Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_110 ID=scaffold_110-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: 20208
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.21
Warning! 7103 characters in sequence are not A, C, G, or T
Found at i:1516 original size:624 final size:623
Alignment explanation
Indices: 1--1569 Score: 2800
Period size: 623 Copynumber: 2.5 Consensus size: 623
* *
1 GTAATTAAATGGAAATTAAAACAAACTGAAAGACAAAAATGTAATCATCTCCTCTAATTTGCTAT
1 GTAATTAAATGGAAATTAAAACAAACTAAAAGACAAAAATGTTATCATCTCCTCTAATTTGCTAT
** *
66 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTTTGGTCATGTAGTTTTTACATGCATGATCAAG
66 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGAGTTTTTACATGCATGATCAAG
*
131 AAACGAACCAACCGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
131 AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
*
196 TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATGTAATATATATGTTTGTTTCCTTATGATTA
196 TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
*
261 TGTATATCAATTGTTAGTTAAATTATAAATAATGTGGAAATTTCATTGTTTGCTTGTAAATTATT
261 TGTATATCAATTGTTAGTTAAATTATAATTAATGTGGAAATTTCATTGTTTGCTTGTAAATTATT
*
326 AAATGTTGGAATTAAGTACAAATGGAAAATGAATACTTGGTCGTGGCAAATCTTGTGGTTTCACA
326 AAATGTTGGAATTAAGTACAAATGAAAAATGAATACTTGGTCGTGGCAAATCTTGTGGTTTCACA
* *
391 ATTTTGAAATGAATGTAATAGATTAGTATTACGTGTACAGATAATTAATTAAGTAAAAATCACTA
391 ATTTTGAAATGAATCTAACAGATTAGTATTACGTGTACAGATAATTAATTAAGTAAAAATCACTA
*
456 AATTGAAAAAGGTGAAAAAATAGATTTCTAATAGGTAAAGGGGTCAATTTATAATGGATTATCAA
456 AATTGAAAAAGGTGAAAAAATAAATTTCTAATAGGTAAAGGGGTCAATTTATAATGGATTATCAA
521 ACTAATGGACTTAAATGGTAAATGCACCAAATGAACTTAGACTGGATGTTTTGGGTGATTAAATG
521 ACTAATGGACTTAAATGGTAAATGCACCAAATGAACTTAGACTGGATGTTTTGGGTGATTAAATG
*
586 GATGAAATTTTATTTTTTAAGGGAAAAATTGTAAATTT
586 GATGAAATTTGATTTTTTAAGGGAAAAATTGTAAATTT
* * * * *
624 GTAATTAAATGGAAATTTAAACAAATTAAAAAACAAAAATTTTATCATCTCCTCGAATTTGCTAT
1 GTAATTAAATGGAAATTAAAACAAACTAAAAGACAAAAATGTTATCATCTCCTCTAATTTGCTAT
689 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGAGTTTTTACATGCATGATCAAG
66 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGAGTTTTTACATGCATGATCAAG
754 AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
131 AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
819 TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
196 TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
884 TGTATATCAATTGTTAGTTAAATTATAATTAATGTGGAAATTTCATTGTTTGCTTGTAAATTATT
261 TGTATATCAATTGTTAGTTAAATTATAATTAATGTGGAAATTTCATTGTTTGCTTGTAAATTATT
*
949 AAATGTTGGAATTAAGTACAAATGAAAAATGAATATTTGGTCGTGGCAAATCTTGTGGTTTCACA
326 AAATGTTGGAATTAAGTACAAATGAAAAATGAATACTTGGTCGTGGCAAATCTTGTGGTTTCACA
*
1014 ATTTTGAAATGAATCTAACAGATTTA-TATTAGGTGTACAGATAATTAATTAAGTAAAAATCACT
391 ATTTTGAAATGAATCTAACAGA-TTAGTATTACGTGTACAGATAATTAATTAAGTAAAAATCACT
* * * *
1078 AAATTGATAAAGGT-ACAAAAATAAATTTCTATTTGGTAAAGGGGTCAATTTATTATGGATTATC
455 AAATTGAAAAAGGTGA-AAAAATAAATTTCTAATAGGTAAAGGGGTCAATTTATAATGGATTATC
*
1142 AAACTAATGGACTTAAATGGTAAATGCACCAAATGAACTTAGAGTGGATGGTTTTGGGTGATTAA
519 AAACTAATGGACTTAAATGGTAAATGCACCAAATGAACTTAGACTGGAT-GTTTTGGGTGATTAA
* *
1207 ATGGATGAAATTTGATTTTTTAAGGGAAAAGTTGTATATTT
583 ATGGATGAAATTTGATTTTTTAAGGGAAAAATTGTAAATTT
* *
1248 GTAATTAAATGGAAATTAAAACAAACTAAAAGACAAAAATGTTATTATCTCCTCTAATTGGCTAT
1 GTAATTAAATGGAAATTAAAACAAACTAAAAGACAAAAATGTTATCATCTCCTCTAATTTGCTAT
*
1313 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGATTTTTTACATGCATGATCAAG
66 TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGAGTTTTTACATGCATGATCAAG
1378 AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
131 AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
*
1443 TTACAGCTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
196 TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
* *
1508 TGTATATCAATTGTTAGTTAAATTATAATTATTGTGAAAATTTCATTGTTTGCTTGTAAATT
261 TGTATATCAATTGTTAGTTAAATTATAATTAATGTGGAAATTTCATTGTTTGCTTGTAAATT
1570 NNNNNNNNNN
Statistics
Matches: 905, Mismatches: 38, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
622 1 0.00
623 537 0.59
624 367 0.41
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (623 bp):
GTAATTAAATGGAAATTAAAACAAACTAAAAGACAAAAATGTTATCATCTCCTCTAATTTGCTAT
TTTGCAAACCGAATAACAGAGAGGAAGAAGCTTCCGGTCATGGAGTTTTTACATGCATGATCAAG
AAACGAACCAAACGGATCTAAACCGAGGAAAAGCTAATGTGTCAGATTAGTCGGCTGCTTCATTT
TTACAACTATATTTGTCGAGGTAAGTTTGTAGTATATAATATATATGTTTGTTTCCTTATGATTA
TGTATATCAATTGTTAGTTAAATTATAATTAATGTGGAAATTTCATTGTTTGCTTGTAAATTATT
AAATGTTGGAATTAAGTACAAATGAAAAATGAATACTTGGTCGTGGCAAATCTTGTGGTTTCACA
ATTTTGAAATGAATCTAACAGATTAGTATTACGTGTACAGATAATTAATTAAGTAAAAATCACTA
AATTGAAAAAGGTGAAAAAATAAATTTCTAATAGGTAAAGGGGTCAATTTATAATGGATTATCAA
ACTAATGGACTTAAATGGTAAATGCACCAAATGAACTTAGACTGGATGTTTTGGGTGATTAAATG
GATGAAATTTGATTTTTTAAGGGAAAAATTGTAAATTT
Found at i:3757 original size:27 final size:26
Alignment explanation
Indices: 3704--3782 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
3694 GTATTATAGC
* **
3704 CCCCATAGGATAAAATGACCGAAATA
1 CCCCATAGGATAAAATGACTGTTATA
3730 CCCCAATAGGATAAAATGACTGTTATA
1 CCCC-ATAGGATAAAATGACTGTTATA
*
3757 CCCC-TAGGAGATGAAATGACTGTTAT
1 CCCCATA-G-GATAAAATGACTGTTAT
3783 GGCCATAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 2 0.04
26 5 0.11
27 39 0.85
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (26 bp):
CCCCATAGGATAAAATGACTGTTATA
Found at i:5633 original size:23 final size:22
Alignment explanation
Indices: 5602--5646 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5592 ATAAAAGAAA
*
5602 GAAATTAATAAATAAAATAAAAC
1 GAAAGTAATAAA-AAAATAAAAC
*
5625 GAAAGTAATAAAAAAATGAAAC
1 GAAAGTAATAAAAAAATAAAAC
5647 AAAATTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (22 bp):
GAAAGTAATAAAAAAATAAAAC
Found at i:5641 original size:27 final size:26
Alignment explanation
Indices: 5592--5650 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
5582 GAAATGTTAT
* *
5592 ATAAAAGAAAGAAATTAATAAATAAA
1 ATAAAAGAAAGAAATAAAAAAATAAA
* *
5618 ATAAAACGAAAGTAATAAAAAAATGAA
1 ATAAAA-GAAAGAAATAAAAAAATAAA
*
5645 ACAAAA
1 ATAAAA
5651 TTTAGAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (26 bp):
ATAAAAGAAAGAAATAAAAAAATAAA
Found at i:17514 original size:10 final size:10
Alignment explanation
Indices: 17499--17545 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
17489 TGAATGCTTG
17499 ATGAAATGGA
1 ATGAAATGGA
17509 ATGAAATGGA
1 ATGAAATGGA
*
17519 ATGATATGGA
1 ATGAAATGGA
* *
17529 ATGGAATGCA
1 ATGAAATGGA
17539 ATGAAAT
1 ATGAAAT
17546 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (10 bp):
ATGAAATGGA
Done.