Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_pilon, whole genome shotgun sequence
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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 25
Found at i:497231 original size:81 final size:80
Alignment explanation
Indices: 497044--497235 Score: 258
Period size: 81 Copynumber: 2.4 Consensus size: 80
497034 TGGCATATGT
* *
497044 AAATCGCATTGCGATTTACGTATTCACATTACGATTTACGTAATCGCATTGCGATTTACGTATTC
1 AAATCGCATTGCGATTTACGTATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAATC
* *
497109 GCATTGCGATTTACG
66 ACATTGCGATTTACC
* * * **
497124 TAATCGCATTGCAATTTTCCAAATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAAT
1 AAATCGCATTGCGA-TTTACGTATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAAT
* *
497189 CACATTGCTATTTTCC
65 CACATTGCGATTTACC
*
497205 AAATTCGCGTTGCGATTTACGTATTCGCATT
1 AAA-TCGCATTGCGATTTACGTATTCGCATT
497236 GCGAATTTGG
Statistics
Matches: 93, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
80 12 0.13
81 72 0.77
82 9 0.10
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (80 bp):
AAATCGCATTGCGATTTACGTATTCGCATTACGATTTACGTAATCGCATTGCGATTTACGTAATC
ACATTGCGATTTACC
Found at i:516218 original size:19 final size:19
Alignment explanation
Indices: 516194--516239 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
516184 AATTAGGTAT
516194 AAGCCTTAAGGAATTGAAA
1 AAGCCTTAAGGAATTGAAA
516213 AAGCCTTAAGGAATTGAAA
1 AAGCCTTAAGGAATTGAAA
*
516232 AGGCCTTA
1 AAGCCTTA
516240 CATTCTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGCCTTAAGGAATTGAAA
Found at i:517919 original size:2 final size:2
Alignment explanation
Indices: 517912--517953 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
517902 CACGTTACTT
* *
517912 TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
517954 GTTTTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:519590 original size:33 final size:33
Alignment explanation
Indices: 519550--519617 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
519540 ATATTCTGAT
*
519550 ATCTTTTATTTTAGT-TTCTTACTTTATATTTTA
1 ATCTTTTATTTTAGTCAT-TTACTTTATATTTTA
519583 ATCTTTTATTTTAGTCATTTACTTTATATTTTA
1 ATCTTTTATTTTAGTCATTTACTTTATATTTTA
519616 AT
1 AT
519618 TTATGTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (33 bp):
ATCTTTTATTTTAGTCATTTACTTTATATTTTA
Found at i:519603 original size:21 final size:22
Alignment explanation
Indices: 519579--519640 Score: 54
Period size: 25 Copynumber: 2.7 Consensus size: 22
519569 TACTTTATAT
519579 TTTAATCTTTTATTTTA-GTCA
1 TTTAATCTTTTATTTTATGTCA
* *
519600 TTTACTTTATATTTTAATTTATGTCA
1 TTTA----ATCTTTTATTTTATGTCA
*
519626 TTTATTCTTTTATTT
1 TTTAATCTTTTATTT
519641 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
21 4 0.13
22 8 0.26
25 11 0.35
26 8 0.26
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTAATCTTTTATTTTATGTCA
Found at i:520977 original size:46 final size:46
Alignment explanation
Indices: 520905--520994 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
520895 ATTTGATTTC
* * * *
520905 AATTTTTCTAAACAAAGCATGGAACTAGAAATCATGCGGTTAGGTT
1 AATTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGGTT
520951 AATTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGG
1 AATTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGG
520995 ATTTTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (46 bp):
AATTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGGTT
Found at i:528159 original size:23 final size:24
Alignment explanation
Indices: 528133--528178 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
528123 CACCATAGCA
528133 CGTATAA-TTGCACCGAAGTGCCG
1 CGTATAATTTGCACCGAAGTGCCG
*
528156 CGTATAATTTGCACCGTAGTGCC
1 CGTATAATTTGCACCGAAGTGCC
528179 ATATAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (24 bp):
CGTATAATTTGCACCGAAGTGCCG
Found at i:528408 original size:105 final size:104
Alignment explanation
Indices: 528195--528417 Score: 239
Period size: 105 Copynumber: 2.1 Consensus size: 104
528185 GATTGTCCAT
* * * * *
528195 AAGGACCACATATAAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGCCTCAAA
1 AAGGACCACATAAAAATTCATTAAGAACCATATACATATACCAAGGACCAAATAAGTGCCGCAAA
*
528260 AGACCTCATACATGCTCCAAAGAATACATATACGTCCCA
66 AGACCTCATACATGCTCCAAAGAATACATATACATCCCA
* * * * * * *
528299 AAGGACGACATAGAAAATTCATTAAGAATCATATACATATGCTAATGACCAAATACGTGTCGCAA
1 AAGGACCACATA-AAAATTCATTAAGAACCATATACATATACCAAGGACCAAATAAGTGCCGCAA
* * * * * * * *
528364 AGGACCTCATAGATGTTCCATAGGATACTTATATATCCCG
65 AAGACCTCATACATGCTCCAAAGAATACATATACATCCCA
*
528404 AAGGACCACGTAAA
1 AAGGACCACATAAA
528418 CCCTCGACTC
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
104 13 0.14
105 82 0.86
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (104 bp):
AAGGACCACATAAAAATTCATTAAGAACCATATACATATACCAAGGACCAAATAAGTGCCGCAAA
AGACCTCATACATGCTCCAAAGAATACATATACATCCCA
Found at i:529912 original size:22 final size:22
Alignment explanation
Indices: 529886--529986 Score: 134
Period size: 21 Copynumber: 4.7 Consensus size: 22
529876 TCGGTTGAGG
* *
529886 GGGTATCGATTCCCCTTTGAAT
1 GGGTACCGATTCCCCATTGAAT
* * *
529908 AGGTATCGATTCCCCCTTGAAT
1 GGGTACCGATTCCCCATTGAAT
*
529930 GGGTACCGATT-CTCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
529951 GGGTACCGATT-CCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
529972 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
529987 TAGCCCAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
21 39 0.55
22 32 0.45
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (22 bp):
GGGTACCGATTCCCCATTGAAT
Found at i:531707 original size:27 final size:27
Alignment explanation
Indices: 531677--531738 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
531667 GAACTGAGTT
*
531677 TTCATCTATTTTGTTTATCATGTGTGA
1 TTCATCTATTTTGTATATCATGTGTGA
*
531704 TTCATCTATTTTGTATATCATGTGTGT
1 TTCATCTATTTTGTATATCATGTGTGA
531731 TTCATCTA
1 TTCATCTA
531739 CAATAGTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (27 bp):
TTCATCTATTTTGTATATCATGTGTGA
Found at i:532500 original size:22 final size:22
Alignment explanation
Indices: 532472--532528 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
532462 ACATCTACAT
532472 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATATATTCTC
532494 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATATATTCTC
532516 TCTTCAAAGATGA
1 TCTTCAAAGATGA
532529 AAGCTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATATATTCTC
Found at i:533230 original size:45 final size:45
Alignment explanation
Indices: 533165--533345 Score: 254
Period size: 45 Copynumber: 4.0 Consensus size: 45
533155 CTATTTCTCA
* * *
533165 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACATGCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
533210 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
533255 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * * *
533300 CATCCATAGGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
533346 AAATTTTTGA
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 111 0.90
46 4 0.03
47 8 0.07
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:533404 original size:45 final size:45
Alignment explanation
Indices: 533353--533449 Score: 176
Period size: 45 Copynumber: 2.2 Consensus size: 45
533343 GGGAAATTTT
*
533353 TGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTATCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
533398 TTATGTTATCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTATCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
533443 TGATGTT
1 TGATGTT
533450 TTAAAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTATCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:533404 original size:76 final size:74
Alignment explanation
Indices: 533277--533419 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 74
533267 CTTCAGTGCA
* *
533277 TGATGTTATCAAAACCTTCGGGTCATCCATAGGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTATCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTATC-AAAA-CCTT
533342 CGGGAAATTTT
64 CGGGAAATTTT
** * * **
533353 TGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATTATGTTATCAAAACCTTCG
1 TGATGTTATCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTATCAAAACCTTCG
533418 GG
66 GG
533420 TCATCTATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
74 8 0.14
75 4 0.07
76 47 0.80
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (74 bp):
TGATGTTATCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTATCAAAACCTTCG
GGAAATTTT
Found at i:533448 original size:121 final size:121
Alignment explanation
Indices: 533232--533849 Score: 516
Period size: 121 Copynumber: 4.9 Consensus size: 121
533222 CTTCAGTGCA
533232 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCG
* *
533297 GGTCATCCATAGGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAATTTT
66 GGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAATTTT
* *
533353 TGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATTATGTTATCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCG
* * * * * **
533418 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTAAAAAAAACCTTCGGGAGCTTTT
66 GGTCATCCATAAGACCTTCAGTGCAGGATGTTTT-CAAAAAGCCTTCGGGAAATTTT
* * *
533475 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATC-AAAA-CCTT
* *** * * ** * * *** * *
533540 CGGGAGC-TTTTTGATATTTTCAAAGT-CTTCGG--GTTATCTGTAAGACCTTCAGTG-CA----
64 CGGG-TCATCCATAAGACCTTC--AGTGC--AGGATGTTTTCAAAAAG-CCTTC-GGGAAATTTT
* *
533596 GGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTATCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCG
*
533661 GGTCATCCAAAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGTCATCTATAAGACCTT
66 GGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGG--------AA-A--TT
*
533726 CAGTGCA
120 ---T--T
* * * ** * * *
533733 GGATGTTTTCAAAAAGCATTCGGATCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCC
1 TGATGTTTTCAA-AA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATC-AAAA-CC
* *
533798 TTCGGGTAATCCATAAGACCTTTAGTGCAGGATGTTTTCAAAAAGCCTTCGG
62 TTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGG
533850 ATCATTCATA
Statistics
Matches: 393, Mismatches: 65, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
116 4 0.01
117 8 0.02
118 10 0.03
119 14 0.04
120 4 0.01
121 142 0.36
122 68 0.17
123 4 0.01
124 17 0.04
125 11 0.03
126 6 0.02
127 1 0.00
137 12 0.03
138 2 0.01
139 35 0.09
140 4 0.01
141 51 0.13
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCG
GGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAATTTT
Found at i:533534 original size:77 final size:77
Alignment explanation
Indices: 533406--533609 Score: 329
Period size: 76 Copynumber: 2.7 Consensus size: 77
533396 CATTATGTTA
* * *
533406 TCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTAAAAAAAACCTTCGGGAGC
1 TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGC
533471 TTTTTGATATTT
66 TTTTTGATATTT
*
533483 TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGC
1 TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGC
533547 TTTTTGATATTT
66 TTTTTGATATTT
* * * *
533559 TCAAAGTCTTCGGGTTATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAA
1 TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
533610 CCTTCGGGTC
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 71 0.60
77 47 0.40
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (77 bp):
TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAAACCTTCGGGAGC
TTTTTGATATTT
Found at i:533636 original size:198 final size:198
Alignment explanation
Indices: 533285--533647 Score: 546
Period size: 198 Copynumber: 1.8 Consensus size: 198
533275 CATGATGTTA
*
533285 TCAAAACCTTCGGGTCATCCATAGGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAAT
1 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAAT
* * **
533350 TTTTGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATTATGTTATCAAAACCT
66 TTTTGATATTATCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTATCAAAACCT
*
533415 TCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTAAAAAAAACCTTCGGGAGCTTTTTGATA
131 TCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTAAAAAAAACCTTCGGGAGCTTTTTGATA
533480 TTT
196 TTT
* ** * * * **
533483 TCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCT
1 TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAAT
* ** * *
533548 TTTTGATATTTTCAAAGTCTTCGGGTTATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCT
66 TTTTGATATTATCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTATCAAAACCT
*
533613 TCGGGTCATCTGTAAGACCTTCAGTGCATGATGTT
131 TCGGGTCATCTATAAGACCTTCAGTGCATGATGTT
533648 ATCAAAACCT
Statistics
Matches: 145, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
198 145 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (198 bp):
TCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAAAT
TTTTGATATTATCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATGTTATCAAAACCT
TCGGGTCATCTATAAGACCTTCAGTGCATGATGTTTTAAAAAAAACCTTCGGGAGCTTTTTGATA
TTT
Found at i:533724 original size:47 final size:47
Alignment explanation
Indices: 533561--534005 Score: 597
Period size: 47 Copynumber: 9.7 Consensus size: 47
533551 TGATATTTTC
* * *
533561 AAAGTCTTCGGGTTATCTGTAAGACCTTCAGTGCAGGATGTTTTC-A
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* * *
533607 AAA-CCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTATC-A
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* *
533652 AAA-CCTTCGGGTCATCCAAAAGACCTTCAGTGCAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
533698 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* * *
533745 AAAGCATTCGGATCATCCATAAGACCTTCAGTGCAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* * *
533792 AAAGCCTTCGGGTAATCCATAAGACCTTTAGTGCAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* *
533839 AAAGCCTTCGGATCAT-TCATAAGACCTTCAGTGCAAGATGTTTTCAA
1 AAAGCCTTCGGGTCATCT-ATAAGACCTTCAGTGCAGGATGTTTTCAA
* *
533886 AAAGCCTTCGGTTCATCTATAAGACCTTCAGTACAGGATGTTTTCAA
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
* * * *
533933 AAAGCCTTC-GGTCATCTGTAAAACCTTTAGTGCAAGATG--TT---
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
*
533974 AAAGCCTTCGGGTCGTCTATAAGACCTTCAGT
1 AAAGCCTTCGGGTCATCTATAAGACCTTCAGT
534006 ACTGTATATT
Statistics
Matches: 358, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
41 9 0.03
42 18 0.05
44 2 0.01
45 77 0.22
46 31 0.09
47 220 0.61
48 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (47 bp):
AAAGCCTTCGGGTCATCTATAAGACCTTCAGTGCAGGATGTTTTCAA
Found at i:537858 original size:33 final size:33
Alignment explanation
Indices: 537818--537885 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
537808 ATATTCTGAT
*
537818 ATCTTTTATTTTAGTTC-CTTACTTTATATTTTA
1 ATCTTTTAATTTAG-TCACTTACTTTATATTTTA
*
537851 ATCTTTTAATTTAGTCATTTACTTTATATTTTA
1 ATCTTTTAATTTAGTCACTTACTTTATATTTTA
537884 AT
1 AT
537886 TTATGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (33 bp):
ATCTTTTAATTTAGTCACTTACTTTATATTTTA
Found at i:537886 original size:25 final size:26
Alignment explanation
Indices: 537854--537907 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
537844 TATTTTAATC
537854 TTTTAATTTA-GTCATTTACTTTATA
1 TTTTAATTTATGTCATTTACTTTATA
*
537879 TTTTAATTTATGTCATTTACTTTTTA
1 TTTTAATTTATGTCATTTACTTTATA
537905 TTT
1 TTT
537908 ATTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTAATTTATGTCATTTACTTTATA
Found at i:537919 original size:30 final size:28
Alignment explanation
Indices: 537854--537916 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 28
537844 TATTTTAATC
*
537854 TTTTAATTTA-GTCATTTAC--TTTATA
1 TTTTAATTTATGTCATTTACTTTTTATT
537879 TTTTAATTTATGTCATTTACTTTTTATT
1 TTTTAATTTATGTCATTTACTTTTTATT
537907 TATTTAATTT
1 T-TTTAATTT
537917 TATTACTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 10 0.30
26 9 0.27
28 6 0.18
29 8 0.24
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTAATTTATGTCATTTACTTTTTATT
Found at i:537937 original size:30 final size:30
Alignment explanation
Indices: 537894--537964 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
537884 ATTTATGTCA
*
537894 TTTACTTTTTATTTATTTAATT-TTATTAC
1 TTTAATTTTTATTTATTTAATTATTATTAC
* * *
537923 TTTAATTTTCTATTTTTTTAATTATTTTTGC
1 TTTAATTTT-TATTTATTTAATTATTATTAC
537954 TTTACATTTTT
1 TTTA-ATTTTT
537965 CAATACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.23
30 12 0.34
31 10 0.29
32 5 0.14
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.70
Consensus pattern (30 bp):
TTTAATTTTTATTTATTTAATTATTATTAC
Found at i:539811 original size:21 final size:21
Alignment explanation
Indices: 539769--539811 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
539759 AATTAGTTAG
**
539769 AAAAAAATAATATTTTTGATA
1 AAAAAAATAATATTTTAAATA
*
539790 AAAAAAATACTATTTTAAATA
1 AAAAAAATAATATTTTAAATA
539811 A
1 A
539812 TATTTTACCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAAAATAATATTTTAAATA
Found at i:568750 original size:14 final size:14
Alignment explanation
Indices: 568715--568758 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
568705 TGTCTTTTCA
*
568715 TGTAGAAAACAGATTG
1 TGTAGAAAACAGA--C
568731 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
568745 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
568759 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:570849 original size:16 final size:16
Alignment explanation
Indices: 570828--570887 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
570818 CCTGATACCA
570828 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
570844 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
570860 TGTAGAAAACAGAC--
1 TGTAGAAAACAGACTG
570874 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
570888 AAGTCTGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.32
16 30 0.68
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:570864 original size:32 final size:30
Alignment explanation
Indices: 570828--570887 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 30
570818 CCTGATACCA
570828 TGTAGAAAACAGACTGTGTAGAAAACAGACTG
1 TGTAGAAAACAGAC--TGTAGAAAACAGACTG
570860 TGTAGAAAACAGACTGTAGAAAACAGAC
1 TGTAGAAAACAGACTGTAGAAAACAGAC
570888 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 14 0.50
32 14 0.50
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (30 bp):
TGTAGAAAACAGACTGTAGAAAACAGACTG
Found at i:577973 original size:23 final size:23
Alignment explanation
Indices: 577944--577993 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
577934 ATTCATCTTC
577944 TAAAATAGAGACTACAAGACTTA
1 TAAAATAGAGACTACAAGACTTA
577967 TAAAATAGAGACTACAAGACTTA
1 TAAAATAGAGACTACAAGACTTA
577990 TAAA
1 TAAA
577994 CAAAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (23 bp):
TAAAATAGAGACTACAAGACTTA
Found at i:582363 original size:81 final size:81
Alignment explanation
Indices: 582273--582434 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
582263 CGTATGAGTG
582273 GTTATTCTCCTTTTTGTCGATGAGCCTCCTCCCCTTTTCAGTTTTCAGTAGTTAATTCCCAATAA
1 GTTATTCTCCTTTTTGTCGATGAGCCTCCTCCCCTTTTCAGTTTTCAGTAGTTAATTCCCAATAA
582338 AAAAAACCAACTCTTT
66 AAAAAACCAACTCTTT
582354 GTTATTCTCCTTTTTGTCGATGAGCCTCCTCCCCTTTTCAGTTTTCAGTAGTTAATTCCCAATAA
1 GTTATTCTCCTTTTTGTCGATGAGCCTCCTCCCCTTTTCAGTTTTCAGTAGTTAATTCCCAATAA
582419 AAAAAACCAACTCTTT
66 AAAAAACCAACTCTTT
582435 TAGTTTCCTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.40
Consensus pattern (81 bp):
GTTATTCTCCTTTTTGTCGATGAGCCTCCTCCCCTTTTCAGTTTTCAGTAGTTAATTCCCAATAA
AAAAAACCAACTCTTT
Found at i:582853 original size:55 final size:55
Alignment explanation
Indices: 582771--583194 Score: 396
Period size: 55 Copynumber: 7.9 Consensus size: 55
582761 TGACGAGCCT
* ** *
582771 GCTCCTTATTCCTTCA-AGAAGTATAAGACTCGAACAATCTTCATA-AAATATGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCA-ACAAACGTGTCC
* * * * * *
582826 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAAACGTGTCC
* * * * *
582882 GCTCTCTATTCCTTTAGAGAGTAT-AGAACTCGAAAAATCTTCAATAAACATGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* * * *
582937 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* ** *
582988 GCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAGCAATCTTCATGAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* * *
583043 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* * *
583098 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* *
583149 GCTTCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
583195 AATTTGCTTC
Statistics
Matches: 315, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
50 1 0.00
51 106 0.34
54 1 0.00
55 159 0.50
56 48 0.15
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
Found at i:583027 original size:106 final size:107
Alignment explanation
Indices: 582771--583194 Score: 436
Period size: 106 Copynumber: 4.0 Consensus size: 107
582761 TGACGAGCCT
* * * *
582771 GCTCCTTATTCCTTCA-AGAAGTATA-AGACTCGAACAATCTTCATAAAATATGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACATGTCCGCTCCCTA
* * * * *
582834 TTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAATGGGTCC
64 TTCCTTCAGAGAGTATAGGAC-T--ACAATCTTCAA-CAAACGTGTCC
* * *
582882 GCTCTCTATTCCTTTAGAGAGTATAGAACTCGAAAAATCTTCA-ATAAACATGTCCGCTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACATGTCCGCTCCCTAT
* * *
582946 TCTTTCAGAGAGTATAGGACT-CAATCTTTAACAAACGTGTTC
65 TCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACGTGTCC
* * ** *
582988 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACATGTCCGCTCCCTATT
* * *
583053 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
66 CCTTCAGAGAGTATAGGACT---ACAATCTTCAACAAACGTGTCC
* * * *
583098 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCCGCTTCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACATGTCCGCTCCCTAT
583158 TCCTTCAGAGAGTATAGGACT-CAATCTTCAACAAACG
65 TCCTTCAGAGAGTATAGGACTACAATCTTCAACAAACG
583195 AATTTGCTTC
Statistics
Matches: 266, Mismatches: 38, Indels: 27
0.80 0.11 0.08
Matches are distributed among these distances:
102 14 0.05
106 124 0.47
107 9 0.03
110 48 0.18
111 68 0.26
112 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (107 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACATGTCCGCTCCCTATT
CCTTCAGAGAGTATAGGACTACAATCTTCAACAAACGTGTCC
Found at i:583071 original size:161 final size:162
Alignment explanation
Indices: 582821--583179 Score: 524
Period size: 161 Copynumber: 2.2 Consensus size: 162
582811 TCATAAAATA
* * * * *
582821 TGTCTGCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAATGGGTCCGCT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAAACGGGTCCGCT
* * *
582885 CTCTATTCCTTTAGAGAGTATAGAACTCGAAAAATCTTCAATAAACATGTCCGCTCCCTATTCTT
65 CTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAACAAACATGTCCGCTCCCTATTCCT
*
582950 TCAGAGAGTATAGGACTCAATCTTTAACAAACG
130 TCAGAGAGTATAGGACTCAATCTTCAACAAACG
* * *
582983 TGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTC-ATGAAACGGGTCCGCTC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCCGCTC
* * *
583047 TCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCCGCTCCCTATTCCTT
66 TCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAACAAACATGTCCGCTCCCTATTCCTT
* *
583112 CAGAGAGTATAGGACTCAATCTTCAACGAACT
131 CAGAGAGTATAGGACTCAATCTTCAACAAACG
* *
583144 TGTCCGCTTCCTATTCCTTCAGAGAGTATAGGACTC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTC
583180 AATCTTCAAC
Statistics
Matches: 176, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
161 136 0.77
162 39 0.22
163 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (162 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCCGCTC
TCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAACAAACATGTCCGCTCCCTATTCCTT
CAGAGAGTATAGGACTCAATCTTCAACAAACG
Found at i:583243 original size:36 final size:36
Alignment explanation
Indices: 583196--583303 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 36
583186 CAACAAACGA
583196 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATG
1 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATG
*
583232 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
1 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG-ATG
* * * *
583269 AATTGCTTCACTGCTCTTTCATGAAGGCTTAAGAT
1 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
583304 TGACCTGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 34 0.52
37 31 0.48
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (36 bp):
ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATG
Found at i:583286 original size:37 final size:36
Alignment explanation
Indices: 583198--583306 Score: 155
Period size: 37 Copynumber: 3.0 Consensus size: 36
583188 ACAAACGAAT
* *
583198 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTGAA
583234 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAG-TTGAA
* * *
583271 TTGCTTCACTGCTCTTTCATGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAG-TTGA
583307 CCTGTTTTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
36 31 0.47
37 35 0.53
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTGAA
Found at i:584626 original size:19 final size:19
Alignment explanation
Indices: 584585--584680 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 19
584575 TCTTTTTTCA
*
584585 TTTTT-CATTTTTTCTTCC
1 TTTTTCCATTTTTTCTTCT
*
584603 ATTTTCCATTTTTTCTT-T
1 TTTTTCCATTTTTTCTTCT
*
584621 TTTTT---TTCTTTTCGT-T
1 TTTTTCCATT-TTTTCTTCT
*
584637 TTTTTCCATCATTTT-TTCT
1 TTTTTCCAT-TTTTTCTTCT
584656 TTTTTCTCATTTTTT-TTCT
1 TTTTTC-CATTTTTTCTTCT
584675 TTTTTC
1 TTTTTC
584681 TTCTTCTCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
15 2 0.03
16 12 0.19
18 9 0.14
19 37 0.59
20 3 0.05
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTCCATTTTTTCTTCT
Found at i:584656 original size:56 final size:55
Alignment explanation
Indices: 584589--584694 Score: 137
Period size: 54 Copynumber: 1.9 Consensus size: 55
584579 TTTTCATTTT
* *
584589 TCATTTTTTCTTCCATTTTC-CATTTTTTCTT-TTTTTT-TTCTTTTCGTTTTTTTCCA
1 TCATTTTTTCTT---TTTTCTCATTTTTT-TTCTTTTTTCTTCTTCTCATTTTTTTCCA
584645 TCATTTTTTCTTTTTTCTCATTTTTTTTCTTTTTTCTTCTTCTCATTTTT
1 TCATTTTTTCTTTTTTCTCATTTTTTTTCTTTTTTCTTCTTCTCATTTTT
584695 ATTATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
53 7 0.16
54 14 0.31
55 12 0.27
56 12 0.27
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.74
Consensus pattern (55 bp):
TCATTTTTTCTTTTTTCTCATTTTTTTTCTTTTTTCTTCTTCTCATTTTTTTCCA
Found at i:584684 original size:10 final size:9
Alignment explanation
Indices: 584611--584685 Score: 55
Period size: 10 Copynumber: 8.0 Consensus size: 9
584601 CCATTTTCCA
584611 TTTTTTC-T
1 TTTTTTCTT
584619 TTTTTT-TT
1 TTTTTTCTT
*
584627 TCTTTTCGTT
1 TTTTTTC-TT
* *
584637 TTTTTCCATCA
1 TTTTTTC-T-T
584648 TTTTTTCTT
1 TTTTTTCTT
*
584657 TTTTCTCATT
1 TTTTTTC-TT
584667 TTTTTTCTT
1 TTTTTTCTT
584676 TTTTCTTCTT
1 TTTT-TTCTT
584686 CTCATTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
8 12 0.23
9 12 0.23
10 22 0.42
11 6 0.12
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:584743 original size:16 final size:15
Alignment explanation
Indices: 584648--584745 Score: 62
Period size: 15 Copynumber: 6.5 Consensus size: 15
584638 TTTTCCATCA
584648 TTTT-TTCTTTTTTC
1 TTTTATTCTTTTTTC
*
584662 --TCATT-TTTTTTC
1 TTTTATTCTTTTTTC
*
584674 TTTT-TTCTTCTTCTC
1 TTTTATTCTT-TTTTC
* *
584689 ATTTTTATTATTATTATTT
1 --TTTTATTCTT-TT-TTC
584708 TTTTATTCTTTTTTC
1 TTTTATTCTTTTTTC
*
584723 ATTTATTCTTTTTTCC
1 TTTTATTCTTTTTT-C
584739 TTTTATT
1 TTTTATT
584746 TCTTCTTCAA
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
12 8 0.13
13 4 0.06
14 3 0.05
15 19 0.30
16 9 0.14
17 13 0.21
18 6 0.10
19 1 0.02
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATTCTTTTTTC
Found at i:594091 original size:51 final size:45
Alignment explanation
Indices: 594045--594136 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
594035 CCATGCTTTG
* *
594045 TTATCCACAAAAATACATCCTAACCTCATGATATCTAATTCGCATGC
1 TTATCCA-AAAAATA-AACCTAACCGCATGATATCTAATTCGCATGC
* *
594092 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATCCAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGC
594137 ATTTATTCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 28 0.68
46 7 0.17
47 6 0.15
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.29
Consensus pattern (45 bp):
TTATCCAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGC
Found at i:600052 original size:3 final size:3
Alignment explanation
Indices: 600044--600078 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
600034 GGAATGTCAC
600044 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
600079 ACTTACAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:609927 original size:2 final size:2
Alignment explanation
Indices: 609920--609955 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
609910 TTTACCCTAG
609920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
609956 CACATGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:610144 original size:33 final size:34
Alignment explanation
Indices: 610088--610153 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
610078 ATAGATTTCA
* *
610088 TATATATTTTAAACAATAACTAAATCAAATAAAT
1 TATATATTATAAAAAATAACTAAATCAAATAAAT
*
610122 TATA-ATTATAAAAAATAACTAAATTAAATAAA
1 TATATATTATAAAAAATAACTAAATCAAATAAA
610154 CTGAGCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (34 bp):
TATATATTATAAAAAATAACTAAATCAAATAAAT
Found at i:610242 original size:17 final size:18
Alignment explanation
Indices: 610196--610242 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
610186 GATCAAAATG
610196 AATTTATTGAAGAGTTAT
1 AATTTATTGAAGAGTTAT
*
610214 CATTTGATTGAAGAGTTA-
1 AATTT-ATTGAAGAGTTAT
610232 AATTTATTGAA
1 AATTTATTGAA
610243 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (18 bp):
AATTTATTGAAGAGTTAT
Found at i:613409 original size:43 final size:43
Alignment explanation
Indices: 613348--613592 Score: 357
Period size: 43 Copynumber: 5.7 Consensus size: 43
613338 GCGTTTGTTA
* *
613348 GCTATTGACTATGTATTTAGCGGCGTTTGTCTTTATAAACACC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
* *
613391 GCTATTTACTGTGTATTTAGCGGCGTTTGTCTTTATAAATGCC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
* ** *
613434 GCTATTGACTATGTA-TTAGCGGTATTTGTCTTTACAAACGCC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
* * * *
613476 GCTATTGATTGTGCATTTAGCGGCGTTTTTCTTTACAAACGCC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
* *
613519 GCTATTGATTGTATATTTAGCGGCGTTTGTCTTTATAAACGCC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
613562 GCTATTGACTGTGTATTTAGCGGCGTTTGTC
1 GCTATTGACTGTGTATTTAGCGGCGTTTGTC
613593 CTATTGATTG
Statistics
Matches: 179, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 35 0.20
43 144 0.80
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (43 bp):
GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTATAAACGCC
Found at i:613577 original size:128 final size:129
Alignment explanation
Indices: 613348--613584 Score: 368
Period size: 128 Copynumber: 1.8 Consensus size: 129
613338 GCGTTTGTTA
* * * *
613348 GCTATTGACTATGTATTTAGCGGCGTTTGTCTTTATAAACACCGCTATTTACTGTGTATTTAGCG
1 GCTATTGACTATGCATTTAGCGGCGTTTGTCTTTACAAACACCGCTATTGACTGTATATTTAGCG
*
613413 GCGTTTGTCTTTATAAATGCCGCTATTGACTATGTA-TTAGCGGTATTTGTCTTTACAAACGCC
66 GCGTTTGTCTTTATAAACGCCGCTATTGACTATGTATTTAGCGGTATTTGTCTTTACAAACGCC
* * * * *
613476 GCTATTGATTGTGCATTTAGCGGCGTTTTTCTTTACAAACGCCGCTATTGATTGTATATTTAGCG
1 GCTATTGACTATGCATTTAGCGGCGTTTGTCTTTACAAACACCGCTATTGACTGTATATTTAGCG
*
613541 GCGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATTTAGCGG
66 GCGTTTGTCTTTATAAACGCCGCTATTGACTATGTATTTAGCGG
613585 CGTTTGTCCT
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
128 90 0.93
129 7 0.07
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (129 bp):
GCTATTGACTATGCATTTAGCGGCGTTTGTCTTTACAAACACCGCTATTGACTGTATATTTAGCG
GCGTTTGTCTTTATAAACGCCGCTATTGACTATGTATTTAGCGGTATTTGTCTTTACAAACGCC
Found at i:613597 original size:30 final size:30
Alignment explanation
Indices: 613563--613619 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
613553 ATAAACGCCG
613563 CTATTGACTGTGTATTTAGCGGCGTTTGTC
1 CTATTGACTGTGTATTTAGCGGCGTTTGTC
*
613593 CTATTGATTGTGTATTTAGCGGCGTTT
1 CTATTGACTGTGTATTTAGCGGCGTTT
613620 TTCTTTACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.46
Consensus pattern (30 bp):
CTATTGACTGTGTATTTAGCGGCGTTTGTC
Found at i:613664 original size:73 final size:73
Alignment explanation
Indices: 613520--613664 Score: 209
Period size: 73 Copynumber: 2.0 Consensus size: 73
613510 ACAAACGCCG
* * * *
613520 CTATTGATTGTATATTTAGCGGCGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATTTAGCGG
1 CTATTGATTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATGTATGTAACGG
*
613585 CGTTTGTC
66 CATTTGTC
* * * *
613593 CTATTGATTGTGTATTTAGCGGCGTTTTTCTTTACAAACGCCGCTATTGACTATGTATGTAATGT
1 CTATTGATTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATGTATGTAACGG
613658 CATTTGT
66 CATTTGT
613665 AATTAAAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (73 bp):
CTATTGATTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATGTATGTAACGG
CATTTGTC
Found at i:616708 original size:40 final size:41
Alignment explanation
Indices: 616623--616901 Score: 154
Period size: 40 Copynumber: 6.9 Consensus size: 41
616613 TTTTGTACTT
* * * * ** *
616623 AAAACGCCGCTAAAATAAGAGCT-TTTAGTGGCGTTTGCACA
1 AAAACGCCACTAAAGTACGAG-TATTTAGCGGCGTTTATATA
** * * *
616664 AAAACGCTGCTAAAGTA-TAGTAATTAGCGGCGTTTATATG
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTATATA
* * * ** * * * *
616704 AAAACGCCACTAATGTAGGGGCCTTTAGCGGCATTTGTGCTT
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTAT-ATA
* * * * * *
616746 AAAATGCCGCTAGAGTACGAGTTTTTAGCGGCGTTTGTACA
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTATATA
* * * * * * * *
616787 AAAATG-CGCTAAATTA-TAGTAATTAGCAGCGTTTCTATG
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTATATA
* * *
616826 AAAACACCACTAAATTA-TAGTATTTAGCGGCGTTTATATA
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTATATA
*
616866 AAAACGCCACTAAAGTACGAGTATTTACCGGCGTTT
1 AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTT
616902 GTTCAAAAAA
Statistics
Matches: 180, Mismatches: 53, Indels: 10
0.74 0.22 0.04
Matches are distributed among these distances:
39 21 0.12
40 79 0.44
41 50 0.28
42 30 0.17
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTATATA
Found at i:616837 original size:122 final size:123
Alignment explanation
Indices: 616614--616838 Score: 326
Period size: 123 Copynumber: 1.8 Consensus size: 123
616604 ATTGGTAGGT
*
616614 TTTGTACTTAAAACGCCGCTAAAATAAGAGCTTTTAGTGGCGTTTGCACAAAAACGCTGCTAAAG
1 TTTGTACTTAAAACGCCGCTAAAATAAGAGCTTTTAGCGGCGTTTGCACAAAAACGCTGCTAAAG
* *
616679 TATAGTAATTAGCGGCGTTTATATGAAAACGCCACTAATGTAGGGGCCTTTAGCGGCA
66 TATAGTAATTAGCAGCGTTTATATGAAAACACCACTAATGTAGGGGCCTTTAGCGGCA
* * * * * * * * *
616737 TTTGTGCTTAAAATGCCGCTAGAGTACGAGTTTTTAGCGGCGTTTGTACAAAAATGC-GCTAAAT
1 TTTGTACTTAAAACGCCGCTAAAATAAGAGCTTTTAGCGGCGTTTGCACAAAAACGCTGCTAAAG
*
616801 TATAGTAATTAGCAGCGTTTCTATGAAAACACCACTAA
66 TATAGTAATTAGCAGCGTTTATATGAAAACACCACTAA
616839 ATTATAGTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
122 41 0.46
123 48 0.54
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (123 bp):
TTTGTACTTAAAACGCCGCTAAAATAAGAGCTTTTAGCGGCGTTTGCACAAAAACGCTGCTAAAG
TATAGTAATTAGCAGCGTTTATATGAAAACACCACTAATGTAGGGGCCTTTAGCGGCA
Found at i:616912 original size:122 final size:123
Alignment explanation
Indices: 616652--616915 Score: 284
Period size: 122 Copynumber: 2.2 Consensus size: 123
616642 AGCTTTTAGT
* * * * *
616652 GGCGTTTGCACAAAAACGCTGCTAAAGTATAGTAATTAGCGGCGTTTATATGAAAACGCCACTAA
1 GGCGTTTGTAAAAAAATGCTGCTAAAGTATAGTAATTAGCAGCGTTTATATGAAAACACCACTAA
* * * * * * * * * *
616717 TGTAGGGGCCTTTAGCGGCATTTGTGCTTAAAATGCCGCTAGAGTACGAGTTTTTAGC
66 TGTAGGAGCATTTAGCGGCATTTATGATAAAAACGCCACTAAAGTACGAGTATTTACC
* * *
616775 GGCGTTTGTACAAAAATGC-GCTAAATTATAGTAATTAGCAGCGTTTCTATGAAAACACCACTAA
1 GGCGTTTGTAAAAAAATGCTGCTAAAGTATAGTAATTAGCAGCGTTTATATGAAAACACCACT-A
* * *
616839 AT-TA-TAGTATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAGTACGAGTATTTACC
65 ATGTAGGAGCATTTAGCGGCATTTATGATAAAAACGCCACTAAAGTACGAGTATTTACC
616895 GGCGTTTGTTCAAAAAAATGC
1 GGCGTTTG-T-AAAAAAATGC
616916 CACTAAAAAT
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
120 33 0.28
121 15 0.13
122 50 0.42
123 20 0.17
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (123 bp):
GGCGTTTGTAAAAAAATGCTGCTAAAGTATAGTAATTAGCAGCGTTTATATGAAAACACCACTAA
TGTAGGAGCATTTAGCGGCATTTATGATAAAAACGCCACTAAAGTACGAGTATTTACC
Found at i:617839 original size:9 final size:10
Alignment explanation
Indices: 617828--617912 Score: 83
Period size: 9 Copynumber: 8.7 Consensus size: 10
617818 TTCATTTGAA
617828 TATTATTTA-
1 TATTATTTAT
617837 TATTA-TTAT
1 TATTATTTAT
617846 TATTA-TTAT
1 TATTATTTAT
617855 TATTA-TTAT
1 TATTATTTAT
617864 TATTA-TTAT
1 TATTATTTAT
*
617873 TATTATATA-
1 TATTATTTAT
617882 TATATATATTAT
1 TAT-TAT-TTAT
617894 TATATATATTAT
1 TAT-TAT-TTAT
617906 TATTATT
1 TATTATT
617913 AAAAAATAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
8 3 0.04
9 40 0.58
10 6 0.09
11 5 0.07
12 15 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTATTTAT
Found at i:617846 original size:6 final size:6
Alignment explanation
Indices: 617828--617913 Score: 113
Period size: 6 Copynumber: 13.8 Consensus size: 6
617818 TTCATTTGAA
617828 TATTAT T-TATAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 TATTAT TAT-TAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
617876 TATATAT ATATATAT TATTA- TATATAT TATTAT TATTA
1 TAT-TAT -TAT-TAT TATTAT TAT-TAT TATTAT TATTA
617914 AAAAATAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.05
6 53 0.72
7 10 0.14
8 7 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATTAT
Found at i:619208 original size:18 final size:20
Alignment explanation
Indices: 619153--619208 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
619143 CACTAATTTC
619153 AATTTTTATTTATT-TTTTA
1 AATTTTTATTTATTGTTTTA
* *
619172 CAATTTTTATATATAGTTTT-
1 -AATTTTTATTTATTGTTTTA
619192 AA-TTTTATTTATTGTTT
1 AATTTTTATTTATTGTTT
619209 AGTTATATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
20 12 0.39
21 4 0.13
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (20 bp):
AATTTTTATTTATTGTTTTA
Found at i:619244 original size:3 final size:3
Alignment explanation
Indices: 619236--619265 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
619226 TTTACTTTTA
*
619236 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
619266 TAGCCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:619487 original size:20 final size:19
Alignment explanation
Indices: 619462--619503 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
619452 CTATTTTATA
619462 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
619482 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
619501 AAT
1 AAT
619504 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:619495 original size:119 final size:116
Alignment explanation
Indices: 619358--619593 Score: 278
Period size: 119 Copynumber: 2.0 Consensus size: 116
619348 ATTTTAATCC
* * * * *
619358 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* *
619421 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTCTAAATAAA-AAATATCCTA-TTTATAAA-TATATATAAAT
* * ** *
619476 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
619541 TTTTTCTGATATTTCTAAATAAAAAATATTTTATTTATAAATATATATAAAT
65 ATTTTCTGATATTTCTAAATAAAAAATATCCTATTTATAAATATATATAAAT
619593 T
1 T
619594 AATATTTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
117 11 0.11
118 16 0.16
119 28 0.28
120 25 0.25
121 20 0.20
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (116 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAATAAAAAATATCCTATTTATAAATATATATAAAT
Found at i:620858 original size:23 final size:23
Alignment explanation
Indices: 620832--620876 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
620822 CACCACAGCT
*
620832 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
620855 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
620877 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:632846 original size:10 final size:10
Alignment explanation
Indices: 632833--632870 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
632823 AGAAAAAATG
632833 AAAAAAGAAA
1 AAAAAAGAAA
632843 AAAAAAGAAA
1 AAAAAAGAAA
*
632853 AAAAATGAAGA
1 AAAAAAGAA-A
632864 AAAAAAG
1 AAAAAAG
632871 GATCAAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:634937 original size:23 final size:22
Alignment explanation
Indices: 634895--634940 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
634885 GTTTATAATG
*
634895 AGAAGAATTCATCTGAAGAAGA
1 AGAAGAATTCATATGAAGAAGA
634917 AGAAGAAGTTCATAATG-AGAAGA
1 AGAAGAA-TTCAT-ATGAAGAAGA
634940 A
1 A
634941 CTTGTTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 12 0.57
24 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AGAAGAATTCATATGAAGAAGA
Found at i:635146 original size:334 final size:333
Alignment explanation
Indices: 634399--635164 Score: 1273
Period size: 334 Copynumber: 2.3 Consensus size: 333
634389 TTAGCAAAGA
* * * * *
634399 CTTAAATCCATCATTTAATGGATCAACATTTTCAGTTAGTGTTCATAATGAGAAGAACTCAACTG
1 CTTAAATTCATCACTTGATGGATCAAC-TTTTCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
634464 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGG
65 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGG
634529 TGGATCAGCAGTGCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTC
130 TGGATCAGCAGTGCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTC
*
634594 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGCCAGT
195 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTGCCAGT
*
634659 TAGAGTTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
260 TAGAGTTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
634724 AACTTTTTG
325 AACCTTTTG
* * * * * **
634733 CTTAAATTCATCCCTCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
1 CTTAAATTCATCACTTGATGGATCAAC-TTTTCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
634798 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGG
65 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGG
* * *
634863 TGGATCAGCAGTGCCAGTTAGAGTTTATAATGAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTC
130 TGGATCAGCAGTGCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTC
634928 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTGCCAGT
195 ATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTGCCAGT
634993 TAGAG-TTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
260 TAGAGTTTCATAATGAAAAGAACTCATCT---GAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
635057 TTCAACCTTTTG
322 TTCAACCTTTTG
** *
635069 CTTAAATTCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 CTTAAATTCATCACTTGATGGATCAACTTTTC-AGTTAGAGTTCATAATGAGAAGAACTCATCTG
635134 AAGAATGAAGAAGAAGTTCATAATGAGAAGA
65 AAGAA-GAAGAAGAAGTTCATAATGAGAAGA
635165 GATTATTCAA
Statistics
Matches: 399, Mismatches: 28, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
333 22 0.06
334 249 0.62
335 2 0.01
336 101 0.25
337 25 0.06
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (333 bp):
CTTAAATTCATCACTTGATGGATCAACTTTTCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCCCTCGGT
GGATCAGCAGTGCCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTGCCAGTT
AGAGTTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTG
Found at i:635194 original size:112 final size:112
Alignment explanation
Indices: 634431--635164 Score: 1258
Period size: 112 Copynumber: 6.6 Consensus size: 112
634421 TCAACATTTT
* *
634431 CAGTTAGTGTTCATAATGAGAAGAACTCAACTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
634496 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
66 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
*
634543 CAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
634608 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
66 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
634655 CAGTTAGAGTTTCATAATGAGAAGAACTCATCT---GAAGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTAGAG-TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
634717 CTTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
65 CTTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
634765 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
634830 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
66 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
* *
634877 CAGTTAGAGTTTATAATGAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
*
634942 TTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCAGTGC
66 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
*
634989 CAGTTAGAGTTCATAATGAAAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
* * * * * ** *
635054 TTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTC
66 TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
* ** *
635101 TAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGA
1 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGA
635165 GATTATTCAA
Statistics
Matches: 595, Mismatches: 22, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
109 23 0.04
110 86 0.14
112 438 0.74
113 48 0.08
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (112 bp):
CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTTGCTTAAATTCATCCCTCGGTGGATCAGCAGTGC
Found at i:635406 original size:3 final size:3
Alignment explanation
Indices: 635400--635454 Score: 60
Period size: 3 Copynumber: 17.7 Consensus size: 3
635390 TTCATTTGAA
635400 TAT TAT T-T ATAT TAT TAT TAT TAT ATAT ATAT TAT TA- TAT ATAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT
635447 TAT TAT TA
1 TAT TAT TA
635455 AAAAAATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 3 0.06
3 33 0.70
4 11 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:636788 original size:3 final size:3
Alignment explanation
Indices: 636780--636809 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
636770 TTTACTTTTA
*
636780 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
636810 TAGCCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:636895 original size:20 final size:20
Alignment explanation
Indices: 636866--636905 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
636856 TTATTAAAAT
*
636866 CTTATTTAATTAT-TTTTAA
1 CTTATTTAATCATGTTTTAA
636885 CTTATTTTAATCATGTTTTAA
1 CTTA-TTTAATCATGTTTTAA
636906 TATTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
CTTATTTAATCATGTTTTAA
Found at i:638242 original size:20 final size:21
Alignment explanation
Indices: 638204--638242 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
638194 AATGACATGT
*
638204 AATATCGATATTGCCTAAGAC
1 AATATCGATACTGCCTAAGAC
638225 AATATCGATACT-CCTAAG
1 AATATCGATACTGCCTAAG
638243 TTAGAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (21 bp):
AATATCGATACTGCCTAAGAC
Found at i:649270 original size:2 final size:2
Alignment explanation
Indices: 649263--649289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
649253 ATTTCGAATA
649263 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
649290 GTAGTTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:654227 original size:26 final size:26
Alignment explanation
Indices: 654162--654229 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
654152 TTTTGAAATA
*
654162 TCAACCAGCAGAGAATTTCCTTTTTG
1 TCAACCAGCAGAGGATTTCCTTTTTG
*
654188 TCAATCAGCAGAGGATTTCC-TTTTG
1 TCAACCAGCAGAGGATTTCCTTTTTG
654213 TCAACCAGCAGGAGGAT
1 TCAACCAGCA-GAGGAT
654230 GCACCACTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (26 bp):
TCAACCAGCAGAGGATTTCCTTTTTG
Found at i:658237 original size:14 final size:14
Alignment explanation
Indices: 658201--658274 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 14
658191 TATATATGTG
*
658201 TATATTTTT-TAAA
1 TATATTTTTAAAAA
658214 T-TATTATTTAAAAA
1 TATATT-TTTAAAAA
*
658228 TATATTTTTAATTAA
1 TATATTTTTAA-AAA
658243 TA-A-TTTTAAAAA
1 TATATTTTTAAAAA
*
658255 AATATTTTTAAAAA
1 TATATTTTTAAAAA
658269 TTATAT
1 -TATAT
658275 AATTTTTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 7 0.14
13 11 0.22
14 19 0.39
15 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATTTTTAAAAA
Found at i:659978 original size:30 final size:30
Alignment explanation
Indices: 659925--660046 Score: 133
Period size: 30 Copynumber: 4.1 Consensus size: 30
659915 ATTTTAAGTT
*
659925 AATATATTTTAA-AATTTAAGATAAAAATAAA
1 AATATA-TTTAATAAGTTAAGATAAAAAT-AA
* *
659956 AATATATTT-TTAAGTGAAGATAAAAATAA
1 AATATATTTAATAAGTTAAGATAAAAATAA
* * * *
659985 ACTATATTTAATAGGTTAATACAAAAATAA
1 AATATATTTAATAAGTTAAGATAAAAATAA
660015 AATATATTTAATAAGTTAAGA-AGAAAATAA
1 AATATATTTAATAAGTTAAGATA-AAAATAA
660045 AA
1 AA
660047 AAATATTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 11 0.14
30 59 0.78
31 6 0.08
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (30 bp):
AATATATTTAATAAGTTAAGATAAAAATAA
Found at i:659991 original size:60 final size:61
Alignment explanation
Indices: 659925--660067 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 61
659915 ATTTTAAGTT
* *
659925 AATATATTTTAAAATTTAAGATAAAAATAAAAATATATTT-TTAAGTGAAGATA-AAAAT-AA
1 AATATATTTTAAAATTTAAGACAAAAAT-AAAATATATTTAATAAGTGAAGA-AGAAAATAAA
* ** * *
659985 ACTATA-TTTAATAGGTTAATACAAAAATAAAATATATTTAATAAGTTAAGAAGAAAATAAA
1 AATATATTTTAA-AATTTAAGACAAAAATAAAATATATTTAATAAGTGAAGAAGAAAATAAA
*
660046 AAAATATTTTAAAAATTTAAGA
1 AATATATTTT-AAAATTTAAGA
660068 ATTCAGATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
59 17 0.26
60 31 0.48
61 6 0.09
62 9 0.14
63 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (61 bp):
AATATATTTTAAAATTTAAGACAAAAATAAAATATATTTAATAAGTGAAGAAGAAAATAAA
Found at i:666059 original size:37 final size:37
Alignment explanation
Indices: 665965--666069 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
665955 CCTTTTCGTC
* *
665965 CTACTAGGATTCAAACTCCTAAAAATAGAATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
666002 TTGCTAGGATTCAAATTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
666039 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
666070 CCACAAGCAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:666796 original size:17 final size:16
Alignment explanation
Indices: 666769--666840 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 16
666759 TTATACATAC
666769 ATTTTTATATTTTTATAT
1 ATTTTT-TA-TTTTATAT
666787 ATTTTTTATTTTAT-T
1 ATTTTTTATTTTATAT
666802 A--TTTTA-TTTATACT
1 ATTTTTTATTTTATA-T
666816 ATTTATTTATTTTAATTAT
1 ATTT-TTTATTTT-A-TAT
666835 ATTTTT
1 ATTTTT
666841 AGTTTCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 2 0.04
15 2 0.04
16 7 0.15
17 6 0.13
18 11 0.24
19 6 0.13
20 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTTTATAT
Found at i:666797 original size:46 final size:48
Alignment explanation
Indices: 666747--666840 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
666737 TACTATTTAG
*
666747 TATTTTATTATATTATACATAC-ATTT-TTATATTTTTA-TATATTTTT
1 TATTTTATTATATTATACATACTATTTATT-TATTTTAATTATATTTTT
* **
666793 TATTTTATTATTTTATTTATACTATTTATTTATTTTAATTATATTTTT
1 TATTTTATTATATTATACATACTATTTATTTATTTTAATTATATTTTT
666841 AGTTTCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 19 0.46
47 11 0.27
48 11 0.27
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (48 bp):
TATTTTATTATATTATACATACTATTTATTTATTTTAATTATATTTTT
Found at i:666808 original size:13 final size:14
Alignment explanation
Indices: 666784--666825 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
666774 TATATTTTTA
666784 TATATT-TTTTATT
1 TATATTATTTTATT
666797 T-TATTATTTTATT
1 TATATTATTTTATT
*
666810 TATACTA-TTTATT
1 TATATTATTTTATT
666823 TAT
1 TAT
666826 TTTAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATATTATTTTATT
Found at i:666945 original size:18 final size:19
Alignment explanation
Indices: 666922--666966 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
666912 TATATATATA
*
666922 TTTTTTCTTC-ATTT-ATT
1 TTTTTTATTCAATTTCATT
666939 TTATTTTATTCAATTTCATT
1 TT-TTTTATTCAATTTCATT
666959 TTTTTTAT
1 TTTTTTAT
666967 ATTTGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 7 0.29
19 10 0.42
20 5 0.21
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTATTCAATTTCATT
Found at i:670390 original size:14 final size:14
Alignment explanation
Indices: 670371--670407 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
670361 TACTTTACCT
670371 TCTTTTACCTTCAA
1 TCTTTTACCTTCAA
670385 TCTTTTACCTTCAA
1 TCTTTTACCTTCAA
670399 TCTTTTACC
1 TCTTTTACC
670408 CACACTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.51
Consensus pattern (14 bp):
TCTTTTACCTTCAA
Found at i:672783 original size:72 final size:72
Alignment explanation
Indices: 672660--672870 Score: 262
Period size: 72 Copynumber: 2.9 Consensus size: 72
672650 CTTCAGCTAT
* * * * * * *
672660 AGTTGCTACGCCTTCACAGTCTGTGTTTGGTAACACCAATCCGGGCCTGGTGCTTGGGTCAACTC
1 AGTTGCTATGCCATCGCAGTCTGTGTTTGGTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
*
672725 CTGCTGC
66 CAGCTGC
* * *
672732 AGTTGCTATGCCATCGCAGTCCGTGTTTGTTAACACCAGTCCCGGCTTGGTGTTTGGGTCAACTC
1 AGTTGCTATGCCATCGCAGTCTGTGTTTGGTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
672797 CAGCTGC
66 CAGCTGC
* ** * *
672804 AGGTGCTACT-CCATCGCAGAATGTGTTTGGCAACACCAGTTCAGGCTTGGTGTTTGGGTCAACT
1 AGTTGCTA-TGCCATCGCAGTCTGTGTTTGGTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACT
672868 CCA
65 CCA
672871 TCTAGTAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
72 119 0.99
73 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (72 bp):
AGTTGCTATGCCATCGCAGTCTGTGTTTGGTAACACCAGTCCAGGCTTGGTGTTTGGGTCAACTC
CAGCTGC
Found at i:675584 original size:28 final size:28
Alignment explanation
Indices: 675523--675576 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
675513 TTTTTAATAT
* * *
675523 ACCCTTAAAATTTTATGAGTTCAAATCC
1 ACCCCTAAAATTTTATAAATTCAAATCC
675551 ACCCCTAAAATTTTATAAATTCAAAT
1 ACCCCTAAAATTTTATAAATTCAAAT
675577 TCATCCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (28 bp):
ACCCCTAAAATTTTATAAATTCAAATCC
Found at i:679176 original size:2 final size:2
Alignment explanation
Indices: 679169--679210 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
679159 TAAATTATCA
679169 AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
679210 A
1 A
679211 TGTGTAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:679838 original size:78 final size:80
Alignment explanation
Indices: 679741--679917 Score: 225
Period size: 84 Copynumber: 2.2 Consensus size: 80
679731 AACCAGAAGT
* * *
679741 TGAAGATGATGTTGAGAAGAAGAATAAAGA-GA-ATACCGGAACTGAAAAGAAGACCGAGGAGGA
1 TGAAGATTATGTTGAGAAGAAGAATAAAGAGGACATACCGAAACTGAAAAGAAGACCGAGGAAGA
679804 GAAGGGAATTATGGA
66 GAAGGGAATTATGGA
* * *
679819 TGAAGATTATGTTGAGAAGAGGAATAAAGAGGACTCTGATGCTGAAACTGAAAAGAAGACCGAGG
1 TGAAGATTATGTTGAGAAGAAGAATAAAGAGGA--C--ATACCGAAACTGAAAAGAAGACCGAGG
*
679884 AAGAGAAGGGAATTGTGGA
62 AAGAGAAGGGAATTATGGA
679903 TGAAG-TTATGGTTGA
1 TGAAGATTAT-GTTGA
679918 AGCTGGTTCT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
78 28 0.33
79 2 0.02
83 4 0.05
84 51 0.60
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.18
Consensus pattern (80 bp):
TGAAGATTATGTTGAGAAGAAGAATAAAGAGGACATACCGAAACTGAAAAGAAGACCGAGGAAGA
GAAGGGAATTATGGA
Found at i:680216 original size:72 final size:73
Alignment explanation
Indices: 680136--680277 Score: 191
Period size: 72 Copynumber: 2.0 Consensus size: 73
680126 AAGGAAGCTA
* * * *
680136 TTGCTGTTGATGATAGAGCTAATGATGCAGGATCT-ATTGTAAGTGAAAAGAA-AAAAG-AATGC
1 TTGCTGTTGATAATAGAGCTAATGATACAGGAGCTGA-TGAAAGTGAAAAGAACAAAAGCAA-GC
680198 AAGGAGGTTG
64 AAGGAGGTTG
* *
680208 TTGCTGTTGCTAATAGTGCTAATGATACAGGAGCTGATGAAAGTGAAAAGAACAAAAGCAAGCAA
1 TTGCTGTTGATAATAGAGCTAATGATACAGGAGCTGATGAAAGTGAAAAGAACAAAAGCAAGCAA
680273 GGAGG
66 GGAGG
680278 CTATTGTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
72 44 0.72
73 15 0.25
74 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (73 bp):
TTGCTGTTGATAATAGAGCTAATGATACAGGAGCTGATGAAAGTGAAAAGAACAAAAGCAAGCAA
GGAGGTTG
Found at i:680678 original size:72 final size:71
Alignment explanation
Indices: 680582--680768 Score: 172
Period size: 66 Copynumber: 2.7 Consensus size: 71
680572 AGAGGAAAAG
* * * * *
680582 CAAAGAGAGTGAAGAGGCAATTGCTGTTGATAATAGTGCTAATGATGCAAG-AGTTGATGGAAGT
1 CAAAGAGAGCGAGGAGGCTATTGCT-TTG-TAATAGTGCTAATGATGCAAGTAGCTGATGAAAGT
*
680646 GGAAAGAA
64 GAAAAGAA
* * *
680654 CCAAGAGAGCGAGGAGGCTGTTGC----TAATAGTGCTAATGATG-TAGTAGCTGATGAAAGTGA
1 CAAAGAGAGCGAGGAGGCTATTGCTTTGTAATAGTGCTAATGATGCAAGTAGCTGATGAAAGTGA
680714 AAAGAA
66 AAAGAA
* * *
680720 CAAAG-GTAGCAAGGAGGCTATTGCTATTGTTGATAGTGCAAATGATGCA
1 CAAAGAG-AGCGAGGAGGCTATTGCT-TTG-TAATAGTGCTAATGATGCA
680769 GGGGTCAATG
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
65 3 0.03
66 54 0.59
72 34 0.37
ACGTcount: A:0.36, C:0.10, G:0.31, T:0.23
Consensus pattern (71 bp):
CAAAGAGAGCGAGGAGGCTATTGCTTTGTAATAGTGCTAATGATGCAAGTAGCTGATGAAAGTGA
AAAGAA
Found at i:680682 original size:66 final size:66
Alignment explanation
Indices: 680604--680745 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 66
680594 AGAGGCAATT
* * * * * *
680604 GCTGTTGATAATAGTGCTAATGATGCAAG-AGTTGATGGAAGTGGAAAGAACCAAGAG-AGCGAG
1 GCTGTTGCTAATAGTGCTAATGATG-AAGTAGCTGATGAAAGTGAAAAGAACAAAG-GTAGCAAG
680667 GAG
64 GAG
*
680670 GCTGTTGCTAATAGTGCTAATGATGTAGTAGCTGATGAAAGTGAAAAGAACAAAGGTAGCAAGGA
1 GCTGTTGCTAATAGTGCTAATGATGAAGTAGCTGATGAAAGTGAAAAGAACAAAGGTAGCAAGGA
680735 G
66 G
*
680736 GCTATTGCTA
1 GCTGTTGCTA
680746 TTGTTGATAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 3 0.05
66 63 0.95
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.23
Consensus pattern (66 bp):
GCTGTTGCTAATAGTGCTAATGATGAAGTAGCTGATGAAAGTGAAAAGAACAAAGGTAGCAAGGA
G
Found at i:681061 original size:385 final size:387
Alignment explanation
Indices: 680438--681175 Score: 1008
Period size: 385 Copynumber: 1.9 Consensus size: 387
680428 AGGGTGTTGT
* *
680438 TGTTGCTAATTGTGCTAATGATGTAAGGGGTGATGAAAGTGAAAAGAACAAAACGAGCAAGGAAG
1 TGTTGCTAATTGTGCTAATGATGTAAGGGCTGATGAAAGTG-AAAGAACAAAACGAGAAAGGAAG
* * * * *
680503 CTATTGCTGTTGCTAATAGTGCTAATGATGCAGTAGCTGGTGGAAGTGAAATGAAGAAAACAAAG
65 CTATTGATGTTGCTAATAGTGCAAATGATACAGGAGCTGATGGAAGTGAAATGAAGAAAACAAAG
*
680568 AAAAAGAGGAAAAGCAAAGAGAGTGAAGAGGCAATTGCTGTTGATAATAGTGCTAATGATGCAAG
130 AAAAAGAAGAAAAGCAAAGAGA--GAAGAGGCAATTGCTGTTGATAATAGTGCTAATGATGCAAG
* * * *
680633 AGTTGATGGAAGTGGAAAGAACCAAGAGAGCGAGGAGGCTGTTGCTAATAGTGCTAATGATGT-A
193 AGCTGATGAAAGTGAAAAGAACAAAGAGAGCGAGGAGGCTGTTGCTAATAGTGCTAATGATGTGA
* * *
680697 GTAGCTGATGAAAGTGAAAAGAACAAAG-GTAGCAAGGAGGCTATTGCTATTGTTGATAGTGCAA
258 -AAACTGATGAAAGTGAAAAGAACAAAGAG-AGCAAGGAGACTATTGCTATTGTTGATAGTGCAA
680761 ATGATGCAGGGGTCAATGAAAGTGAAAAGAAAAAGAAGAAGAAGAGGAAAGGCAAAGAGAGTATT
321 ATGATGCAGGGGTCAATGAAAGTGAAAAGAAAAAGAAGAAGAAGAGGAAAGGCAAAGAGAGTATT
680826 GC
386 GC
* *
680828 TGTTGCT-ATTAGTGCTAATGATGT-AGGAGCTGATGAAAGTG-AAGAACAAAGCGAGAAAGGAG
1 TGTTGCTAATT-GTGCTAATGATGTAAGG-GCTGATGAAAGTGAAAGAACAAAACGAGAAAGGAA
* * * *
680890 GCTATTGATGTTGTTGATAGTGCAAATTG-TACAGGGGGTGATGGAAGTGAAATGAAGAAAACAA
64 GCTATTGATGTTGCTAATAGTGCAAA-TGATACAGGAGCTGATGGAAGTGAAATGAAGAAAACAA
* * * * *
680954 AGAAGAAGAAGAAGAGGAAAG-GCA-AAGAGAG-TATTGCTGTTGATAATAGTTCTAATGATGCA
128 AGAAAAAGAAGAAAAGCAAAGAG-AGAAGAG-GCAATTGCTGTTGATAATAGTGCTAATGATGCA
* *
681016 GGAGCTGATGAAAGTGAAAAGAATAAAGAGAGCGAGGAGGCTGTTGCTAATAGTGCTAATGATGT
191 AGAGCTGATGAAAGTGAAAAGAACAAAGAGAGCGAGGAGGCTGTTGCTAATAGTGCTAATGATGT
* ** * * *
681081 GAAAACTGATGAAAGTGAGAAGAACAAAGAGAGTGAGGAGACTGTTGTTGTTGTTGATAGTGCAA
256 GAAAACTGATGAAAGTGAAAAGAACAAAGAGAGCAAGGAGACTATTGCTATTGTTGATAGTGCAA
*
681146 ATGATGCAGGGGTCGATGAAAGTGAAAAGA
321 ATGATGCAGGGGTCAATGAAAGTGAAAAGA
681176 GGAAAAATAA
Statistics
Matches: 306, Mismatches: 35, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
385 174 0.57
386 3 0.01
387 1 0.00
388 88 0.29
389 8 0.03
390 32 0.10
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.21
Consensus pattern (387 bp):
TGTTGCTAATTGTGCTAATGATGTAAGGGCTGATGAAAGTGAAAGAACAAAACGAGAAAGGAAGC
TATTGATGTTGCTAATAGTGCAAATGATACAGGAGCTGATGGAAGTGAAATGAAGAAAACAAAGA
AAAAGAAGAAAAGCAAAGAGAGAAGAGGCAATTGCTGTTGATAATAGTGCTAATGATGCAAGAGC
TGATGAAAGTGAAAAGAACAAAGAGAGCGAGGAGGCTGTTGCTAATAGTGCTAATGATGTGAAAA
CTGATGAAAGTGAAAAGAACAAAGAGAGCAAGGAGACTATTGCTATTGTTGATAGTGCAAATGAT
GCAGGGGTCAATGAAAGTGAAAAGAAAAAGAAGAAGAAGAGGAAAGGCAAAGAGAGTATTGC
Found at i:681067 original size:66 final size:66
Alignment explanation
Indices: 680989--681127 Score: 181
Period size: 66 Copynumber: 2.1 Consensus size: 66
680979 AGAGAGTATT
* * * *
680989 GCTGTTGATAATAGTTCTAATGATGCAG-GAGCTGATGAAAGTGAAAAGAATAAAGAGAGCGAGG
1 GCTGTTGATAATAGTGCTAATGATG-AGAAAACTGATGAAAGTGAAAAGAACAAAGAGAGCGAGG
681053 AG
65 AG
* * * *
681055 GCTGTTGCTAATAGTGCTAATGATGTGAAAACTGATGAAAGTGAGAAGAACAAAGAGAGTGAGGA
1 GCTGTTGATAATAGTGCTAATGATGAGAAAACTGATGAAAGTGAAAAGAACAAAGAGAGCGAGGA
681120 G
66 G
*
681121 ACTGTTG
1 GCTGTTG
681128 TTGTTGTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (66 bp):
GCTGTTGATAATAGTGCTAATGATGAGAAAACTGATGAAAGTGAAAAGAACAAAGAGAGCGAGGA
G
Found at i:681198 original size:84 final size:85
Alignment explanation
Indices: 681099--681349 Score: 292
Period size: 84 Copynumber: 2.9 Consensus size: 85
681089 ATGAAAGTGA
681099 GAAGAACAAAGAGAGTGAGGAGACTGTTGTTGTTGTTGATAGTGCAAATGATGCAGGGGTCGATG
1 GAAGAACAAAGAGAGTGAGGAGACTGTTGTTGTTGTTGATAGTGCAAATGATGCAGGGGT-GATG
*
681164 AAAGTGAAAAGAGGAAAA-AT
65 AAAGTGAAAAGAGAAAAAGAT
* * * ** *
681184 -AAGAACACAGAGAGTAAGGAGACTGTTTTTGTTGTTGATAGTGCAGGTGATGTAAGGGGTGATG
1 GAAGAACAAAGAGAGTGAGGAGACTGTTGTTGTTGTTGATAGTGCAAATGATG-CAGGGGTGATG
681248 AAAGTGAAAAGAAGAAAAAGAT
65 AAAGTGAAAAG-AGAAAAAGAT
* * * * * *
681270 GAAGGACAAAGAGAGTGACGATG-CTATTGTTGTTGATAATGTTAGTGCTAATGATGCATGGAGT
1 GAAGAACAAAGAGAGTGAGGA-GACTGTTGTTGTTG-T--TGATAGTGCAAATGATGCA-GGGGT
681334 GATGAAAGTGAAAAGA
61 GATGAAAGTGAAAAGA
681350 ACAATGTGAA
Statistics
Matches: 138, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
84 62 0.45
85 12 0.09
86 2 0.01
87 26 0.19
88 2 0.01
89 2 0.01
90 32 0.23
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.24
Consensus pattern (85 bp):
GAAGAACAAAGAGAGTGAGGAGACTGTTGTTGTTGTTGATAGTGCAAATGATGCAGGGGTGATGA
AAGTGAAAAGAGAAAAAGAT
Found at i:681395 original size:72 final size:72
Alignment explanation
Indices: 681311--681493 Score: 197
Period size: 71 Copynumber: 2.6 Consensus size: 72
681301 GTTGATAATG
* * * ** * *
681311 TTAGTGCTAATGATGCATGGAGTGATGAAAGTGAAAAGAACAATGTGAACAAGGAGGCGGTTGCT
1 TTAGTGCAAATGATGCAAGGAGTGATGAAAGTGAAAAGAACAAAGACAACAACGACGCGGTTGCT
*
681376 GTTGTTC
66 GTTGTTA
* * * *
681383 TTAGTGCAAATGATGCAAGGGGTGATGGAAGTG-AAAGAACAAAGACAGCAACGACGTGGTTGCT
1 TTAGTGCAAATGATGCAAGGAGTGATGAAAGTGAAAAGAACAAAGACAACAACGACGCGGTTGCT
681447 GTTGTTA
66 GTTGTTA
* * * * * *
681454 ATAGTGCAAATGATGCAGGGTGTGGTTAAAGTGACAAGAA
1 TTAGTGCAAATGATGCAAGGAGTGATGAAAGTGAAAAGAA
681494 GAAAAAGAAG
Statistics
Matches: 91, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 57 0.63
72 34 0.37
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Consensus pattern (72 bp):
TTAGTGCAAATGATGCAAGGAGTGATGAAAGTGAAAAGAACAAAGACAACAACGACGCGGTTGCT
GTTGTTA
Found at i:685205 original size:29 final size:29
Alignment explanation
Indices: 685163--685485 Score: 133
Period size: 30 Copynumber: 11.0 Consensus size: 29
685153 AGTATAGAAT
* * *
685163 TTTACAAATTATATTTTATTTTAATTTTAA
1 TTTA-AAAATATATTTTATTTTTATCTTAA
* * *
685193 TTTAAAAATATATTTTAATCTTATCATAA
1 TTTAAAAATATATTTTATTTTTATCTTAA
*
685222 CTTAAAAATATATTTTATTTTTTATCTTAA
1 TTTAAAAATATATTTTA-TTTTTATCTTAA
* *
685252 CTTTTAAAAATATATCTTATTTTTATTTTAA
1 --TTTAAAAATATATTTTATTTTTATCTTAA
* * * * * **
685283 CTTATTACATATATTATATTCTTAAATTAA
1 TTTA-AAAATATATTTTATTTTTATCTTAA
* ** * * * *
685313 ATTATTTAATATATTCTAGTCTTACCTTAA
1 TTTA-AAAATATATTTTATTTTTATCTTAA
* * * ** *
685343 ATTATTAAATATAATTTATCCTTATTTTAA
1 TTTA-AAAATATATTTTATTTTTATCTTAA
** * * *
685373 CATAAAATATATATTTTATTCTTATTTTTA
1 TTTAAAA-ATATATTTTATTTTTATCTTAA
* * *
685403 -TTAATATATATATATATATTATT-T-TT-A
1 TTTAA-AAATATAT-TTTATTTTTATCTTAA
685430 TTTAAAAATGTATATTTTA--TTT-T-TT-A
1 TTTAAAAA--TATATTTTATTTTTATCTTAA
*
685456 TTTTAAAATATATTTTATTTTTATCTTAA
1 TTTAAAAATATATTTTATTTTTATCTTAA
685485 T
1 T
685486 GTTGAAATAT
Statistics
Matches: 229, Mismatches: 49, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
24 9 0.04
26 16 0.07
27 4 0.02
28 11 0.05
29 57 0.25
30 106 0.46
31 11 0.05
32 15 0.07
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (29 bp):
TTTAAAAATATATTTTATTTTTATCTTAA
Found at i:685443 original size:27 final size:24
Alignment explanation
Indices: 685389--685484 Score: 88
Period size: 26 Copynumber: 3.8 Consensus size: 24
685379 ATATATATTT
685389 TATTCTTATTTTTA-TTAATATATATATA
1 TATT-TTATTTTTATTTAA-A-A-AT-TA
*
685417 TATATTATTTTTATTTAAAAATGTA
1 TATTTTATTTTTATTTAAAAAT-TA
*
685442 TATTTTATTTTTTATTTTAAAA-TA
1 TATTTTA-TTTTTATTTAAAAATTA
685466 TATTTTATTTTTATCTTAA
1 TATTTTATTTTTAT-TTAA
685485 TGTTGAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
23 7 0.12
24 12 0.20
25 10 0.17
26 14 0.23
27 10 0.17
28 7 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (24 bp):
TATTTTATTTTTATTTAAAAATTA
Found at i:685467 original size:24 final size:24
Alignment explanation
Indices: 685414--685477 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
685404 TAATATATAT
*
685414 ATATATATTA-TTTTTATTTAAAA
1 ATATATTTTATTTTTTATTTAAAA
*
685437 ATGTATATTTTATTTTTTATTTTAAA
1 A--TATATTTTATTTTTTATTTAAAA
685463 ATATATTTTATTTTT
1 ATATATTTTATTTTT
685478 ATCTTAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 14 0.39
25 8 0.22
26 13 0.36
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATATTTTATTTTTTATTTAAAA
Found at i:685610 original size:26 final size:25
Alignment explanation
Indices: 685581--685631 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
685571 ATTTTATAAG
685581 TTAAAATAAGAATAA-AATATAAATAT
1 TTAAAATAAG-ATAATAATA-AAATAT
**
685607 TTAAGTTAAGATAATAATAAAATAT
1 TTAAAATAAGATAATAATAAAATAT
685632 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (25 bp):
TTAAAATAAGATAATAATAAAATAT
Found at i:685615 original size:31 final size:31
Alignment explanation
Indices: 685497--685653 Score: 139
Period size: 31 Copynumber: 5.2 Consensus size: 31
685487 TTGAAATATT
* *
685497 ATAAGAATAAAATATAAATATTTAAGCTAAG
1 ATAAGAATAAAATATAAATTTTTAAGTTAAG
* * *
685528 GTGAGAAT-AAAT-T-ATTTTTTAAAGTTAA-
1 ATAAGAATAAAATATAAATTTTT-AAGTTAAG
* *
685556 A-AAAAATTAAAATAT--ATTTTATAAGTTAAA
1 ATAAGAA-TAAAATATAAATTTT-TAAGTTAAG
*
685586 ATAAGAATAAAATATAAATATTTAAGTTAAG
1 ATAAGAATAAAATATAAATTTTTAAGTTAAG
* *
685617 ATAATAATAAAATATATATTTTTAATGTTAAG
1 ATAAGAATAAAATATAAATTTTTAA-GTTAAG
685649 ATAAG
1 ATAAG
685654 TTTAGACTAA
Statistics
Matches: 100, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
27 3 0.03
28 6 0.06
29 22 0.22
30 15 0.15
31 40 0.40
32 14 0.14
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (31 bp):
ATAAGAATAAAATATAAATTTTTAAGTTAAG
Found at i:686357 original size:3 final size:3
Alignment explanation
Indices: 686349--686375 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
686339 CTTGTATTTA
686349 GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT
686376 TTCATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:691293 original size:21 final size:20
Alignment explanation
Indices: 691252--691298 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
691242 TAAGTATAAA
* *
691252 TATAATTTAAATTTTATATT
1 TATAATTTAAATATAATATT
*
691272 TTTAATTTACAATATAATATT
1 TATAATTTA-AATATAATATT
691293 TATAAT
1 TATAAT
691299 AGACATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTAAATATAATATT
Found at i:694632 original size:17 final size:16
Alignment explanation
Indices: 694610--694665 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
694600 TTAAAATATC
694610 TAAAATATATGAAAATT
1 TAAAATATAT-AAAATT
* *
694627 TAAAATATTATCAAATC
1 TAAAATA-TATAAAATT
*
694644 TAAAATATATAAGAAAT
1 TAAAATATATAA-AATT
694661 TAAAA
1 TAAAA
694666 ATTTTCAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.12
17 25 0.78
18 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (16 bp):
TAAAATATATAAAATT
Found at i:694667 original size:42 final size:42
Alignment explanation
Indices: 694589--694669 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
694579 GAGATAAAAC
* * *
694589 ATATTATCAATTTAAAATATCTAAAATATATGAAAATTTAAA
1 ATATTATCAATCTAAAATATATAAAATATATAAAAATTTAAA
694631 ATATTATCAAATCTAAAATATATAAGAA-AT-TAAAAATTT
1 ATATTATC-AATCTAAAATATATAA-AATATATAAAAATTT
694670 TCAAGAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 16 0.47
43 16 0.47
44 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (42 bp):
ATATTATCAATCTAAAATATATAAAATATATAAAAATTTAAA
Found at i:697442 original size:20 final size:20
Alignment explanation
Indices: 697417--697461 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
697407 TCTTAGGACA
*
697417 CATTTAGGATCATATAGA-TG
1 CATTTAGGAGCATATA-ATTG
697437 CATTTAGGAGCATATAATTG
1 CATTTAGGAGCATATAATTG
697457 CATTT
1 CATTT
697462 GGTGGATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (20 bp):
CATTTAGGAGCATATAATTG
Found at i:700963 original size:18 final size:17
Alignment explanation
Indices: 700936--700969 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
700926 TGACAGAAGA
*
700936 GAAAGAACAAGTGATAT
1 GAAAGAACAAATGATAT
700953 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
700970 ATGCCCATGT
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:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:701086 original size:22 final size:21
Alignment explanation
Indices: 701038--701095 Score: 89
Period size: 22 Copynumber: 2.7 Consensus size: 21
701028 GGGTTTACGC
*
701038 GGTCCTTCGGGACAACTCATA
1 GGTCCTTCGGGACAACTCACA
*
701059 GGTCCTTCGGGACATATTCACA
1 GGTCCTTCGGGACA-ACTCACA
701081 GGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
701096 AATTTCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (21 bp):
GGTCCTTCGGGACAACTCACA
Found at i:702458 original size:64 final size:63
Alignment explanation
Indices: 702390--702570 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
702380 TTGGAACACT
* **
702390 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
* * * **
702454 TGATGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * *
702518 AGAGTGCATCGATGCATGTAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
702571 CAATTAATTC
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
64 55 0.55
65 45 0.45
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:702542 original size:19 final size:19
Alignment explanation
Indices: 702518--702554 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
702508 GAAAATATTC
702518 AGAGTGCATCGATGCATGT
1 AGAGTGCATCGATGCATGT
*
702537 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
702555 GAATGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGT
Found at i:702610 original size:65 final size:63
Alignment explanation
Indices: 702412--702619 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
702402 GCACCAAGTG
* * *
702412 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGATTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGTA-TGA
*
702476 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGTA-G
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGTATG
702539 A
63 A
* * * *
702540 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGTA-T
702604 GA
62 GA
*
702606 TGCATCGGTGCATG
1 TGCATCGATGCATG
702620 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
63 10 0.08
64 46 0.37
65 65 0.52
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGTATGA
Found at i:707671 original size:21 final size:21
Alignment explanation
Indices: 707601--707682 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
707591 CAGAACCCCA
* *
707601 GGGGGTATCGATTCCC-CTGTG
1 GGGGGAATCGATTCCCTC-ATG
* **
707622 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCATG
707645 GGGGGAATCGATTCCCTCATG
1 GGGGGAATCGATTCCCTCATG
707666 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
707683 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 12 0.24
21 19 0.38
22 6 0.12
23 12 0.24
24 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCATG
Found at i:707674 original size:20 final size:20
Alignment explanation
Indices: 707622--707682 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
707612 TTCCCCTGTG
* *
707622 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
707645 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
707665 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
707683 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:711524 original size:20 final size:20
Alignment explanation
Indices: 711477--711524 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
711467 TTCATGTTTC
*
711477 AATATTTTTTAATTTTGAAA
1 AATAATTTTTAATTTTGAAA
* *
711497 CATCATTTTTATATTTT-AAA
1 AATAATTTTTA-ATTTTGAAA
711517 AATAATTT
1 AATAATTT
711525 CTCATAATCC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
AATAATTTTTAATTTTGAAA
Found at i:714401 original size:2 final size:2
Alignment explanation
Indices: 714396--714451 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
714386 ATATACATCC
714396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
714437 -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
714452 CTCCATCCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:716730 original size:16 final size:16
Alignment explanation
Indices: 716706--716737 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
716696 GGTTGCCCGT
716706 TATGAACTAGAAGAGC
1 TATGAACTAGAAGAGC
*
716722 TATGGACTAGAAGAGC
1 TATGAACTAGAAGAGC
716738 AATACAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (16 bp):
TATGAACTAGAAGAGC
Found at i:725151 original size:359 final size:359
Alignment explanation
Indices: 724477--725180 Score: 1358
Period size: 359 Copynumber: 2.0 Consensus size: 359
724467 TGTTTCTTAG
724477 TTTGATGGTAGGAGAAATTGGAGCCTTAGTTACTGCCAAGGACATTATGGTTAGATGGATTCCTA
1 TTTGATGGTAGGAGAAATTGGAGCCTTAGTTACTGCCAAGGACATTATGGTTAGATGGATTCCTA
*
724542 GGAGCTGTAATTTGGAGGCAGATAAGCTAGCTAAGTAAGGGATAGGCTGATGGTTGTTTGTTTCC
66 GGAGCTGTAATTTGGAGGCAGATAAGCTAGCTAAGGAAGGGATAGGCTGATGGTTGTTTGTTTCC
724607 CGTCGTTATTGTAGTTATGTTCTGTTTTTTCTAGGAGGGCTAGAGTGTAATGTGTATCTTATGTA
131 CGTCGTTATTGTAGTTATGTTCTGTTTTTTCTAGGAGGGCTAGAGTGTAATGTGTATCTTATGTA
*
724672 ATTCGGGGTTAGAGTGCAATGTTTATCCTTTGTAATTCAGGTTTATTAATAAATTGAGGTACTTT
196 ATTCGGGGTTAGAGTGCAATGTGTATCCTTTGTAATTCAGGTTTATTAATAAATTGAGGTACTTT
724737 TTCCTCCTTCAATTAGTTGCCTCTTATAAGAGCCAACTATGAGGGAGGTTTTTAATGAGACCTCC
261 TTCCTCCTTCAATTAGTTGCCTCTTATAAGAGCCAACTATGAGGGAGGTTTTTAATGAGACCTCC
724802 TATTCCTATAAAAAAAAGGTTTGTAATTCAGGTT
326 TATTCCTATAAAAAAAAGGTTTGTAATTCAGGTT
724836 TTTGATGGTAGGAGAAATTGGAGCCTTAGTTACTGCCAAGGACATTATGGTTAGATGGATTCCTA
1 TTTGATGGTAGGAGAAATTGGAGCCTTAGTTACTGCCAAGGACATTATGGTTAGATGGATTCCTA
724901 GGAGCTGTAATTTGGAGGCAGATAAGCTAGCTAAGGAAGGGATAGGCTGATGGTTGTTTGTTTCC
66 GGAGCTGTAATTTGGAGGCAGATAAGCTAGCTAAGGAAGGGATAGGCTGATGGTTGTTTGTTTCC
724966 CGT-GTTATTGTAGTTATGTTCTGTTTTTTCTAGGAGGGCTAGAGTGTAATGTGTATCTTATGTA
131 CGTCGTTATTGTAGTTATGTTCTGTTTTTTCTAGGAGGGCTAGAGTGTAATGTGTATCTTATGTA
725030 ATTCGGGGTTAGAGTGCAATGTGTATCCTTTGTAATTCAGGTTTATTAATAAATTGAGGTACTCT
196 ATTCGGGGTTAGAGTGCAATGTGTATCCTTTGTAATTCAGGTTTATTAATAAATTGAGGTACT-T
725095 TTTCCTCCTTCAATTAGTTGCCTCTTGATAAGAGCCAACTATGAGGGAGG-TTTTAATGAGACCT
260 TTTCCTCCTTCAATTAGTTGCCTCTT-ATAAGAGCCAACTATGAGGGAGGTTTTTAATGAGACCT
725159 CCTATTCCTATAAAAAAAAGGT
324 CCTATTCCTATAAAAAAAAGGT
725181 GATCTGTCCT
Statistics
Matches: 341, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
358 123 0.36
359 195 0.57
360 23 0.07
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (359 bp):
TTTGATGGTAGGAGAAATTGGAGCCTTAGTTACTGCCAAGGACATTATGGTTAGATGGATTCCTA
GGAGCTGTAATTTGGAGGCAGATAAGCTAGCTAAGGAAGGGATAGGCTGATGGTTGTTTGTTTCC
CGTCGTTATTGTAGTTATGTTCTGTTTTTTCTAGGAGGGCTAGAGTGTAATGTGTATCTTATGTA
ATTCGGGGTTAGAGTGCAATGTGTATCCTTTGTAATTCAGGTTTATTAATAAATTGAGGTACTTT
TTCCTCCTTCAATTAGTTGCCTCTTATAAGAGCCAACTATGAGGGAGGTTTTTAATGAGACCTCC
TATTCCTATAAAAAAAAGGTTTGTAATTCAGGTT
Found at i:728495 original size:14 final size:16
Alignment explanation
Indices: 728465--728497 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
728455 TGTTTTCCTG
728465 TTTCTTTCTGTGTTGT
1 TTTCTTTCTGTGTTGT
728481 TTTCTTT-TG-GTTGT
1 TTTCTTTCTGTGTTGT
728495 TTT
1 TTT
728498 AATTAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTGTGTTGT
Found at i:729857 original size:9 final size:9
Alignment explanation
Indices: 729843--729867 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
729833 ACACCTTGTA
729843 GATGAAGAT
1 GATGAAGAT
729852 GATGAAGAT
1 GATGAAGAT
729861 GATGAAG
1 GATGAAG
729868 TTGTTATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GATGAAGAT
Found at i:731379 original size:249 final size:245
Alignment explanation
Indices: 730942--731671 Score: 952
Period size: 249 Copynumber: 3.0 Consensus size: 245
730932 GTTGAGAGAG
*
730942 CAGGTGACTAATCTGAATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACAATGGCCTCGC
1 CAGGTGACTAATCTGCATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACAATGGCCTCGC
731007 TGCCGAACA-CCCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAATTGTGATGAAAATG
66 TGCCGAACACCCCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAA-TGTGATGAAAATG
* * * *
731071 ACAATGGTGAATGTAATGTAGAACGTGTATCTGCAAAGAAGAAACCTTCCAAGAGGTCAAAGAAA
130 ATAATGGTGAAT-TAATGTAG-ACATGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
* *
731136 CCCGTGAATGAAAGTGAAAAACTTCCTCGAAAACATAAGATAGCTAACGAATCT
193 CCCGTGAATGAAAGTGAAAAAC-TCCTCGAAAACATAAGATAGCTAATGAAGCT
* * ** * *
731190 CAGGTGACTAATCTGCATGTTGTTGATGATCTTCAGGATGGGACTTGTAAACACGATAGCCTCGC
1 CAGGTGACTAATCTGCATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACAATGGCCTCGC
* *
731255 TGCCAAACACCCCCTTAGTTATGCTATTAATGAGGATAAAGACGACAACAATGATGATGAAAATG
66 TGCCGAACACCCCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAATG-TGATGAAAATG
**
731320 ATAATGGTGAATATAATGTAGAGCACATATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
130 ATAATGGTGAAT-TAATGTAGA-CATGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAA
* * * * *
731385 CCCATGAATGAAAGTGAAAAAACTCCTCGAAATCATTAGATATCTAGTGAAGCT
193 CCCGTGAATGAAAGTG-AAAAACTCCTCGAAAACATAAGATAGCTAATGAAGCT
* * *
731439 CAGGTGATTAATCTGCATATTGTTGATGATCTTGAGGATGGGACTGGTAATGACAATGGCCTCGT
1 CAGGTGACTAATCTGCATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACAATGGCCTCGC
* * * *
731504 TGCCGAACACCCCTTTAGTTAAGCTATCAATGAGGATAAAAATGACAACAATG-G-TG--AAT-A
66 TGCCGAACACCCCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAATGTGATGAAAATGA
* * *
731564 TAA---TG---T-A-G-A-ACATGTATCGGCAAAGAGTAAACCTTCTAAGAGGTCGAAGAAACCC
131 TAATGGTGAATTAATGTAGACATGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAACCC
* * *
731619 GTGAATGAAAGTGAAAAACCTCCTCAAAAACGTGAGATAGCTAATGAAGCT
196 GTGAATGAAAGTGAAAAA-CTCCTCGAAAACATAAGATAGCTAATGAAGCT
731670 CA
1 CA
731672 AAATCATAAG
Statistics
Matches: 427, Mismatches: 50, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
230 5 0.01
231 80 0.19
232 1 0.00
233 1 0.00
234 1 0.00
235 1 0.00
236 1 0.00
240 2 0.00
243 4 0.01
244 3 0.01
246 2 0.00
247 1 0.00
248 69 0.16
249 250 0.59
250 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (245 bp):
CAGGTGACTAATCTGCATATTGTTGATGATCTTGAGGATGGGACTTGTAATGACAATGGCCTCGC
TGCCGAACACCCCCTTAGTTATGCTATCAATGAGGATAAAGACGACAACAATGTGATGAAAATGA
TAATGGTGAATTAATGTAGACATGTATCTGCAAAGAGGAAACCTTCTAAGAGGTCAAAGAAACCC
GTGAATGAAAGTGAAAAACTCCTCGAAAACATAAGATAGCTAATGAAGCT
Found at i:733032 original size:27 final size:27
Alignment explanation
Indices: 733000--733059 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
732990 GCAGGAAGAA
733000 GTAGCAAAACCCGAGCAGGATGAGGAT
1 GTAGCAAAACCCGAGCAGGATGAGGAT
*
733027 GTAGCAAAACCGGAGCAGGATGAGGAT
1 GTAGCAAAACCCGAGCAGGATGAGGAT
733054 GTAGCA
1 GTAGCA
733060 GTGAGAGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.35, T:0.12
Consensus pattern (27 bp):
GTAGCAAAACCCGAGCAGGATGAGGAT
Found at i:737503 original size:64 final size:63
Alignment explanation
Indices: 737409--737549 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
737399 CACATTCAAT
* * * *
737409 GTGCATCGATACACTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATTGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCAT-AGGTA
* * * * * *
737472 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAAATGGTGCATCGATGCATAGGTA
737536 GTGCATCGATGCAC
1 GTGCATCGATGCAC
737550 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 17 0.26
64 48 0.74
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCATAGGTA
Found at i:737585 original size:20 final size:22
Alignment explanation
Indices: 737537--737594 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
737527 GCATGGGTAG
737537 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
737561 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
737581 TGCATCGATGCACT
1 TGCATCGATGCACT
737595 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:738342 original size:31 final size:31
Alignment explanation
Indices: 738284--738348 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
738274 AAAGTCGAGG
*
738284 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
* * *
738315 GTTTACCTAGGT-TCTTCGGGACCTATGGATA
1 GTTTACCTAGGTCT-TTCGAGACATATGGACA
738346 GTT
1 GTT
738349 GCTGAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGACA
Found at i:738358 original size:30 final size:30
Alignment explanation
Indices: 738323--738379 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
738313 CAGTTTACCT
*
738323 AGGTTCTTCGGGACCTATGGATAGTTGCTG
1 AGGTTCTTCAGGACCTATGGATAGTTGCTG
* * *
738353 AGGTTCTTTATGACCTCTGGATAGTTG
1 AGGTTCTTCAGGACCTATGGATAGTTG
738380 TCGGGGTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.37
Consensus pattern (30 bp):
AGGTTCTTCAGGACCTATGGATAGTTGCTG
Found at i:738400 original size:30 final size:30
Alignment explanation
Indices: 738334--738406 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
738324 GGTTCTTCGG
* *
738334 GACCTATGGATAGTTGCTGAGGTTCTTTAT
1 GACCTCTGGATAGTTGCTGAGGGTCTTTAT
*
738364 GACCTCTGGATAGTTG-TCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGCT-GAGGGTCTTTAT
*
738393 GACCCTCTAGATAG
1 GA-CCTCTGGATAG
738407 GTCATTCGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.36
Consensus pattern (30 bp):
GACCTCTGGATAGTTGCTGAGGGTCTTTAT
Found at i:741381 original size:63 final size:64
Alignment explanation
Indices: 741310--741446 Score: 165
Period size: 63 Copynumber: 2.2 Consensus size: 64
741300 ATTGAATGTG
*
741310 CATCGATGCACT-CTTTAAAGAAG-AAACATCGAATGCAAATGGTGTATCGATGCATAAGG-AGT
1 CATCGATGCACTCCTTTAAA-AAGAAAACATCGAAGGCAAATGGTGTATCGATGCAT-AGGTAGT
741372 A
64 A
* * * * * *
741373 CATCGATGCA-TCCTTTAAAATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAGTG
1 CATCGATGCACTCCTTTAAAAAGAAAACATCGAAGGCAAATGGTGTATCGATGCATAGGTAGTA
741436 CATCGATGCAC
1 CATCGATGCAC
741447 ATGTTAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
62 5 0.08
63 58 0.92
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (64 bp):
CATCGATGCACTCCTTTAAAAAGAAAACATCGAAGGCAAATGGTGTATCGATGCATAGGTAGTA
Found at i:741482 original size:20 final size:22
Alignment explanation
Indices: 741434--741491 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
741424 GCATGGGTAG
741434 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
741458 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
741478 TGCATCGATGCACT
1 TGCATCGATGCACT
741492 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:742293 original size:29 final size:30
Alignment explanation
Indices: 742231--742302 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
742221 GGTTATTCGG
* * *
742231 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
* *
742261 GACCTCTGGATAGTTGTCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
742290 GACCTCTGGATAG
1 GACCTCTGGATAG
742303 GTCTTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTGCCGAGGGTCTTTAT
Found at i:743494 original size:13 final size:14
Alignment explanation
Indices: 743460--743495 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
743450 GTCACATCTG
743460 TAATTTATTT--AA
1 TAATTTATTTAAAA
743472 TAATTTATTTAAAA
1 TAATTTATTTAAAA
743486 TAA-TTATTTA
1 TAATTTATTTA
743496 TATTATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.45
13 7 0.32
14 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTTATTTAAAA
Done.