Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2259
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: 410483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:347565 original size:61 final size:62
Alignment explanation
Indices: 346858--347564 Score: 770
Period size: 62 Copynumber: 11.6 Consensus size: 62
346848 ATAAAGTACA
* * *
346858 TCCTGCTCTTTGAGGACAAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAA-AAAAAGTGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAG-GCG
* * * * * * * *
346919 TCTTGCTTTTTAAGGACTAAAAGGTGCCACTAACTCGTGTGAGCTTTAAAAAGAGAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * * * *
346981 TCTTGCTTTTTGAGCACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGAG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * * **
347043 TCCTGCTTTTTAATGACAAAAAGGTGCCACCAACTCATACGGGCTTT-AAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * * * *
347104 TCCTACTCTGTGAGGACTAAAAGGTGCCACCAGCTCTTGTGAGCTTTAAAAAGGAAAA--CG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * * * *
347164 TCATGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGACTTTAAAAGGAAAAA-GCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * *
347225 TCCTGCTCTTTGAAGACAAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAATAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* ** **
347287 TCCTACTCGATGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGGGAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * * *
347349 TCCTGCTTTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * * *
347411 TCCTACTCTTTGAGGATTAAAAGGT-ACACCAACTCATGTGGGCTTT--AAA-AAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * ** * *
347469 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTATGCTTT-GAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
* * *
347530 TCTTACTCTTTAAGGACTAAAAGGTGCCACCAACT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
347565 TTCTTTTTGA
Statistics
Matches: 544, Mismatches: 94, Indels: 16
0.83 0.14 0.02
Matches are distributed among these distances:
58 31 0.06
59 20 0.04
60 53 0.10
61 199 0.37
62 236 0.43
63 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (62 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAAGGCG
Found at i:347577 original size:93 final size:94
Alignment explanation
Indices: 347477--347646 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 94
347467 CATCCTACTC
* * * * *
347477 TTTGAGGACTAAAAGGTGCCACCAACTTATGTATGCTTT-GAAAGAAAAAGGTGTCTTACTCTTT
1 TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTACTCTTT
347541 AAGGACTAAAAGGTGCCACCAACTTTCTT
66 AAGGACTAAAAGGTGCCACCAACTTTCTT
* *
347570 TTTGAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTCTTT
1 TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTACTCTTT
*
347635 GAGGACTAAAAG
66 AAGGACTAAAAG
347647 TTACACCAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
93 35 0.51
94 33 0.49
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (94 bp):
TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTACTCTTT
AAGGACTAAAAGGTGCCACCAACTTTCTT
Found at i:347613 original size:213 final size:215
Alignment explanation
Indices: 347354--347781 Score: 671
Period size: 215 Copynumber: 2.0 Consensus size: 215
347344 AGGCGTCCTG
* * * *
347354 CTTTTTGAGGACTAAAAAGTGTCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTC
1 CTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCCTACTC
* *
347419 TTTGAGGATTAAAAGGTACACCAACTCATGTGGGCTTT-AAA-AAAAAGGCATCCTACTCTTTGA
66 TTTGAGGACTAAAAGGTACACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTAA
* * * ** *
347482 GGACTAAAAGGTGCCACCAACTTATGTATGCTTTGAAAGAAAAAGGTGTCTTACTCTTTAAGGAC
131 GGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTAAGGAC
347547 TAAAAGGTGCCACCAACTTT
196 TAAAAGGTGCCACCAACTTT
* * *
347567 CTTTTTGAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTC
1 CTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCCTACTC
* * *
347632 TTTGAGGACTAAAAGTTACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTAA
66 TTTGAGGACTAAAAGGTACACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTAA
*
347697 GGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTGAGGAC
131 GGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTAAGGAC
347762 TAAAAGGTGCCACCAACTTT
196 TAAAAGGTGCCACCAACTTT
347782 TGTGGGGTTT
Statistics
Matches: 194, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
213 93 0.48
214 3 0.02
215 98 0.51
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (215 bp):
CTTTTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCCTACTC
TTTGAGGACTAAAAGGTACACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTAA
GGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTAAGGAC
TAAAAGGTGCCACCAACTTT
Found at i:347668 original size:61 final size:60
Alignment explanation
Indices: 347570--348021 Score: 509
Period size: 61 Copynumber: 7.4 Consensus size: 60
347560 CAACTTTCTT
* * * * *
347570 TTTGAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTC
1 TTTGAGGACT-AAAAGTGCCACCAACTCATGTGGGCTTT-AAAAGAAAAAGGCATCCTACTC
** * *
347632 TTTGAGGACTAAAAGTTACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTC
1 TTTGAGGACTAAAAGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
* * * * *
347692 TTTAAGGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTC
1 TTTGAGGACTAAAA-GTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
** * * *
347753 TTTGAGGACTAAAAGGTGCCACCAACTTTTGTGGGGTTTAGAAAG-GAAA-GCATCCTGCTC
1 TTTGAGGACTAAAA-GTGCCACCAACTCATGTGGGCTTTA-AAAGAAAAAGGCATCCTACTC
* * *
347813 TTTGAGGACTTAAAGGTGCCACCAACTCGTGTAGGCTTTAAAAGAAAAAGGCATCCTGA-TC
1 TTTGAGGAC-TAAAAGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCT-ACTC
* * * * *
347874 TTTGAGGACTAAAAG-GTACACCAACTCGTATGGGCTTTAAATGAAAAAGGCGTCCTACT-
1 TTTGAGGACTAAAAGTG-CCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
347933 TTTAGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
1 TTT-GAGGACTAAAA-GTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
* *
347995 TTTCAAGACTAAAAGGTGCCACCAACT
1 TTTGAGGACTAAAA-GTGCCACCAACT
348022 TTCTCTTTGA
Statistics
Matches: 336, Mismatches: 42, Indels: 25
0.83 0.10 0.06
Matches are distributed among these distances:
59 9 0.03
60 126 0.38
61 183 0.54
62 18 0.05
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (60 bp):
TTTGAGGACTAAAAGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTC
Found at i:347692 original size:154 final size:151
Alignment explanation
Indices: 347419--347719 Score: 397
Period size: 154 Copynumber: 2.0 Consensus size: 151
347409 TGTCCTACTC
* * *
347419 TTTGAGGATTAAAAGGTACACCAACTCATGTGGGCTTTAAAAAAAAGGCATCCTACTCTTTGAGG
1 TTTGAGGACTAAAAAGTACACCAACTCATGTAGGCTTTAAAAAAAAGGCATCCTACTCTTTGAGG
* * * * * *
347484 ACTAAAAGGTGCCACCAACTTATGTATGCTTTGAAAGAAAAAGGTGTCTTACTCTTTAAGGACTA
66 ACTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTAAGGACTA
*
347549 AAAGGTGCCACCAACTTTCTT
131 AAAGGTGACACCAACTTTCTT
* * * * *
347570 TTTGAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTCTTT
1 TTTGAGGACTAAAAAGT-ACACCAACTCATGTAGGCTTT--AAA-AAAAAGGCATCCTACTCTTT
* * *
347635 GAGGACTAAAA-GTTACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTAAGG
62 GAGGACTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTAAGG
347699 ACTAAAAGGTGACACCAACTT
127 ACTAAAAGGTGACACCAACTT
347720 ATGTAGGCTT
Statistics
Matches: 128, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
151 15 0.12
152 18 0.14
154 67 0.52
155 28 0.22
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (151 bp):
TTTGAGGACTAAAAAGTACACCAACTCATGTAGGCTTTAAAAAAAAGGCATCCTACTCTTTGAGG
ACTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTAAGGACTA
AAAGGTGACACCAACTTTCTT
Found at i:347896 original size:242 final size:243
Alignment explanation
Indices: 347570--348023 Score: 741
Period size: 242 Copynumber: 1.9 Consensus size: 243
347560 CAACTTTCTT
* * * *
347570 TTTGAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTCTTT
1 TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCATCCTGATCTTT
* *
347635 GAGGACTAAAAGTTACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTA-AGG
66 GAGGACTAAAAGGTACACCAACTCGTATGGGCTTTAAAAGAAAAAGGCGTCCTACT-TTTAGAGG
* * *
347699 ACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTGAGGACTA
130 ACTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTCAAGACTA
347764 AAAGGTGCCACCAACTTTTGTGGGGTTTAGAAAGGAAAGCATCCTGCTC
195 AAAGGTGCCACCAACTTTTGTGGGGTTTAGAAAGGAAAGCATCCTGCTC
* * *
347813 TTTGAGGACTTAAAGGTGCCACCAACTCGTGTAGGCTTT-AAAAGAAAAAGGCATCCTGATCTTT
1 TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCATCCTGATCTTT
*
347877 GAGGACTAAAAGGTACACCAACTCGTATGGGCTTTAAATGAAAAAGGCGTCCTACTTTTAGAGGA
66 GAGGACTAAAAGGTACACCAACTCGTATGGGCTTTAAAAGAAAAAGGCGTCCTACTTTTAGAGGA
* * *
347942 CTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAGACTAA
131 CTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTCAAGACTAA
348007 AAGGTGCCACCAACTTT
196 AAGGTGCCACCAACTTT
348024 CTCTTTGAGG
Statistics
Matches: 194, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
241 4 0.02
242 155 0.80
243 35 0.18
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (243 bp):
TTTGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTTTAAAAAGAAAAAGGCATCCTGATCTTT
GAGGACTAAAAGGTACACCAACTCGTATGGGCTTTAAAAGAAAAAGGCGTCCTACTTTTAGAGGA
CTAAAAGGTGACACCAACTCATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTCAAGACTAA
AAGGTGCCACCAACTTTTGTGGGGTTTAGAAAGGAAAGCATCCTGCTC
Found at i:348010 original size:121 final size:123
Alignment explanation
Indices: 347573--348021 Score: 599
Period size: 121 Copynumber: 3.7 Consensus size: 123
347563 CTTTCTTTTT
* * * * *
347573 GAGGACTAAAAAGTGCCACGAACTCATGTAGGCTTTAAAAAGAAAAAGGCGTCTTGCTCTTTGAG
1 GAGGACTAAAAGGTGCCACCAACTCATGTAGGCTTT-AAAAGAAAAAGGCATCCTACTCTTTGAG
*
347638 GACTAAAA-GTTACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTA
65 GACTAAAAGGTGACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTA
* * *
347696 -AGGACTAAAAGGTGACACCAACTTATGTAGGCTTTAAAAGAAAAAGGAATCCTACTCTTTGAGG
1 GAGGACTAAAAGGTGCCACCAACTCATGTAGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGG
* ** * * * *
347760 ACTAAAAGGTGCCACCAACTTTTGTGGGGTTTAGAAAG-GAAA-GCATCCTGCTCTTT-
66 ACTAAAAGGTGACACCAACTCGTGTGGGCTTTA-AAAGAAAAAGGCGTCCTACTCTTTA
* *
347816 GAGGACTTAAAGGTGCCACCAACTCGTGTAGGCTTTAAAAGAAAAAGGCATCCTGA-TCTTTGAG
1 GAGGACTAAAAGGTGCCACCAACTCATGTAGGCTTTAAAAGAAAAAGGCATCCT-ACTCTTTGAG
* *
347880 GACTAAAAGGT-ACACCAACTCGTATGGGCTTTAAATGAAAAAGGCGTCCTACT-TTTA
65 GACTAAAAGGTGACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTA
* * *
347937 GAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAG
1 GAGGACTAAAAGGTGCCACCAACTCATGTAGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGG
*
348002 ACTAAAAGGTGCCACCAACT
66 ACTAAAAGGTGACACCAACT
348022 TTCTCTTTGA
Statistics
Matches: 281, Mismatches: 36, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
119 3 0.01
120 24 0.09
121 187 0.67
122 63 0.22
123 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (123 bp):
GAGGACTAAAAGGTGCCACCAACTCATGTAGGCTTTAAAAGAAAAAGGCATCCTACTCTTTGAGG
ACTAAAAGGTGACACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTA
Found at i:348028 original size:32 final size:32
Alignment explanation
Indices: 347992--348053 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
347982 AGGCATCCTA
347992 CTCTTTCAAGACTAAAAGGTGCCACCAACTTT
1 CTCTTTCAAGACTAAAAGGTGCCACCAACTTT
* *
348024 CTCTTTGAGGACTAAAAGGTGCCACCAACT
1 CTCTTTCAAGACTAAAAGGTGCCACCAACT
348054 CACGTGGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (32 bp):
CTCTTTCAAGACTAAAAGGTGCCACCAACTTT
Found at i:348047 original size:93 final size:93
Alignment explanation
Indices: 347937--348115 Score: 286
Period size: 93 Copynumber: 1.9 Consensus size: 93
347927 CCTACTTTTA
*
347937 GAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAG
1 GAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAG
*
348002 ACTAAAAGGTGCCACCAACTTTCTCTTT
66 ACTAAAAAGTGCCACCAACTTTCTCTTT
* ** * * *
348030 GAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGG
1 GAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAG
348095 ACTAAAAAGTGCCACCAACTT
66 ACTAAAAAGTGCCACCAACTT
348116 GTGTAGGCTG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (93 bp):
GAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGAAAAAGGCATCCTACTCTTTCAAG
ACTAAAAAGTGCCACCAACTTTCTCTTT
Found at i:348083 original size:154 final size:154
Alignment explanation
Indices: 347872--348177 Score: 384
Period size: 154 Copynumber: 2.0 Consensus size: 154
347862 GGCATCCTGA
** *
347872 TCTTTGAGGACTAAAAGGTACACCAACTCGTATGGGCTTTAAATGAAAAAGGCGTCCTACT-TTT
1 TCTTTGAGGACTAAAAGGTACACCAACTCACATGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTT
* * * *
347936 AGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGA-AAAA-GGCATCCTACTCTTTC
66 -GAGGACTAAAAAGTGCCACCAACTCATGTAGGCTGTAAAA-ATAAAATGGCATCCTACTATTTC
347999 AAGACTAAAAGGTGCCACCAACTTTC
129 AAGACTAAAAGGTGCCACCAACTTTC
* * * * *
348025 TCTTTGAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTT
1 TCTTTGAGGACTAAAAGGT-ACACCAACTCACATGGGCTTTAAAAGAAAAAGGCGTCCTACTCTT
** * * *
348090 TGAGGACTAAAAAGTGCCACCAACTTGTGTAGGCTGTAAAAATAAAATGGCGTCCTGCTATTTGA
65 TGAGGACTAAAAAGTGCCACCAACTCATGTAGGCTGTAAAAATAAAATGGCATCCTACTATTTCA
* * *
348155 GGACTAAAGGGTGCTACCAACTT
130 AGACTAAAAGGTGCCACCAACTT
348178 ATGTGAGCTT
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
153 20 0.16
154 73 0.57
155 36 0.28
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (154 bp):
TCTTTGAGGACTAAAAGGTACACCAACTCACATGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTT
GAGGACTAAAAAGTGCCACCAACTCATGTAGGCTGTAAAAATAAAATGGCATCCTACTATTTCAA
GACTAAAAGGTGCCACCAACTTTC
Found at i:348091 original size:61 final size:61
Alignment explanation
Indices: 348024--348227 Score: 239
Period size: 62 Copynumber: 3.3 Consensus size: 61
348014 CACCAACTTT
* * * *
348024 CTCTTTGAGGACTAAAAGGTGCCACCAACTCACGTGGGCTTTAAAAGGAAAAGGTGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCGTCCTG
* * * *
348085 CTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTAGGCTGTAAAA-ATAAAATGGCGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGA-AAAA-GGCGTCCTG
* * * * *
348147 CTATTTGAGGACTAAAGGGTGCTACCAACTTATGTGAGCTTTAAAAAGAAAAAAGCGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTT-AAAAGAAAAAGGCGTCCTG
* *
348209 CGCTTTGAGGTCTAAAAGG
1 CTCTTTGAGGACTAAAAGG
348228 CTAAAAGAGG
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
61 44 0.37
62 65 0.55
63 8 0.07
64 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (61 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCGTCCTG
Found at i:354856 original size:10 final size:10
Alignment explanation
Indices: 354841--354898 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
354831 CCTTTTATTC
354841 TTTCTTTTTG
1 TTTCTTTTTG
354851 TTTCTTTTTG
1 TTTCTTTTTG
*
354861 TTT-TTTGATTT
1 TTTCTTT--TTG
354872 TTTCATTTTTG
1 TTTC-TTTTTG
*
354883 TTTCTCTTGTG
1 TTTCT-TTTTG
354894 TTTCT
1 TTTCT
354899 CATTTTTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.08
10 14 0.35
11 20 0.50
13 3 0.08
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.76
Consensus pattern (10 bp):
TTTCTTTTTG
Found at i:354882 original size:32 final size:31
Alignment explanation
Indices: 354833--354896 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
354823 GTCGTTCCCC
*
354833 TTTTATTCTTTCTTTTTGTTTCT-TTTTGTT
1 TTTTATTCTTTCTTTTTGTTTCTCTTGTGTT
*
354863 TTTTGATTTTTTCATTTTTGTTTCTCTTGTGTT
1 TTTT-ATTCTTTC-TTTTTGTTTCTCTTGTGTT
354896 T
1 T
354897 CTCATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 7 0.24
32 11 0.38
33 7 0.24
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (31 bp):
TTTTATTCTTTCTTTTTGTTTCTCTTGTGTT
Found at i:354904 original size:32 final size:31
Alignment explanation
Indices: 354841--354912 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
354831 CCTTTTATTC
* * *
354841 TTTCTTTTTGTTTCTTTTTGTTTTTTGATTT
1 TTTCTTTTTGTTTCTTTGTGTTTTCTCATTT
354872 TTTCATTTTTGTTTCTCTTGTG-TTTCTCATTT
1 TTTC-TTTTTGTTTCT-TTGTGTTTTCTCATTT
354904 TTTGCTTTT
1 TTT-CTTTT
354913 ACCTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 4 0.11
32 26 0.74
33 5 0.14
ACGTcount: A:0.04, C:0.11, G:0.10, T:0.75
Consensus pattern (31 bp):
TTTCTTTTTGTTTCTTTGTGTTTTCTCATTT
Found at i:358776 original size:13 final size:13
Alignment explanation
Indices: 358758--358783 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
358748 GTCCAACATC
358758 TAGCTAATCTATT
1 TAGCTAATCTATT
358771 TAGCTAATCTATT
1 TAGCTAATCTATT
358784 CATACATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TAGCTAATCTATT
Found at i:364586 original size:13 final size:13
Alignment explanation
Indices: 364568--364593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
364558 TACAGCAAGT
364568 ATGTATCGATACA
1 ATGTATCGATACA
364581 ATGTATCGATACA
1 ATGTATCGATACA
364594 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:366839 original size:21 final size:21
Alignment explanation
Indices: 366806--366850 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
366796 TTGCAAGTTG
*
366806 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
366828 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
366848 AAA
1 AAA
366851 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:370744 original size:20 final size:20
Alignment explanation
Indices: 370665--370744 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
370655 AATGTCCAAA
*
370665 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
370685 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
370710 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
370730 TTGTATCGATACATT
1 ATGTATCGATACATT
370745 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:370748 original size:13 final size:13
Alignment explanation
Indices: 370730--370768 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
370720 ACATTTTTCT
370730 TTGTATCGATACA
1 TTGTATCGATACA
370743 TTGTATCGATACA
1 TTGTATCGATACA
*
370756 CTGTATCGATACA
1 TTGTATCGATACA
370769 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:373280 original size:13 final size:13
Alignment explanation
Indices: 373262--373287 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
373252 TACAGCAAGT
373262 ATGTATCGATACA
1 ATGTATCGATACA
373275 ATGTATCGATACA
1 ATGTATCGATACA
373288 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:375970 original size:8 final size:8
Alignment explanation
Indices: 375957--376005 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
375947 ATACCAAAAT
375957 AAAAACAA
1 AAAAACAA
*
375965 AAAAAC-C
1 AAAAACAA
*
375972 AAGAA--A
1 AAAAACAA
375978 AAAAACAA
1 AAAAACAA
375986 AAAAACAA
1 AAAAACAA
*
375994 ACAAACAA
1 AAAAACAA
376002 AAAA
1 AAAA
376006 GGGTTCCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 4 0.12
7 4 0.12
8 25 0.76
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:375983 original size:21 final size:20
Alignment explanation
Indices: 375949--375991 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
375939 CGACTTTCAT
*
375949 ACCAAAATAAAAACAAAAAA
1 ACCAAAAAAAAAACAAAAAA
375969 ACCAAGAAAAAAAACAAAAAA
1 ACCAA-AAAAAAAACAAAAAA
375990 AC
1 AC
375992 AAACAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.02
Consensus pattern (20 bp):
ACCAAAAAAAAAACAAAAAA
Found at i:376003 original size:21 final size:21
Alignment explanation
Indices: 375957--376004 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
375947 ATACCAAAAT
* *
375957 AAAAACAAAAAAACCAAGAAA
1 AAAAACAAAAAAACAAACAAA
375978 AAAAACAAAAAAACAAACAAA
1 AAAAACAAAAAAACAAACAAA
375999 CAAAAA
1 -AAAAA
376005 AGGGTTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAAACAAACAAA
Found at i:376773 original size:13 final size:13
Alignment explanation
Indices: 376755--376854 Score: 71
Period size: 13 Copynumber: 8.6 Consensus size: 13
376745 GTAACCCATA
*
376755 TATCGATACATTG
1 TATCGATACAATG
376768 TATCGATACAATG
1 TATCGATACAATG
*
376781 TATCGATAGAA--
1 TATCGATACAATG
*
376792 -A--GA-ACATTG
1 TATCGATACAATG
376801 TATCGATACAATG
1 TATCGATACAATG
*
376814 TATCGATAGAA--
1 TATCGATACAATG
*
376825 -A--GA-ACATTG
1 TATCGATACAATG
376834 TATCGATACAATG
1 TATCGATACAATG
376847 TATCGATA
1 TATCGATA
376855 GAAAGAACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
7 4 0.06
8 4 0.06
10 4 0.06
12 4 0.06
13 50 0.76
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:376804 original size:20 final size:20
Alignment explanation
Indices: 376779--376874 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
376769 ATCGATACAA
376779 TGTATCGATAGAAAGAACAT
1 TGTATCGATAGAAAGAACAT
*
376799 TGTATCGAT-------ACAA
1 TGTATCGATAGAAAGAACAT
376812 TGTATCGATAGAAAGAACAT
1 TGTATCGATAGAAAGAACAT
*
376832 TGTATCGAT-------ACAA
1 TGTATCGATAGAAAGAACAT
376845 TGTATCGATAGAAAGAACAT
1 TGTATCGATAGAAAGAACAT
376865 TGTATCGATA
1 TGTATCGATA
376875 CATTCTGGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
13 24 0.41
20 34 0.59
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATAGAAAGAACAT
Found at i:376804 original size:33 final size:33
Alignment explanation
Indices: 376762--376876 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
376752 ATATATCGAT
376762 ACATTGTATCGATACAATGTATCGATAGAAAGA
1 ACATTGTATCGATACAATGTATCGATAGAAAGA
376795 ACATTGTATCGATACAATGTATCGATAGAAAGA
1 ACATTGTATCGATACAATGTATCGATAGAAAGA
376828 ACATTGTATCGATACAATGTATCGATAGAAAGA
1 ACATTGTATCGATACAATGTATCGATAGAAAGA
376861 ACATTGTATCGATACA
1 ACATTGTATCGATACA
376877 TTCTGGAAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (33 bp):
ACATTGTATCGATACAATGTATCGATAGAAAGA
Found at i:382094 original size:83 final size:80
Alignment explanation
Indices: 381923--382242 Score: 282
Period size: 83 Copynumber: 4.0 Consensus size: 80
381913 CATTTACGAT
* * * ** * *
381923 AAATCTTGAATTTATATTCTTGGGGATACTCCAACCCTATCTCT-C--TGAGAGGATACTCCAAC
1 AAATCTTGAATTTACATTC-TGGGGATACTTCAA-CCTATCTTTCCAAAAAAAAGATACTCCAAC
* *
381985 CCTATTTTTCTTATAAC
64 CCTATTTTTCTTACAAA
*
382002 AAATCTTGAATTTACATTCTCGGGGATACTTCAACCTTATCTTTTCGAAAAAAAAGATACTCCAA
1 AAATCTTGAATTTACATTCT-GGGGATACTTCAACC-TATC-TTTCCAAAAAAAAGATACTCCAA
382067 CCCTATTTTTCTTACAAA
63 CCCTATTTTTCTTACAAA
* ** * * * *
382085 AAATCTTGAATTT--A---TGGGGATACTTCAACCCTATCTCTCCAAAATGAGGACATTCTAACC
1 AAATCTTGAATTTACATTCTGGGGATACTTCAA-CCTATCTTTCCAAAAAAAAGATACTCCAACC
*
382145 CTATTTTTCTTATAAAA
65 CTATTTTTCTTA-CAAA
* * **
382162 AAATCTTGAATTTACATTCTTGGGGATACTTCAACCTA--TTTCTACAAAAAGAGATACTTTAAC
1 AAATCTTGAATTTACATTC-TGGGGATACTTCAACCTATCTTTCCA-AAAAAAAGATACTCCAAC
*
382225 CCTATTTTTCATACAAA
64 CCTATTTTTCTTACAAA
382242 A
1 A
382243 TGACTTGTTT
Statistics
Matches: 196, Mismatches: 30, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
76 29 0.15
77 33 0.17
78 6 0.03
79 35 0.18
80 10 0.05
81 24 0.12
82 4 0.02
83 55 0.28
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (80 bp):
AAATCTTGAATTTACATTCTGGGGATACTTCAACCTATCTTTCCAAAAAAAAGATACTCCAACCC
TATTTTTCTTACAAA
Found at i:382189 original size:160 final size:153
Alignment explanation
Indices: 381943--382242 Score: 404
Period size: 160 Copynumber: 1.9 Consensus size: 153
381933 TTTATATTCT
** * *
381943 TGGGGATACTCCAACCCTATCTCTCTGAGAGGATACTCCAACCCTATTTTTCTTATAACAAATCT
1 TGGGGATACTCCAACCCTATCTCTCAAAGAGGACACTCCAACCCTATTTTTCTTATAAAAAATCT
382008 TGAATTTACATTCTCGGGGATACTTCAACCTTATCTTTTCGA-AAAAAAAGATACTCCAACCCTA
66 TGAATTTACATTCTCGGGGATACTTCAACC-TA---TTTCGACAAAAAAAGATACTCCAACCCTA
*
382072 TTTTTCTTACAAAAAATCTTGAATTTA
127 TTTTTCATACAAAAAATCTTGAATTTA
* * *
382099 TGGGGATACTTCAACCCTATCTCTCCAAAATGAGGACATTCTAACCCTATTTTTCTTATAAAAAA
1 TGGGGATACTCCAACCCTATCTCT-C-AAA-GAGGACACTCCAACCCTATTTTTCTTAT-AAAAA
* * * **
382164 ATCTTGAATTTACATTCTTGGGGATACTTCAACCTATTTCTACAAAAAGAGATACTTTAACCCTA
62 ATCTTGAATTTACATTCTCGGGGATACTTCAACCTATTTCGACAAAAAAAGATACTCCAACCCTA
382229 TTTTTCATACAAAA
127 TTTTTCATACAAAA
382243 TGACTTGTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
156 28 0.22
157 33 0.26
158 1 0.01
159 27 0.21
160 37 0.29
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (153 bp):
TGGGGATACTCCAACCCTATCTCTCAAAGAGGACACTCCAACCCTATTTTTCTTATAAAAAATCT
TGAATTTACATTCTCGGGGATACTTCAACCTATTTCGACAAAAAAAGATACTCCAACCCTATTTT
TCATACAAAAAATCTTGAATTTA
Found at i:383749 original size:6 final size:6
Alignment explanation
Indices: 383740--383819 Score: 63
Period size: 6 Copynumber: 12.8 Consensus size: 6
383730 TGGGTTTTTG
* *
383740 TTTTAT TTTTAT TTTAAT TTTTATT TTTTAAT TTTTAAT TTTTA- TTTAAT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTT-AT TTTT-AT TTTTAT TTTTAT
* * * *
383790 TTTAAT TTTTGT TTTTTT TCTTTTT TTTTA
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTA
383820 GGCATAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
5 4 0.06
6 35 0.56
7 23 0.37
8 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:383767 original size:7 final size:7
Alignment explanation
Indices: 383740--383799 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
383730 TGGGTTTTTG
383740 TTTT-AT
1 TTTTAAT
383746 TTTT-A-
1 TTTTAAT
383751 TTTTAAT
1 TTTTAAT
*
383758 TTTTATT
1 TTTTAAT
383765 TTTTAAT
1 TTTTAAT
383772 TTTTAAT
1 TTTTAAT
383779 TTTT-A-
1 TTTTAAT
383784 -TTTAA-
1 TTTTAAT
383789 TTTTAAT
1 TTTTAAT
383796 TTTT
1 TTTT
383800 GTTTTTTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
4 3 0.06
5 5 0.11
6 12 0.26
7 27 0.57
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTAAT
Found at i:383814 original size:32 final size:31
Alignment explanation
Indices: 383734--383819 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
383724 TGGGTTTGGG
* *
383734 TTTTTGTTTTATTTTTATTTTAATTTTTATTT
1 TTTTTTTTTTATTTTTA-TTTAATTTTAATTT
* *
383766 TTTAATTTTTAATTTTTATTTAATTTTAATTT
1 TTT-TTTTTTTATTTTTATTTAATTTTAATTT
* *
383798 TTGTTTTTTTTCTTTTTTTTTA
1 TT-TTTTTTTTATTTTTATTTA
383820 GGCATAATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 32 0.73
33 12 0.27
ACGTcount: A:0.17, C:0.01, G:0.02, T:0.79
Consensus pattern (31 bp):
TTTTTTTTTTATTTTTATTTAATTTTAATTT
Found at i:387161 original size:33 final size:33
Alignment explanation
Indices: 387116--387195 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
387106 TAACATTTTC
** *
387116 TTCAAAATCGACCTCATTCAAGCAAATGACTTA
1 TTCAAAATCGACCTCATTCAAGCAAACAACTCA
* *
387149 TTTAAAATCGACCTCGTTCAAGCAAACAACTCA
1 TTCAAAATCGACCTCATTCAAGCAAACAACTCA
387182 TTCAAAATCGACCT
1 TTCAAAATCGACCT
387196 TTGAATCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (33 bp):
TTCAAAATCGACCTCATTCAAGCAAACAACTCA
Found at i:394733 original size:20 final size:20
Alignment explanation
Indices: 394708--394761 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
394698 GTTAGAAGCA
*
394708 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
394728 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
394748 ATGTATCGATACAA
1 ATGTATCGATACAA
394762 ACAATGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:394834 original size:19 final size:20
Alignment explanation
Indices: 394790--394837 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
394780 CTGCCAGTTT
**
394790 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
394810 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
394829 CATGTATCG
1 CATGTATCG
394838 TTACTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:395559 original size:13 final size:13
Alignment explanation
Indices: 395541--395566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
395531 TACACTAACT
395541 ATGTATCGATACA
1 ATGTATCGATACA
395554 ATGTATCGATACA
1 ATGTATCGATACA
395567 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:395564 original size:32 final size:33
Alignment explanation
Indices: 395523--395586 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
395513 TAGCCAAACT
* **
395523 TGTATCGATACACTAACTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
395555 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
395587 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:401728 original size:13 final size:13
Alignment explanation
Indices: 401710--401747 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
401700 GGAAATTCAA
*
401710 TGTATCGATACAT
1 TGTATCGATACAC
401723 TGTATCGATACAC
1 TGTATCGATACAC
401736 TGTATCGATACA
1 TGTATCGATACA
401748 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:406567 original size:13 final size:13
Alignment explanation
Indices: 406547--406586 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
406537 ATAGTAACCC
406547 ACGTATCGATACA
1 ACGTATCGATACA
*
406560 ATGTATCGATACA
1 ACGTATCGATACA
*
406573 ACATATCGATACA
1 ACGTATCGATACA
406586 A
1 A
406587 GGAATATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (13 bp):
ACGTATCGATACA
Found at i:406644 original size:20 final size:20
Alignment explanation
Indices: 406619--406656 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
406609 GGGTTTTTCA
406619 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
406639 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
406657 AGAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:407926 original size:155 final size:155
Alignment explanation
Indices: 407714--408167 Score: 454
Period size: 158 Copynumber: 2.9 Consensus size: 155
407704 ACAACGTGGC
* *
407714 TGGAGTATCCCTGATTAT-GAAAAATCGGTGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCGT
1 TGGAGTATCCCT-ATTATAG-AAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCC-T
*
407778 CGAAAATAATAGGGTTGGAGTATCCTCGATTATAGAAAATTGGTGTTTTGAAAATAAATCGAGGT
63 CGAAAATAACAGGGTTGGAGTATCCTCGATTATAGAAAATTGGTGTTTTGAAAATAAATCGAGGT
** * *
407843 TGGAGTATTGCTTC-AAAATAATAGGGT
128 TGGAGTATCCCTACGAAAATAACAGGGT
* *
407870 TGGAGTATCCCTATTATAGAAAATCGATGTTTTGAAAATCAAATCGAGGTTAGAGTATCCCCTCG
1 TGGAGTATCCCTATTATAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTAT-CCCTCG
* * * * * ** *
407935 AAAATAACAGGGTTGGAGTATCCCCGATTA-CGAAAAATCGATGCTTT-AGAAATAAGGCCTAGG
65 AAAATAACAGGGTTGGAGTATCCTCGATTATAG-AAAATTGGTGTTTTGA-AAATAA-ATCGA-G
*
407998 GTTGGAGTATCCCTACGAAAATAACGGGGT
126 GTTGGAGTATCCCTACGAAAATAACAGGGT
* * * * * * *
408028 TGGAGTATCCCGATTGTGAAAAAAT-AATATTTTAAAAATAAAACCG-GGATTGGAGTATCCC-C
1 TGGAGTATCCCTATTAT-AGAAAATCGATGTTTTGAAAATAAAATCGAGG-TTGGAGTATCCCTC
* * * * * * *
408090 AATGAAATAACAAGGTTGGAGTGTCCTCGATTGTAAAAAATTGGTGTTTTGGAAATAAAATCGGG
64 GA--AAATAACAGGGTTGGAGTATCCTCGATTATAGAAAATTGGTGTTTTGAAAAT-AAATCGAG
408155 GTTGGAGTATCCC
126 GTTGGAGTATCCC
408168 CGATTGTGGA
Statistics
Matches: 242, Mismatches: 42, Indels: 27
0.78 0.14 0.09
Matches are distributed among these distances:
154 2 0.01
155 88 0.36
156 20 0.08
157 33 0.14
158 91 0.38
159 8 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (155 bp):
TGGAGTATCCCTATTATAGAAAATCGATGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCTCGA
AAATAACAGGGTTGGAGTATCCTCGATTATAGAAAATTGGTGTTTTGAAAATAAATCGAGGTTGG
AGTATCCCTACGAAAATAACAGGGT
Found at i:407970 original size:78 final size:79
Alignment explanation
Indices: 407714--408168 Score: 400
Period size: 79 Copynumber: 5.8 Consensus size: 79
407704 ACAACGTGGC
* * * *
407714 TGGAGTATCCCTGATTAT-GAAAAATCGGTGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCGT
1 TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGAAAAT-AAATCGAGGTTGGAGTATCCCCT
*
407778 CGAAAATAATAGGGT
65 CGAAAATAACAGGGT
* * * ** *
407793 TGGAGTATCCTCGATTATAG-AAAATTGGTGTTTTGAAAATAAATCGAGGTTGGAGTATTGCTTC
1 TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGAAAATAAATCGAGGTTGGAGTATCCCCTC
*
407857 -AAAATAATAGGGT
66 GAAAATAACAGGGT
* *
407870 TGGAGTAT-CCCTATTATAG-AAAATCGATGTTTTGAAAATCAAATCGAGGTTAGAGTATCCCCT
1 TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGAAAAT-AAATCGAGGTTGGAGTATCCCCT
407933 CGAAAATAACAGGGT
65 CGAAAATAACAGGGT
* * ** *
407948 TGGAGTATCCCCGATTA-CGAAAAATCGATGCTTT-AGAAATAAGGCCTAGGGTTGGAGTAT-CC
1 TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGA-AAATAA-ATCGA-GGTTGGAGTATCCC
*
408010 CTACGAAAATAACGGGGT
63 CT-CGAAAATAACAGGGT
* * * * *
408028 TGGAGTAT-CCCGATTGT-GAAAAAAT-AATATTTTAAAAATAAAACCG-GGATTGGAGTATCCC
1 TGGAGTATCCCCGATTATAG-AAAAATCGATGTTTTGAAAAT-AAATCGAGG-TTGGAGTATCCC
*
408089 CAAT-G-AAATAACAAGGT
63 C--TCGAAAATAACAGGGT
* * * * * * *
408106 TGGAGTGTCCTCGATTGTA-AAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCC
1 TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGAAAAT-AAATCGAGGTTGGAGTATCCCC
408169 GATTGTGGAA
Statistics
Matches: 315, Mismatches: 40, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
76 27 0.09
77 43 0.14
78 77 0.24
79 123 0.39
80 44 0.14
81 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATAGAAAAATCGATGTTTTGAAAATAAATCGAGGTTGGAGTATCCCCTC
GAAAATAACAGGGT
Found at i:408160 original size:51 final size:51
Alignment explanation
Indices: 408102--408219 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
408092 TGAAATAACA
* * *
408102 AGGTTGGAGTGTCCTCGATTGTAAAAAATTGGTGTTTTGGAAATAAAATCG
1 AGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAATCG
* **
408153 GGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCG
1 AGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAATCG
*
408204 AGGTTAGAGTATCCCC
1 AGGTTGGAGTATCCCC
408220 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTAGAAATAAAATCG
Found at i:408171 original size:130 final size:130
Alignment explanation
Indices: 408022--408297 Score: 344
Period size: 130 Copynumber: 2.1 Consensus size: 130
408012 ACGAAAATAA
*
408022 CGGGGTTGGAGTAT-CCCGATTGTGAAAAAATAATATTTTAAAAATAAAACCG-GGATTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAAAAATAAAACCGAGG-TTAGAGTA
* * * * * *
408085 TCCCCAAT-G-AAATAACAAGGTTGGAGTGTCCTCGATTGTAAAAAATTGGTGTTTTGGAAATAA
65 TCCCC--TCGAAAATAACAAGATTGGAGTATCCCCGACTATAAAAAATTGATGTTTTGGAAATAA
408148 AAT
128 AAT
* * ** * * *
408151 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAAATAAAATCGAGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAAAAATAAAACCGAGGTTAGAGTAT
* *
408216 CCCCTCGAAAATAACGAGATTGGAGTATCCCCGACTATGAAAAATTGATGTTTTGGAAATAAAAT
66 CCCCTCGAAAATAACAAGATTGGAGTATCCCCGACTATAAAAAATTGATGTTTTGGAAATAAAAT
*
408281 CGAGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
408298 TGAGATGAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
128 1 0.01
129 15 0.12
130 108 0.86
131 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAAATAATATTTTAAAAATAAAACCGAGGTTAGAGTAT
CCCCTCGAAAATAACAAGATTGGAGTATCCCCGACTATAAAAAATTGATGTTTTGGAAATAAAAT
Done.