Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018517.1 Corchorus olitorius cultivar O-4 contig18550, 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: 33375
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:6297 original size:2 final size:2
Alignment explanation
Indices: 6290--6332 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6280 TACATAAATG
6290 AT AT 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 AT AT
6332 A
1 A
6333 CACGTTTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8753 original size:173 final size:173
Alignment explanation
Indices: 8457--8801 Score: 645
Period size: 173 Copynumber: 2.0 Consensus size: 173
8447 TATTTGAAAA
8457 ACCCAGAAAATTTACCAAAAACCCCTTTTAAGGATCGATGAGGAGGCTCCATTTGAACTTTTCTT
1 ACCCAGAAAATTTACCAAAAACCCCTTTTAAGGATCGATGAGGAGGCTCCATTTGAACTTTTCTT
*
8522 ATCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGTAAGT
66 ATCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGT
8587 TCCTATCCTTGAGCCCTTTTTTGTAATTATCCTTTCTTTTCAG
131 TCCTATCCTTGAGCCCTTTTTTGTAATTATCCTTTCTTTTCAG
* * *
8630 ACCCAGGAAATTTACCAAAAACCCCTTTTGAGGATCGATGAGGAGGCTCCATTTGAACTTTTTTT
1 ACCCAGAAAATTTACCAAAAACCCCTTTTAAGGATCGATGAGGAGGCTCCATTTGAACTTTTCTT
*
8695 GTCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGT
66 ATCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGT
8760 TCCTATCCTTGAGCCCTTTTTTGTAATTATCCTTTCTTTTCA
131 TCCTATCCTTGAGCCCTTTTTTGTAATTATCCTTTCTTTTCA
8802 CATAAAATGT
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
173 167 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (173 bp):
ACCCAGAAAATTTACCAAAAACCCCTTTTAAGGATCGATGAGGAGGCTCCATTTGAACTTTTCTT
ATCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGT
TCCTATCCTTGAGCCCTTTTTTGTAATTATCCTTTCTTTTCAG
Found at i:8780 original size:86 final size:86
Alignment explanation
Indices: 8523--8780 Score: 201
Period size: 86 Copynumber: 3.0 Consensus size: 86
8513 ACTTTTCTTA
*
8523 TCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGTAAGTT
1 TCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTT
8588 CCTATCCTTGAGCCCTTTTTTG
66 CCTATCCTTGAGCCC-TTTTTG
** * * ** * * * **
8610 TAATTATCCTT-TCTTTTCAGACCCAG-GAAATTTACCAA-AA-ACCCCT--TTTGAGGATCGAT
1 TCCTT-T-TTTGTCTTTTCACA-CTTGCTAAA-TTACTAAGAAGA-CCCTAGGTT-A-G-TTTAT
* * * * **
8669 GAGGAGGCTCC-AT--TTGAACTTTTTTTG
58 -AGCAAGTTCCTATCCTTGAGCCCTTTTTG
8696 TCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTT
1 TCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTT
8761 CCTATCCTTGAGCCCTTTTT
66 CCTATCCTTGAGCCCTTTTT
8781 TGTAATTATC
Statistics
Matches: 119, Mismatches: 34, Indels: 37
0.63 0.18 0.19
Matches are distributed among these distances:
83 7 0.06
84 15 0.13
85 20 0.17
86 23 0.19
87 12 0.10
88 20 0.17
89 15 0.13
90 7 0.06
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (86 bp):
TCCTTTTTTGTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTT
CCTATCCTTGAGCCCTTTTTG
Found at i:8798 original size:88 final size:88
Alignment explanation
Indices: 8533--8803 Score: 240
Period size: 88 Copynumber: 3.1 Consensus size: 88
8523 TCCTTTTTTG
*
8533 TCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGTAAGTTCCTATCCTTG
1 TCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTTCCTATCCTTG
8598 AGCCCTTTTTTGTAATTATCCTT
66 AGCCCTTTTTTGTAATTATCCTT
* ** * * * ** * * *
8621 TCTTTTCAGACCCAG-GAAATTTACCAA-AA-ACCCCT--TTTGAGGATCGATGAGGAGGCTCC-
1 TCTTTTCACA-CTTGCTAAA-TTACTAAGAAGA-CCCTAGGTT-A-G-TTTAT-AGCAAGTTCCT
* * ** *
8680 AT--TTGA-ACTTTTTTTGTCCTT-T-TTT
59 ATCCTTGAGCCCTTTTTTGTAATTATCCTT
8705 GTCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTTCCTATCCTT
1 -TCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTTCCTATCCTT
8770 GAGCCCTTTTTTGTAATTATCCTT
65 GAGCCCTTTTTTGTAATTATCCTT
8794 TCTTTTCACA
1 TCTTTTCACA
8804 TAAAATGTTA
Statistics
Matches: 132, Mismatches: 32, Indels: 38
0.65 0.16 0.19
Matches are distributed among these distances:
83 7 0.05
84 15 0.11
85 20 0.15
86 19 0.14
87 19 0.14
88 30 0.23
89 15 0.11
90 7 0.05
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (88 bp):
TCTTTTCACACTTGCTAAATTACTAAGAAGACCCTAGGTTAGTTTATAGCAAGTTCCTATCCTTG
AGCCCTTTTTTGTAATTATCCTT
Found at i:12839 original size:20 final size:20
Alignment explanation
Indices: 12814--12852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12804 TTATTCGAAC
12814 CCGAAACTTTAATTAAAAAG
1 CCGAAACTTTAATTAAAAAG
* *
12834 CCGAAATTTTATTTAAAAA
1 CCGAAACTTTAATTAAAAA
12853 ACTTCAAATC
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:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (20 bp):
CCGAAACTTTAATTAAAAAG
Found at i:12983 original size:8 final size:8
Alignment explanation
Indices: 12970--12997 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
12960 ACCCGAAGGC
12970 AAAAAAGA
1 AAAAAAGA
12978 AAAAAAGA
1 AAAAAAGA
12986 AAAAAAGA
1 AAAAAAGA
12994 AAAA
1 AAAA
12998 GAAAAAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:13857 original size:30 final size:31
Alignment explanation
Indices: 13805--13865 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
13795 TTACTGGCAC
* *
13805 TTTTACTGGCTTTTTTTTTTTAACCTAAAAA
1 TTTTACTGGCTTTTTCTTTTTAACCAAAAAA
13836 TTTTACTGGC-TTTTCTTTTTAACCAAAAAA
1 TTTTACTGGCTTTTTCTTTTTAACCAAAAAA
13866 GTGAGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTTACTGGCTTTTTCTTTTTAACCAAAAAA
Found at i:26311 original size:6 final size:6
Alignment explanation
Indices: 26300--26333 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
26290 CATAAAGCTC
26300 AAATGA AAATGA AAATGA AAATGA AAATGA AAAT
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAAT
26334 TTGTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:27483 original size:21 final size:21
Alignment explanation
Indices: 27457--27497 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27447 TTAATCCGAC
*
27457 AATTCCTTAATTCGATTGTAT
1 AATTCCTTAATCCGATTGTAT
27478 AATTCCTTAATCCGATTGTA
1 AATTCCTTAATCCGATTGTA
27498 CAGTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (21 bp):
AATTCCTTAATCCGATTGTAT
Found at i:30428 original size:2 final size:2
Alignment explanation
Indices: 30421--30445 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30411 GAACACAATC
30421 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 T
30446 GCTGGATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32889 original size:29 final size:31
Alignment explanation
Indices: 32857--32923 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
32847 ATGCAATTTG
32857 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
**
32886 GGATATAACGTTACGAAAAGTGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
32917 GGATATA
1 GGATATA
32924 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:33090 original size:31 final size:31
Alignment explanation
Indices: 33055--33129 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
33045 CTAACTGATT
*
33055 ATATCCTTAATTGCTTGAAATCGAAAACGCC
1 ATATCCTTAATTGCTTGAAATAGAAAACGCC
**
33086 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGCC
*
33117 ATATCTTTAATTG
1 ATATCCTTAATTG
33130 ATTGTTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGCC
Done.