Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014249.1 Corchorus olitorius cultivar O-4 contig14282, 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: 54812
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:203 original size:111 final size:111
Alignment explanation
Indices: 9--233 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
1 TTCGAGGT
*
9 GGAAGCCATAGATGTGGAAGCCGGCTGGATTGGGTGAGGATCGTTAGAGGGAGCCTCCGCAGGGT
1 GGAAGCCATAGATGTGGAAGCCGGCTGGATTGGGCGAGGATCGTTAGAGGGAGCCTCCGCAGGGT
74 AAGGAGCGGAAGACAGAGATGAGGAAGGAGGGGTCAAGGTGGAAGG
66 AAGGAGCGGAAGACAGAGATGAGGAAGGAGGGGTCAAGGTGGAAGG
120 GGAAGCCATAGATGTGGAAGCCGGCTGGATTGGGCGAGGATCGTTAGAGGGAGCCTCCGCAGGGT
1 GGAAGCCATAGATGTGGAAGCCGGCTGGATTGGGCGAGGATCGTTAGAGGGAGCCTCCGCAGGGT
185 AAGGAGCGGAAGACAGAGATGAGGAAGGAGGGGTCAAGGTGGAAGG
66 AAGGAGCGGAAGACAGAGATGAGGAAGGAGGGGTCAAGGTGGAAGG
231 GGA
1 GGA
234 TGAGGGAAGA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.28, C:0.13, G:0.46, T:0.13
Consensus pattern (111 bp):
GGAAGCCATAGATGTGGAAGCCGGCTGGATTGGGCGAGGATCGTTAGAGGGAGCCTCCGCAGGGT
AAGGAGCGGAAGACAGAGATGAGGAAGGAGGGGTCAAGGTGGAAGG
Found at i:531 original size:36 final size:36
Alignment explanation
Indices: 458--540 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
448 GGTAAGTAGT
*
458 GGCTTGTTCAAGAATGGAGGGAGGAGGGAAAGTTGG
1 GGCTTGTTCAAGAATGGAGGGAGGAGGGAAAGGTGG
* * * *
494 GGCTTGTTGAAG-ATGGAGAGGGGGGGGGGAAGGTGG
1 GGCTTGTTCAAGAATGGAG-GGAGGAGGGAAAGGTGG
530 GGCTTGATTCA
1 GGCTTG-TTCA
541 GATTCTGCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 6 0.15
36 30 0.77
37 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.51, T:0.20
Consensus pattern (36 bp):
GGCTTGTTCAAGAATGGAGGGAGGAGGGAAAGGTGG
Found at i:1223 original size:50 final size:49
Alignment explanation
Indices: 1168--1264 Score: 167
Period size: 50 Copynumber: 2.0 Consensus size: 49
1158 GTATTTTTCG
*
1168 ATGCTTGTTTGTAAGTTAAACTTCTTTTTTTCGATAAATCCTATCGTTTT
1 ATGCTTGTTTGTAAGTTAAACTTC-TTTTATCGATAAATCCTATCGTTTT
*
1218 ATGCTTGTTTGTAAGTTAAACTTCTTTTATCTATAAATCCTATCGTT
1 ATGCTTGTTTGTAAGTTAAACTTCTTTTATCGATAAATCCTATCGTT
1265 ATATTGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 21 0.47
50 24 0.53
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (49 bp):
ATGCTTGTTTGTAAGTTAAACTTCTTTTATCGATAAATCCTATCGTTTT
Found at i:2968 original size:2 final size:2
Alignment explanation
Indices: 2961--3012 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
2951 GCAATGTAGA
2961 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
3003 AT AT GAT AT A
1 AT AT -AT AT A
3013 ATAAATCTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13629 original size:3 final size:3
Alignment explanation
Indices: 13621--13652 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13611 TGTCACCTTA
*
13621 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
13653 GATTGAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:20406 original size:5 final size:6
Alignment explanation
Indices: 20377--20403 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20367 AGATAAGCCA
20377 AAAACT AAAACT AAAACT AAAACT AAA
1 AAAACT AAAACT AAAACT AAAACT AAA
20404 CTAGAAGGTG
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:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAACT
Found at i:47486 original size:14 final size:13
Alignment explanation
Indices: 47467--47505 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
47457 ACTCAACACT
47467 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
47481 AACTGACTCAACA
1 AACTGACTCAAAA
47494 AACTGACT-AAAA
1 AACTGACTCAAAA
47506 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:47498 original size:13 final size:13
Alignment explanation
Indices: 47456--47501 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
47446 GGTAGACTCA
47456 GACTCAACACTAACT
1 GACTCAACA--AACT
*
47471 GACTCGAAAAAACT
1 GACTC-AACAAACT
47485 GACTCAACAAACT
1 GACTCAACAAACT
47498 GACT
1 GACT
47502 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:47815 original size:2 final size:2
Alignment explanation
Indices: 47808--47835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47798 TGTGAAAACA
47808 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
47836 GAATAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48316 original size:29 final size:29
Alignment explanation
Indices: 48284--48340 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
48274 TTTGATCATT
*
48284 ATTTATAAAAAATATATATAT-AAAATTTA
1 ATTTAAAAAAAATATATAT-TGAAAATTTA
48313 ATTTAAAAAAAATATATATTGAAAATTT
1 ATTTAAAAAAAATATATATTGAAAATTT
48341 TACAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTTAAAAAAAATATATATTGAAAATTTA
Found at i:54634 original size:228 final size:228
Alignment explanation
Indices: 54237--54812 Score: 850
Period size: 228 Copynumber: 2.5 Consensus size: 228
54227 TTCAAAATAG
* * * * * * *
54237 ATGCAAATCTTCGTTAAGACCCTCACTGGCAAGACCATCACCCTT-GAGGTGGAAAGTTCCGACA
1 ATGCAAATCTTTGTTAAGACCCTTACTGGAAAGACCATCA-CCTTGGAAGTTGAGAGCTCCGACA
* * * *
54301 CTATTGACAATGTAAAGGCCAAGATCCAGGATAAGGAGGGTATCCCCCCAGACCAGCAAAGGTTG
65 CAATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATCCCCCCAGACCAGCAAAGGTTG
54366 ATCTTTGCCGGTAAGCAACTTGAGGATGGCCGCACCCTGGCTGACTACAACATCCAAAAGGAATC
130 ATCTTTGCCGGTAAGCAACTTGAGGATGGCCGCACCCTGGCTGACTACAACATCCAAAAGGAATC
*
54431 CACCCTCCACTTGGTGCTCCGTCTTCGAGGTGGC
195 CACCCTCCACTTGGTGCTCCGTCTCCGAGGTGGC
* * *
54465 ATGCAAATCTTTGTTAAGACCCTTACTGGGAAGACTATCACCTTGGAAGTTGAGAGCTCGGACAC
1 ATGCAAATCTTTGTTAAGACCCTTACTGGAAAGACCATCACCTTGGAAGTTGAGAGCTCCGACAC
* * *
54530 AATTGACAATGTCAAGGCTAAGATTCAGGACAAGGAGGGTATCCCCCCAGATCAGCAGAGGCTT-
66 AATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATCCCCCCAGACCAGCAAAGG-TTG
* * *
54594 ATCTTTGCCGGTAAGCAGCTTGAGGATGGCCGTACCCTGGCTGACTACAACATCCAAAAGGAGTC
130 ATCTTTGCCGGTAAGCAACTTGAGGATGGCCGCACCCTGGCTGACTACAACATCCAAAAGGAATC
* * *
54659 CACCCTCCACTTGGTTCTCCGTCTCCGTGGTGGT
195 CACCCTCCACTTGGTGCTCCGTCTCCGAGGTGGC
* * * * *
54693 ATGCAGATTTTTGTGAAGACACTTACTGGAAAGACCATCACCTTGGAAGTTGAGAGCTCTGACAC
1 ATGCAAATCTTTGTTAAGACCCTTACTGGAAAGACCATCACCTTGGAAGTTGAGAGCTCCGACAC
*
54758 AATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATCCCCCAAGACCAG
66 AATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATCCCCCCAGACCAG
Statistics
Matches: 313, Mismatches: 33, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
227 4 0.01
228 307 0.98
229 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (228 bp):
ATGCAAATCTTTGTTAAGACCCTTACTGGAAAGACCATCACCTTGGAAGTTGAGAGCTCCGACAC
AATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATCCCCCCAGACCAGCAAAGGTTGA
TCTTTGCCGGTAAGCAACTTGAGGATGGCCGCACCCTGGCTGACTACAACATCCAAAAGGAATCC
ACCCTCCACTTGGTGCTCCGTCTCCGAGGTGGC
Done.