Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021397.1 Corchorus olitorius cultivar O-4 contig21430, 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: 65347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4174 original size:16 final size:16
Alignment explanation
Indices: 4153--4183 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4143 ATTGGATATA
*
4153 TATATATATATATGTT
1 TATATATATAAATGTT
4169 TATATATATAAATGT
1 TATATATATAAATGT
4184 ACACATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATATATAAATGTT
Found at i:4542 original size:3 final size:3
Alignment explanation
Indices: 4534--4564 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4524 TATTCTCTAC
4534 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4565 AAAGAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4720 original size:15 final size:15
Alignment explanation
Indices: 4700--4754 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
4690 GGTGTCCAGA
**
4700 TCCAAAACTGCAAAT
1 TCCAAAACCCCAAAT
4715 TCCAAAACCCCAAAT
1 TCCAAAACCCCAAAT
*
4730 TCGAAAACCCCAAAT
1 TCCAAAACCCCAAAT
4745 TCCAAAACCC
1 TCCAAAACCC
4755 TAAACCCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.45, C:0.36, G:0.04, T:0.15
Consensus pattern (15 bp):
TCCAAAACCCCAAAT
Found at i:5367 original size:101 final size:101
Alignment explanation
Indices: 5193--5484 Score: 415
Period size: 101 Copynumber: 2.9 Consensus size: 101
5183 TTCTATATTA
* * * * *
5193 GTAATTGACCTTAGATTTCTATCCAG-TTCCCCGTGAGAACACCGAAACTAAGTTGTGGCCAAGC
1 GTAATTGACCTTAGATTTCGATCCGGACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCCGAGC
*
5257 GTAAGCCCTGGACTCTTTGTGAGAACAGCGACGTTC
66 GTAAGCCCTGGACTCTTTGTAAGAACAGCGACGTTC
* * *
5293 GTAATTGACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCTGAGT
1 GTAATTGACCTTAGATTTCGATCCGGACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCCGAGC
** *
5358 GTAAGCCCTGGACTCTTTGTAAGAATGGTGACGTTC
66 GTAAGCCCTGGACTCTTTGTAAGAACAGCGACGTTC
* * * * *
5394 GTAATTGACCTTAGATTTCGATCCGAACTCCCCGTGAGGACATCAAAACTAAATTGTGGCCGAAC
1 GTAATTGACCTTAGATTTCGATCCGGACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCCGAGC
*
5459 GTAAGCCCTGAACTCTTTGTAAGAAC
66 GTAAGCCCTGGACTCTTTGTAAGAAC
5485 GACAACATTC
Statistics
Matches: 169, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 23 0.14
101 146 0.86
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (101 bp):
GTAATTGACCTTAGATTTCGATCCGGACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCCGAGC
GTAAGCCCTGGACTCTTTGTAAGAACAGCGACGTTC
Found at i:15867 original size:3 final size:3
Alignment explanation
Indices: 15859--15884 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15849 CAATTTTAAT
15859 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
15885 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16845 original size:38 final size:36
Alignment explanation
Indices: 16764--16846 Score: 96
Period size: 38 Copynumber: 2.3 Consensus size: 36
16754 CGACTAGGAA
* ** *
16764 ATTGTCGAC-TTAAGGAAGAAGTAACGTCGACTAAG
1 ATTGTCGACTTTAAGGAAAAAACAACATCGACTAAG
16799 ATTGTCGACTTTAAGGAAAAAACAAGCATCGACTTAAG
1 ATTGTCGACTTTAAGGAAAAAACAA-CATCGAC-TAAG
*
16837 CTTGTCGACT
1 ATTGTCGACT
16847 ATCCAAGGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 9 0.22
36 12 0.30
37 6 0.15
38 13 0.32
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (36 bp):
ATTGTCGACTTTAAGGAAAAAACAACATCGACTAAG
Found at i:19490 original size:11 final size:11
Alignment explanation
Indices: 19474--19499 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19464 AAATTCGTGT
19474 TTGAAGACTTA
1 TTGAAGACTTA
19485 TTGAAGACTTA
1 TTGAAGACTTA
19496 TTGA
1 TTGA
19500 TGACAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
TTGAAGACTTA
Found at i:23747 original size:2 final size:2
Alignment explanation
Indices: 23740--23784 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
23730 CCTTCCAAAA
* *
23740 AT AT AT AT AC AT AT AT AT AT AT AT AT AT -T A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23780 AT AT A
1 AT AT A
23785 AGAATGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27595 original size:3 final size:3
Alignment explanation
Indices: 27587--27618 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27577 TTTTCACGTT
*
27587 TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
27619 ACCTAGCCCG
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:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:28280 original size:14 final size:14
Alignment explanation
Indices: 28261--28292 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28251 TTGGTTGTTG
28261 TGTTTGCATCTCCC
1 TGTTTGCATCTCCC
28275 TGTTTGCATCTCCC
1 TGTTTGCATCTCCC
28289 TGTT
1 TGTT
28293 AAATGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.31, G:0.16, T:0.47
Consensus pattern (14 bp):
TGTTTGCATCTCCC
Found at i:28511 original size:16 final size:16
Alignment explanation
Indices: 28457--28575 Score: 98
Period size: 16 Copynumber: 7.5 Consensus size: 16
28447 CAGACAGTTT
**
28457 TCTCGGGTCATTCAAG
1 TCTCGGGTCATTCGGG
* * *
28473 TTTCAGGTCATCCGGG
1 TCTCGGGTCATTCGGG
*
28489 T-TCGGGTAATTCGGG
1 TCTCGGGTCATTCGGG
* *
28504 TCTCGGGTCATACGAG
1 TCTCGGGTCATTCGGG
*
28520 TTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
* *
28536 TCTCAGGTCATTCAGG
1 TCTCGGGTCATTCGGG
* *
28552 T-TCTGGATCATTCGGA
1 TCTC-GGGTCATTCGGG
28568 TCTCGGGT
1 TCTCGGGT
28576 TGGGCGGATT
Statistics
Matches: 78, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
15 14 0.18
16 62 0.79
17 2 0.03
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:28563 original size:32 final size:31
Alignment explanation
Indices: 28459--28571 Score: 109
Period size: 32 Copynumber: 3.6 Consensus size: 31
28449 GACAGTTTTC
** * * *
28459 TCGGGTCATTCAAGTTTCAGGTCATCCGGGT
1 TCGGGTCATTCGGGTCTCAGGTCATACAGGT
* * *
28490 TCGGGTAATTCGGGTCTCGGGTCATACGAGTT
1 TCGGGTCATTCGGGTCTCAGGTCATAC-AGGT
*
28522 TCGGGTCATTCGGGTCTCAGGTCATTCAGGT
1 TCGGGTCATTCGGGTCTCAGGTCATACAGGT
* *
28553 TCTGGATCATTCGGATCTC
1 TC-GGGTCATTCGGGTCTC
28572 GGGTTGGGCG
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
31 26 0.39
32 40 0.61
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (31 bp):
TCGGGTCATTCGGGTCTCAGGTCATACAGGT
Found at i:29381 original size:23 final size:22
Alignment explanation
Indices: 29353--29406 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
29343 TCTCGGGTTA
*
29353 TTTGGGTTTCGGGTCATACGGG
1 TTTGGGTTACGGGTCATACGGG
* *
29375 TCTTGGGTTACTGGTCATTCGGG
1 T-TTGGGTTACGGGTCATACGGG
29398 TTTCGGGTT
1 TTT-GGGTT
29407 GGGCGGGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (22 bp):
TTTGGGTTACGGGTCATACGGG
Found at i:34874 original size:18 final size:19
Alignment explanation
Indices: 34835--34874 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
34825 GTGCTCCCAT
34835 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
34856 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
34874 T
1 T
34875 TCTCACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:40760 original size:26 final size:25
Alignment explanation
Indices: 40731--40783 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
40721 AATTTCCTTA
40731 TTCACCAGAAAAAAATATTTAATTTC
1 TTCA-CAGAAAAAAATATTTAATTTC
****
40757 TTCATTTCAAAAAATATTTAATTTC
1 TTCACAGAAAAAAATATTTAATTTC
40782 TT
1 TT
40784 AAATCAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (25 bp):
TTCACAGAAAAAAATATTTAATTTC
Found at i:40790 original size:24 final size:25
Alignment explanation
Indices: 40740--40790 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
40730 ATTCACCAGA
**
40740 AAAAAATATTTAATTTCTTCATTTC
1 AAAAAATATTTAATTTCTTCAAATC
40765 AAAAAATATTTAATTTCTT-AAATC
1 AAAAAATATTTAATTTCTTCAAATC
40789 AA
1 AA
40791 TAATTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAAATATTTAATTTCTTCAAATC
Found at i:49383 original size:34 final size:35
Alignment explanation
Indices: 49321--49388 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
49311 CCCCAACTGC
*
49321 TGCCCCATGAGTTCTTCACCAACTAATATTTAGTTGT
1 TGCCCCATGAG-T-TTCACCAACCAATATTTAGTTGT
49358 TGCCCCATGAG-TTCACCAACCAATATTTAGT
1 TGCCCCATGAGTTTCACCAACCAATATTTAGT
49389 CCCATCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 19 0.63
37 11 0.37
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (35 bp):
TGCCCCATGAGTTTCACCAACCAATATTTAGTTGT
Found at i:60867 original size:6 final size:6
Alignment explanation
Indices: 60856--60882 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
60846 ATTAGTGTAA
60856 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
60883 TATGCAAAGA
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:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Done.