Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold413
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: 166130
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:153699 original size:29 final size:29
Alignment explanation
Indices: 153659--154533 Score: 1162
Period size: 29 Copynumber: 30.1 Consensus size: 29
153649 TTTTCATCCC
*
153659 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153688 TTTCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153717 TTTCAAAGCCCACACGAGTTAGTGGCACTCC
1 TTTCAAAGCCCACA--AGTCAGTGGCACTCT
153748 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153777 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153806 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153835 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153863 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153892 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153920 TTTCAAAGCCCACAATTTAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153948 TTTCAAAGCCCATAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
153977 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
154005 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154034 TTTCAAAGCCCACACGAGTTAGTGGCAACT-T
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
* *
154065 CTTTCAAAGCCCACGTAAGTTAGTGGCAC-CC
1 -TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
* *
154096 TTTCGAAGCCCACAAGTTAGTGGCACTCGT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-T
* *
154126 TTT-AAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154153 TTTCAAAGCCCACAAGTCAGTGGCACTCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154182 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154211 TTCCAAAGCTCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154240 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154269 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154297 TTTCAAAGTCCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154326 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154354 TTTCAAAGCCCATAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* ** *
154383 TTTCAAAGTCCACACGAGTTGGTGGCAACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCT
*
154415 TTTCAAAGCCCACGTAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
*
154445 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154474 TTTCAGAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
154502 TTTAAAAGCCTACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
154531 TTT
1 TTT
154534 GTCGCAACGT
Statistics
Matches: 752, Mismatches: 68, Indels: 52
0.86 0.08 0.06
Matches are distributed among these distances:
27 3 0.00
28 225 0.30
29 390 0.52
30 35 0.05
31 52 0.07
32 46 0.06
34 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:153894 original size:57 final size:58
Alignment explanation
Indices: 153659--154533 Score: 1157
Period size: 57 Copynumber: 15.1 Consensus size: 58
153649 TTTTCATCCC
*
153659 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153717 TTTCAAAGCCCACACGAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACA--AGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153777 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153835 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
153892 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAATTTAGTGGCACT-T
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153948 TTTCAAAGCCCATAA-TTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTT-AGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154005 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACT-T
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
* * *
154065 CTTTCAAAGCCCACGTAAGTTAGTGGCAC-CCTTTCGAAGCCCACAAGTTAGTGGCACTCGT
1 -TTTCAAAGCCCAC--AAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-T
* *
154126 TTT-AAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCA
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154182 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTCCAAAGCTCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
154240 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154297 TTTCAAAGTCCACAA-TTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTT-AGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * ** *
154354 TTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGTCCACACGAGTTGGTGGCAACTCC
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACTCT
* * *
154415 TTTCAAAGCCCACGTAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCAC--AAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
154474 TTTCAGAGCCCACAAGTCAGTGGCAC-CTTTTAAAAGCCTACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
154531 TTT
1 TTT
154534 GTCGCAACGT
Statistics
Matches: 740, Mismatches: 52, Indels: 51
0.88 0.06 0.06
Matches are distributed among these distances:
55 1 0.00
56 27 0.04
57 337 0.46
58 163 0.22
59 48 0.06
60 86 0.12
61 30 0.04
62 23 0.03
63 25 0.03
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (58 bp):
TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:154333 original size:349 final size:347
Alignment explanation
Indices: 153656--154527 Score: 1376
Period size: 349 Copynumber: 2.5 Consensus size: 347
153646 GAATTTTCAT
* * *
153656 CCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACA--AGTCAATGGC-AC-TCT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACTTC-
*** *
153717 TTTCAAAGCCCACACGAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
65 TTTCAAAGCCCACGTAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCA
* *
153782 AAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
129 AAGCCCACAAGTTAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACTCATTTCAAAGCCCA
*
153847 CAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAG
193 CAAGTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAG
* ** *
153912 TGGCACCCTTTCAAAGCCCACAATTTAGTGGCACTTTTTCAAAGCCCATAATTCAGTGGCACTCT
258 TGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAATTCAGTGGCACTCT
153977 TTTCAAAGCCCACAAGTCAGTGGCA
323 TTTCAAAGCCCACAAGTCAGTGGCA
*
154002 CCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACTTCT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACTTCT
*
154067 TTCAAAGCCCACGTAAGTTAGTGGCACCCTTTCGAAGCCCACAAGTTAGTGGCACTCGTTTT-AA
66 TTCAAAGCCCACGTAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTC-TTTTCAA
*
154131 AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCATTTCAAAGCCCACA
130 AGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCATTTCAAAGCCCACA
* * *
154196 AGTTAGTGGCACTCTTTCCAAAGCTCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGT
195 AGTTAGTGGCACCCTTT-CAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGT
* *
154261 GGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGTCCACAATTCAGTGGCACTCT
259 GGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAATTCAGTGGCACTCT
154326 TTTCAAAGCCCACAAGTCAGTGGCA
323 TTTCAAAGCCCACAAGTCAGTGGCA
* * * *
154351 CCCTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGTCCACACGAGTTGGTGGCAACTCCT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACTTCT
* *
154416 TTCAAAGCCCACGTAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAGA
66 TTCAAAGCCCACGTAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
* * *
154481 GCCCACAAGTCAGTGGCACCTTTTAAAAGCCTACAAGTCAGTGGCAC
131 GCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC
154528 CCTTTTGTCG
Statistics
Matches: 484, Mismatches: 34, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
346 44 0.09
347 58 0.12
348 111 0.23
349 269 0.56
350 2 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (347 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTTAGTGGCAACTTCT
TTCAAAGCCCACGTAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
GCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTCATTTCAAAGCCCACAA
GTTAGTGGCACCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGG
CACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAATTCAGTGGCACTCTTTT
CAAAGCCCACAAGTCAGTGGCA
Found at i:157131 original size:10 final size:10
Alignment explanation
Indices: 157116--157146 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
157106 CCATTTCATA
157116 TTTTTTTCTT
1 TTTTTTTCTT
157126 TTTTTTTCTT
1 TTTTTTTCTT
*
157136 TTTCTTTCTT
1 TTTTTTTCTT
157146 T
1 T
157147 CTTCTTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:157145 original size:20 final size:21
Alignment explanation
Indices: 157116--157173 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 21
157106 CCATTTCATA
*
157116 TTTT-TTTCTTTTTTT-TTCT
1 TTTTCTTTCTTTTTTTCATCT
157135 TTTTCTTTCTTTCTTCTTCATCT
1 TTTTCTTTCTTT-TT-TTCATCT
157158 TCTTTCTTTCTTTTTT
1 T-TTTCTTTCTTTTTT
157174 ACCTAACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 4 0.12
20 7 0.21
21 2 0.06
22 3 0.09
23 6 0.18
24 11 0.33
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTCTTTTTTTCATCT
Found at i:158456 original size:32 final size:32
Alignment explanation
Indices: 158401--158810 Score: 590
Period size: 32 Copynumber: 12.8 Consensus size: 32
158391 AAAATGGTGA
* * **
158401 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158433 TTTTAAATGGGTTTCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158465 TTTGAAAAGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158497 TTTGAAATGGGTTGCCACTGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158529 TTTGGAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
158561 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158593 TTTGAAAAGGGTTGCCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
158625 TTTGAAATGGGTTGCCACCGACATGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
158657 TTTGAAAAGGGTTGCCACTGACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
158689 TTTGAAAAT-GGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
*
158721 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158753 TTTGAAATGGGTTACCACCAACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
158785 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
158811 GATTTTAAAA
Statistics
Matches: 338, Mismatches: 38, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
31 14 0.04
32 321 0.95
33 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:158918 original size:27 final size:27
Alignment explanation
Indices: 158793--159986 Score: 1749
Period size: 27 Copynumber: 44.0 Consensus size: 27
158783 GCTTTGAAAT
* *
158793 GGGTGCCACAGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
* * * *
158821 GAGTTCCACGGAGTTATGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
* *
158849 GGGTGCCACAGAATTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
158876 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
158904 GGGTGCCACGGAG-T-T-G---T--AA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
158923 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
158950 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
158977 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159004 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159031 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
159058 GGGGGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159085 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
159113 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
159140 GAGATGCCATGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
159168 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
159195 GAGTGGCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159222 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
159250 GGGTGCCACGGAGTTGTTGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159277 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
159304 GGGGGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159331 GGGTGCCACGGAG-TGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
159358 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
159385 GAGATGCCATGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
* *
159413 GGGTGCCACGAAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
159440 GAGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159467 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
159495 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159522 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159549 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
159576 GGGGGCCACGGAGTTATGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
159603 GGGTGCCATGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
159631 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
159658 GAGATGCCATGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
159686 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
159713 GAGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159740 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
159768 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159795 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
159822 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
159849 AGGTGCGACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
159876 GAATGCCCACGAAGTTGTGGACTTAAAA
1 GGGTG-CCACGGAGTTGTGGACTTAAAA
159904 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
159932 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
159959 GGGTGCCACGGAGTTGTGGGCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
159987 AGGTCATAGT
Statistics
Matches: 1060, Mismatches: 84, Indels: 44
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.01
20 1 0.00
21 2 0.00
22 1 0.00
24 1 0.00
25 2 0.00
26 8 0.01
27 714 0.67
28 315 0.30
29 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:158929 original size:19 final size:19
Alignment explanation
Indices: 158902--158939 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
158892 ATGGACTTAA
*
158902 AAGGGTGCCACGGAGTTGT
1 AAGGATGCCACGGAGTTGT
158921 AAGGATGCCACGGAGTTGT
1 AAGGATGCCACGGAGTTGT
158940 GGACTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.21
Consensus pattern (19 bp):
AAGGATGCCACGGAGTTGT
Found at i:159314 original size:273 final size:271
Alignment explanation
Indices: 158797--159973 Score: 1755
Period size: 273 Copynumber: 4.3 Consensus size: 271
158787 TGAAATGGGT
* * * * * * * *
158797 GCCACAGAGTTGTGGATTTTAAAAGAGTTCCACGGAGTTATGGATTTTAAAAGGGTGCCACAGAA
1 GCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAG
* * *
158862 TTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAG-T-T-G---T
64 TTGTGGACTTAAAAG-GGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTT
158921 --AAG-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
128 AAAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGC
*
158983 CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGT
193 CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGT
*
159048 GGACTTAAAAGGGG
258 GGACTAAAAAGGGG
* *
159062 GCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGT
1 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGT
* * * * *
159127 TGTGGACTTAAAAGAGATGCCATGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTATGGACTTA
65 TGTGGACTTAAAAG-GGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTA
* *
159192 AAAGAG-TGGCACGGAGTTATGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGC
129 AAAGAGATGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGC
*
159256 CACGGAGTTGTTGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGT
193 CACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGT
*
159321 GGACTAAAAAGGGT
258 GGACTAAAAAGGGG
* * *
159335 GCCACGGAG-TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCATGGAG
1 GCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAG
* *
159399 TTATGGACTTAAAAGGGTGCCACGAAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTA
64 TTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTA
*
159464 AAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
129 AAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
159529 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTATG
194 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGTG
*
159594 GACTAAAAAGGGT
259 GACTAAAAAGGGG
* * * *
159607 GCCATGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCATGGAG
1 GCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAG
*
159672 TTATGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTA
64 TTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTA
*
159737 AAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
129 AAAGAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
159802 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGTGCGACGGAGTTGTG
194 ACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGTG
* **
159867 GACTTAAAAGAATG
259 GACTAAAAAG-GGG
* *
159881 CCCACGAAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 GCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
159946 TGTGGACTTAAAAGGGTGCCACGGAGTT
65 TGTGGACTTAAAAGGGTGCCACGGAGTT
159974 GTGGGCTTTA
Statistics
Matches: 846, Mismatches: 49, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
264 94 0.11
265 16 0.02
266 1 0.00
267 1 0.00
270 1 0.00
272 206 0.24
273 489 0.58
274 38 0.04
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.22
Consensus pattern (271 bp):
GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
GTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGAGTGCCACAGAGTTGTGGACTTAAA
AGAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGTGGA
CTAAAAAGGGG
Found at i:161023 original size:14 final size:14
Alignment explanation
Indices: 161004--161042 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
160994 AGGGTGAAAA
161004 GGTTTTTTTTTTTT
1 GGTTTTTTTTTTTT
161018 GGTTTTTTTTTGTTT
1 GGTTTTTTTTT-TTT
161033 --TTTTTTTTTT
1 GGTTTTTTTTTT
161043 AGGATTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 9 0.38
14 11 0.46
15 3 0.12
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
GGTTTTTTTTTTTT
Found at i:161038 original size:10 final size:10
Alignment explanation
Indices: 161009--161042 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
160999 GAAAAGGTTT
161009 TTTTTTTTTGG
1 TTTTTTTTT-G
161020 TTTTTTTTTG
1 TTTTTTTTTG
161030 TTTTTTTTT-
1 TTTTTTTTTG
161039 TTTT
1 TTTT
161043 AGGATTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 10 0.43
11 9 0.39
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:161350 original size:23 final size:24
Alignment explanation
Indices: 161324--161369 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
161314 TGCTTTTGCA
*
161324 CTTTTTCTTTTCA-TTTTTTTGTG
1 CTTTTGCTTTTCACTTTTTTTGTG
*
161347 CTTTTGCTTTTGACTTTTTTTGT
1 CTTTTGCTTTTCACTTTTTTTGT
161370 CATTTAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (24 bp):
CTTTTGCTTTTCACTTTTTTTGTG
Done.