Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020636.1 Corchorus olitorius cultivar O-4 contig20669, 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: 19697
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:979 original size:8 final size:8
Alignment explanation
Indices: 966--997 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
956 CATTTCCTTC
966 TTCTTTTT
1 TTCTTTTT
974 TTCTTTTT
1 TTCTTTTT
982 TT-TTTTT
1 TTCTTTTT
989 TTCTTTTT
1 TTCTTTTT
997 T
1 T
998 GCCTACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTCTTTTT
Found at i:987 original size:15 final size:15
Alignment explanation
Indices: 969--997 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
959 TTCCTTCTTC
969 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
984 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
998 GCCTACACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (15 bp):
TTTTTTTCTTTTTTT
Found at i:4396 original size:4 final size:4
Alignment explanation
Indices: 4379--4565 Score: 61
Period size: 4 Copynumber: 47.0 Consensus size: 4
4369 ATAGGTTTTT
4379 TAAA -AAA T-AA TAAA TAAA TAAA TAAA TAAAA TAGGAA TAGAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TA--AA TA-A-A TAAA
* ** ** * * *
4426 TAGA TAAA TAGG TAGG TAAA -AAA -AAG TAGA TAATA GTAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA
** * * * *
4474 T-AA TAGC TAAA TTAA TAAA TAAA -AGGA TAAA T-AG TAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA
** * *
4520 T-AA TAGT TAAA TTAA TAAA TAAA -AATA TAAA T-AG TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA
4566 AAAAATCTTT
Statistics
Matches: 134, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
3 22 0.16
4 90 0.67
5 12 0.09
6 10 0.07
ACGTcount: A:0.64, C:0.01, G:0.11, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:4502 original size:27 final size:27
Alignment explanation
Indices: 4462--4565 Score: 93
Period size: 27 Copynumber: 4.1 Consensus size: 27
4452 TAGATAATAG
*
4462 TAAATAAATAGAT-AATAGCTAAATTAA
1 TAAATAAATAGATAAATAG-TAAATAAA
4489 TAAATAAA-AGGATAAATAGTAAATAAA
1 TAAATAAATA-GATAAATAGTAAATAAA
* *
4516 TAGAT-AATAGTTAAAT--T-AATAAA
1 TAAATAAATAGATAAATAGTAAATAAA
4539 T-AA-AAAT--ATAAATAGTAAATAAA
1 TAAATAAATAGATAAATAGTAAATAAA
4562 TAAA
1 TAAA
4566 AAAAATCTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
20 5 0.08
22 5 0.08
23 14 0.22
24 3 0.05
26 9 0.14
27 23 0.36
28 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAATAAATAGATAAATAGTAAATAAA
Found at i:4514 original size:46 final size:46
Alignment explanation
Indices: 4453--4563 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
4443 AAAAAAAAGT
4453 AGAT-AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
* *
4498 GGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
*
4544 ATATAAATAGTAAATAAATA
1 AGATAAATAGTAAATAAATA
4564 AAAAAAATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 3 0.05
46 58 0.95
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (46 bp):
AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
Found at i:13343 original size:2 final size:2
Alignment explanation
Indices: 13293--13328 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13283 AGCATACTGC
13293 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
13329 TGATTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17091 original size:22 final size:22
Alignment explanation
Indices: 17049--17092 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17039 TATTCATATG
* *
17049 AAATTATGATAATCTTCCTATT
1 AAATTATAATAATCTACCTATT
17071 AAATTATAATAAT-TACACTATT
1 AAATTATAATAATCTAC-CTATT
17093 TTTGATGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTATAATAATCTACCTATT
Found at i:17461 original size:57 final size:57
Alignment explanation
Indices: 17373--17488 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
17363 GGTGTTGCTA
*
17373 GGTTTTGTTGTGTGAAAGAGATTTTTGAGAGCAAAGTATCTGTATAATGTGAATAAT
1 GGTTTTGTTGTGTGAAAAAGATTTTTGAGAGCAAAGTATCTGTATAATGTGAATAAT
* * *
17430 GGTTTTGTTGTGTGAAAAAGATTTTTTAGAGCAAAGTCTGTGTATAATGTGAATAAT
1 GGTTTTGTTGTGTGAAAAAGATTTTTGAGAGCAAAGTATCTGTATAATGTGAATAAT
17487 GG
1 GG
17489 AAGAATGATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (57 bp):
GGTTTTGTTGTGTGAAAAAGATTTTTGAGAGCAAAGTATCTGTATAATGTGAATAAT
Found at i:17673 original size:25 final size:24
Alignment explanation
Indices: 17625--17693 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 24
17615 TTTGGTGGGT
17625 GTGTTTA-TGGTATACCTTTGATGG
1 GTGTTTACT-GTATACCTTTGATGG
17649 GTGTTTACTGTATACCCTTTGATGG
1 GTGTTTACTGTATA-CCTTTGATGG
17674 GTGTTTAC-GTTATACCTTTG
1 GTGTTTACTG-TATACCTTTG
17694 GTTGGTACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
24 19 0.45
25 23 0.55
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.46
Consensus pattern (24 bp):
GTGTTTACTGTATACCTTTGATGG
Found at i:18633 original size:16 final size:15
Alignment explanation
Indices: 18595--18636 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
18585 ACAGAGATTG
*
18595 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
18610 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
18625 ACTAGAAAACAA
1 AC-AGAAAACAA
18637 AGAAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.