Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 16 of 16
Found at i:2015572 original size:86 final size:85
Alignment explanation
Indices: 2015406--2017209 Score: 2398
Period size: 86 Copynumber: 21.0 Consensus size: 85
2015396 TGAAAAGGGT
* * * * *
2015406 TGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACGTGCGTGGGCTTTG-AAAGAATGCC
1 TGCCACTGACTTG--TGGGCTTTGAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAG-GTGCC
* *
2015470 ACTAACTCGTGGGCTTTGAAAGGA-
61 ACTGACTTGTGGGCTTTGAAAGGAG
* *
2015494 TGCCATTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGA
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
* *
2015559 CTTGCGTGAGCTTTAAAAGGAG
66 CTT--GTGGGCTTTGAAAGGAG
* *
2015581 TGCCACTGACTTGTGTGAGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCAC
1 TGCCACTGACTTGTG-G-GCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCAC
* * * *
2015645 TGAATTGTGGGCTTCGCAATG-G
63 TGACTTGTGGGCTTTGAAAGGAG
* * * * * *
2015667 TGCCACTGACTTGTGGGCTTCGAAAGGGTGCTACTGACTTGTGGGCTCTGAAAGGGTGCCACTAA
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
2015732 CTTGTGGGCTTTGAAAGG-G
66 CTTGTGGGCTTTGAAAGGAG
* * * *
2015751 TGCCACTGACTTATGGGCTTTGAAAAGAGCGTCACTGATTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACT
*
2015816 GACTTATGGGCTTTGAAAGGAG
64 GACTTGTGGGCTTTGAAAGGAG
* * * * * *
2015838 TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAATAGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTG
* *
2015903 ATTTGTGGGCTTTGAAAAGAG
65 ACTTGTGGGCTTTGAAAGGAG
* *
2015924 TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
*
2015989 ACTTGTGGGCTCTGAAAGG-G
65 ACTTGTGGGCTTTGAAAGGAG
* * * *
2016009 TGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCACTGAGTTGTGGGCTTTGAAAGGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTG
2016074 ACTTGTGGGCTTTGAAAGGAG
65 ACTTGTGGGCTTTGAAAGGAG
* * *
2016095 TGCCACTAACTTATGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
* * * *
2016160 AATTGTGGGCTTCGCAATG-G
65 ACTTGTGGGCTTTGAAAGGAG
* * * * *
2016180 TGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAA
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
2016245 CTTGTGGGCTTTGAAAGG-G
66 CTTGTGGGCTTTGAAAGGAG
* *
2016264 TGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACT
*
2016329 AACTTGTGGGCTTTGAAAGGAG
64 GACTTGTGGGCTTTGAAAGGAG
* * *
2016351 TGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTG
* * *
2016416 ATTTATGGGCTTTGAAAAGAG
65 ACTTGTGGGCTTTGAAAGGAG
*
2016437 TGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTG-AAAGGAATGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGG--TGCCAC
2016501 TGACTTGTGGGCTTTGAAAGG-G
63 TGACTTGTGGGCTTTGAAAGGAG
* *
2016523 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACT
2016588 GACTTGTGGGCTTTGAAAGGAG
64 GACTTGTGGGCTTTGAAAGGAG
*
2016610 TGCCACTGACTTGTGGGCTTTGAAATG-GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACT
* * *
2016674 GATTTATGGGCTTTGAAAAGAG
64 GACTTGTGGGCTTTGAAAGGAG
*
2016696 TGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTG-AAAGGAATGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGG--TGCCAC
2016760 TGACTTGTGGGCTTTGAAAGG-G
63 TGACTTGTGGGCTTTGAAAGGAG
* *
2016782 TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACT
1 TGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACT
2016847 GACTTGTGGGCTTTGAAAGGAG
64 GACTTGTGGGCTTTGAAAGGAG
* *
2016869 TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTG
* * *
2016934 ATTTATGGGCTTTGAAAAGAG
65 ACTTGTGGGCTTTGAAAGGAG
*
2016955 TGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTG-AAAGGAATGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGG--TGCCAC
2017019 TGACTTGTGGGCTTTGAAA-GAG
63 TGACTTGTGGGCTTTGAAAGGAG
* * *
2017041 TGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA
1 TGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
*
2017106 ACTTGTAGGCTTTGAAAGGAG
65 ACTTGTGGGCTTTGAAAGGAG
*
2017127 TGCCACTGACTTGTGGGCTTTGAAA-AGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
2017191 ACTTGTGGGCTTTGAAAGG
65 ACTTGTGGGCTTTGAAAGG
2017210 GATGAACATT
Statistics
Matches: 1530, Mismatches: 146, Indels: 83
0.87 0.08 0.05
Matches are distributed among these distances:
84 193 0.13
85 218 0.14
86 738 0.48
87 318 0.21
88 20 0.01
89 43 0.03
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.28
Consensus pattern (85 bp):
TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGA
CTTGTGGGCTTTGAAAGGAG
Found at i:2015787 original size:29 final size:29
Alignment explanation
Indices: 2015394--2017207 Score: 2392
Period size: 29 Copynumber: 63.2 Consensus size: 29
2015384 ACAGTGGTGA
* *
2015394 TTTGAAAAGGGTTGCCATTGACTTGCATGGGC
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGC
* *
2015426 TTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
* * *
2015456 TTTG-AAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2015484 TTTGAAAGGA-TGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2015512 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2015540 TTTGAAAAG-GTACCACTGACTTGCGTGAGC
1 TTTGAAAAGAGTGCCACTGACTT--GTGGGC
2015570 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAA-GAGTGCCACTGACTTGTG-G-GC
*
2015601 TTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2015629 TTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015657 TTCGCAATG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015685 TTCG-AAAGGGTGCTACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015713 TCTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2015741 TTTG-AAAGGGTGCCACTGACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015769 TTTGAAAAGAGCGTCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2015798 TTTGAAAAGAGTGCCACTGACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2015827 TTTGAAAGGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015856 TTTG-AAAGGGTGCCATTGACTTGTGGTC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015884 TTTGAAAATAGTGCCACTAATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2015913 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2015942 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2015971 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2015999 TCTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016027 TTTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016055 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2016084 TTTGAAAGGAGTGCCACTAACTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016113 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016142 TTTG-AAAGGGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2016170 TTCGCAATG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016198 TTCG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2016226 TCTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016254 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016282 TTTAAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016311 TTTGAAAAGAGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016340 TTTGAAAGGAGTGCCAATGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016369 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016397 TTTGAAAAGAGTGCCACTGATTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2016426 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016455 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016484 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016513 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016541 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016570 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016599 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016628 TTTGAAATG-GTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016656 TTTGAAAAGAGTGCCACTGATTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2016685 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016714 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016743 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016772 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016800 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016829 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2016858 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016887 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016915 TTTGAAAAGAGTGCCACTGATTTATGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2016944 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2016973 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2017002 TTTGAAAGGAATGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2017031 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
2017059 TTTGAAAGGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
2017088 TTTG-AAAGGGTGCCACTAACTTGTAGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2017116 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2017145 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
2017173 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
2017201 TTTGAAA
1 TTTGAAA
2017208 GGGATGAACA
Statistics
Matches: 1601, Mismatches: 151, Indels: 63
0.88 0.08 0.03
Matches are distributed among these distances:
27 14 0.01
28 627 0.39
29 871 0.54
30 56 0.03
31 29 0.02
32 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:2015860 original size:115 final size:115
Alignment explanation
Indices: 2015394--2017209 Score: 2488
Period size: 115 Copynumber: 15.8 Consensus size: 115
2015384 ACAGTGGTGA
* * *
2015394 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACGTGCGTGGGCTT
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTT
* * * *
2015458 TG-AAAGAATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCATTGACTTGTGGGC
60 TGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2015512 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTT-AA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAA
*
2015575 AAGGAGTGCCACTGACTTGTGTGAGCTTTAAAAGG-GTGCCACTGACTTGTGGGC
64 AA-GAGTGCCACTGACTTGTG-G-GCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * * * *
2015629 TTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGCTTCG-AAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* * * *
2015692 GGGTGCTACTGACTTGTGGGCTCTGAAAGG-GTGCCACTAACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
2015741 TTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGAGCGTCACTGATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* *
2015806 GAGTGCCACTGACTTATGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * * *
2015856 TTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAATAGTGCCACTAATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
2015921 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
2015971 TTTGAAAGGGTGCCACTAACTTGTGGGCTCTG-AAAGGGTGCCACTGAGTTGTGGGCTTTG-AAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* *
2016034 GGGTGCCACTGAGTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2016084 TTTGAAAGGAGTGCCACTAACTTATGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * * *
2016148 AGGGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
2016198 TTCGAAAGGGTGCCACTGACTTGTGGGCTCTG-AAAGGGTGCCACTAACTTGTGGGCTTTG-AAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
* * * *
2016261 GGGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGATTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * * *
2016311 TTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCAATGACTTGTGGGCTTTG-AA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * * *
2016375 AGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2016426 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGCTTTGAAA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* *
2016491 GGAATGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2016541 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * *
2016606 GGAGTGCCACTGACTTGTGGGCTTTGAAATG-GTGCCACTAACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2016656 TTTGAAAAGAGTGCCACTGATTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * *
2016721 GGAATGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* *
2016772 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
2016837 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
* * *
2016887 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
*
2016952 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAATGCCACTGACTTGTGGGC
66 GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
*
2017002 TTTGAAAGGAATGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * *
2017066 GGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTAACTTGTAGGC
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
2017116 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTG-AA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
*
2017179 AGGGTGCCACTGACTTGTGGGCTTTGAAAGG
65 AGAGTGCCACTGACTTGTGGGCTTTGAAAGG
2017210 GATGAACATT
Statistics
Matches: 1547, Mismatches: 130, Indels: 47
0.90 0.08 0.03
Matches are distributed among these distances:
112 111 0.07
113 154 0.10
114 242 0.16
115 876 0.57
116 83 0.05
117 77 0.05
118 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.28
Consensus pattern (115 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAA
GAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
Found at i:2018436 original size:1 final size:1
Alignment explanation
Indices: 2018430--2018503 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
2018420 GACCCTTCTA
* * * * * * * * *
2018430 TTTTTTTTTTTTCTATTTTTTCTTTTTTTGTTTTTTGTTTTGTTTTTTTTTGTGTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2018495 TTTTTTTTT
1 TTTTTTTTT
2018504 GGGTGTAAAG
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.03, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:2018450 original size:12 final size:12
Alignment explanation
Indices: 2018447--2018504 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
2018437 TTTTTCTATT
*
2018447 TTTTCTTTTTTTG
1 TTTT-TTTTTGTG
2018460 TTTTTTGTTT-TG
1 TTTTTT-TTTGTG
2018472 TTTTTTTTTGTG
1 TTTTTTTTTGTG
2018484 TTTTTTTTTGT-
1 TTTTTTTTTGTG
2018495 TTTTTTTTTG
1 TTTTTTTTTG
2018505 GGTGTAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 13 0.30
12 23 0.53
13 7 0.16
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTGTG
Found at i:2031595 original size:22 final size:22
Alignment explanation
Indices: 2031567--2031621 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2031557 TGGACATGTT
2031567 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2031589 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2031611 AAAAATGCATG
1 AAAAATGCATG
2031622 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:2032578 original size:20 final size:20
Alignment explanation
Indices: 2032531--2032605 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2032521 AAAAAGACAT
*
2032531 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2032550 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2032571 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2032591 AATGTATCGATACAT
1 AATGTATCGATACAT
2032606 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2032599 original size:40 final size:39
Alignment explanation
Indices: 2032528--2032605 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2032518 GGTAAAAAGA
* *
2032528 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2032567 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2032606 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2032892 original size:16 final size:17
Alignment explanation
Indices: 2032863--2032896 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2032853 ATTAGATTAC
2032863 TTTTAAAAAAATAAATA
1 TTTTAAAAAAATAAATA
*
2032880 TTTT-AAAATATAAATA
1 TTTTAAAAAAATAAATA
2032896 T
1 T
2032897 CCTAATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAATAAATA
Found at i:2033077 original size:2 final size:2
Alignment explanation
Indices: 2033070--2033158 Score: 144
Period size: 2 Copynumber: 45.0 Consensus size: 2
2033060 GTAAAGTTTA
*
2033070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT AT
* *
2033112 AT AT AT GT AT AT AT AT AT AT AT AT GT 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 AT AT
2033154 A- AT AT
1 AT AT AT
2033159 CATAATAAGG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2033093 original size:18 final size:18
Alignment explanation
Indices: 2033070--2033153 Score: 159
Period size: 18 Copynumber: 4.7 Consensus size: 18
2033060 GTAAAGTTTA
*
2033070 ATATATATATATATATAT
1 ATATATATATATGTATAT
2033088 ATATATATATATGTATAT
1 ATATATATATATGTATAT
2033106 ATATATATATATGTATAT
1 ATATATATATATGTATAT
2033124 ATATATATATATGTATAT
1 ATATATATATATGTATAT
2033142 ATATATATATAT
1 ATATATATATAT
2033154 AATATCATAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
ATATATATATATGTATAT
Found at i:2034104 original size:64 final size:65
Alignment explanation
Indices: 2034001--2034130 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 65
2033991 ATTTCATATC
*
2034001 TTAAGAATATTAAAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAGGAGTTATGTA
1 TTAAGAATATT-AAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTA
2034066 A
65 A
* * ***
2034067 TTAAGAATATT-CAAAAAAAAATCATTTGTCCTTATAAATAAACTCTTTTATAAGAGTTATGTAA
1 TTAAGAATATTAAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTAA
2034131 AATTTATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 47 0.81
66 11 0.19
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (65 bp):
TTAAGAATATTAAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTAA
Found at i:2039049 original size:13 final size:13
Alignment explanation
Indices: 2039031--2039069 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2039021 TTTCCTAGTT
2039031 AGATAAGAAAGAA
1 AGATAAGAAAGAA
2039044 AGATAAGAGAAGAA
1 AGATAAGA-AAGAA
*
2039058 AG-GAAGAAAGAA
1 AGATAAGAAAGAA
2039070 GAAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 5 0.21
13 12 0.50
14 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (13 bp):
AGATAAGAAAGAA
Found at i:2039072 original size:18 final size:18
Alignment explanation
Indices: 2039035--2039068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2039025 CTAGTTAGAT
2039035 AAGAAAGAAAGATAAGAG
1 AAGAAAGAAAGATAAGAG
*
2039053 AAGAAAGGAAGA-AAGA
1 AAGAAAGAAAGATAAGA
2039069 AGAAAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (18 bp):
AAGAAAGAAAGATAAGAG
Done.