAT
Found at i:226 original size:22 final size:22
Alignment explanation
Indices: 184--226 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
174 CGTAGGAATG
*
184 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAAGGAGA
*
206 TTATCAAAATTTTATAAGGAG
1 TTATCAAAATTTCATAAGGAG
227 GTCATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGA
Found at i:15349 original size:2 final size:2
Alignment explanation
Indices: 15342--15379 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15332 GTACCACCAA
15342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15380 TATGCTAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16268 original size:17 final size:16
Alignment explanation
Indices: 16216--16264 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
16206 CACCCCCCAT
*
16216 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
*
16233 ATCATCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
16250 ATCACCAGTGATCAA
1 ATCACCAGTGATCAA
16265 AGATTACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:16990 original size:96 final size:96
Alignment explanation
Indices: 16862--17045 Score: 334
Period size: 96 Copynumber: 1.9 Consensus size: 96
16852 TTTCTTATTT
*
16862 GAATTTACTAAAAAAACTACAGGGCTATTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
1 GAATTTACTAAAAAAACTACAGGGCTACTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
16927 -ATCGATCTCTGATGCAAGAAGAAGAAGAAA
66 AATCGATCTCTGATGCAAGAAGAAGAAGAAA
*
16957 GAATTTACTAAAAAGAACTACAGGGCTACTAAGAACGAAGTTAAATATTAATCAATTAAGAAGGT
1 GAATTTACTAAAAA-AACTACAGGGCTACTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGT
17022 TAATCGATCTCTGATGCAAGAAGA
65 TAATCGATCTCTGATGCAAGAAGA
17046 TTATCAATTT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 14 0.16
96 49 0.58
97 22 0.26
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (96 bp):
GAATTTACTAAAAAAACTACAGGGCTACTAAGAACGAAGTTAAACATTAATCAATTAAGAAGGTT
AATCGATCTCTGATGCAAGAAGAAGAAGAAA
Found at i:18961 original size:180 final size:180
Alignment explanation
Indices: 18653--18998 Score: 611
Period size: 180 Copynumber: 1.9 Consensus size: 180
18643 AAAAGTTATG
18653 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* *
18718 TGATCAATAATGAAAGTTGCCAATTTAATTACTTAAGTAATCTACTATAAAAGCTAAAAAAGTTA
66 TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
18783 TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTTGCCGA
131 TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTTGCCGA
* *
18833 AAAACATTATAGTACTATCTAGATTCAAGTAATCTTACATCCTTATTAATTTTAGTAACTTTTTA
1 AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
* * * *
18898 TGATTAATAATGAAAGTTACCAATTTAATTACTTGAGTAATCTACTAAAAAAGCTATAAAAGTTT
66 TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
*
18963 TTTAAATTGTATTTACCAATCCTTACATTCTTAATA
131 TTAAAATTGTATTTACCAATCCTTACATTCTTAATA
18999 ACATTAGTAA
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 157 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (180 bp):
AAAACATTATAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTTTAGTAACTTTGTA
TGATCAATAATGAAAGTTACCAATTTAATTACTTAAGTAATCTACTAAAAAAGCTAAAAAAGTTA
TTAAAATTGTATTTACCAATCCTTACATTCTTAATATTTTTTTTTGCCGA
Found at i:19498 original size:36 final size:36
Alignment explanation
Indices: 19451--19520 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
19441 TTCAATAACC
* *
19451 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
19487 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
19521 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.