Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019273.1 Corchorus olitorius cultivar O-4 contig19306, 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: 22670
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Found at i:3286 original size:76 final size:75
Alignment explanation
Indices: 3204--3605 Score: 214
Period size: 77 Copynumber: 5.2 Consensus size: 75
3194 CGGTCTCATT
* ** * *
3204 GGAGACGTTCGTCTATTTTGCTT-TTACATGGGGACACCTGGGCCGGTGTTCGACCGTTTGTGAC
1 GGAGACGATCGTCTATTTTGCTTGTTAC--GGGGACACCAAGGCCGGTGCTCGACCGTTTGCGAC
3268 GAAAGTCTCTAA
64 GAAAGTCTCTAA
* * * ** *
3280 GGAGACGATCGTTTTGTTTTGTTTGTTACGGGGACACCAAGGTTGGTGCTCGGCCGTTTGCGACG
1 GGAGACGATCG-TCTATTTTGCTTGTTACGGGGACACCAAGGCCGGTGCTCGACCGTTTGCGACG
3345 AAAGTCTCTAA
65 AAAGTCTCTAA
* * * ** * *
3356 GGAGACGATCGTTTTGTTTTGTTTTGTTTCTTTTACGGGGACACCAAGGTTGGTGTTCGGCCGTT
1 GGAGACGATCG-TCTATTTTG-CTTG------TTACGGGGACACCAAGGCCGGTGCTCGACCGTT
* ** * *
3421 CGTAACGAGAGTCTCTGA
58 TGCGACGAAAGTCTCTAA
* * * ** * * **
3439 GGAGACGATCGTTTTATTTTGTTTTTTTACGGGGACACCAAGGTTGGTGTTC-AGCCGTTGGTAA
1 GGAGACGATCG-TCTATTTTG-CTTGTTACGGGGACACCAAGGCCGGTGCTCGA-CCGTTTGCGA
*
3503 CGAGAGTCTCTAA
63 CGAAAGTCTCTAA
* * ** * ** * * * **
3516 GGAGACGATCGTTTTGTTTTTTTTTTTTCACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGTAA
1 GGAGACGATCG-TCT-ATTTTGCTTGTT-ACGGGGACACCAAGGCCGGTGCTCGACCGTTTGCGA
* *
3581 CGAGAGTCTCAAA
63 CGAAAGTCTCTAA
3594 GGAGACGATCGT
1 GGAGACGATCGT
3606 TTTGTTTGCT
Statistics
Matches: 286, Mismatches: 27, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
76 71 0.25
77 82 0.29
78 64 0.22
83 69 0.24
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.34
Consensus pattern (75 bp):
GGAGACGATCGTCTATTTTGCTTGTTACGGGGACACCAAGGCCGGTGCTCGACCGTTTGCGACGA
AAGTCTCTAA
Found at i:3503 original size:77 final size:77
Alignment explanation
Indices: 3248--3612 Score: 516
Period size: 78 Copynumber: 4.7 Consensus size: 77
3238 CACCTGGGCC
* * * * *
3248 GGTGTTCGACCGTTTGTGACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTTG-TTTGTTACGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTTTTACGGG
3312 GACACCAAGGTT
66 GACACCAAGGTT
* * ** *
3324 GGTGCTCGGCCGTTTGCGACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTGTTTCTTT
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATC-----GTTTTGTTTTGTTT-TTT
3389 TACGGGGACACCAAGGTT
60 TACGGGGACACCAAGGTT
* *
3407 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTGAGGAGACGATCGTTTTATTTTGTTTTTTTACGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTTTTACGGG
3472 GACACCAAGGTT
66 GACACCAAGGTT
* * *
3484 GGTGTTCAGCCGTTGGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTTCACGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTTTT-ACGG
3549 GGACACCAAGGTT
65 GGACACCAAGGTT
*
3562 GGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACGATCGTTTTGTTT
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTT
3613 GCTTCTTCAA
Statistics
Matches: 262, Mismatches: 19, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
76 39 0.15
77 76 0.29
78 78 0.30
81 11 0.04
82 2 0.01
83 56 0.21
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.35
Consensus pattern (77 bp):
GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTTTTACGGG
GACACCAAGGTT
Found at i:3580 original size:155 final size:158
Alignment explanation
Indices: 3248--3608 Score: 541
Period size: 155 Copynumber: 2.3 Consensus size: 158
3238 CACCTGGGCC
* * * * *
3248 GGTGTTCGACCGTTTGTGACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTGTTACGGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTATTTTGTTTGTTACGGGG
* * *
3313 ACACCAAGGTTGGTGCTCGGCCGTTTGCGACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTTGT
66 ACACCAAGGTTGGTGCTCAGCCGTTGGCAACGAAAGTCTCTAAGGAGACGATCGTTTTG-TTTGT
*
3378 TTTGTTTCTTTTACGGGGACACCAAGGTT
130 TTTGTTTCTTTCACGGGGACACCAAGGTT
* *
3407 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTGAGGAGACGATCGTTTTATTTTGTTTTTTTACGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTATTTTG-TTTGTTACGGG
* * *
3472 GACACCAAGGTTGGTGTTCAGCCGTTGGTAACGAGAGTCTCTAAGGAGACGATCGTTTTG-TT-T
65 GACACCAAGGTTGGTGCTCAGCCGTTGGCAACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTGT
3535 TTT-TTT-TTTCACGGGGACACCAAGGTT
130 TTTGTTTCTTTCACGGGGACACCAAGGTT
*
3562 GGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACGATCGTTTT
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTT
3609 GTTTGCTTCT
Statistics
Matches: 185, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
155 65 0.35
156 3 0.02
157 4 0.02
158 2 0.01
159 47 0.25
160 64 0.35
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (158 bp):
GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTATTTTGTTTGTTACGGGG
ACACCAAGGTTGGTGCTCAGCCGTTGGCAACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTGTT
TTGTTTCTTTCACGGGGACACCAAGGTT
Found at i:3581 original size:78 final size:77
Alignment explanation
Indices: 3248--3612 Score: 507
Period size: 77 Copynumber: 4.7 Consensus size: 77
3238 CACCTGGGCC
* * * * * *
3248 GGTGTTCGACCGTTTGTGACGAAAGTCTCTAAGGAGACGATCGTTTTG-TTTTGTTTGTTACGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTTACGGG
3312 GACACCAAGGTT
66 GACACCAAGGTT
* * ** *
3324 GGTGCTCGGCCGTTTGCGACGAAAGTCTCTAAGGAGACGATCGTTTTGTTTTGTTTTGTTTCTTT
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTG---T-TTTT-TTT-TTT
3389 TACGGGGACACCAAGGTT
60 TACGGGGACACCAAGGTT
* * *
3407 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTGAGGAGACGATCGTTTTATTTTGTTTTTTTACGGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTTACGGG
3472 GACACCAAGGTT
66 GACACCAAGGTT
* *
3484 GGTGTTCAGCCGTTGGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTTCACGG
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTT-ACGG
3549 GGACACCAAGGTT
65 GGACACCAAGGTT
*
3562 GGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACGATCGTTTTGTTT
1 GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTT
3613 GCTTCTTCAA
Statistics
Matches: 260, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
76 45 0.17
77 76 0.29
78 68 0.26
79 3 0.01
80 1 0.00
81 4 0.02
82 2 0.01
83 61 0.23
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.35
Consensus pattern (77 bp):
GGTGTTCGGCCGTTCGTAACGAGAGTCTCTAAGGAGACGATCGTTTTGTTTTTTTTTTTTACGGG
GACACCAAGGTT
Found at i:18765 original size:20 final size:17
Alignment explanation
Indices: 18727--18774 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
18717 AAGAAAGGAG
*
18727 AAAAAAAAAAACTTCCT
1 AAAAAAAAAAACTACCT
*
18744 AATTAAAAAAAAACTAAGCT
1 AA--AAAAAAAAACT-ACCT
18764 AAAAAAAAAAA
1 AAAAAAAAAAA
18775 GAACCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 11 0.42
20 4 0.15
ACGTcount: A:0.73, C:0.10, G:0.02, T:0.15
Consensus pattern (17 bp):
AAAAAAAAAAACTACCT
Found at i:21753 original size:13 final size:13
Alignment explanation
Indices: 21735--21760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21725 CGAAAGTTCT
21735 TATAAACTAATCA
1 TATAAACTAATCA
21748 TATAAACTAATCA
1 TATAAACTAATCA
21761 AACTTACTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TATAAACTAATCA
Done.