Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014229.1 Corchorus olitorius cultivar O-4 contig14262, 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: 30813
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1794 original size:45 final size:45
Alignment explanation
Indices: 1743--1836 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
1733 GCACATACCA
*
1743 ATTATCATCATTTATATTTGTGGATTTGACATGAAATACCTTGAT
1 ATTATCATCAATTATATTTGTGGATTTGACATGAAATACCTTGAT
*
1788 ATTATCATCAATTATATTTGTGGATTTGACATGAAATTCCTTGAT
1 ATTATCATCAATTATATTTGTGGATTTGACATGAAATACCTTGAT
1833 ATTA
1 ATTA
1837 ATAGAGATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (45 bp):
ATTATCATCAATTATATTTGTGGATTTGACATGAAATACCTTGAT
Found at i:3870 original size:168 final size:169
Alignment explanation
Indices: 3588--3904 Score: 444
Period size: 168 Copynumber: 1.9 Consensus size: 169
3578 AAAATGTCTG
* *
3588 TTTTAGCTAAAAGAAAGAAGAAAGATAGTGATAAATTCTGATCGGATAGTAATTTGCCAGAAAAT
1 TTTTAGCTAAAAGAAAGAAGAAAAATAGTGATAAATTCTGATCGGATAGTAATTTACCAGAAAA-
* **
3653 TATAACTATTAGGAAAATTAACATTTTCCGTTTATGATTTTCAGGTAAATTGCTGATCCGACTAG
65 TATAACTACTAGGAAAATTAACATTTTCCGTTTATGATTTTCAGGTAAATCACTGATCCGACTAG
3718 AAATT-ATTTCTACATGGAATAGATCTAGAATTTCATGCTA
130 -AATTCATTTCTACATGGAATAGATCTAGAATTTCATGCTA
* * * **
3758 TTTTAGCTGAAAGAAAGAA-AATATAATAGTGATGAATTCTGATCGGTTAGTGGTTTACCA-AAA
1 TTTTAGCTAAAAGAAAGAAGAA-A-AATAGTGATAAATTCTGATCGGATAGTAATTTACCAGAAA
* * *
3821 A-ATAATTACTAGGAAAATTAACATTTTCCGTTTATGATTTTCTGGTAAATCACTGATCCGATTA
64 ATATAACTACTAGGAAAATTAACATTTTCCGTTTATGATTTTCAGGTAAATCACTGATCCGACTA
*
3885 GAATTCGTTTCTACATGGAA
129 GAATTCATTTCTACATGGAA
3905 AACTCACATC
Statistics
Matches: 130, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
167 4 0.03
168 71 0.55
169 2 0.02
170 23 0.18
171 30 0.23
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (169 bp):
TTTTAGCTAAAAGAAAGAAGAAAAATAGTGATAAATTCTGATCGGATAGTAATTTACCAGAAAAT
ATAACTACTAGGAAAATTAACATTTTCCGTTTATGATTTTCAGGTAAATCACTGATCCGACTAGA
ATTCATTTCTACATGGAATAGATCTAGAATTTCATGCTA
Found at i:9659 original size:32 final size:33
Alignment explanation
Indices: 9623--9703 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
9613 TACACGATTC
9623 AACCCCTTTCAAATGTATTATA-AAAAAAAAAA
1 AACCCCTTTCAAATGTATTATATAAAAAAAAAA
9655 AACCCCATTT-AAATGTATTATATAAAAAAAAAA
1 AACCCC-TTTCAAATGTATTATATAAAAAAAAAA
9688 AA-CCC-TTCAAATGTAT
1 AACCCCTTTCAAATGTAT
9704 ATACCACACG
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
30 2 0.04
31 8 0.17
32 21 0.46
33 15 0.33
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (33 bp):
AACCCCTTTCAAATGTATTATATAAAAAAAAAA
Found at i:16959 original size:28 final size:28
Alignment explanation
Indices: 16919--16974 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
16909 AAAAAAAGTC
*
16919 TTCTCCTTTTATGATTTGGATTTGACTA
1 TTCTCCTTCTATGATTTGGATTTGACTA
16947 TTCTCCTTCTATGATTTGGATTTGACTA
1 TTCTCCTTCTATGATTTGGATTTGACTA
16975 CAACTACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (28 bp):
TTCTCCTTCTATGATTTGGATTTGACTA
Found at i:27642 original size:191 final size:192
Alignment explanation
Indices: 27316--27675 Score: 607
Period size: 191 Copynumber: 1.9 Consensus size: 192
27306 TATAACTTAT
*
27316 TACAGCTCCCTCTAAATTTTGTCCACATTTTGCCATTGAAACAAGATGCCAGAACATCCTAGGAA
1 TACAGCTCCCTCTAAATTTTCTCCACATTTTGCCATTGAAACAAGATGCCAGAACATCCTAGGAA
* *
27381 AACGAATATAACTTAGATTATGGCATCCAACACCCGGGTTCTATGGTTTCAAACTACCTTCAATT
66 AACGAACATAACTTAAATTATGGCATCCAACACCCGGGTTCTATGGTTTCAAACTACCTTCAATT
*
27446 TCAAAAAATCTACCCCTAAGATGTTATAGGCCAAGTATTGTATGGCATCCAACAAGATGTTA
131 TCAAAAAATCTACCCCTAAGATGTTAAAGGCCAAGTATTGTATGGCATCCAACAAGATGTTA
** * *
27508 TACAGCTCCCTCTCTATTTTCTGCACATTTTGCCATTG-AACAAGATGGCAGAACATCCTAGGAA
1 TACAGCTCCCTCTAAATTTTCTCCACATTTTGCCATTGAAACAAGATGCCAGAACATCCTAGGAA
*
27572 AACGAACATAACTTAAATTATGGCATCCAACACCCGGGTTCTATGGTTTCAAACTACCTT-TATG
66 AACGAACATAACTTAAATTATGGCATCCAACACCCGGGTTCTATGGTTTCAAACTACCTTCAAT-
*
27636 TTCAAAAAATCTACCCCTAAGATGTTAAAGGGCAAGTATT
130 TTCAAAAAATCTACCCCTAAGATGTTAAAGGCCAAGTATT
27676 TTTGTACTTC
Statistics
Matches: 157, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
190 2 0.01
191 121 0.77
192 34 0.22
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (192 bp):
TACAGCTCCCTCTAAATTTTCTCCACATTTTGCCATTGAAACAAGATGCCAGAACATCCTAGGAA
AACGAACATAACTTAAATTATGGCATCCAACACCCGGGTTCTATGGTTTCAAACTACCTTCAATT
TCAAAAAATCTACCCCTAAGATGTTAAAGGCCAAGTATTGTATGGCATCCAACAAGATGTTA
Found at i:29602 original size:2 final size:2
Alignment explanation
Indices: 29595--29650 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
29585 TTAAGTTCTA
29595 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29637 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
29651 TTCAGCTATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.