Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024160.1 Corchorus olitorius cultivar O-4 contig24193, 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: 29776
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1403 original size:23 final size:23
Alignment explanation
Indices: 1372--1420 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
1362 CTTATCGATG
*
1372 ATTTGCTTCCACTTAAGTCGACTA
1 ATTTGCTT-CACTTAAGTCGACCA
* *
1396 ATTT-CTTCTCTTTAGTCGACCA
1 ATTTGCTTCACTTAAGTCGACCA
1418 ATT
1 ATT
1421 AGCTCCTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 3 0.14
24 4 0.18
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (23 bp):
ATTTGCTTCACTTAAGTCGACCA
Found at i:1573 original size:35 final size:38
Alignment explanation
Indices: 1493--1575 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 38
1483 TTCCTTGTAT
* * * *
1493 AGTCGACAAGCTTAAGTCGATGCTTGCTTTTTCCTTAA
1 AGTCGACAATCTTAAGTCGACGCTTACTTCTTCCTTAA
1531 AGTCGACAATCTT-AGTCGACG-TTACTTCTTCCTT-A
1 AGTCGACAATCTTAAGTCGACGCTTACTTCTTCCTTAA
1566 AGTCGACAAT
1 AGTCGACAAT
1576 TTTCTACTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 11 0.27
36 11 0.27
37 7 0.17
38 12 0.29
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (38 bp):
AGTCGACAATCTTAAGTCGACGCTTACTTCTTCCTTAA
Found at i:6701 original size:19 final size:18
Alignment explanation
Indices: 6668--6703 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6658 TTGAAATTAT
*
6668 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
6686 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
6704 TAAGTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:8643 original size:22 final size:22
Alignment explanation
Indices: 8615--8658 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8605 TTTCCCTGTT
8615 TCGACCTTCATCAGGGTC-AAAC
1 TCGACCTTC-TCAGGGTCGAAAC
*
8637 TCGACCTTCTCTGGGTCGAAAC
1 TCGACCTTCTCAGGGTCGAAAC
8659 AGGGCTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (22 bp):
TCGACCTTCTCAGGGTCGAAAC
Found at i:9906 original size:18 final size:19
Alignment explanation
Indices: 9885--9924 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
9875 CTCTTGAAAT
*
9885 AATTCTTCAAA-AATCTTC
1 AATTCTCCAAATAATCTTC
*
9903 AATTCTCCAAATTATCTTC
1 AATTCTCCAAATAATCTTC
9922 AAT
1 AAT
9925 AAGTCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCTCCAAATAATCTTC
Found at i:10781 original size:18 final size:18
Alignment explanation
Indices: 10748--10782 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10738 AAGGCTTCGT
* *
10748 TTTTTTTTGTGTGAGAGA
1 TTTTTTTTATGGGAGAGA
10766 TTTTTTTTATGGGAGAG
1 TTTTTTTTATGGGAGAG
10783 GATGATCCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (18 bp):
TTTTTTTTATGGGAGAGA
Found at i:12644 original size:26 final size:26
Alignment explanation
Indices: 12580--12650 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
12570 TAAAATGCCC
*
12580 AAAATGACCAAAACGCCCTTGAGTATG
1 AAAATGACCAAAATGCCCTTGAGTA-G
* *
12607 CAAATGACCAAAATGCCCTTAGGGTA-
1 AAAATGACCAAAATGCCCTT-GAGTAG
12633 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
12651 CCCTAGGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 17 0.44
27 18 0.46
28 4 0.10
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTTGAGTAG
Found at i:14378 original size:31 final size:31
Alignment explanation
Indices: 14343--14403 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
14333 TAGACTTGGA
*
14343 TTATTATGTTTTTGAATTTTCAAATTCCATG
1 TTATTATGATTTTGAATTTTCAAATTCCATG
* * *
14374 TTATTCTGATTTTGTATTTTCAACTTCCAT
1 TTATTATGATTTTGAATTTTCAAATTCCAT
14404 TTTCTTTTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (31 bp):
TTATTATGATTTTGAATTTTCAAATTCCATG
Found at i:18166 original size:78 final size:78
Alignment explanation
Indices: 18037--18195 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
18027 GATATAACCT
18037 TGATGTATGAGGGCTCTAAATCTCAAATTTCAGCTCAATCGAAGCAACAGTGAATATAGAATAAA
1 TGATGTATGAGGGCTCTAAATCTCAAATTTCAGCTCAATCGAAGCAACAGTGAATATAGAATAAA
18102 AATCACAAGTTTC
66 AATCACAAGTTTC
18115 TGATGTATGAGGGCTCTAAATCTCAAATTTCAGCTCAATCGAAGCAACAGTGAATATAGAATAAA
1 TGATGTATGAGGGCTCTAAATCTCAAATTTCAGCTCAATCGAAGCAACAGTGAATATAGAATAAA
18180 AATCACAAGTTTC
66 AATCACAAGTTTC
18193 TGA
1 TGA
18196 ATTTTTTATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (78 bp):
TGATGTATGAGGGCTCTAAATCTCAAATTTCAGCTCAATCGAAGCAACAGTGAATATAGAATAAA
AATCACAAGTTTC
Found at i:20517 original size:22 final size:22
Alignment explanation
Indices: 20489--20535 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
20479 GATTTACAAA
20489 TGAGATTTGAAAGCACAGAGCT
1 TGAGATTTGAAAGCACAGAGCT
* *
20511 TGAGATTTGTAAGCACGGAGCT
1 TGAGATTTGAAAGCACAGAGCT
20533 TGA
1 TGA
20536 TTTGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (22 bp):
TGAGATTTGAAAGCACAGAGCT
Found at i:24762 original size:169 final size:173
Alignment explanation
Indices: 24466--24850 Score: 452
Period size: 169 Copynumber: 2.3 Consensus size: 173
24456 TTTCTATATT
* * *
24466 TATATTA-A-ATAAGGCTAAACTCTAAAACTTGTGCGGAAATATCTAAAATATCACCCTTAATTT
1 TATATTATATATAAGGCTAAACTCTAAAACTTGAGCAGAAATATCTAAAATACCACCCTTAATTT
** * * *
24529 GTCTTACCTCCTTATATATGTGATATATAAAATTTGAGCAAAAATATCTAAAATACCATTCTTAA
66 GTCTTACCTCAGTATATATATAATATATAAAACTTGAGCAAAAATATCTAAAATACCATTCTTAA
*
24594 TTTGT-CTTAGCTCTCAATG-GTATATCTCTA-AC-TATCTATCTG
131 TTTGTACTTAGCTCT-AAGGAGTATATCTCTATACATATCTA--TG
* ***
24636 TATATTATATATAAGGCTAAACTCT-AAACTTAAGCAGAAATATCTAAAATACCTTTCTTAATTT
1 TATATTATATATAAGGCTAAACTCTAAAACTTGAGCAGAAATATCTAAAATACCACCCTTAATTT
* *
24700 GTCTTA-C-CAGTATATATATAATATATAAAACTTGAAG-AGAAATATCTAAAATACCCTTCTTA
66 GTCTTACCTCAGTATATATATAATATATAAAACTTG-AGCAAAAATATCTAAAATACCATTCTTA
* * * *
24762 ATTTGTATTTATCTCTGAGGAGTATATCTCTATTCATATCTATG
130 ATTTGTACTTAGCTCTAAGGAGTATATCTCTATACATATCTATG
* * *
24806 TATA-T-TATACAAGGCTAAATTCTAAAATTTGAGCAGAAATATCTA
1 TATATTATATATAAGGCTAAACTCTAAAACTTGAGCAGAAATATCTA
24851 CCCTTATCAC
Statistics
Matches: 184, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
168 16 0.09
169 73 0.40
170 34 0.18
171 40 0.22
172 21 0.11
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (173 bp):
TATATTATATATAAGGCTAAACTCTAAAACTTGAGCAGAAATATCTAAAATACCACCCTTAATTT
GTCTTACCTCAGTATATATATAATATATAAAACTTGAGCAAAAATATCTAAAATACCATTCTTAA
TTTGTACTTAGCTCTAAGGAGTATATCTCTATACATATCTATG
Found at i:25107 original size:49 final size:49
Alignment explanation
Indices: 25054--25150 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 49
25044 GATAAGAGGA
* *
25054 TGCGACGAAAAGTAAATATTCAATTTTGTCT-TAAAAATTGAGAAAAAGG
1 TGCGACGAAAAGTAAAGATTCAATTTTGT-TGCAAAAATTGAGAAAAAGG
* * *
25103 TGCGAGGAAAATTAAAGGTTCAATTTTGTTGCAAAAATTGAGAAAAAG
1 TGCGACGAAAAGTAAAGATTCAATTTTGTTGCAAAAATTGAGAAAAAG
25151 TGCAGGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.02
49 41 0.98
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCGACGAAAAGTAAAGATTCAATTTTGTTGCAAAAATTGAGAAAAAGG
Found at i:28031 original size:11 final size:10
Alignment explanation
Indices: 28015--28066 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
28005 AAGTTCGTGT
28015 TTGAAGACTTA
1 TTGAAGA-TTA
*
28026 TTGAAGATAA
1 TTGAAGATTA
28036 TTTGAAGA-T-
1 -TTGAAGATTA
28045 TTGAAGATTA
1 TTGAAGATTA
28055 TTGAAGAATTA
1 TTGAAG-ATTA
28066 T
1 T
28067 CTCAAGAGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:28050 original size:19 final size:18
Alignment explanation
Indices: 28026--28061 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28016 TGAAGACTTA
28026 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
28045 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
28062 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.