Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_951 ID=scaffold_951-JGI_221_v2.0
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: 2116
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:89 original size:54 final size:54
Alignment explanation
Indices: 3--174 Score: 148
Period size: 54 Copynumber: 3.2 Consensus size: 54
1 TA
* * * ** *
3 TTACGAATCTCGAGGTCTAATGATTTACGATCACGGCCTTCTACTTACCGTATT
1 TTACGAATCTCGTGGTCCAATAATTTACGATCACAACCTTCTACTTACCGGATT
* * * **
57 TTATGAATCTCGTGGTCCATTAATTTATGATCACAACCTTCTACTTATGGGATT
1 TTACGAATCTCGTGGTCCAATAATTTACGATCACAACCTTCTACTTACCGGATT
* ** * ** * *
111 TTACGAATCTCGTAGTCCGCTAATTTACAATCATGACGTTCTACTGA-CGTGATT
1 TTACGAATCTCGTGGTCCAATAATTTACGATCACAACCTTCTACTTACCG-GATT
*
165 CTACGAATCT
1 TTACGAATCT
175 AAACATGTCG
Statistics
Matches: 94, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
53 1 0.01
54 93 0.99
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.37
Consensus pattern (54 bp):
TTACGAATCTCGTGGTCCAATAATTTACGATCACAACCTTCTACTTACCGGATT
Found at i:506 original size:54 final size:53
Alignment explanation
Indices: 446--622 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 53
436 CACGAGCTTT
* * * *
446 TACTTACGGGTTATTATGAATCTCGAGGTTTGTTGATTTACGATGACTACTTTC
1 TACTTACGGGTT-TTACGAATCTCGAGGTTTGCTGATTTACGATGACAACCTTC
* * * * * *
500 TACTTACGGGATTTTACGAATCTTGCA-ATTCGGTGATTTACGATGACGACCATC
1 TACTTACGGG-TTTTACGAATCTCG-AGGTTTGCTGATTTACGATGACAACCTTC
* * * * *
554 TATTTACAGGATTTTACGAATCTCGTGGTCTGCTGATTTACGATCACAACCTTC
1 TACTTAC-GGGTTTTACGAATCTCGAGGTTTGCTGATTTACGATGACAACCTTC
* *
608 TACTTATGGGATTTA
1 TACTTACGGGTTTTA
623 ACAAATCTTG
Statistics
Matches: 96, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
53 6 0.06
54 85 0.89
55 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (53 bp):
TACTTACGGGTTTTACGAATCTCGAGGTTTGCTGATTTACGATGACAACCTTC
Found at i:619 original size:108 final size:108
Alignment explanation
Indices: 463--735 Score: 280
Period size: 108 Copynumber: 2.5 Consensus size: 108
453 GGGTTATTAT
* * * * * * * *
463 GAATCTCGAGGTTTGTTGATTTACGATGACTACTTTCTACTTACGGGATTTTACGAATCTTGCAA
1 GAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACAAATCTTGCAA
**** * *
528 TTCGGTGATTTACGATGACGACCATCTA-TTTA-CAGGATTTTAC
66 TGAACTGATTTACGATCACGACCATCTACTTAATCA--ATTTTAC
* ***
571 GAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTAACAAATCTTGTGG
1 GAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACAAATCTTGCAA
** *
636 TGAACTGATTTGTGATCACGACCTTCTACTTAATCAATTTTAC
66 TGAACTGATTTACGATCACGACCATCTACTTAATCAATTTTAC
* * * * *
679 GAATCTCGTGGTCTGCTAATTCACAATCACAATCGTCTACTTATGGGATTTTACAAA
1 GAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACAAA
736 CCTCTCAATC
Statistics
Matches: 136, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
108 131 0.96
109 3 0.02
110 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (108 bp):
GAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACAAATCTTGCAA
TGAACTGATTTACGATCACGACCATCTACTTAATCAATTTTAC
Found at i:630 original size:54 final size:54
Alignment explanation
Indices: 464--735 Score: 188
Period size: 54 Copynumber: 5.0 Consensus size: 54
454 GGTTATTATG
* * * * * * * *
464 AATCTCGAGGTTTGTTGATTTACGATGACTACTTTCTACTTACGGGATTTTACG
1 AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACA
* *** * * * * * ** *
518 AATCTTGCAAT-TCGGTGATTTACGATGACGACCATCTATTTACAGGATTTTACG
1 AATCTCGTGGTCT-GCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACA
*
572 AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTAACA
1 AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACA
* *** ** * ** *
626 AATCTTGTGGTGAACTGATTTGTGATCACGACCTTCTACTTAAT-CAATTTTACG
1 AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTT-ATGGGATTTTACA
* * * * *
680 AATCTCGTGGTCTGCTAATTCACAATCACAATCGTCTACTTATGGGATTTTACA
1 AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACA
734 AA
1 AA
736 CCTCTCAATC
Statistics
Matches: 165, Mismatches: 49, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
53 3 0.02
54 159 0.96
55 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (54 bp):
AATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTTACA
Found at i:767 original size:108 final size:108
Alignment explanation
Indices: 564--775 Score: 237
Period size: 108 Copynumber: 2.0 Consensus size: 108
554 TATTTACAGG
* * * * *
564 ATTTTACGAATCTCGTGGTCTGCTGATTTACGATCACAACCTTCTACTTATGGGATTTAACAAAT
1 ATTTTACGAATCTCGTGGTCTGCTAATTCACAATCACAACCGTCTACTTATGGGATTTAACAAAC
*** * * ***
629 CTTGTGGTGAACTGATTTGTGATCACGACCTTCTACTTAATCA
66 CTTGCAATCAACTAATTTACAATCACGACCTTCTACTTAATCA
* *
672 ATTTTACGAATCTCGTGGTCTGCTAATTCACAATCACAATCGTCTACTTATGGGATTTTACAAAC
1 ATTTTACGAATCTCGTGGTCTGCTAATTCACAATCACAACCGTCTACTTATGGGATTTAACAAAC
** * *
737 CTCT-CAATCCGCTAATTTACAATCATGACCTTTTACTTA
66 CT-TGCAATCAACTAATTTACAATCACGACCTTCTACTTA
776 CTGGCTTTTA
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
108 83 0.99
109 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (108 bp):
ATTTTACGAATCTCGTGGTCTGCTAATTCACAATCACAACCGTCTACTTATGGGATTTAACAAAC
CTTGCAATCAACTAATTTACAATCACGACCTTCTACTTAATCA
Found at i:1456 original size:54 final size:54
Alignment explanation
Indices: 1398--1735 Score: 227
Period size: 54 Copynumber: 6.3 Consensus size: 54
1388 TTGATTTACA
* * *** * *
1398 ATCACAACCTTTTACTTATGGGATTTTTTGAATCTCAAGGTCTATTTATTTATG
1 ATCACGACCTTCTACTTATGGGATTTTAACAATCTCAAGGTCTACTAATTTATG
* *
1452 ATCACGACCTTCTACTTATGGGATTTTAACAATCTCATGGTCTGCTAATTTATG
1 ATCACGACCTTCTACTTATGGGATTTTAACAATCTCAAGGTCTACTAATTTATG
* ** * * *
1506 ATCACGACCTTCTACTTACT-AGATTTT-ACAAATCTCGTGGTCTGCTGATTTACG
1 ATCACGACCTTCTACTTA-TGGGATTTTAAC-AATCTCAAGGTCTACTAATTTATG
* ** ** * *
1560 ATCACAACCTTCTACTTACAGGATTTT-ACGAATCTCGCGGTCCACTAGTTTATG
1 ATCACGACCTTCTACTTATGGGATTTTAAC-AATCTCAAGGTCTACTAATTTATG
* * * * ** * * *
1614 ATCATGATCTTCTACTTAAGGAATTTT-ACAAATCTCGTGGTCTGCTGATTTACG
1 ATCACGACCTTCTACTTATGGGATTTTAAC-AATCTCAAGGTCTACTAATTTATG
* * * ** ** * * *
1668 ATCACTACCTTTTGCTTATCAGATTTT-ACGAATCTCGTGGTCCACTGATTTACG
1 ATCACGACCTTCTACTTATGGGATTTTAAC-AATCTCAAGGTCTACTAATTTATG
1722 ATCACGACCTTCTA
1 ATCACGACCTTCTA
1736 GTGACGTAAT
Statistics
Matches: 230, Mismatches: 51, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
53 2 0.01
54 227 0.99
55 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (54 bp):
ATCACGACCTTCTACTTATGGGATTTTAACAATCTCAAGGTCTACTAATTTATG
Found at i:1584 original size:108 final size:108
Alignment explanation
Indices: 1445--1735 Score: 374
Period size: 108 Copynumber: 2.7 Consensus size: 108
1435 AGGTCTATTT
* * ** * **
1445 ATTTATGATCACGACCTTCTACTTATGGGATTTTAAC-AATCTCATGGTCTGCTAATTTATGATC
1 ATTTACGATCACAACCTTCTACTTACAGGATTTT-ACGAATCTCGTGGTCCACTAATTTATGATC
1509 ACGACCTTCTACTTACTA-G-ATTTTACAAATCTCGTGGTCTGCTG
65 ACGACCTTCTACTTA--AGGAATTTTACAAATCTCGTGGTCTGCTG
* *
1553 ATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCGCGGTCCACTAGTTTATGATCA
1 ATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCGTGGTCCACTAATTTATGATCA
* *
1618 TGATCTTCTACTTAAGGAATTTTACAAATCTCGTGGTCTGCTG
66 CGACCTTCTACTTAAGGAATTTTACAAATCTCGTGGTCTGCTG
* * * * *
1661 ATTTACGATCACTACCTTTTGCTTATCA-GATTTTACGAATCTCGTGGTCCACTGATTTACGATC
1 ATTTACGATCACAACCTTCTACTTA-CAGGATTTTACGAATCTCGTGGTCCACTAATTTATGATC
1725 ACGACCTTCTA
65 ACGACCTTCTA
1736 GTGACGTAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
106 1 0.01
107 3 0.02
108 153 0.96
109 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (108 bp):
ATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCGTGGTCCACTAATTTATGATCA
CGACCTTCTACTTAAGGAATTTTACAAATCTCGTGGTCTGCTG
Found at i:1657 original size:162 final size:162
Alignment explanation
Indices: 1389--1735 Score: 430
Period size: 162 Copynumber: 2.1 Consensus size: 162
1379 GAGTTTTAGT
* * ** ** * *
1389 TGATTTACAATCACAACCTTTTACTTATGGGATTTTTTGAATCTCAAGGTCTATTTATTTATGAT
1 TGATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCAAGGTCCATCTATTTATGAT
* * *
1454 CACGACCTTCTACTTATGGGATTTTAACAATCTCATGGTCTGCTAATTTATGATCACGACCTTCT
66 CACGACCTTCTACTTAAGGAATTTTAACAATCTCATGGTCTGCTAATTTACGATCACGACCTTCT
**
1519 ACTTA-CTAGATTTTACAAATCTCGTGGTCTGC
131 ACTTATC-AGATTTTACAAATCTCGTGGTCCAC
**
1551 TGATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCGCGGTCCA-CTAGTTTATGA
1 TGATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCAAGGTCCATCTA-TTTATGA
* * * * *
1615 TCATGATCTTCTACTTAAGGAATTTT-ACAAATCTCGTGGTCTGCTGATTTACGATCACTACCTT
65 TCACGACCTTCTACTTAAGGAATTTTAAC-AATCTCATGGTCTGCTAATTTACGATCACGACCTT
* * *
1679 TTGCTTATCAGATTTTACGAATCTCGTGGTCCAC
129 CTACTTATCAGATTTTACAAATCTCGTGGTCCAC
*
1713 TGATTTACGATCACGACCTTCTA
1 TGATTTACGATCACAACCTTCTA
1736 GTGACGTAAT
Statistics
Matches: 158, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
161 4 0.03
162 153 0.97
163 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (162 bp):
TGATTTACGATCACAACCTTCTACTTACAGGATTTTACGAATCTCAAGGTCCATCTATTTATGAT
CACGACCTTCTACTTAAGGAATTTTAACAATCTCATGGTCTGCTAATTTACGATCACGACCTTCT
ACTTATCAGATTTTACAAATCTCGTGGTCCAC
Found at i:1755 original size:54 final size:54
Alignment explanation
Indices: 1445--1756 Score: 258
Period size: 54 Copynumber: 5.8 Consensus size: 54
1435 AGGTCTATTT
* * ** * ** *
1445 ATTTATGATCACGACCTTCTACTTATGGGATTTTAAC-AATCTCATGGTCTGCTA
1 ATTTACGATCACGACCTTCTACTTACGTAATTTT-ACGAATCTCGTGGTCCACTG
* * **
1499 ATTTATGATCACGACCTTCTACTTAC-TAGATTTTACAAATCTCGTGGTCTGCTG
1 ATTTACGATCACGACCTTCTACTTACGTA-ATTTTACGAATCTCGTGGTCCACTG
* * *
1553 ATTTACGATCACAACCTTCTACTTACAG-GATTTTACGAATCTCGCGGTCCACT-
1 ATTTACGATCACGACCTTCTACTTAC-GTAATTTTACGAATCTCGTGGTCCACTG
* * * * * * **
1606 AGTTTATGATCATGATCTTCTACTTAAGGAATTTTACAAATCTCGTGGTCTGCTG
1 A-TTTACGATCACGACCTTCTACTTACGTAATTTTACGAATCTCGTGGTCCACTG
* * *
1661 ATTTACGATCACTACCTTTTGCTTA--TCAGATTTTACGAATCTCGTGGTCCACTG
1 ATTTACGATCACGACCTTCTACTTACGT-A-ATTTTACGAATCTCGTGGTCCACTG
* * * *
1715 ATTTACGATCACGACCTTCTAGTGACGTAATTTAATGAATCT
1 ATTTACGATCACGACCTTCTACTTACGTAATTTTACGAATCT
1757 AGGCATGTTG
Statistics
Matches: 208, Mismatches: 39, Indels: 22
0.77 0.14 0.08
Matches are distributed among these distances:
53 5 0.02
54 200 0.96
55 2 0.01
56 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (54 bp):
ATTTACGATCACGACCTTCTACTTACGTAATTTTACGAATCTCGTGGTCCACTG
Done.