Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011360.1 Corchorus olitorius cultivar O-4 contig11393, 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: 52720
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:17223 original size:2 final size:2
Alignment explanation
Indices: 17216--17252 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
17206 AATTATTATC
17216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
17253 TATTTTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19601 original size:27 final size:27
Alignment explanation
Indices: 19571--19638 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
19561 GGTCATCCAG
*
19571 GGGCATTTTGGTCATTTGTACATTCAA
1 GGGCATTTTGGTCATTTGCACATTCAA
*
19598 GGGCATTTTGGTCATTTGCACATTCAG
1 GGGCATTTTGGTCATTTGCACATTCAA
19625 GGGCATTTTGGTCA
1 GGGCATTTTGGTCA
19639 CTTTAGTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.38
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTGCACATTCAA
Found at i:23771 original size:16 final size:16
Alignment explanation
Indices: 23736--23786 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
23726 TTTAAAAATC
*
23736 ACAATTAAA-AAGAAA
1 ACAATTAAACTAGAAA
*
23751 GCAATTAAACTAGAAA
1 ACAATTAAACTAGAAA
*
23767 ACAATTATACTAGAAA
1 ACAATTAAACTAGAAA
23783 ACAA
1 ACAA
23787 AACAAAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.18
Consensus pattern (16 bp):
ACAATTAAACTAGAAA
Found at i:31692 original size:48 final size:48
Alignment explanation
Indices: 31606--31698 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
31596 GTGAATATGA
* * *
31606 GAGCACTCAAATTGATAAATGTACCATTTGGAGTAATGCTGAATGAATG
1 GAGCACTCAAATTGATAAATG-ACCATGTGGAGGAATGCTAAATGAATG
* *
31655 GAGCTCTCAAATTGATAATATG-CTATGTGGAGGAATGCTAAATG
1 GAGCACTCAAATTGATAA-ATGACCATGTGGAGGAATGCTAAATG
31699 GAGGAACTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 18 0.47
49 17 0.45
50 3 0.08
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (48 bp):
GAGCACTCAAATTGATAAATGACCATGTGGAGGAATGCTAAATGAATG
Found at i:32056 original size:22 final size:21
Alignment explanation
Indices: 31993--32090 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 21
31983 AGGAAGGTTA
* * *
31993 CAAAATTCATATGGAGTTTAT
1 CAAATTTCATATGGTGATTAT
* *
32014 CACAATTTTATA-GGTAATTAT
1 CA-AATTTCATATGGTGATTAT
32035 CGAAATTTCATATGGTGATTAT
1 C-AAATTTCATATGGTGATTAT
* *
32057 CAAAATTCAATAAGGT-AGTTAT
1 CAAATTTC-ATATGGTGA-TTAT
32079 CCAAATTTCATA
1 -CAAATTTCATA
32091 AAAATATTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
21 24 0.39
22 30 0.49
23 7 0.11
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (21 bp):
CAAATTTCATATGGTGATTAT
Found at i:32057 original size:43 final size:44
Alignment explanation
Indices: 31993--32090 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
31983 AGGAAGGTTA
* * * **
31993 CAAAATTCATATGGAGTTTATCACAATTTTAT-AGGTAATTATC
1 CAAATTTCATATGGAGATTATCAAAATTCAATAAGGTAATTATC
* * *
32036 GAAATTTCATATGGTGATTATCAAAATTCAATAAGGTAGTTATC
1 CAAATTTCATATGGAGATTATCAAAATTCAATAAGGTAATTATC
32080 CAAATTTCATA
1 CAAATTTCATA
32091 AAAATATTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 25 0.56
44 20 0.44
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (44 bp):
CAAATTTCATATGGAGATTATCAAAATTCAATAAGGTAATTATC
Found at i:32085 original size:44 final size:43
Alignment explanation
Indices: 31965--32090 Score: 116
Period size: 43 Copynumber: 3.0 Consensus size: 43
31955 ATCTCACAGA
* *
31965 GAGATTATCAAAAATC-ATAGG-AAGGTTA--CAAAATTCATATG
1 GAGATTATCAAAATTCAATAGGTAA--TTATCCAAATTTCATATG
* * ** *
32006 GAGTTTATCACAATTTTATAGGTAATTATCGAAATTTCATATG
1 GAGATTATCAAAATTCAATAGGTAATTATCCAAATTTCATATG
* *
32049 GTGATTATCAAAATTCAATAAGGTAGTTATCCAAATTTCATA
1 GAGATTATCAAAATTCAAT-AGGTAATTATCCAAATTTCATA
32091 AAAATATTCA
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
41 15 0.22
42 5 0.07
43 27 0.40
44 20 0.30
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (43 bp):
GAGATTATCAAAATTCAATAGGTAATTATCCAAATTTCATATG
Found at i:37608 original size:15 final size:15
Alignment explanation
Indices: 37588--37617 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37578 CTAACCCTTA
37588 ATTTTTGTTTCTTTT
1 ATTTTTGTTTCTTTT
37603 ATTTTTGTTTCTTTT
1 ATTTTTGTTTCTTTT
37618 TTTAGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (15 bp):
ATTTTTGTTTCTTTT
Found at i:38413 original size:18 final size:18
Alignment explanation
Indices: 38390--38426 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38380 AAAGGGTAAT
*
38390 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
38408 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
38426 T
1 T
38427 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:39293 original size:22 final size:21
Alignment explanation
Indices: 39268--39321 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
39258 GAAGTTCGTG
39268 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
39290 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
39309 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
39322 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:46360 original size:29 final size:29
Alignment explanation
Indices: 46327--46383 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
46317 TTCTGAATTC
*
46327 TGAAGTGAATCGATGAATGGGAGTGGTGG
1 TGAAGTGAATCGATGAATGAGAGTGGTGG
*
46356 TGAAGTGAATCGGTGAATGAGAGTGGTG
1 TGAAGTGAATCGATGAATGAGAGTGGTG
46384 AAGCCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.44, T:0.25
Consensus pattern (29 bp):
TGAAGTGAATCGATGAATGAGAGTGGTGG
Found at i:46502 original size:2 final size:2
Alignment explanation
Indices: 46495--46532 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
46485 TTGCCACATC
46495 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
46533 TCTATTAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50083 original size:42 final size:43
Alignment explanation
Indices: 50028--50121 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
50018 AGTGCATTAC
*
50028 CTAA-ATTGTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTGTACCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
50069 CTAATATTTTACTCCTCCATCTCTAGATAATTCGTCAAAATAAAG
1 CTAATATTGTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
50114 CTAATATT
1 CTAATATT
50122 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 37 0.80
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.35
Consensus pattern (43 bp):
CTAATATTGTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:50816 original size:51 final size:51
Alignment explanation
Indices: 50735--50838 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
50725 TTAATCCTCA
50735 ATTTCGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
1 ATTTCGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
*
50786 ATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
1 ATTTCGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
50837 AT
1 AT
50839 GTTACCAAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (51 bp):
ATTTCGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
Done.