Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012965.1 Corchorus olitorius cultivar O-4 contig12998, 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: 26555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1094 original size:36 final size:36
Alignment explanation
Indices: 1047--1116 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1037 TTCAATAACC
* *
1047 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
1083 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
1117 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:2469 original size:30 final size:28
Alignment explanation
Indices: 2416--2472 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
2406 GACTTCAACA
* *
2416 AATAGATGATAAATAATGGAAATAGATG
1 AATAGATAATAAATAAGGGAAATAGATG
2444 AATAGATAATAGAATTAAGGGAAATAGAT
1 AATAGATAATA-AA-TAAGGGAAATAGAT
2473 TAAATGGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 2 0.08
30 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (28 bp):
AATAGATAATAAATAAGGGAAATAGATG
Found at i:2935 original size:25 final size:25
Alignment explanation
Indices: 2862--3012 Score: 213
Period size: 25 Copynumber: 6.0 Consensus size: 25
2852 CACCAATGTG
2862 TTGCCACGTATGATAGTGGGCTTTGTA
1 TTGCCACGTA-G-TAGTGGGCTTTGTA
2889 TTGCCACGTA-TAGTGGGCTTTGTA
1 TTGCCACGTAGTAGTGGGCTTTGTA
2913 TTGCCACGTAGGT-GTGGGCTTTGTA
1 TTGCCACGTA-GTAGTGGGCTTTGTA
*
2938 TTTCCACGTA-TAGTGGGCTTTGTA
1 TTGCCACGTAGTAGTGGGCTTTGTA
2962 TTGCCACGTAG-ATGTGGGCTTTGTA
1 TTGCCACGTAGTA-GTGGGCTTTGTA
2987 TTGCCACGTAGGTA-TGGGCTTTGTA
1 TTGCCACGTA-GTAGTGGGCTTTGTA
3012 T
1 T
3013 CGAACCATGG
Statistics
Matches: 115, Mismatches: 2, Indels: 16
0.86 0.02 0.12
Matches are distributed among these distances:
23 1 0.01
24 46 0.40
25 55 0.48
26 2 0.02
27 11 0.10
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (25 bp):
TTGCCACGTAGTAGTGGGCTTTGTA
Found at i:2936 original size:49 final size:49
Alignment explanation
Indices: 2862--3012 Score: 241
Period size: 49 Copynumber: 3.0 Consensus size: 49
2852 CACCAATGTG
2862 TTGCCACGTATGATAGTGGGCTTTGTATTGCCACGTATAGTGGGCTTTGTA
1 TTGCCACGTA-GAT-GTGGGCTTTGTATTGCCACGTATAGTGGGCTTTGTA
* *
2913 TTGCCACGTAGGTGTGGGCTTTGTATTTCCACGTATAGTGGGCTTTGTA
1 TTGCCACGTAGATGTGGGCTTTGTATTGCCACGTATAGTGGGCTTTGTA
2962 TTGCCACGTAGATGTGGGCTTTGTATTGCCACGTAGGTA-TGGGCTTTGTA
1 TTGCCACGTAGATGTGGGCTTTGTATTGCCACGTA--TAGTGGGCTTTGTA
3012 T
1 T
3013 CGAACCATGG
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
49 68 0.72
50 14 0.15
51 12 0.13
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (49 bp):
TTGCCACGTAGATGTGGGCTTTGTATTGCCACGTATAGTGGGCTTTGTA
Found at i:7740 original size:39 final size:40
Alignment explanation
Indices: 7684--7764 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
7674 TTTAATTTCT
* *
7684 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACCAAAATACTTACATTAATTAA
* *
7724 ATGTAATA-CTATAATAACCGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACCAAAATACTTACATTAATTAA
7763 AT
1 AT
7765 TCTTAGGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACCAAAATACTTACATTAATTAA
Found at i:8781 original size:36 final size:36
Alignment explanation
Indices: 8741--8810 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
8731 GAGATTTTGG
* *
8741 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
8777 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
8811 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:10179 original size:58 final size:58
Alignment explanation
Indices: 10078--10190 Score: 183
Period size: 58 Copynumber: 1.9 Consensus size: 58
10068 AGCATCATGC
*
10078 CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAAGT
1 CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAAGT
* *
10136 CTCGGTCCGAAAACGTCTTTTTTAATGCATCTAAT-AAAGAACATGTCACTTGATA
1 CTCGGTCCGAAAACGTCTTTTTT-AGGCATCTAATAAAAAAACATGTCACTTGATA
10191 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 41 0.80
59 10 0.20
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (58 bp):
CTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTTGATAAGT
Found at i:13191 original size:11 final size:11
Alignment explanation
Indices: 13167--13200 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
13157 TTCCATAATA
13167 TTCTTTTCTTTT
1 TTCTTTT-TTTT
13179 TTCTTTTTTTT
1 TTCTTTTTTTT
13190 TTCTTTTTTTT
1 TTCTTTTTTTT
13201 CGTGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:13290 original size:5 final size:5
Alignment explanation
Indices: 13275--13303 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
13265 ATTAGAAACG
13275 TAAAA -AAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
13304 ATTCAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:15824 original size:11 final size:11
Alignment explanation
Indices: 15808--15842 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
15798 TTTTTCTATT
15808 TTTTGTTTTTG
1 TTTTGTTTTTG
*
15819 TTTTGTTTTCG
1 TTTTGTTTTTG
15830 TTTTGTTTTTG
1 TTTTGTTTTTG
15841 TT
1 TT
15843 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:22845 original size:26 final size:28
Alignment explanation
Indices: 22802--22854 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
22792 TTTTCCTGGC
*
22802 AGGCTTATTCAAATCCTTT-TTCTTTGT
1 AGGCTTATCCAAATCCTTTCTTCTTTGT
*
22829 AGGCTTCTCCAAA-CCTTTCTTCTTTG
1 AGGCTTATCCAAATCCTTTCTTCTTTG
22855 AAGTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (28 bp):
AGGCTTATCCAAATCCTTTCTTCTTTGT
Done.