Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010922.1 Corchorus olitorius cultivar O-4 contig10954, 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: 76084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:65 original size:2 final size:2
Alignment explanation
Indices: 58--88 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48 TAGGTAGACG
58 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 A
89 GTCTTCTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1454 original size:30 final size:29
Alignment explanation
Indices: 1409--1476 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
1399 TTAGTTTTAC
* *
1409 TATTGATTAAATAATTAAAATGGTATTGAT
1 TATTAATTAAATAATTAAAATGG-AGTGAT
*
1439 TATTAATTAATTAATTAAAATGGAGTGAT
1 TATTAATTAAATAATTAAAATGGAGTGAT
1468 TAATTAATT
1 T-ATTAATT
1477 TATGATGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 6 0.18
30 28 0.82
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (29 bp):
TATTAATTAAATAATTAAAATGGAGTGAT
Found at i:5969 original size:15 final size:16
Alignment explanation
Indices: 5949--5981 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5939 CTCCAATATT
5949 AGAAAGA-AAAGAAAA
1 AGAAAGATAAAGAAAA
*
5964 AGAAAGATAAATAAAA
1 AGAAAGATAAAGAAAA
5980 AG
1 AG
5982 GACATCGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AGAAAGATAAAGAAAA
Found at i:7659 original size:63 final size:63
Alignment explanation
Indices: 7560--7684 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
7550 GAGCTACACC
*
7560 GAATATAAACCATATTAACAAGAATAGAAGAACCCAGCCGCCAAAACAATCCAATTAATCCCT
1 GAATATAAACCATATTAACAAGAATAGAAGAACCCAGCCCCCAAAACAATCCAATTAATCCCT
*
7623 GAATATAAACCATGTTAACAAGAATAGAAGAACCCAGCCCCCAAAACAATCCAATTAATCCC
1 GAATATAAACCATATTAACAAGAATAGAAGAACCCAGCCCCCAAAACAATCCAATTAATCCC
7685 CAAAAAGGGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.47, C:0.26, G:0.10, T:0.17
Consensus pattern (63 bp):
GAATATAAACCATATTAACAAGAATAGAAGAACCCAGCCCCCAAAACAATCCAATTAATCCCT
Found at i:20407 original size:13 final size:13
Alignment explanation
Indices: 20389--20413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20379 AATCACTTGA
20389 ATTAACCATTTGG
1 ATTAACCATTTGG
20402 ATTAACCATTTG
1 ATTAACCATTTG
20414 TGGGTCTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTAACCATTTGG
Found at i:25193 original size:2 final size:2
Alignment explanation
Indices: 25182--25220 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
25172 TGACTTTTCC
25182 AT AT -T 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 AT
25221 TGATGGAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30879 original size:20 final size:21
Alignment explanation
Indices: 30854--30901 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
30844 AGCTTATTTT
30854 CCGTTAACAAATTACTTAAC-
1 CCGTTAACAAATTACTTAACA
*
30874 CCGTTAGCAAATTACTTAACA
1 CCGTTAACAAATTACTTAACA
30895 CCGTTAA
1 CCGTTAA
30902 TTTTACCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (21 bp):
CCGTTAACAAATTACTTAACA
Found at i:31470 original size:21 final size:20
Alignment explanation
Indices: 31444--31502 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
31434 GCTGCTCTAA
*
31444 TAATCTCATCTGTACAGTATC
1 TAATCTCATTTGTACAGT-TC
* *
31465 TAATCTAATTTGTACAG-TG
1 TAATCTCATTTGTACAGTTC
31484 TAATCTCATTTGTACAGTT
1 TAATCTCATTTGTACAGTT
31503 GATAAACAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 17 0.52
20 1 0.03
21 15 0.45
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
TAATCTCATTTGTACAGTTC
Found at i:37624 original size:18 final size:19
Alignment explanation
Indices: 37573--37624 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
37563 AATGTGATAT
37573 TTGTA-TTATTAATATGTA
1 TTGTATTTATTAATATGTA
* * *
37591 TTATATTAATTTAATA-GTG
1 TTGTATTTA-TTAATATGTA
37610 TTGTATTTATTAATA
1 TTGTATTTATTAATA
37625 ATATACACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
TTGTATTTATTAATATGTA
Found at i:60764 original size:29 final size:29
Alignment explanation
Indices: 60732--60802 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
60722 AAAATATCCC
*
60732 TTTTTTTATTTTTCCTTTAGACTA-TTACA
1 TTTTTTTATTTTT-CTTTAGACAAGTTACA
* * *
60761 TTTTTTTAATTTTCTTTGGAGAAGTTACA
1 TTTTTTTATTTTTCTTTAGACAAGTTACA
*
60790 TTTTTTAATTTTT
1 TTTTTTTATTTTT
60803 ATTATCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.63
Consensus pattern (29 bp):
TTTTTTTATTTTTCTTTAGACAAGTTACA
Found at i:60777 original size:28 final size:30
Alignment explanation
Indices: 60732--60801 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
60722 AAAATATCCC
* *
60732 TTTTTTTATTTTTCCTTTAGACTA-TTACA
1 TTTTTTTAATTTTCCTTTAGACAAGTTACA
* *
60761 TTTTTTTAATTTT-CTTTGGAGAAGTTACA
1 TTTTTTTAATTTTCCTTTAGACAAGTTACA
60790 -TTTTTTAATTTT
1 TTTTTTTAATTTT
60802 TATTATCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTTTTAATTTTCCTTTAGACAAGTTACA
Found at i:62215 original size:25 final size:24
Alignment explanation
Indices: 62194--62240 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
62184 TTACATTTAC
62194 ATTT-ACATTTGTAAAAGACA-TT
1 ATTTAACATTTGTAAAAGACATTT
62216 ATTTCAAACATTTGTAAAAGACATT
1 ATTT--AACATTTGTAAAAGACATT
62241 AAAGTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
25 16 0.76
26 1 0.05
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
ATTTAACATTTGTAAAAGACATTT
Found at i:72435 original size:6 final size:6
Alignment explanation
Indices: 72426--72452 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
72416 CAGTATGTTT
72426 TCTTTC TCTTTC TCTTTC TCTTTC TCT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCT
72453 ATTTTGCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Done.