Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014473.1 Corchorus capsularis cultivar CVL-1 contig14494, 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: 39657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1258 original size:51 final size:51
Alignment explanation
Indices: 1171--1276 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
1161 ACATATCAAC
* *
1171 TATAAATATGAATCACTGCCTTTGCACTTTATAACTTTTATCTTTCTATTAA
1 TATAAATAT-AATCACTGCCTCTGCACTTTACAACTTTTATCTTTCTATTAA
*
1223 TATAAATAT-ATCCACTGCCTCTGCATTTTACAACTTTTATCTTTCTATTAA
1 TATAAATATAAT-CACTGCCTCTGCACTTTACAACTTTTATCTTTCTATTAA
1274 TAT
1 TAT
1277 CCCAACATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 2 0.04
51 39 0.78
52 9 0.18
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (51 bp):
TATAAATATAATCACTGCCTCTGCACTTTACAACTTTTATCTTTCTATTAA
Found at i:5086 original size:40 final size:40
Alignment explanation
Indices: 5039--5119 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5029 CGTGTTTCGT
5039 ATCATAATCATGTTAAAGACACGATTGACACGTTTATGAC
1 ATCATAATCATGTTAAAGACACGATTGACACGTTTATGAC
5079 ATCATAATCATGTTAAAGACACGATTGACACGTTTATGAC
1 ATCATAATCATGTTAAAGACACGATTGACACGTTTATGAC
5119 A
1 A
5120 CGAGTGACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (40 bp):
ATCATAATCATGTTAAAGACACGATTGACACGTTTATGAC
Found at i:5121 original size:20 final size:20
Alignment explanation
Indices: 5056--5135 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
5046 TCATGTTAAA
5056 GACACGATTGACACGTTTAT
1 GACACGATTGACACGTTTAT
* * * *
5076 GACATC-A-TAATCATGTTAAA
1 GACA-CGATTGA-CACGTTTAT
5096 GACACGATTGACACGTTTAT
1 GACACGATTGACACGTTTAT
*
5116 GACACGAGTGACACGCTTTA
1 GACACGATTGACACG-TTTA
5136 ATAACCGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 36 0.78
21 7 0.15
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (20 bp):
GACACGATTGACACGTTTAT
Found at i:7842 original size:57 final size:58
Alignment explanation
Indices: 7774--7882 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 58
7764 TATCAACTAT
* *
7774 AAATATGAATCATTGACTTTGCACTTTACAACTTTTATCTTTCTATTAATATAAAATA
1 AAATATGAATCACTGACTCTGCACTTTACAACTTTTATCTTTCTATTAATATAAAATA
* *
7832 AAATAT-AATCACTGTCTCTGCATTTTACAACTTTTATCTTTCTATTAATAT
1 AAATATGAATCACTGACTCTGCACTTTACAACTTTTATCTTTCTATTAATAT
7883 CCCAACATGG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 41 0.87
58 6 0.13
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.45
Consensus pattern (58 bp):
AAATATGAATCACTGACTCTGCACTTTACAACTTTTATCTTTCTATTAATATAAAATA
Found at i:23255 original size:19 final size:19
Alignment explanation
Indices: 23209--23265 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
23199 CATTGCTCTA
* *
23209 ATAATCTCATCTGTACAGT
1 ATAATCTAATCTGTACAAT
23228 ACTTAATCTAATCTGTACAAT
1 A--TAATCTAATCTGTACAAT
23249 ATAATCTAATCTGTACA
1 ATAATCTAATCTGTACA
23266 GTTGCTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (19 bp):
ATAATCTAATCTGTACAAT
Found at i:31248 original size:31 final size:31
Alignment explanation
Indices: 31161--31314 Score: 164
Period size: 31 Copynumber: 5.0 Consensus size: 31
31151 TTTTGTGCAC
* * **
31161 GTGGCATGCCACGTGCCACTTTTTGAAACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
31192 GTGGCATGTCACGTGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
31223 ATGGCGTGCCACATGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* ** * * *
31254 GTAGCGTGATATGTGTCACTTTCTGGTATAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
31285 GTGGTGTGCCACATGTCACTTTTTGGTACA
1 GTGGCGTGCCACGTGTCACTTTTTGGTACA
31315 CGTTGCATGT
Statistics
Matches: 99, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (31 bp):
GTGGCGTGCCACGTGTCACTTTTTGGTACAT
Found at i:31490 original size:2 final size:2
Alignment explanation
Indices: 31483--31511 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31473 TATTTATGCC
31483 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31512 ATTATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32346 original size:70 final size:70
Alignment explanation
Indices: 32270--32499 Score: 280
Period size: 70 Copynumber: 3.1 Consensus size: 70
32260 TAACTAAAAT
* *
32270 AGTAAAATTGTAAAATATAATAGTTATAAGGATGTTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
32335 AGTTG
66 AGTTG
32340 AGTAAAATAGTAAAATGGTAAAATATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAA
1 AGT-AAA-A-T----T-GT-AAA-AT-ATAATAGTTATAAGGATATTAGATTTAATTATATAAAA
*
32405 ATAGAGTTTTTAATTG
55 ATAGAGTTTTTAGTTG
* * * * * *
32421 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
32486 AGTTG
66 AGTTG
32491 AGTAAAATT
1 AGTAAAATT
32500 ATTAAAACCT
Statistics
Matches: 138, Mismatches: 11, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
70 59 0.43
71 5 0.04
72 4 0.03
73 3 0.02
77 1 0.01
78 3 0.02
79 4 0.03
80 5 0.04
81 54 0.39
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:32394 original size:81 final size:78
Alignment explanation
Indices: 32264--32498 Score: 326
Period size: 81 Copynumber: 3.1 Consensus size: 78
32254 TTTTTTTAAC
* *
32264 TAAAATAGTAAAATTGTAAAAT-ATAATAGTTATAAGGATGTTAGATTTAATTATATAAAAATTG
1 TAAAATAGTAAAA-TGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAG
32328 AGTTTTTAGTTGAG
65 AGTTTTTAGTTGAG
32342 TAAAATAGTAAAATGGTAAAATATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAT
1 TAAAATAGTAAAAT-GT-AAA-ATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAAT
*
32407 AGAGTTTTTAATTGAG
63 AGAGTTTTTAGTTGAG
* *
32423 TAAAATAGTAAAA--TAAAATAAT--TA--TA-AA-GATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
32480 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
32493 TAAAAT
1 TAAAAT
32499 TATTAAAACC
Statistics
Matches: 147, Mismatches: 6, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
70 45 0.31
71 2 0.01
72 2 0.01
74 2 0.01
76 5 0.03
77 4 0.03
78 16 0.11
79 3 0.02
80 2 0.01
81 66 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (78 bp):
TAAAATAGTAAAATGTAAAATAATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:32610 original size:6 final size:6
Alignment explanation
Indices: 32593--32635 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
32583 GTACTTTTTA
32593 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT
32636 TAATTAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Done.