Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024918.1 Corchorus olitorius cultivar O-4 contig24951, 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: 35822
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5059 original size:12 final size:13
Alignment explanation
Indices: 5031--5085 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
5021 TCATGCACCC
5031 AAAATCATTTAAT
1 AAAATCATTTAAT
5044 AAAATCATTT-AT
1 AAAATCATTTAAT
*
5056 AAAAACAATTTAAT
1 AAAATC-ATTTAAT
*
5070 AAAA-CA-ATAAT
1 AAAATCATTTAAT
5081 AAAAT
1 AAAAT
5086 AGTTTCTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 15 0.41
14 6 0.16
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATCATTTAAT
Found at i:6184 original size:2 final size:2
Alignment explanation
Indices: 6177--6202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6167 TTCATTCTCA
6177 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
6203 CATTCTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6267 original size:24 final size:24
Alignment explanation
Indices: 6240--6291 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6230 TTCATCAATT
* *
6240 TAAACTTTTAAACTCTATATACCA
1 TAAACTTATAAACTCTAGATACCA
* * *
6264 TAAAGTTATCAACTCTAGATTCCA
1 TAAACTTATAAACTCTAGATACCA
6288 TAAA
1 TAAA
6292 AGAGAAGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (24 bp):
TAAACTTATAAACTCTAGATACCA
Found at i:9017 original size:15 final size:15
Alignment explanation
Indices: 8997--9027 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8987 CCTTTCTTCA
8997 CCTTTCCCCTCTACC
1 CCTTTCCCCTCTACC
9012 CCTTTCCCCTCTACC
1 CCTTTCCCCTCTACC
9027 C
1 C
9028 AAACTTGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.61, G:0.00, T:0.32
Consensus pattern (15 bp):
CCTTTCCCCTCTACC
Found at i:9717 original size:19 final size:19
Alignment explanation
Indices: 9690--9732 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
9680 CCTAATTCAA
9690 AAAAAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAG
* * *
9709 AAAAGAAAAGAAAAAGAAG
1 AAAAAAAAAAAAAAAAAAG
9728 AAAAA
1 AAAAA
9733 GGAAAAATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAG
Found at i:9732 original size:10 final size:10
Alignment explanation
Indices: 9689--9732 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
9679 CCCTAATTCA
*
9689 AAAAAAAAAA
1 AAAAAAAAAG
9699 AAAAAAAAAG
1 AAAAAAAAAG
*
9709 AAAAGAAAAG
1 AAAAAAAAAG
*
9719 -AAAAAGAAG
1 AAAAAAAAAG
9728 AAAAA
1 AAAAA
9733 GGAAAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:9733 original size:9 final size:9
Alignment explanation
Indices: 9688--9732 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
9678 ACCCTAATTC
9688 AAAA-AAAA
1 AAAAGAAAA
9696 AAAA-AAAA
1 AAAAGAAAA
9704 AAAAGAAAA
1 AAAAGAAAA
9713 GAAAAGAAAA
1 -AAAAGAAAA
*
9723 AGAAGAAAA
1 AAAAGAAAA
9732 A
1 A
9733 GGAAAAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 12 0.35
9 13 0.38
10 9 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:9737 original size:16 final size:16
Alignment explanation
Indices: 9688--9739 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
9678 ACCCTAATTC
* *
9688 AAAAA-AAAAAAAAAA
1 AAAAAGAAAAGAAAAG
9703 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
*
9719 AAAAAGAAGAA-AAAGG
1 AAAAAGAA-AAGAAAAG
9735 AAAAA
1 AAAAA
9740 TGGGCTAGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 5 0.16
16 25 0.78
17 2 0.06
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:9765 original size:43 final size:44
Alignment explanation
Indices: 9718--9803 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
9708 GAAAAGAAAA
9718 GAAAAAGAAGAAAAAGGAAA-AATGGGCT-AGGCCC-AACTTTAAG
1 GAAAAAGAA-AAAAA-GAAATAATGGGCTAAGGCCCGAACTTTAAG
* * *
9761 GAAAAGGAAAAGAAGAAATAATGGGCTAAGGCCCGAATTTTAA
1 GAAAAAGAAAAAAAGAAATAATGGGCTAAGGCCCGAACTTTAA
9804 AATAAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 4 0.11
42 12 0.32
43 14 0.38
44 7 0.19
ACGTcount: A:0.50, C:0.10, G:0.26, T:0.14
Consensus pattern (44 bp):
GAAAAAGAAAAAAAGAAATAATGGGCTAAGGCCCGAACTTTAAG
Found at i:13291 original size:29 final size:30
Alignment explanation
Indices: 13259--13335 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
13249 TTCAAATTGT
13259 AAGTTCAGGGGACAAAACGTCCAAAAT-TA-
1 AAGTTCAGGGGACAAAACGT-CAAAATCTAC
*
13288 AAGTTCAGGGGGCAAAACGTCAAAATCGTAC
1 AAGTTCAGGGGACAAAACGTCAAAATC-TAC
*
13319 AAGTTCAGTGGACAAAA
1 AAGTTCAGGGGACAAAA
13336 AGGACATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.14
29 19 0.45
30 2 0.05
31 15 0.36
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGACAAAACGTCAAAATCTAC
Found at i:13414 original size:18 final size:18
Alignment explanation
Indices: 13391--13430 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13381 ACTACCACCT
13391 TTAACCCTAGTTTACAAG
1 TTAACCCTAGTTTACAAG
* *
13409 TTAACCCTTGTTTACGAG
1 TTAACCCTAGTTTACAAG
13427 TTAA
1 TTAA
13431 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (18 bp):
TTAACCCTAGTTTACAAG
Found at i:14111 original size:19 final size:20
Alignment explanation
Indices: 14066--14111 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14056 TTAATTTTCC
*
14066 TAAACTATAATTAATTTAGG
1 TAAATTATAATTAATTTAGG
* *
14086 AAAATTATAATTAATTT-GT
1 TAAATTATAATTAATTTAGG
14105 TAAATTA
1 TAAATTA
14112 AATAGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
TAAATTATAATTAATTTAGG
Found at i:22929 original size:2 final size:2
Alignment explanation
Indices: 22922--22946 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22912 AATTTCCATT
22922 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
22947 TATGTGAATG
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:26407 original size:11 final size:11
Alignment explanation
Indices: 26364--26401 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
26354 TTCCTATATA
*
26364 AAATAAATTAT
1 AAATTAATTAT
26375 CAAA-TAATTAT
1 -AAATTAATTAT
26386 AAATTAATTAT
1 AAATTAATTAT
26397 AAATT
1 AAATT
26402 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:29315 original size:43 final size:43
Alignment explanation
Indices: 29254--29338 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
29244 TATCTTTCCC
* *
29254 AACTTATTATCTTTGGTTCGTGGAAAGTAATGGGAAAATATGA
1 AACTTATTACCTTAGGTTCGTGGAAAGTAATGGGAAAATATGA
29297 AACTTATTACCTTAGGTTCGTGGAAAGTAATGGGAAAATATG
1 AACTTATTACCTTAGGTTCGTGGAAAGTAATGGGAAAATATG
29339 GTAAGTTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (43 bp):
AACTTATTACCTTAGGTTCGTGGAAAGTAATGGGAAAATATGA
Found at i:34458 original size:36 final size:35
Alignment explanation
Indices: 34330--34462 Score: 160
Period size: 35 Copynumber: 3.8 Consensus size: 35
34320 AAAAACCGAA
** *
34330 TGGGAACTTTCCCAATT-TGAAAACTTAAAAGCTGA
1 TGGGAACTTTCCCAATTAAAAAAACTTAAAA-CTGG
* * ** *
34365 CGGGAACTTTCCCCATTTAAAAAAGTTTAAACCTGG
1 TGGGAACTTT-CCCAATTAAAAAAACTTAAAACTGG
34401 TGGGAACTTTCCCAATTAAAAAAACTTAAAACTGG
1 TGGGAACTTTCCCAATTAAAAAAACTTAAAACTGG
*
34436 TGGGAACTTTCCCAATAAAAAAAACTT
1 TGGGAACTTTCCCAATTAAAAAAACTT
34463 GGTGCAATTC
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
35 56 0.68
36 18 0.22
37 8 0.10
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (35 bp):
TGGGAACTTTCCCAATTAAAAAAACTTAAAACTGG
Done.