Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012433.1 Corchorus capsularis cultivar CVL-1 contig12454, 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: 52393
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:866 original size:26 final size:27
Alignment explanation
Indices: 817--867 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
807 TTAATAAAAA
*
817 GGGATAATTAAAAAGGAACAAGAGGTT
1 GGGACAATTAAAAAGGAACAAGAGGTT
844 GGGACAATTAAAAAGGAAC-AGAGG
1 GGGACAATTAAAAAGGAACAAGAGG
868 GAGTACCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.49, C:0.06, G:0.31, T:0.14
Consensus pattern (27 bp):
GGGACAATTAAAAAGGAACAAGAGGTT
Found at i:947 original size:2 final size:2
Alignment explanation
Indices: 940--966 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
930 AGTTTAGTAT
940 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
967 TCGAAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4666 original size:21 final size:18
Alignment explanation
Indices: 4629--4667 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
4619 GTTTTGCTTC
4629 GCTTTGCTGTCAAAATTA
1 GCTTTGCTGTCAAAATTA
4647 GCTTATGCATGTCATAAATTA
1 GCTT-TGC-TGTCA-AAATTA
4668 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 5 0.28
21 6 0.33
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (18 bp):
GCTTTGCTGTCAAAATTA
Found at i:6726 original size:6 final size:6
Alignment explanation
Indices: 6717--6741 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6707 TTCTTCCTCT
6717 TCTTCG TCTTCG TCTTCG TCTTCG T
1 TCTTCG TCTTCG TCTTCG TCTTCG T
6742 TTTTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TCTTCG
Found at i:10404 original size:2 final size:2
Alignment explanation
Indices: 10397--10433 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10387 CACTGAAAGA
10397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10434 ATCAATGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16525 original size:15 final size:14
Alignment explanation
Indices: 16502--16531 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
16492 ATGAAAGTTA
16502 AATATTTTTATTTT
1 AATATTTTTATTTT
16516 AATATATTTTATTTT
1 AATAT-TTTTATTTT
16531 A
1 A
16532 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:16953 original size:20 final size:20
Alignment explanation
Indices: 16919--16956 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16909 AGTTTTTTAA
**
16919 AAATATATTTCAATAAAATG
1 AAATATATTAAAATAAAATG
16939 AAATATATTAAAATAAAA
1 AAATATATTAAAATAAAA
16957 ATATCTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATATATTAAAATAAAATG
Found at i:17947 original size:37 final size:37
Alignment explanation
Indices: 17897--17976 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
17887 TTTATTTACA
17897 ATATATATTAATATTCTTGTTTTGTTGTAAAAATAAC
1 ATATATATTAATATTCTTGTTTTGTTGTAAAAATAAC
17934 ATATATATTAATATTCTTGTTTTGTTGTAAAAATAAC
1 ATATATATTAATATTCTTGTTTTGTTGTAAAAATAAC
*
17971 GTATAT
1 ATATAT
17977 TAATATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.49
Consensus pattern (37 bp):
ATATATATTAATATTCTTGTTTTGTTGTAAAAATAAC
Found at i:18389 original size:34 final size:34
Alignment explanation
Indices: 18346--18452 Score: 205
Period size: 34 Copynumber: 3.1 Consensus size: 34
18336 AAGATAAATC
18346 ACATACCACTATCTAAGTGAAATTTTGTTACAAA
1 ACATACCACTATCTAAGTGAAATTTTGTTACAAA
18380 ACATACCACTATCTAAGTGAAATTTTGTTACAAA
1 ACATACCACTATCTAAGTGAAATTTTGTTACAAA
*
18414 ACATACCACTATCTAAGTGAAATTTTGTTACAAT
1 ACATACCACTATCTAAGTGAAATTTTGTTACAAA
18448 ACATA
1 ACATA
18453 AGATAAATCA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (34 bp):
ACATACCACTATCTAAGTGAAATTTTGTTACAAA
Found at i:19395 original size:15 final size:15
Alignment explanation
Indices: 19351--19398 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
19341 TTCCTCCTCA
* *
19351 TCTTCGTCATCATCC
1 TCTTCATCATCATCT
*
19366 TCATCATCATCATCT
1 TCTTCATCATCATCT
*
19381 TCTTCATCTTCATCT
1 TCTTCATCATCATCT
19396 TCT
1 TCT
19399 ATCTCAAGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.02, T:0.46
Consensus pattern (15 bp):
TCTTCATCATCATCT
Found at i:32240 original size:33 final size:33
Alignment explanation
Indices: 32174--32241 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
32164 ATCAGAACTC
* * *
32174 AATGTAACTATCGGATATTGAAGCTCTCTTACA
1 AATGTAACTACCGGATATTGAAACTCTCCTACA
* *
32207 AATGTAATTACCGGATATTGAAACTTTCCTACA
1 AATGTAACTACCGGATATTGAAACTCTCCTACA
32240 AA
1 AA
32242 ATATATAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
AATGTAACTACCGGATATTGAAACTCTCCTACA
Found at i:37071 original size:21 final size:21
Alignment explanation
Indices: 37046--37090 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
37036 AAAACGACGT
*
37046 ACCGAAACCGACAAAACCGAG
1 ACCGAAACCAACAAAACCGAG
*
37067 ACCGAAACCAACAAAACTGAG
1 ACCGAAACCAACAAAACCGAG
37088 ACC
1 ACC
37091 AAATGGATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.33, G:0.16, T:0.02
Consensus pattern (21 bp):
ACCGAAACCAACAAAACCGAG
Found at i:37123 original size:18 final size:19
Alignment explanation
Indices: 37100--37169 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 19
37090 CAAATGGATC
37100 TATATATTAATTTAAATT-
1 TATATATTAATTTAAATTA
* *
37118 TATATATTATAATTATATTA
1 TATATATTA-ATTTAAATTA
**
37138 TATATGATTAATTATAAAAAA
1 TATAT-ATTAATT-TAAATTA
37159 TATATA-TAATT
1 TATATATTAATT
37170 ATATATATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
18 9 0.21
19 12 0.29
20 8 0.19
21 13 0.31
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (19 bp):
TATATATTAATTTAAATTA
Found at i:37192 original size:35 final size:38
Alignment explanation
Indices: 37119--37194 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
37109 ATTTAAATTT
*
37119 ATATATTATAATTATATTATATATGATTAATTATAAAAA
1 ATATATTATAATTATATTATAAATGATT-ATTATAAAAA
37158 ATATA-TATAATTATATATATAAAT-ATT-TTA-AAAAA
1 ATATATTATAATTATAT-TATAAATGATTATTATAAAAA
37193 AT
1 AT
37195 TGGTCGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 7 0.20
36 3 0.09
38 14 0.40
39 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
ATATATTATAATTATATTATAAATGATTATTATAAAAA
Found at i:43133 original size:20 final size:20
Alignment explanation
Indices: 43108--43146 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43098 TTGAACCGCT
43108 TTGTACCGGACTGTTTCGGC
1 TTGTACCGGACTGTTTCGGC
* *
43128 TTGTACTGGCCTGTTTCGG
1 TTGTACCGGACTGTTTCGG
43147 GCGTTTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (20 bp):
TTGTACCGGACTGTTTCGGC
Done.