Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015122.1 Corchorus olitorius cultivar O-4 contig15155, 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: 16788
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:638 original size:39 final size:39
Alignment explanation
Indices: 584--1593 Score: 1571
Period size: 39 Copynumber: 25.9 Consensus size: 39
574 AGGTCAGAAC
* *
584 TTATCAAAGTTGACTGGAAACATGTAATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
623 TTATCAAAGTTGACTGGAAACAGGTAATCTTTTTAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
662 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGTAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
701 TTA-CAAAGTTAACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
739 TTATCAAAGTTGACTGGAAACAGATCATCTTTTTAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
778 TTATCAAAATTGACTAGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
817 TTATCAAAGTTGATTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
856 TTATCAAAATTGACTGGAAACAAGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* * *
895 TTATTAAAGTTGACTGGAAACAGATCATCTTTTCAACAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
934 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
973 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1012 TTAT-ACAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCA-AAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1051 TTATCAAAGTTGACTGGAAACAGATCATCTTTTTAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
1090 TTATTAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* **
1129 TTATTAAAGTTGACTGGAAACAGGTCATCTTTTCATTAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1168 TTATCTAAA-TTGACTAGAAACAGGTCATCTTTTCAGCAA
1 TTATC-AAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
1207 TTATTAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1246 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTTAGTAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
1285 TTATTAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1324 TTATCAAAGTTGACTGGAAACAGGTCACCATTTT-AGTAT
1 TTATCAAAGTTGACTGGAAACAGGTCATC-TTTTCAGCAT
*
1363 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTTAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
*
1402 TTATTAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1441 TTATCAAAGTTGACTGCAAACAGGTCATCTCTTT-AGTAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCT-TTTCAGCAT
* * *
1480 TTATTAAAATTAACTGGAAACAGGTCATCTTTTCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* *
1519 TTATCAAAGTTGATTGGAAACAGGTCATCTTTGCAGCAT
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
* * *
1558 TTGTCAAAGTTGACTGGAGATAGGTCATCTTTTCAG
1 TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAG
1594 TAATTACTAA
Statistics
Matches: 888, Mismatches: 74, Indels: 18
0.91 0.08 0.02
Matches are distributed among these distances:
38 47 0.05
39 830 0.93
40 11 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (39 bp):
TTATCAAAGTTGACTGGAAACAGGTCATCTTTTCAGCAT
Found at i:1691 original size:33 final size:31
Alignment explanation
Indices: 1654--1775 Score: 120
Period size: 33 Copynumber: 3.8 Consensus size: 31
1644 TTCATTTTTT
1654 ATTCCAGACCTCAGACAGGTCTTTATCTTTCAA
1 ATTCCAGACCTCAGACAGGTCTTT-TCTTTC-A
* * *
1687 ATTCCAAACCTCAGACAGGTTTTTCTCCGTTTTA
1 ATTCCAGACCTCAGACAGGTCTTT-T-C-TTTCA
* *
1721 ATTTC-GACCTCAGACATGTCATTTTCTTTCA
1 ATTCCAGACCTCAGACAGGTC-TTTTCTTTCA
* *
1752 GTTTCAGACCTCAGACAGGTCTTT
1 ATTCCAGACCTCAGACAGGTCTTT
1776 CTTAGTTTCC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
31 11 0.15
32 15 0.20
33 36 0.49
34 9 0.12
35 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (31 bp):
ATTCCAGACCTCAGACAGGTCTTTTCTTTCA
Found at i:4117 original size:2 final size:2
Alignment explanation
Indices: 4110--4141 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4100 TTTAACATTG
4110 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
4142 CTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4148 original size:2 final size:2
Alignment explanation
Indices: 4143--4167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4133 TATATATATC
4143 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
4168 CTACTTTCAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5792 original size:35 final size:35
Alignment explanation
Indices: 5752--5917 Score: 201
Period size: 35 Copynumber: 4.7 Consensus size: 35
5742 AATTTCATTC
5752 AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT
*
5787 AAGTTTTCAAATTGGGAAAGTTCCCATCAG-TTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT
* * *
5821 AAATTTTCAAATCGGGAAAGTTCCCACCAGTTTTCA
1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTT-T
* * * * *
5857 AAGTTTTTTAAGTCGGGAAAGTTCCCATCAGGTTTT
1 AAG-TTTTCAAATTGGGAAAGTTCCCACCAGTTTTT
*
5893 -AGTTTTCAATTTAGGGAAAGTTCCC
1 AAGTTTTCAAATT-GGGAAAGTTCCC
5918 GTCATTTTCA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
34 38 0.34
35 46 0.41
36 2 0.02
37 27 0.24
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (35 bp):
AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT
Found at i:14303 original size:14 final size:15
Alignment explanation
Indices: 14277--14306 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
14267 CTAAGTCCAA
14277 TCCTTGCTTATTTAT
1 TCCTTGCTTATTTAT
14292 TCCTTG-TTATTTAT
1 TCCTTGCTTATTTAT
14306 T
1 T
14307 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (15 bp):
TCCTTGCTTATTTAT
Found at i:15536 original size:14 final size:16
Alignment explanation
Indices: 15517--15552 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
15507 AAGGACCTTG
15517 CCCAGGCGCGGG-T-C
1 CCCAGGCGCGGGCTAC
15531 CCCAGGCGCGGGCTAC
1 CCCAGGCGCGGGCTAC
15547 CCCAGG
1 CCCAGG
15553 AGGAGTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.11, C:0.44, G:0.39, T:0.06
Consensus pattern (16 bp):
CCCAGGCGCGGGCTAC
Found at i:15603 original size:21 final size:21
Alignment explanation
Indices: 15577--15624 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
15567 TTGCTTCGAG
15577 ACCTTGCCTAGGCACGGGTCA
1 ACCTTGCCTAGGCACGGGTCA
*
15598 ACCTTGCCTAGGCGCGGGTCA
1 ACCTTGCCTAGGCACGGGTCA
15619 ACCTTG
1 ACCTTG
15625 TCCAGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (21 bp):
ACCTTGCCTAGGCACGGGTCA
Found at i:16439 original size:29 final size:28
Alignment explanation
Indices: 16274--16456 Score: 197
Period size: 28 Copynumber: 6.4 Consensus size: 28
16264 TTGCTTCTCG
16274 TTTTGGTCATTTTTCATGACCAGGGGCA
1 TTTTGGTCATTTTTCATGACCAGGGGCA
*
16302 TTTTGGTCATTTTACATGACCAGGGG-A
1 TTTTGGTCATTTTTCATGACCAGGGGCA
* *
16329 TTTTTGGTCATTTTACATGTCCAGGGGCA
1 -TTTTGGTCATTTTTCATGACCAGGGGCA
* ** * * *
16358 TTCTGGTCATCCTTCTAGGTCTAGGGGGCA
1 TTTTGGTCATTTTTC-ATGACCA-GGGGCA
* * * *
16388 TTGTGATCATTATTCATGTCCAGGGGCA
1 TTTTGGTCATTTTTCATGACCAGGGGCA
*
16416 TTTTGGTCATTTTGTCAGGACCAGGGGCA
1 TTTTGGTCATTTT-TCATGACCAGGGGCA
16445 TTTTGGTCATTT
1 TTTTGGTCATTT
16457 CAAGTTTATT
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.01
28 77 0.59
29 36 0.27
30 17 0.13
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (28 bp):
TTTTGGTCATTTTTCATGACCAGGGGCA
Found at i:16442 original size:58 final size:55
Alignment explanation
Indices: 16274--16456 Score: 206
Period size: 58 Copynumber: 3.2 Consensus size: 55
16264 TTGCTTCTCG
* * *
16274 TTTTGGTCATTTTTCATGACCAGGGGCATTTTGGTCATTTTACATGACCAGGGG-A
1 TTTTGGTCA-TTTTCATGTCCAGGGGCATTTTGGTCATTTTTCAGGACCAGGGGCA
* ** * *
16329 TTTTTGGTCATTTTACATGTCCAGGGGCATTCTGGTCATCCTTCTAGGTCTAGGGGGCA
1 -TTTTGGTCATTTT-CATGTCCAGGGGCATTTTGGTCATTTTTC-AGGACCA-GGGGCA
* *
16388 TTGTGATCATTATTCATGTCCAGGGGCATTTTGGTCATTTTGTCAGGACCAGGGGCA
1 TTTTGGTCATT-TTCATGTCCAGGGGCATTTTGGTCATTTT-TCAGGACCAGGGGCA
16445 TTTTGGTCATTT
1 TTTTGGTCATTT
16457 CAAGTTTATT
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
55 4 0.04
56 34 0.33
57 19 0.18
58 42 0.40
59 5 0.05
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (55 bp):
TTTTGGTCATTTTCATGTCCAGGGGCATTTTGGTCATTTTTCAGGACCAGGGGCA
Done.