Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 30 of 145
Found at i:9658904 original size:5 final size:6
Alignment explanation
Indices: 9658885--9658941 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
9658875 TTCAAAAAAC
* *
9658885 AAATAA AAATAA AAATAA AACACTAC AAATAG AAAT-A AAATGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAAT-AA AAATAA
*
9658935 AGATAA A
1 AAATAA A
9658942 CTAAATTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 4 0.09
6 28 0.65
7 7 0.16
8 4 0.09
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:9660088 original size:12 final size:12
Alignment explanation
Indices: 9660071--9660115 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
9660061 AGGTTATGTA
9660071 TTATTATGTAAG
1 TTATTATGTAAG
*
9660083 TTATTATGTAGG
1 TTATTATGTAAG
*
9660095 TTATTATATAAG
1 TTATTATGTAAG
*
9660107 TCATTATGT
1 TTATTATGT
9660116 TGGTTATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:9660101 original size:24 final size:24
Alignment explanation
Indices: 9660064--9660122 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
9660054 TTTATGTAGG
* *
9660064 TTATGTA--TTATTATGTAAGTTA
1 TTATGTAGGTTATTATATAAGTCA
9660086 TTATGTAGGTTATTATATAAGTCA
1 TTATGTAGGTTATTATATAAGTCA
*
9660110 TTATGTTGGTTAT
1 TTATGTAGGTTAT
9660123 GTAAGTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
24 25 0.78
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.53
Consensus pattern (24 bp):
TTATGTAGGTTATTATATAAGTCA
Found at i:9660306 original size:19 final size:18
Alignment explanation
Indices: 9660256--9660309 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 18
9660246 TCAATTTTTA
*
9660256 AAAATATATATAAATTTT
1 AAAATATATATAAATATT
*
9660274 AAAA-ATAT-T-TATATT
1 AAAATATATATAAATATT
9660289 AAAACTATATATAAATATT
1 AAAA-TATATATAAATATT
9660308 AA
1 AA
9660310 TAAGTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 8 0.28
18 5 0.17
19 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATATAAATATT
Found at i:9660324 original size:9 final size:9
Alignment explanation
Indices: 9660310--9660389 Score: 58
Period size: 9 Copynumber: 8.9 Consensus size: 9
9660300 TAAATATTAA
9660310 TAAGTTATG
1 TAAGTTATG
9660319 TAAGTTATG
1 TAAGTTATG
* *
9660328 TATTA-TAAATT
1 TA--AGT-TATG
*
9660339 TAAATTATG
1 TAAGTTATG
9660348 TAAGTTATG
1 TAAGTTATG
*
9660357 -GA-TTATG
1 TAAGTTATG
9660364 TAAGTTATG
1 TAAGTTATG
* *
9660373 TAAATTACG
1 TAAGTTATG
9660382 TAAGTTAT
1 TAAGTTAT
9660390 AATATTTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 40 0.74
10 2 0.04
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:9660363 original size:16 final size:16
Alignment explanation
Indices: 9660342--9660372 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9660332 ATAAATTTAA
9660342 ATTATGTAAGTTATGG
1 ATTATGTAAGTTATGG
9660358 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
9660373 TAAATTACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (16 bp):
ATTATGTAAGTTATGG
Found at i:9663234 original size:6 final size:7
Alignment explanation
Indices: 9663214--9663248 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
9663204 CTATAGAAAA
9663214 CTAAACC
1 CTAAACC
9663221 CTAAACC
1 CTAAACC
9663228 C-AAACC
1 CTAAACC
9663234 CTAAACC
1 CTAAACC
*
9663241 ATAAACC
1 CTAAACC
9663248 C
1 C
9663249 CAAATCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.46, C:0.43, G:0.00, T:0.11
Consensus pattern (7 bp):
CTAAACC
Found at i:9663234 original size:13 final size:13
Alignment explanation
Indices: 9663216--9663240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9663206 ATAGAAAACT
9663216 AAACCCTAAACCC
1 AAACCCTAAACCC
9663229 AAACCCTAAACC
1 AAACCCTAAACC
9663241 ATAAACCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (13 bp):
AAACCCTAAACCC
Found at i:9664217 original size:74 final size:73
Alignment explanation
Indices: 9663995--9664247 Score: 326
Period size: 74 Copynumber: 3.4 Consensus size: 73
9663985 CAGAGCATTA
* * * *
9663995 GCGGCGCTGTATTAAAAATGCCGCTAAATCCCCCGAAAGGTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTTATCAAAAACGCCGCTAAAT-CCCCGAAAAGTCAGAAAACGGCGTCGTTGGGCTTA
* *
9664060 TGTCTTTTT
65 GGTTTTTTT
* * * * * *
9664069 GCAGTGCTTTACCAAAAACGCCGCTAAATCCCCGAAACGTCAAAAAATGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAAGTCAGAAAACGGCGTCGTTGGGCTTAG
9664134 GTTTTTTT
66 GTTTTTTT
* * * * *
9664142 GCGGCGCTTTATTAAAAATGCCACTAAATCCCAGAAAAGATCAGAAAACGGCGTCGTTGAGCTTA
1 GCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAAG-TCAGAAAACGGCGTCGTTGGGCTTA
9664207 GGTTTTTTT
65 GGTTTTTTT
*
9664216 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCC
1 GCGGCGCTTTATCAAAAACGCCGCTAAATCCC
9664248 TGAGCATTAG
Statistics
Matches: 152, Mismatches: 26, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
73 70 0.46
74 82 0.54
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (73 bp):
GCGGCGCTTTATCAAAAACGCCGCTAAATCCCCGAAAAGTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTTT
Found at i:9664320 original size:114 final size:116
Alignment explanation
Indices: 9664155--9664362 Score: 303
Period size: 115 Copynumber: 1.8 Consensus size: 116
9664145 GCGCTTTATT
* * * *
9664155 AAAAATGCCACTAAATCCCAGAAAAGATCAGAAAACGGCGTCGTTGAGCTTAGG-TTTTTTTGCG
1 AAAAACGCCACTAAATCCCAGAAAAGATCAGAAAACAGCATCGTTGAGCTTAGGTTTTTTTTACG
*
9664219 GCGCTTTCTCAAAAACGCCGCTAAATCCCTGAGCATTAGCGGTGCTTTCTG
66 GCGCTTTCTCAAAAACGCCACTAAATCCCTGAGCATTAGCGGTGCTTTCTG
* * * * *
9664270 AAAAACGCCGCTAAATCCCCGAATA-CTCAGAAAACAGCATCGTTGGGCTTAGGTTTTTTTTACG
1 AAAAACGCCACTAAATCCCAGAAAAGATCAGAAAACAGCATCGTTGAGCTTAGGTTTTTTTTACG
*
9664334 GCGCTTTCTCAAAATCGCCACTAAATCCC
66 GCGCTTTCTCAAAAACGCCACTAAATCCC
9664363 CGAATGCTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 24 0.30
115 57 0.70
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (116 bp):
AAAAACGCCACTAAATCCCAGAAAAGATCAGAAAACAGCATCGTTGAGCTTAGGTTTTTTTTACG
GCGCTTTCTCAAAAACGCCACTAAATCCCTGAGCATTAGCGGTGCTTTCTG
Found at i:9664387 original size:74 final size:74
Alignment explanation
Indices: 9664262--9664430 Score: 218
Period size: 74 Copynumber: 2.3 Consensus size: 74
9664252 CATTAGCGGT
* *
9664262 GCTTTCTGAAAAACGCCGCTAAATCCCCGAATACTCAGAAAACAGCATCGTTGGGCTTAGGTTTT
1 GCTTTCTCAAAAACGCCACTAAATCCCCGAATACTCAGAAAACAGCATCGTTGGGCTTAGGTTTT
9664327 TTTTACGGC
66 TTTTACGGC
* * * *
9664336 GCTTTCTCAAAATCGCCACTAAATCCCCGAATGCTTAGAAAAC-GACGTCGTTGGGCTTAGG--T
1 GCTTTCTCAAAAACGCCACTAAATCCCCGAATACTCAGAAAACAG-CATCGTTGGGCTTAGGTTT
* **
9664398 TTTTTGCGAT
65 TTTTTACGGC
*
9664408 GCTTTCTCAAAAACGCCGCTAAA
1 GCTTTCTCAAAAACGCCACTAAA
9664431 GCCCTGAGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 29 0.35
73 1 0.01
74 53 0.64
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (74 bp):
GCTTTCTCAAAAACGCCACTAAATCCCCGAATACTCAGAAAACAGCATCGTTGGGCTTAGGTTTT
TTTTACGGC
Found at i:9664480 original size:187 final size:187
Alignment explanation
Indices: 9664081--9664548 Score: 638
Period size: 187 Copynumber: 2.5 Consensus size: 187
9664071 AGTGCTTTAC
* * * *
9664081 CAAAAACGCCGCTAAATCCCCGAA-ACGTCAAAAAATGGCGTCGTTGGGCTTAGGTTTTTTTGCG
1 CAAAAACGCCGCTAAATCCCCGAATAC-TCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTTCG
* * *
9664145 GCGCTTTATTAAAAATGCCACTAAATCCCAGAAAAGATCAGAAAACGGCGTCGTTGAGCTTAGGT
65 GCGCTTT-CTCAAAATGCCACTAAATCCCAGAAAAGATCAGAAAACGACGTCGTTGAGCTTAGGT
* * * * *
9664210 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCTGAGCATTAGCGGTGCTTTCT
129 TTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCCT
* *
9664269 GAAAAACGCCGCTAAATCCCCGAATACTCAGAAAACAGCATCGTTGGGCTTAGGTTTTTTTTACG
1 CAAAAACGCCGCTAAATCCCCGAATACTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTT-CG
* * * * *
9664334 GCGCTTTCTCAAAATCGCCACTAAATCCCCG-AATGCTTAGAAAACGACGTCGTTGGGCTTAGG-
65 GCGCTTTCTCAAAAT-GCCACTAAATCCCAGAAAAGATCAGAAAACGACGTCGTTGAGCTTAGGT
*
9664397 TTTTTTGCGATGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCCT
129 TTTTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCCT
* * *
9664456 CAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGGTTTTTTGT-G
1 CAAAAACGCCGCTAAATCCCCGAATACTCAGAAAACGGCATCGTTGGGCTTA-GGTTTTTTTTCG
*
9664520 GCGCTTTCTCAAAAATGCCGCTAAATCCC
65 GCGCTTTCTC-AAAATGCCACTAAATCCC
9664549 TGAGCATTAG
Statistics
Matches: 249, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
186 23 0.09
187 106 0.43
188 95 0.38
189 25 0.10
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (187 bp):
CAAAAACGCCGCTAAATCCCCGAATACTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTTCGG
CGCTTTCTCAAAATGCCACTAAATCCCAGAAAAGATCAGAAAACGACGTCGTTGAGCTTAGGTTT
TTTTGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCCT
Found at i:9664555 original size:114 final size:113
Alignment explanation
Indices: 9664332--9664769 Score: 639
Period size: 114 Copynumber: 3.9 Consensus size: 113
9664322 GTTTTTTTTA
* * * *
9664332 CGGCGCTTTCTC-AAAATCGCCACTAAATCCCCGAATGCTTAGAAAACGACGTCGTTGGGCTTAG
1 CGGCGCTTCCTCAAAAAT-GCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAG
**
9664396 GTTTTTTGCGATGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
65 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* *
9664445 CAGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAACGGCATCGTTGGGCTTAGG
1 CGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTA-G
* * *
9664510 GTTTTTTGTGGCGCTTTCTCAAAAATGCCGCTAAATCCCTGAGCATTAG
65 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
*
9664559 CGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAATC-GTGTCGTTGGGCTTAG
1 CGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAA-CGGCGTCGTTGGGCTTAG
*
9664623 GTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTAG
65 G-TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
* ** *
9664673 CGGCGCTTCCGCAAAAATGCCGCTAAATCCCTAAATGCTCAGAAAATGGCGTCGTTGGGCTTAGG
1 CGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
** *
9664738 -TTTTTGCGGCGCTTTCTGGAAAATGCCGCTAA
66 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
9664770 TGCTTATTTT
Statistics
Matches: 294, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
112 29 0.10
113 53 0.18
114 211 0.72
115 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (113 bp):
CGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAG
Found at i:9671770 original size:23 final size:23
Alignment explanation
Indices: 9671728--9671771 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
9671718 GTAAAACCAA
*
9671728 ATAATTGTCACATGTGTATTACC
1 ATAATTGTCACATGTATATTACC
9671751 ATAATTG-CACATGTAATATTA
1 ATAATTGTCACATGT-ATATTA
9671772 TTAACCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (23 bp):
ATAATTGTCACATGTATATTACC
Found at i:9675204 original size:25 final size:24
Alignment explanation
Indices: 9675171--9675219 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
9675161 TTTTAATATT
9675171 TATATTAATATCAAATAAATATAAA
1 TATATTAATATCAAATAAA-ATAAA
*
9675196 TATATTAATATTAAATAAAATAAA
1 TATATTAATATCAAATAAAATAAA
9675220 AATCTCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATTAATATCAAATAAAATAAA
Found at i:9675925 original size:269 final size:270
Alignment explanation
Indices: 9675435--9675975 Score: 1075
Period size: 269 Copynumber: 2.0 Consensus size: 270
9675425 ATTGCTTATA
9675435 ATTCTTGCATCTATCCTATATGGCTTCTGTTAAAGAATAAACAACTTAAGATAGAATTTTCATGG
1 ATTCTTGCATCTATCCTATATGGCTTCTGTTAAAGAATAAACAACTTAAGATAGAATTTTCATGG
9675500 TTGATAGGAGGGGATTTTGAACCATAAAAACATCCGCTATGATTGTTGTTGGAATCTTTTTAATT
66 TTGATAGGAGGGGATTTTGAACCATAAAAACATCCGCTATGATTGTTGTTGGAATCTTTTTAATT
9675565 TGTGTACTACACTGTTAGACAACAAAATTTATTAAATAAAATTTCGAGTTAAAACTTACATAGTA
131 TGTGTACTACACTGTTAGACAACAAAATTTATTAAATAAAATTTCGAGTTAAAACTTACATAGTA
9675630 AACTCACGCATGTAAGTCTTGTCTAAAAAAGGTCACTTCATAATCTTGTTTCGACAAGATAAGGG
196 AACTCACGCATGTAAGTCTTGTCTAAAAAAGGTCACTTCATAATCTTGTTTCGACAAGATAAGGG
9675695 ACAAATTGTT
261 ACAAATTGTT
9675705 ATTCTTGCAT-TATCCTATATGGCTTCTGTTAAAGAATAAACAACTTAAGATAGAATTTTCATGG
1 ATTCTTGCATCTATCCTATATGGCTTCTGTTAAAGAATAAACAACTTAAGATAGAATTTTCATGG
9675769 TTGATAGGAGGGGATTTTGAACCATAAAAACATCCGCTATGATTGTTGTTGGAATCTTTTTAATT
66 TTGATAGGAGGGGATTTTGAACCATAAAAACATCCGCTATGATTGTTGTTGGAATCTTTTTAATT
9675834 TGTGTACTACACTGTTAGACAACAAAATTTATTAAATAAAATTTCGAGTTAAAACTTACATAGTA
131 TGTGTACTACACTGTTAGACAACAAAATTTATTAAATAAAATTTCGAGTTAAAACTTACATAGTA
9675899 AACTCACGCATGTAAGTCTTGTCTAAAAAAGGTCACTTCATAATCTTGTTTCGACAAGATAAGGG
196 AACTCACGCATGTAAGTCTTGTCTAAAAAAGGTCACTTCATAATCTTGTTTCGACAAGATAAGGG
9675964 ACAAATTGTT
261 ACAAATTGTT
9675974 AT
1 AT
9675976 AGAATATATC
Statistics
Matches: 271, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
269 261 0.96
270 10 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (270 bp):
ATTCTTGCATCTATCCTATATGGCTTCTGTTAAAGAATAAACAACTTAAGATAGAATTTTCATGG
TTGATAGGAGGGGATTTTGAACCATAAAAACATCCGCTATGATTGTTGTTGGAATCTTTTTAATT
TGTGTACTACACTGTTAGACAACAAAATTTATTAAATAAAATTTCGAGTTAAAACTTACATAGTA
AACTCACGCATGTAAGTCTTGTCTAAAAAAGGTCACTTCATAATCTTGTTTCGACAAGATAAGGG
ACAAATTGTT
Found at i:9676451 original size:16 final size:17
Alignment explanation
Indices: 9676419--9676461 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
9676409 TTTTTATTTT
9676419 ATTTAATATTAATATAAA
1 ATTTAA-ATTAATATAAA
9676437 ATTTAAATT-ATATAAA
1 ATTTAAATTAATATAAA
*
9676453 TTTTAAATT
1 ATTTAAATT
9676462 TATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
17 3 0.12
18 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATTAATATAAA
Found at i:9677742 original size:25 final size:24
Alignment explanation
Indices: 9677709--9677757 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
9677699 TTTTAATATT
9677709 TATATTAATATCAAATAAATATAAA
1 TATATTAATATCAAATAAA-ATAAA
*
9677734 TATATTAATATTAAATAAAATAAA
1 TATATTAATATCAAATAAAATAAA
9677758 AATCTCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATTAATATCAAATAAAATAAA
Found at i:9681915 original size:2 final size:2
Alignment explanation
Indices: 9681908--9681940 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9681898 AACGCAACAT
9681908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9681941 GTTGTCACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9683214 original size:23 final size:23
Alignment explanation
Indices: 9683184--9683241 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
9683174 AAAAATAATG
*
9683184 AAATTATAATTTAATACATGATA
1 AAATTATAATTTAATACATGAAA
* **
9683207 AAATTATATTTTAATTTATGAAA
1 AAATTATAATTTAATACATGAAA
9683230 AAATATATAATT
1 AAAT-TATAATT
9683242 AAATTCCAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATTATAATTTAATACATGAAA
Found at i:9683302 original size:39 final size:39
Alignment explanation
Indices: 9683238--9683314 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
9683228 AAAAATATAT
9683238 AATTAAATTCCAGACCATGTTAAAAAAATTTCTAGATTC
1 AATTAAATTCCAGACCATGTTAAAAAAATTTCTAGATTC
9683277 AATTAAATT-CAGACCATGTTAAAAAAATTTCTAGATTC
1 AATTAAATTCCAGACCATGTTAAAAAAATTTCTAGATTC
9683315 TCATAGCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 29 0.76
39 9 0.24
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (39 bp):
AATTAAATTCCAGACCATGTTAAAAAAATTTCTAGATTC
Found at i:9684282 original size:22 final size:20
Alignment explanation
Indices: 9684257--9684302 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
9684247 TTTAATAGTT
9684257 TTTTGAATATATATTTATAAAA
1 TTTTGAA-ATATATTT-TAAAA
*
9684279 TTTTGGAAAAATATTTTAAAA
1 TTTT-GAAATATATTTTAAAA
9684300 TTT
1 TTT
9684303 GAAGATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTTGAAATATATTTTAAAA
Found at i:9685106 original size:2 final size:2
Alignment explanation
Indices: 9685099--9685129 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9685089 TTGTCTGGTT
9685099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9685130 GTTTCCAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9705125 original size:40 final size:40
Alignment explanation
Indices: 9705070--9705347 Score: 304
Period size: 40 Copynumber: 7.0 Consensus size: 40
9705060 TATTGAATGA
* *
9705070 ATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTG
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* * ***
9705110 ATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCAAA
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* ** ** *
9705150 ATTGCACAAACATGCCCCTATTTGTACTTCAATACCTCTG
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * *
9705190 ATTGCACTTATGTGCCCATGTTTGTAGTTCGGTACCCCTG
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * *
9705230 ATTACACATGTGTGTCCCTATTTGTACTTCGATACCCCTG
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* * * *
9705270 ATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCGG
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
* **
9705310 ATTGCACATATGTGCCCCTGTTTGTACTTTAGTACCCC
1 ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
9705348 CTGAACACAT
Statistics
Matches: 193, Mismatches: 45, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 193 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (40 bp):
ATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTG
Found at i:9705286 original size:120 final size:120
Alignment explanation
Indices: 9705070--9705347 Score: 340
Period size: 120 Copynumber: 2.3 Consensus size: 120
9705060 TATTGAATGA
* * *
9705070 ATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGATTGCACATACGTGCCCCTATTTGT
1 ATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACATACGTGCCCCTATTTGT
* * * *
9705135 ACTTTGGTACCCAAAATTGCACAAACATGCCCCTATTTGTACTTCAATACCTCTG
66 ACTTCGATACCCAAAATTGCACAAACATGCCCCTATTTGTACTTCAATACCCCGG
* * * ** *
9705190 ATTGCACTTATGTGCCCATGTTTGTAGTTCGGTACCCCTGATTACACATGTGTGTCCCTATTTGT
1 ATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACATACGTGCCCCTATTTGT
*** * * * * **
9705255 ACTTCGATACCCCTGATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCGG
66 ACTTCGATACCCAAAATTGCACAAACATGCCCCTATTTGTACTTCAATACCCCGG
**
9705310 ATTGCACATATGTGCCCCTGTTTGTACTTTAGTACCCC
1 ATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
9705348 CTGAACACAT
Statistics
Matches: 131, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 131 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (120 bp):
ATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCCCTGATTACACATACGTGCCCCTATTTGT
ACTTCGATACCCAAAATTGCACAAACATGCCCCTATTTGTACTTCAATACCCCGG
Found at i:9717563 original size:33 final size:33
Alignment explanation
Indices: 9717493--9717659 Score: 178
Period size: 33 Copynumber: 5.1 Consensus size: 33
9717483 GTAGAAGTCA
*
9717493 CACCCTCCCTATCAGCTTCTA-CCCTTCAACAT
1 CACCCTCCCAATCAGCTTCTACCCCTTCAACAT
* * *
9717525 CACCCTACCCAAT-AGCTTGTACCCTTTCTACAT
1 CACCCT-CCCAATCAGCTTCTACCCCTTCAACAT
* * *
9717558 CACCCTCCCCATCAGCTTCTCCCCCTTCAGCAT
1 CACCCTCCCAATCAGCTTCTACCCCTTCAACAT
* * * *
9717591 CACCCTCCCCATCAACTTGTACCCCTTCAACTT
1 CACCCTCCCAATCAGCTTCTACCCCTTCAACAT
* *
9717624 CACCCTTCCC-ATCAGCTTCTACTCCTTCAAAAT
1 CACCC-TCCCAATCAGCTTCTACCCCTTCAACAT
9717657 CAC
1 CAC
9717660 TTTCTCCAGC
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
32 18 0.16
33 89 0.80
34 4 0.04
ACGTcount: A:0.22, C:0.47, G:0.04, T:0.28
Consensus pattern (33 bp):
CACCCTCCCAATCAGCTTCTACCCCTTCAACAT
Found at i:9717610 original size:66 final size:65
Alignment explanation
Indices: 9717493--9717659 Score: 201
Period size: 66 Copynumber: 2.5 Consensus size: 65
9717483 GTAGAAGTCA
* * * * *
9717493 CACCCTCCCTATCAGCTTCTACCCTTCAACATCACCCTACCCAATAGCTTGTACCCTTTCTACAT
1 CACCCTCCCCATCAGCTTCTCCCCTTCAACATCACCCTACCCAATAACTTGTACCCCTTCAACAT
* *
9717558 CACCCTCCCCATCAGCTTCTCCCCCTTCAGCATCACCCT-CCCCATCAACTTGTACCCCTTCAAC
1 CACCCTCCCCATCAGCTTCT-CCCCTTCAACATCACCCTACCCAAT-AACTTGTACCCCTTCAAC
*
9717622 TT
64 AT
* * *
9717624 CACCCTTCCCATCAGCTTCTACTCCTTCAAAATCAC
1 CACCCTCCCCATCAGCTTCT-CCCCTTCAACATCAC
9717660 TTTCTCCAGC
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
65 24 0.28
66 63 0.72
ACGTcount: A:0.22, C:0.47, G:0.04, T:0.28
Consensus pattern (65 bp):
CACCCTCCCCATCAGCTTCTCCCCTTCAACATCACCCTACCCAATAACTTGTACCCCTTCAACAT
Found at i:9717720 original size:42 final size:42
Alignment explanation
Indices: 9717648--9717729 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
9717638 GCTTCTACTC
* * * *
9717648 CTTCAAAATCACTTTCTCCAGCACTTAATAGTAACATATCAT
1 CTTCAAAATCACTCTCCCCAACACTCAATAGTAACATATCAT
9717690 CTTCAAAATCACTCTCCCCAACAAC-CAATAGTAACATATC
1 CTTCAAAATCACTCTCCCCAAC-ACTCAATAGTAACATATC
9717730 TCCCTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (42 bp):
CTTCAAAATCACTCTCCCCAACACTCAATAGTAACATATCAT
Found at i:9734857 original size:6 final size:6
Alignment explanation
Indices: 9734846--9734876 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
9734836 AAACAAACAT
9734846 ATCAGA ATCAGA ATCAGA ATCATGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCA-GA ATCAGA
9734877 GATTGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:9740879 original size:21 final size:19
Alignment explanation
Indices: 9740843--9740881 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
9740833 AGTAAGATTA
9740843 AATTTCAAATAAAAAAAGT
1 AATTTCAAATAAAAAAAGT
*
9740862 AATTTACATAATATAAAAAG
1 AATTT-CA-AATAAAAAAAG
9740882 GGTTATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AATTTCAAATAAAAAAAGT
Found at i:9745028 original size:21 final size:21
Alignment explanation
Indices: 9744989--9745030 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9744979 TTTTCCTAGG
*
9744989 ATGTGAATTGGATGGAATTGA
1 ATGTGAATTGGATGAAATTGA
* *
9745010 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATGAAATTGA
9745031 GTTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
ATGTGAATTGGATGAAATTGA
Found at i:9747856 original size:39 final size:39
Alignment explanation
Indices: 9747813--9747891 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
9747803 TAACTGGCCC
9747813 TGATAAAATCATTTGGGTACATACAACAAATGGAAGATT
1 TGATAAAATCATTTGGGTACATACAACAAATGGAAGATT
9747852 TGATAAAATCATTTGGGTACATACAACAAATGGAAGATT
1 TGATAAAATCATTTGGGTACATACAACAAATGGAAGATT
9747891 T
1 T
9747892 TTAGTTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (39 bp):
TGATAAAATCATTTGGGTACATACAACAAATGGAAGATT
Found at i:9765695 original size:9 final size:9
Alignment explanation
Indices: 9765681--9765864 Score: 87
Period size: 9 Copynumber: 20.1 Consensus size: 9
9765671 AAGTTGTGTA
9765681 TTATGTAAG
1 TTATGTAAG
9765690 TTATGTAAG
1 TTATGTAAG
*
9765699 TTATGT-AT
1 TTATGTAAG
*
9765707 TTAAGTGTATG
1 TT-A-TGTAAG
*
9765718 TTATGTAAC
1 TTATGTAAG
*
9765727 TTGTGT-A-
1 TTATGTAAG
* *
9765734 TAATGTTAG
1 TTATGTAAG
**
9765743 TTATCAAAG
1 TTATGTAAG
9765752 TTATGT-A-
1 TTATGTAAG
*
9765759 CTATGTAAG
1 TTATGTAAG
*
9765768 TTATTTAAG
1 TTATGTAAG
9765777 TTATGTAAG
1 TTATGTAAG
*
9765786 TTGTGT-A-
1 TTATGTAAG
9765793 TTATGTAAG
1 TTATGTAAG
*
9765802 TTATTCTGTTA-
1 TTA---TGTAAG
9765813 TTATGTAAG
1 TTATGTAAG
*
9765822 TTATGCAAG
1 TTATGTAAG
*
9765831 TTTATATATAAG
1 --T-TATGTAAG
9765843 TTTATAGATAAG
1 -TTAT-G-TAAG
9765855 TTATGTAAG
1 TTATGTAAG
9765864 T
1 T
9765865 ATATCACTTT
Statistics
Matches: 131, Mismatches: 26, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
7 14 0.11
8 13 0.10
9 70 0.53
10 8 0.06
11 12 0.09
12 14 0.11
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:9765705 original size:25 final size:25
Alignment explanation
Indices: 9765670--9765832 Score: 123
Period size: 25 Copynumber: 6.2 Consensus size: 25
9765660 NNNNNNNNNT
*
9765670 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
9765695 TAAGTTATGTATTTAAGTGTATGTTATG
1 TAAGTTATGTA-TT-A-TGTAAGTTATG
* * * * *
9765723 TAACTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATTATGTAAGTTATG
* * *
9765748 AAAGTTATGTACTATGTAAGTTATT
1 TAAGTTATGTATTATGTAAGTTATG
*
9765773 TAAGTTATGTAAGTTGTGT-A-TTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
9765798 TAAGTTATTCTGTTATTATGTAAGTTATG
1 TAAGTTA---TG-TATTATGTAAGTTATG
*
9765827 CAAGTT
1 TAAGTT
9765833 TATATATAAG
Statistics
Matches: 106, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
25 56 0.53
26 5 0.05
27 11 0.10
28 23 0.22
29 11 0.10
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:9765779 original size:34 final size:34
Alignment explanation
Indices: 9765741--9765806 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
9765731 GTATAATGTT
9765741 AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
1 AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
** * *
9765775 AGTTATGTAAGTTGTGTATTATGTAAGTTATT
1 AGTTATCAAAGTTATGTACTATGTAAGTTATT
9765807 CTGTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (34 bp):
AGTTATCAAAGTTATGTACTATGTAAGTTATTTA
Found at i:9766681 original size:47 final size:47
Alignment explanation
Indices: 9766612--9766782 Score: 214
Period size: 47 Copynumber: 3.8 Consensus size: 47
9766602 GGATAAGTAC
*
9766612 AGTAATGTAAGTAATGTAATATATGCTTAAAAATATATATTTCGGTA
1 AGTAATGTAAGTAATGTAATATATGCTTAAGAATATATATTTCGGTA
* *
9766659 AGTAAAGTAAGTAATGTAATATATACTTAAGAATATATA-TT---TA
1 AGTAATGTAAGTAATGTAATATATGCTTAAGAATATATATTTCGGTA
* * *
9766702 AGTAATGTAAGTAAAGTAA-ACTGA-G-TTATGTA-ATATATTTCGGTA
1 AGTAATGTAAGTAATGTAATA-T-ATGCTTAAGAATATATATTTCGGTA
9766747 AGTAATGTAAGTAATGTAATATATGCTTAAGAATAT
1 AGTAATGTAAGTAATGTAATATATGCTTAAGAATAT
9766783 TGCGTTTTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
41 5 0.05
42 8 0.08
43 20 0.19
44 2 0.02
45 22 0.21
46 8 0.08
47 38 0.37
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.37
Consensus pattern (47 bp):
AGTAATGTAAGTAATGTAATATATGCTTAAGAATATATATTTCGGTA
Found at i:9767479 original size:16 final size:16
Alignment explanation
Indices: 9767435--9767483 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 16
9767425 GATTTTAGTA
9767435 AAGTATATATTCCAGC
1 AAGTATATATTCCAGC
*
9767451 AACTGGAATATATTCCAGC
1 AA---GTATATATTCCAGC
9767470 AAGTATATATTCCA
1 AAGTATATATTCCA
9767484 AAGTTATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 13 0.46
19 15 0.54
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (16 bp):
AAGTATATATTCCAGC
Found at i:9769412 original size:21 final size:21
Alignment explanation
Indices: 9769370--9769452 Score: 70
Period size: 21 Copynumber: 4.2 Consensus size: 21
9769360 CCTTAACCTT
** *
9769370 TAAAGCATAACCTTTAACCCC
1 TAAAGCATAACCCCTAAACCC
9769391 TAAAGCATAACCCCTAAACCC
1 TAAAGCATAACCCCTAAACCC
* *
9769412 T-AA--AT--CCCCTTAGCCC
1 TAAAGCATAACCCCTAAACCC
9769428 ATAAAGCATAACCCCT-AACCC
1 -TAAAGCATAACCCCTAAACCC
9769449 TAAA
1 TAAA
9769453 CCACAAAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 9 0.18
17 1 0.02
18 4 0.08
20 8 0.16
21 23 0.46
22 5 0.10
ACGTcount: A:0.40, C:0.36, G:0.05, T:0.19
Consensus pattern (21 bp):
TAAAGCATAACCCCTAAACCC
Found at i:9769447 original size:59 final size:59
Alignment explanation
Indices: 9769338--9769452 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
9769328 CCCAAATCCC
* ** **
9769338 TAACCCATAACCCCTAAATCCCCCTTAACCTTTAAAGCATAACCTTTAACCCCTAAAGCA
1 TAACCCATAAACCCTAAATCCCCCTTAACCCATAAAGCATAACCCCTAA-CCCTAAAGCA
* *
9769398 TAACCCCTAAACCCTAAAT-CCCCTTAGCCCATAAAGCATAACCCCTAACCCTAAA
1 TAACCCATAAACCCTAAATCCCCCTTAACCCATAAAGCATAACCCCTAACCCTAAA
9769453 CCACAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 7 0.15
59 24 0.50
60 17 0.35
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.21
Consensus pattern (59 bp):
TAACCCATAAACCCTAAATCCCCCTTAACCCATAAAGCATAACCCCTAACCCTAAAGCA
Found at i:9770552 original size:7 final size:7
Alignment explanation
Indices: 9770540--9770638 Score: 60
Period size: 7 Copynumber: 13.7 Consensus size: 7
9770530 CTAATCGTTG
9770540 AAACCCT
1 AAACCCT
9770547 AAACCCT
1 AAACCCT
9770554 AAATCCCT
1 AAA-CCCT
* *
9770562 TAACACAT
1 AAAC-CCT
*
9770570 AACCCCT
1 AAACCCT
9770577 AAATCTCCT
1 AAA-C-CCT
*
9770586 AACCCCT
1 AAACCCT
* *
9770593 AAAGCAT
1 AAACCCT
9770600 -AACACCT
1 AAAC-CCT
9770607 -AACCCT
1 AAACCCT
*
9770613 AAACCTT
1 AAACCCT
9770620 AAATCCC-
1 AAA-CCCT
9770627 AAACCCT
1 AAACCCT
9770634 AAACC
1 AAACC
9770639 ATACACCGAC
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
6 8 0.11
7 43 0.61
8 14 0.20
9 5 0.07
ACGTcount: A:0.41, C:0.39, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:9771071 original size:114 final size:112
Alignment explanation
Indices: 9770851--9771423 Score: 505
Period size: 114 Copynumber: 5.0 Consensus size: 112
9770841 AAATTATTTT
* * * *
9770851 TAAATCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAA
1 TAAATCCCTGAGCATTAGCGGCGC-TT-CTAAAAACGCCACTAAATCCCCGGAAAGCTCAAAAAA
* * *
9770916 CGGTGCCGTTGGGCTTA-GTTTTTCTTGCGGCGCTACCCCAAAAACGCCGC
64 CGGCGTCGTTGGGCTTAGGTTTTT-TTGCGGCGCT-TCCCAAAAACGCCGC
* * * *
9770966 TAAATCCCTGAGCAGTAGCGGTGCTTCTAGAGAAACGCCACTAGAT-CCCGGAAATCTCAAAAAA
1 TAAATCCCTGAGCATTAGCGGCGCTTCTA-A-AAACGCCACTAAATCCCCGGAAAGCTCAAAAAA
* *
9771030 CGGCATCGTTGGGCTTAGGTTATTTTGCGGCGCTTCGCCAAAAACGCCGC
64 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTC-CCAAAAACGCCGC
* * * * *
9771080 TAAAGCCATGAGCATTAGCGGTGCTCCCTTAAAAACG-CAGCTAAATCCCCGAAAAGCTCAAAAA
1 TAAATCCCTGAGCATTAGCGGCGCT-TC-TAAAAACGCCA-CTAAATCCCCGGAAAGCTCAAAAA
* ** *
9771144 A-GGTGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCTTAAAAAAAGCCGC
63 ACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTC-CCAAAAACGCCGC
* * * * * * *
9771194 TAAAGCCTTGAGCATTAGCGGCACTT-TAATAAATACGCCGCTAAA-CCCCTGAATGCTCAGAAA
1 TAAATCCCTGAGCATTAGCGGCGCTTCT-A-AAA-ACGCCACTAAATCCCCGGAAAGCTCAAAAA
* * * * *
9771257 ATGGCGTCGTTGGGCTGAGGTTTTTTTGCGGCGCTTTCTCAAAAATGCCAC
63 ACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC-TTCCCAAAAACGCCGC
* * * * * ***
9771308 TAAATCCCTGAGCATTAGCGGCGCTTTATGAAAAACACCGCTAAATCCCC-TAAAGTTCGGTAAA
1 TAAATCCCTGAGCATTAGCGGCGC-TTCT-AAAAACGCCACTAAATCCCCGGAAAGCTCAAAAAA
* * ***
9771372 TGGCGTTGTTGGGCTTAGG-TTTTTTGCGGCGCTTTCTGGAAAACGCCGC
64 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGC-TTCCCAAAAACGCCGC
9771421 TAA
1 TAA
9771424 TTCTTATTTT
Statistics
Matches: 384, Mismatches: 57, Indels: 36
0.81 0.12 0.08
Matches are distributed among these distances:
111 1 0.00
112 1 0.00
113 53 0.14
114 255 0.66
115 70 0.18
116 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (112 bp):
TAAATCCCTGAGCATTAGCGGCGCTTCTAAAAACGCCACTAAATCCCCGGAAAGCTCAAAAAACG
GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTCCCAAAAACGCCGC
Found at i:9771269 original size:228 final size:227
Alignment explanation
Indices: 9770859--9771405 Score: 577
Period size: 228 Copynumber: 2.4 Consensus size: 227
9770849 TTTAAATCCC
* * *
9770859 TGAGCATTAGCGGCGCTTTCC-TAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAACGGTGCC
1 TGAGCATTAGCGGCGC-TTCCTTAAAAACGCCGCTAAAT-CCCCGAAAGCTCA-AAAAAGGTGTC
* * * *
9770923 GTTGGGCTTA-GTTTTTCTTGCGGCGCTACCCCAAAAACGCCGCTAAATCCCTGAGCAGTAGCGG
63 GTTGGGCTTAGGTTTTT-TTGCGGCGCTTCCCAAAAAAAGCCGCTAAAGCCCTGAGCAGTAGCGG
** * * * *
9770987 TGCTTCTAGAGAAACGCCACTAGATCCCGGAAATCTCAAAAAACGGCATCGTTGGGCTTAGGTTA
127 CACTTCTAGAAAAACGCCACTAAACCCCGGAAATCTCAAAAAACGGCATCGTTGGGCTGAGGTTA
*
9771052 TTTTGCGGCGC-TTCGCCAAAAACGCCGCTAAAGCCA
192 TTTTGCGGCGCTTTC-CCAAAAACGCCACTAAAGCCA
* * *
9771088 TGAGCATTAGCGGTGCTCCCTTAAAAACGCAGCTAAATCCCCGAAAAGCTCAAAAAAGGTGTCGT
1 TGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCG-AAAGCTCAAAAAAGGTGTCGT
** * *
9771153 TGGGCTTAGGTTTTTTTGCGGCGCTTCTTAAAAAAAGCCGCTAAAGCCTTGAGCATTAGCGGCAC
65 TGGGCTTAGGTTTTTTTGCGGCGCTTCCCAAAAAAAGCCGCTAAAGCCCTGAGCAGTAGCGGCAC
* * * * * *
9771218 TT-TA-ATAAATACGCCGCTAAACCCCTG-AATGCTCAGAAAATGGCGTCGTTGGGCTGAGGTTT
130 TTCTAGA-AAA-ACGCCACTAAACCCCGGAAAT-CTCAAAAAACGGCATCGTTGGGCTGAGGTTA
* * * *
9771280 TTTTGCGGCGCTTTCTCAAAAATGCCACTAAATCCC
192 TTTTGCGGCGCTTTCCCAAAAACGCCACTAAAGCCA
** * * * * ** * * *
9771316 TGAGCATTAGCGGCGCTTTATGAAAAACACCGCTAAATCCCCTAAAGTTCGGTAAATGGCGTTGT
1 TGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTC-AAAAAAGGTGTCGT
9771381 TGGGCTTAGG-TTTTTTGCGGCGCTT
65 TGGGCTTAGGTTTTTTTGCGGCGCTT
9771406 TCTGGAAAAC
Statistics
Matches: 265, Mismatches: 45, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
226 1 0.00
227 28 0.11
228 189 0.71
229 47 0.18
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.25
Consensus pattern (227 bp):
TGAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAAAAAAGGTGTCGTT
GGGCTTAGGTTTTTTTGCGGCGCTTCCCAAAAAAAGCCGCTAAAGCCCTGAGCAGTAGCGGCACT
TCTAGAAAAACGCCACTAAACCCCGGAAATCTCAAAAAACGGCATCGTTGGGCTGAGGTTATTTT
GCGGCGCTTTCCCAAAAACGCCACTAAAGCCA
Found at i:9772608 original size:44 final size:44
Alignment explanation
Indices: 9772560--9772654 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 44
9772550 TGAACTACTG
* * *
9772560 ATCAGTAGGCATCAAAGCGCTGAGTAGTAGGCACCAAAGTGTGA
1 ATCAGTAGGCATCAAAGCGCTGAATAATAGGCACCAAAGTGAGA
* * * * *
9772604 ATCAGTAGGCATCGAAGTGTTGAATAATAGGCATCGAAGTGAGA
1 ATCAGTAGGCATCAAAGCGCTGAATAATAGGCACCAAAGTGAGA
9772648 ATCAGTA
1 ATCAGTA
9772655 AGAACCGAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (44 bp):
ATCAGTAGGCATCAAAGCGCTGAATAATAGGCACCAAAGTGAGA
Found at i:9772621 original size:22 final size:23
Alignment explanation
Indices: 9772560--9772654 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 23
9772550 TGAACTACTG
*
9772560 ATCAGTAGGCATCAAAGCGCTGA
1 ATCAGTAGGCATCAAAGTGCTGA
* *
9772583 GT-AGTAGGCACCAAAGTG-TGA
1 ATCAGTAGGCATCAAAGTGCTGA
* *
9772604 ATCAGTAGGCATCGAAGTGTTGA
1 ATCAGTAGGCATCAAAGTGCTGA
* * *
9772627 AT-AATAGGCATCGAAGTG-AGA
1 ATCAGTAGGCATCAAAGTGCTGA
9772648 ATCAGTA
1 ATCAGTA
9772655 AGAACCGAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.13
22 46 0.77
23 6 0.10
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (23 bp):
ATCAGTAGGCATCAAAGTGCTGA
Found at i:9790430 original size:43 final size:43
Alignment explanation
Indices: 9790161--9790427 Score: 203
Period size: 43 Copynumber: 6.2 Consensus size: 43
9790151 GGCATCGCAA
* ** * * * * * *
9790161 TGCATCATCGGATAAATTGAAGGAAATATAATGGCACACATAA
1 TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
* * * * * *
9790204 TGCATCATCGGATAAACTGAAGGAAATATATTGGCACACACAG
1 TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
* * * ** *
9790247 TGCATCATCGGTCATG-TCGAAGTAATTATACTGACATACACAG
1 TGCATCATCGGACAAGCT-GAAGCAATTATACTGGTACACACAG
* * *
9790290 TGCATCATCGGACAAGCTGAAGCAATTATATTAGAACACACAG
1 TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
* * ** * * *
9790333 TTCATCATTGGACAAGCCAAAGCAATTATAATGGTACATACAT
1 TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
** * *
9790376 TGCATCATCAAACAAGCTGAAGTAATTATACCGGTACACACAG
1 TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
9790419 TGCATCATC
1 TGCATCATC
9790428 AAAAAACCGA
Statistics
Matches: 181, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
42 1 0.01
43 179 0.99
44 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (43 bp):
TGCATCATCGGACAAGCTGAAGCAATTATACTGGTACACACAG
Found at i:9793188 original size:35 final size:35
Alignment explanation
Indices: 9793139--9793205 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
9793129 CATACCAATG
9793139 CTCATAAAAGCTAGTCCAACCGAAACACACCATTA
1 CTCATAAAAGCTAGTCCAACCGAAACACACCATTA
**
9793174 CTCA-AAAGAGCTAGTCCCTCCGAAACACACCA
1 CTCATAAA-AGCTAGTCCAACCGAAACACACCA
9793206 AACAGACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.15
Consensus pattern (35 bp):
CTCATAAAAGCTAGTCCAACCGAAACACACCATTA
Found at i:9805453 original size:35 final size:35
Alignment explanation
Indices: 9805414--9805480 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
9805404 TTTTTAAAAA
* *
9805414 TTATTTGATAATTCATAATAAAAATTAAATGAAAT
1 TTATTTGATAATCCATAATAAAAAGTAAATGAAAT
*
9805449 TTATTTGATAATCCATAATAAGAAGTAAATGA
1 TTATTTGATAATCCATAATAAAAAGTAAATGA
9805481 TAGAAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (35 bp):
TTATTTGATAATCCATAATAAAAAGTAAATGAAAT
Found at i:9810352 original size:23 final size:23
Alignment explanation
Indices: 9810305--9810383 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
9810295 GCACGAGCAT
* * *
9810305 GGTTCACATATAACAACATGAAG
1 GGTTCGCATGTAACAACATGTAG
** *
9810328 GGTTCGCATGTTTCAATATGTAG
1 GGTTCGCATGTAACAACATGTAG
* * *
9810351 GGTTTGCATATAACAACATTTAG
1 GGTTCGCATGTAACAACATGTAG
9810374 GGTTCGCATG
1 GGTTCGCATG
9810384 CAATATAGGG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (23 bp):
GGTTCGCATGTAACAACATGTAG
Found at i:9810364 original size:46 final size:41
Alignment explanation
Indices: 9810311--9810422 Score: 129
Period size: 46 Copynumber: 2.6 Consensus size: 41
9810301 GCATGGTTCA
* *
9810311 CATATAACAACATGAAGGGTTCGCATGTTTCAATATGTAGGGTTTG
1 CATATAACAACATTAAGGGTTCGCATG---CAATA--TAGGGTATG
*
9810357 CATATAACAACATTTAGGGTTCGCATGCAATATAGGGTATG
1 CATATAACAACATTAAGGGTTCGCATGCAATATAGGGTATG
9810398 CATA-ATAC-ACATTAAGGGTTCGCAT
1 CATATA-ACAACATTAAGGGTTCGCAT
9810423 ATTAATCACC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
40 17 0.28
41 14 0.23
43 5 0.08
46 25 0.41
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (41 bp):
CATATAACAACATTAAGGGTTCGCATGCAATATAGGGTATG
Found at i:9810633 original size:22 final size:22
Alignment explanation
Indices: 9810608--9810653 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
9810598 AACATAAAGA
* *
9810608 CTCGCATGTAATTACACATAGG
1 CTCGCATGTAATAACACACAGG
9810630 CTCGCATGTAATAACACACAGG
1 CTCGCATGTAATAACACACAGG
9810652 CT
1 CT
9810654 TTTATGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (22 bp):
CTCGCATGTAATAACACACAGG
Found at i:9812584 original size:30 final size:30
Alignment explanation
Indices: 9812549--9812636 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 30
9812539 AACCTCGATA
9812549 TAATGTCAGCTTGTGTGAGCAACTCTATTG
1 TAATGTCAGCTTGTGTGAGCAACTCTATTG
* * * *
9812579 TAATGTTAGTTTGTGTGAGCAACCCTAATG
1 TAATGTCAGCTTGTGTGAGCAACTCTATTG
* *
9812609 TACTGTCAGCTTATGTGAGCAACT-TATT
1 TAATGTCAGCTTGTGTGAGCAACTCTATT
9812637 CCCGGGTATC
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 3 0.06
30 45 0.94
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (30 bp):
TAATGTCAGCTTGTGTGAGCAACTCTATTG
Found at i:9825834 original size:22 final size:22
Alignment explanation
Indices: 9825809--9825854 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
9825799 ATCATCAACA
9825809 TTACACTTAGTCCACTGACCAG
1 TTACACTTAGTCCACTGACCAG
9825831 TTACACTTAGTCCACTGACCAG
1 TTACACTTAGTCCACTGACCAG
9825853 TT
1 TT
9825855 GGTCTCTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (22 bp):
TTACACTTAGTCCACTGACCAG
Found at i:9826218 original size:32 final size:32
Alignment explanation
Indices: 9826149--9826225 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
9826139 ATGCATGTGT
* *
9826149 GTAACTTTTCATCTTCAAGTCTCTTCGCATTA
1 GTAACTTTTCATATTCAAGTCTCTTCACATTA
* * *
9826181 TTAACTCTTCATATTCAAGTCTCCTT-ACATTC
1 GTAACTTTTCATATTCAAGTCT-CTTCACATTA
9826213 GTAACTTTTCATA
1 GTAACTTTTCATA
9826226 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGTCTCTTCACATTA
Found at i:9852033 original size:27 final size:26
Alignment explanation
Indices: 9851988--9852073 Score: 102
Period size: 27 Copynumber: 3.3 Consensus size: 26
9851978 CTTTGAACCC
9851988 TGAACCCAAACCC-AAACTCTAAACT
1 TGAACCCAAACCCTAAACTCTAAACT
* * *
9852013 TGAACCTCGAACCCTAAACTCAAAATT
1 TGAACC-CAAACCCTAAACTCTAAACT
* *
9852040 TAAACCCAAAACCCTAAACTCTAACCT
1 TGAACCC-AAACCCTAAACTCTAAACT
9852067 TGAACCC
1 TGAACCC
9852074 TAATCCAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 6 0.12
26 7 0.14
27 36 0.73
ACGTcount: A:0.42, C:0.35, G:0.05, T:0.19
Consensus pattern (26 bp):
TGAACCCAAACCCTAAACTCTAAACT
Found at i:9865186 original size:25 final size:25
Alignment explanation
Indices: 9865135--9865221 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
9865125 GCACATGTAT
* * *
9865135 GCTCATACGAGCGATA-AACGGTAA
1 GCTCATACGAGCTAAATAATGGTAA
* *
9865159 GCTCCTCCGAGCTAAATAATGGTAA
1 GCTCATACGAGCTAAATAATGGTAA
9865184 GCTCATACGAGCTAAATAATGGTAA
1 GCTCATACGAGCTAAATAATGGTAA
9865209 GCTCATACGAGCT
1 GCTCATACGAGCT
9865222 GAGTATCAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 12 0.22
25 43 0.78
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTAAATAATGGTAA
Found at i:9865233 original size:25 final size:25
Alignment explanation
Indices: 9865155--9865240 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
9865145 GCGATAAACG
* * *
9865155 GTAAGCTCCTCCGAGCTAAATAATG
1 GTAAGCTCATACGAGCTAAATAATA
*
9865180 GTAAGCTCATACGAGCTAAATAATG
1 GTAAGCTCATACGAGCTAAATAATA
* *
9865205 GTAAGCTCATACGAGCTGAGT-ATCA
1 GTAAGCTCATACGAGCTAAATAAT-A
9865230 GTAAGCTCATA
1 GTAAGCTCATA
9865241 AAAGCTAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 2 0.04
25 53 0.96
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTAAATAATA
Found at i:9868337 original size:27 final size:27
Alignment explanation
Indices: 9868307--9868417 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
9868297 GATAAACCCT
* *
9868307 AAAAGAATGCCTTTGTGGCGTAATATG
1 AAAAGAACGCCTTTGTGGCGCAATATG
* *
9868334 AAAAGAACGTCTTTGTCGCGCAATATG
1 AAAAGAACGCCTTTGTGGCGCAATATG
* * *
9868361 AAAGGAAAGCCTCTGTGGCGCAATATG
1 AAAAGAACGCCTTTGTGGCGCAATATG
* * *
9868388 AAAGGAACACCTTTTTGGCGCAATATG
1 AAAAGAACGCCTTTGTGGCGCAATATG
9868415 AAA
1 AAA
9868418 TATAATAAGT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (27 bp):
AAAAGAACGCCTTTGTGGCGCAATATG
Found at i:9873971 original size:54 final size:54
Alignment explanation
Indices: 9873877--9874041 Score: 206
Period size: 54 Copynumber: 3.1 Consensus size: 54
9873867 AGCGAGCCCT
* * *
9873877 AAAAGAAAACCTTTGTGGCTCAATATAAAAGGAACACCTTTGTGGT-GTAATATG
1 AAAAGAACACCTTTGTGGCACAATATAAAAGGAACACCTTTGT-GTCGCAATATG
* * * * *
9873931 AAAAGAACACTTTTGTGGCGCAATATGAAATGAACGCCTTTGTGTCGCAATATG
1 AAAAGAACACCTTTGTGGCACAATATAAAAGGAACACCTTTGTGTCGCAATATG
* * * *
9873985 AAAAGAACCCCTTTGTGGCACAATATAAAAGGAACACCTTTATGGCACAATATG
1 AAAAGAACACCTTTGTGGCACAATATAAAAGGAACACCTTTGTGTCGCAATATG
9874039 AAA
1 AAA
9874042 GGGTATCTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 2 0.02
54 92 0.98
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (54 bp):
AAAAGAACACCTTTGTGGCACAATATAAAAGGAACACCTTTGTGTCGCAATATG
Found at i:9874043 original size:27 final size:27
Alignment explanation
Indices: 9873885--9874043 Score: 183
Period size: 27 Copynumber: 5.9 Consensus size: 27
9873875 CTAAAAGAAA
* *
9873885 ACCTTTGTGGCTCAATATAAAAGGAAC
1 ACCTTTGTGGCGCAATATGAAAGGAAC
* * *
9873912 ACCTTTGTGGTGTAATATGAAAAGAAC
1 ACCTTTGTGGCGCAATATGAAAGGAAC
* *
9873939 ACTTTTGTGGCGCAATATGAAATGAAC
1 ACCTTTGTGGCGCAATATGAAAGGAAC
* * *
9873966 GCCTTTGTGTCGCAATATGAAAAGAAC
1 ACCTTTGTGGCGCAATATGAAAGGAAC
* * *
9873993 CCCTTTGTGGCACAATATAAAAGGAAC
1 ACCTTTGTGGCGCAATATGAAAGGAAC
* *
9874020 ACCTTTATGGCACAATATGAAAGG
1 ACCTTTGTGGCGCAATATGAAAGG
9874044 GTATCTTTTA
Statistics
Matches: 111, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
ACCTTTGTGGCGCAATATGAAAGGAAC
Found at i:9878625 original size:15 final size:15
Alignment explanation
Indices: 9878605--9878634 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9878595 CACAATTATG
*
9878605 TAAATATTATTAAAA
1 TAAATAATATTAAAA
9878620 TAAATAATATTAAAA
1 TAAATAATATTAAAA
9878635 CTATCAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATAATATTAAAA
Found at i:9880409 original size:50 final size:47
Alignment explanation
Indices: 9880355--9880461 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 47
9880345 ATTAATATAC
9880355 TATTATATTAATTAATATTAATTTTATTATTATATGA-TAATAATAAAAAA
1 TATTATATTAATTAATATTAA-TTTA-TA--ATATGATTAATAATAAAAAA
* *
9880405 TA-T-TATT--TTAATATTAATTTATAATATTATTAATAATAAAATA
1 TATTATATTAATTAATATTAATTTATAATATGATTAATAATAAAAAA
9880448 TATTATTATTAATT
1 TATTA-TATTAATT
9880462 TAAAAAATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
42 5 0.10
43 14 0.29
44 3 0.06
45 4 0.08
46 14 0.29
48 6 0.12
49 1 0.02
50 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (47 bp):
TATTATATTAATTAATATTAATTTATAATATGATTAATAATAAAAAA
Found at i:9880419 original size:11 final size:12
Alignment explanation
Indices: 9880403--9880442 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
9880393 AATAATAAAA
9880403 AATATTATTT-T
1 AATATTATTTAT
9880414 AATATTAATTTAT
1 AATATT-ATTTAT
*
9880427 AATATTATTAAT
1 AATATTATTTAT
9880439 AATA
1 AATA
9880443 AAATATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 13 0.50
13 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATATTATTTAT
Found at i:9880467 original size:22 final size:22
Alignment explanation
Indices: 9880398--9880467 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
9880388 ATGATAATAA
9880398 TAAAAA-ATATTATT-TTAATAT
1 TAAAAATATATTATTATTAAT-T
** *
9880419 T-AATTTATAATATTATTAA-T
1 TAAAAATATATTATTATTAATT
*
9880439 AATAAAATATATTATTATTAATT
1 TA-AAAATATATTATTATTAATT
9880462 TAAAAA
1 TAAAAA
9880468 ATTCAAAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.08
21 8 0.22
22 23 0.64
23 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAAATATATTATTATTAATT
Found at i:9881241 original size:13 final size:14
Alignment explanation
Indices: 9881210--9881243 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9881200 TATCACAAAT
* *
9881210 AAAAATTCAAGTCC
1 AAAAATCCAAATCC
9881224 AAAAATCCAAATCC
1 AAAAATCCAAATCC
9881238 AAAAAT
1 AAAAAT
9881244 AAAATCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAAATCCAAATCC
Found at i:9882906 original size:11 final size:11
Alignment explanation
Indices: 9882890--9882914 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9882880 TTCAATTCAA
9882890 ATAATCAATAT
1 ATAATCAATAT
9882901 ATAATCAATAT
1 ATAATCAATAT
9882912 ATA
1 ATA
9882915 TATACCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:9883650 original size:25 final size:25
Alignment explanation
Indices: 9883622--9883683 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
9883612 TTAATTTCTC
* *
9883622 CTTTATTTCTT-TCCCTTTTTCTTTT
1 CTTTATTT-TTCTCCCTGTTTCGTTT
*
9883647 CTTTCTTTTTCTCCCTGTTTCGTTT
1 CTTTATTTTTCTCCCTGTTTCGTTT
*
9883672 CTATTATGTTTC
1 CT-TTATTTTTC
9883684 GTTTCTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.07
25 21 0.70
26 7 0.23
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (25 bp):
CTTTATTTTTCTCCCTGTTTCGTTT
Found at i:9883681 original size:16 final size:16
Alignment explanation
Indices: 9883662--9883692 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9883652 TTTTTCTCCC
9883662 TGTTTCGTTTCTATTA
1 TGTTTCGTTTCTATTA
9883678 TGTTTCGTTTCTATT
1 TGTTTCGTTTCTATT
9883693 TCTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.65
Consensus pattern (16 bp):
TGTTTCGTTTCTATTA
Found at i:9883754 original size:30 final size:31
Alignment explanation
Indices: 9883714--9883792 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 31
9883704 TTTTATTTAT
* *
9883714 TATATTTACTTATTATAATATATA-ATATAA
1 TATATATACTTATTATAATATATAGATAGAA
9883744 TATATATACTTA--ATAAT-TA-AGATAGAA
1 TATATATACTTATTATAATATATAGATAGAA
*
9883771 TAT-TATA-ATATTATAATATATA
1 TATATATACTTATTATAATATATA
9883793 TTTTAACTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 15 0.37
28 7 0.17
29 1 0.02
30 11 0.27
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
TATATATACTTATTATAATATATAGATAGAA
Found at i:9884137 original size:13 final size:14
Alignment explanation
Indices: 9884111--9884145 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
9884101 GATACAAATA
9884111 ACAGAATCAGATAT
1 ACAGAATCAGATAT
*
9884125 GCAGAAT-AGATAT
1 ACAGAATCAGATAT
9884138 ACAGAATC
1 ACAGAATC
9884146 CTACCCCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (14 bp):
ACAGAATCAGATAT
Found at i:9885349 original size:3 final size:3
Alignment explanation
Indices: 9885341--9885382 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
9885331 TGGCAAAAGG
*
9885341 AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
9885383 TGATGATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9885387 original size:3 final size:3
Alignment explanation
Indices: 9885381--9885406 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9885371 AGAAGAAGAA
9885381 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
9885407 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:9888971 original size:15 final size:15
Alignment explanation
Indices: 9888953--9889012 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
9888943 AACCCATATC
9888953 CTATTAGACACATCA
1 CTATTAGACACATCA
*
9888968 CTATTAGATACATCA
1 CTATTAGACACATCA
* *
9888983 TTAATAGACACATCA
1 CTATTAGACACATCA
9888998 CTATTAGACACATCA
1 CTATTAGACACATCA
9889013 AAATCAGACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (15 bp):
CTATTAGACACATCA
Found at i:9889022 original size:30 final size:30
Alignment explanation
Indices: 9888957--9889022 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
9888947 CATATCCTAT
* *
9888957 TAGACACATCACTATTAGATACATCATTAA
1 TAGACACATCACTATTAGACACATCATAAA
9888987 TAGACACATCACTATTAGACACATCA-AAA
1 TAGACACATCACTATTAGACACATCATAAA
9889016 TCAGACA
1 T-AGACA
9889023 TTTCTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (30 bp):
TAGACACATCACTATTAGACACATCATAAA
Found at i:9889597 original size:16 final size:16
Alignment explanation
Indices: 9889578--9889619 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9889568 TTTCAAAATT
*
9889578 TAAATTTAGACAACCC
1 TAAATTTAAACAACCC
* *
9889594 TAAATCTAAATAACCC
1 TAAATTTAAACAACCC
9889610 TAAATTTAAA
1 TAAATTTAAA
9889620 AAATCAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAATTTAAACAACCC
Found at i:9890032 original size:21 final size:21
Alignment explanation
Indices: 9890008--9890067 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
9889998 CAACATGGCA
9890008 AGTTAACTGGCCACATCAACT
1 AGTTAACTGGCCACATCAACT
*
9890029 AGTTAATTGGCCACATCAACT
1 AGTTAACTGGCCACATCAACT
* *
9890050 AGTTAGCTTGCCACATCA
1 AGTTAACTGGCCACATCA
9890068 GCAGTCTCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAACT
Found at i:9890169 original size:30 final size:31
Alignment explanation
Indices: 9890104--9890173 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
9890094 AATGTTAATA
*
9890104 AGTGACTGATTTGTCACTTTTTGATAATGTT
1 AGTGACTGATTTGTCACTTTTTGATAAAGTT
* * *
9890135 AGTGACTGTTTTGTTA-TTTTT-CTAAAGTT
1 AGTGACTGATTTGTCACTTTTTGATAAAGTT
9890164 GAGTGACTGA
1 -AGTGACTGA
9890174 AATGAAACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 6 0.18
30 13 0.39
31 14 0.42
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (31 bp):
AGTGACTGATTTGTCACTTTTTGATAAAGTT
Found at i:9893925 original size:31 final size:30
Alignment explanation
Indices: 9893865--9893999 Score: 91
Period size: 31 Copynumber: 4.4 Consensus size: 30
9893855 TTTTTTTTGT
* * * *
9893865 CTAATTTGATAACTAAATTTGACAATTTTTC
1 CTAATTTGGTACCTAAACTTGAC-CTTTTTC
9893896 CTAATTTGGTACCTAAACTTGACGCTTTTTC
1 CTAATTTGGTACCTAAACTTGAC-CTTTTTC
* ** *
9893927 TTACGTTGGTACTTAAACTT----TTTTGGAGTC
1 CTAATTTGGTACCTAAACTTGACCTTTT----TC
*
9893957 C-AATTTGATACCTAAACTTGACTCTTTTTC
1 CTAATTTGGTACCTAAACTTGAC-CTTTTTC
9893987 CTAATTTGGTACC
1 CTAATTTGGTACC
9894000 GACTTTTTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
26 4 0.05
29 14 0.18
30 5 0.06
31 52 0.66
34 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (30 bp):
CTAATTTGGTACCTAAACTTGACCTTTTTC
Found at i:9894010 original size:60 final size:60
Alignment explanation
Indices: 9893898--9894008 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
9893888 AATTTTTCCT
* * * **
9893898 AATTTGGTACCTAAACTTGACGCTTTTTCTTACGTTGGTACTTAAACTTTTTTGGAGTCC
1 AATTTGATACCTAAACTTGACGCTTTTTCCTAAGTTGGTACCGAAACTTTTTTGGAGTCC
* *
9893958 AATTTGATACCTAAACTTGACTCTTTTTCCTAATTTGGTACCG--ACTTTTTT
1 AATTTGATACCTAAACTTGACGCTTTTTCCTAAGTTGGTACCGAAACTTTTTT
9894009 TTTCGATTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 8 0.18
60 36 0.82
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.45
Consensus pattern (60 bp):
AATTTGATACCTAAACTTGACGCTTTTTCCTAAGTTGGTACCGAAACTTTTTTGGAGTCC
Found at i:9895706 original size:27 final size:27
Alignment explanation
Indices: 9895654--9895705 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
9895644 ATTAAAATTT
* **
9895654 ATAAAAATATTAAATAAAATTCAAAAG
1 ATAAAAATAATAAATAAAATAAAAAAG
9895681 ATAAAAA-AATAAATAAAATAAAAAA
1 ATAAAAATAATAAATAAAATAAAAAA
9895706 AAACTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (27 bp):
ATAAAAATAATAAATAAAATAAAAAAG
Found at i:9896342 original size:21 final size:21
Alignment explanation
Indices: 9896316--9896356 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9896306 CATTCTAAAC
*
9896316 TTAATTTTTAAATATTTTTTA
1 TTAATTATTAAATATTTTTTA
9896337 TTAATTATTAAATATTTTTT
1 TTAATTATTAAATATTTTTT
9896357 TAACTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTAATTATTAAATATTTTTTA
Found at i:9896365 original size:21 final size:21
Alignment explanation
Indices: 9896316--9896383 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
9896306 CATTCTAAAC
9896316 TTAATTT-TTAAATATTTTTTA
1 TTAATTTATTAAATA-TTTTTA
9896337 TTAA-TTATTAAATATTTTT-
1 TTAATTTATTAAATATTTTTA
**
9896356 TTAACTTTATTTCATA-TTTTA
1 TTAA-TTTATTAAATATTTTTA
*
9896377 TAAATTT
1 TTAATTT
9896384 TAATAATGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.10
20 14 0.35
21 22 0.55
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATTTATTAAATATTTTTA
Found at i:9901680 original size:50 final size:49
Alignment explanation
Indices: 9901641--9901783 Score: 130
Period size: 49 Copynumber: 2.9 Consensus size: 49
9901631 CGAGCATGTA
* * *
9901641 ATCAGAAAGCTCTTTCGAGCCATATAACAGGAAGTTCATATGAGCCAATT
1 ATCAGAAAGCTCATACGAGCCATA-AACAGGAAGTTCATACGAGCCAATT
* * * * *
9901691 ATCAGGAAGCTCATACGAGCCATAAACGGGAAGCTCA-AGAGAGCCAAAT
1 ATCAGAAAGCTCATACGAGCCATAAACAGGAAGTTCATA-CGAGCCAATT
* * *
9901740 ATC-GAAAAGCTCATACGAGCCA-AAATCGGGAAGCTCATAGGAGC
1 ATCAG-AAAGCTCATACGAGCCATAAA-CAGGAAGTTCATACGAGC
9901784 TGTAATTAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
48 5 0.06
49 53 0.66
50 22 0.28
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (49 bp):
ATCAGAAAGCTCATACGAGCCATAAACAGGAAGTTCATACGAGCCAATT
Found at i:9901727 original size:24 final size:24
Alignment explanation
Indices: 9901647--9901783 Score: 91
Period size: 25 Copynumber: 5.6 Consensus size: 24
9901637 TGTAATCAGA
* * *
9901647 AAGCTCTTTCGAGCCATATAACAGG
1 AAGCTCATACGAGCCATA-AACGGG
* * * * *
9901672 AAGTTCATATGAGCCAATTATCAGG
1 AAGCTCATACGAGCC-ATAAACGGG
9901697 AAGCTCATACGAGCCATAAACGGG
1 AAGCTCATACGAGCCATAAACGGG
* **
9901721 AAGCTCA-AGAGAGCCA-AATATCGAA
1 AAGCTCATA-CGAGCCATAA-A-CGGG
9901746 AAGCTCATACGAGCCA-AAATCGGG
1 AAGCTCATACGAGCCATAAA-CGGG
*
9901770 AAGCTCATAGGAGC
1 AAGCTCATACGAGC
9901784 TGTAATTAGG
Statistics
Matches: 89, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
23 3 0.03
24 37 0.42
25 46 0.52
26 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (24 bp):
AAGCTCATACGAGCCATAAACGGG
Found at i:9901759 original size:25 final size:24
Alignment explanation
Indices: 9901670--9901783 Score: 106
Period size: 24 Copynumber: 4.7 Consensus size: 24
9901660 CCATATAACA
* * * *
9901670 GGAAGTTCATATGAGCCAATTATCA
1 GGAAGCTCATACGAGCCAA-AATCG
9901695 GGAAGCTCATACGAGCCATAAA-CG
1 GGAAGCTCATACGAGCCA-AAATCG
*
9901719 GGAAGCTCA-AGAGAGCCAAATATCG
1 GGAAGCTCATA-CGAGCCAAA-ATCG
**
9901744 AAAAGCTCATACGAGCCAAAATCG
1 GGAAGCTCATACGAGCCAAAATCG
*
9901768 GGAAGCTCATAGGAGC
1 GGAAGCTCATACGAGC
9901784 TGTAATTAGG
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
23 3 0.04
24 34 0.47
25 34 0.47
26 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (24 bp):
GGAAGCTCATACGAGCCAAAATCG
Found at i:9903128 original size:18 final size:17
Alignment explanation
Indices: 9903090--9903130 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
9903080 CATTAAGTTC
9903090 TTTTTCCTAAGAACTCA
1 TTTTTCCTAAGAACTCA
9903107 TTTTTCCTAAGAACTCA
1 TTTTTCCTAAGAACTCA
9903124 TTTTTCC
1 TTTTTCC
9903131 AGTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (17 bp):
TTTTTCCTAAGAACTCA
Found at i:9914329 original size:12 final size:13
Alignment explanation
Indices: 9914305--9914333 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9914295 ATTTAGTTAG
9914305 TTTTAGATTTTTA
1 TTTTAGATTTTTA
9914318 TTTTAG-TTTTTA
1 TTTTAGATTTTTA
9914330 TTTT
1 TTTT
9914334 CTTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTAGATTTTTA
Found at i:9933949 original size:26 final size:27
Alignment explanation
Indices: 9933920--9933971 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
9933910 TTTGTTTTTC
9933920 TATTTCC-TAAAATAAACTTCTCAATA
1 TATTTCCATAAAATAAACTTCTCAATA
* *
9933946 TATTTCCATTTAAATAATCTTCTCAA
1 TATTTCCA-TAAAATAAACTTCTCAA
9933972 CCCAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
28 15 0.68
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (27 bp):
TATTTCCATAAAATAAACTTCTCAATA
Found at i:9934200 original size:57 final size:57
Alignment explanation
Indices: 9934132--9934256 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
9934122 CATTTCCAGG
*
9934132 TCCATTTTCATTTTTATTTTGGAGAAAA-C-TACATTCATTTCCAAATA-ATTTCATTTC
1 TCCATTTTCATTTTTATTTTGGAGAAAACCGTA-A-TCATTTCCAAATATA-CTCATTTC
*
9934189 TCCATTTTCATTTTTATTTTGGAGAAAACCGTAATCATTTCCAAATGTCACTCATTTC
1 TCCATTTTCATTTTTATTTTGGAGAAAACCGTAATCATTTCCAAATAT-ACTCATTTC
9934247 TCCATTTTCA
1 TCCATTTTCA
9934257 CCATTTCTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
57 40 0.65
58 19 0.31
59 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (57 bp):
TCCATTTTCATTTTTATTTTGGAGAAAACCGTAATCATTTCCAAATATACTCATTTC
Found at i:9942373 original size:92 final size:93
Alignment explanation
Indices: 9942261--9942446 Score: 365
Period size: 92 Copynumber: 2.0 Consensus size: 93
9942251 ATGAATTAAT
9942261 ATTCATAATTTGGATAGTCTTAGGCTGAAAATTTAATTTTCCTTGATGCTTCAAAATTGCTTCTC
1 ATTCATAATTTGGATAGTCTTAGGCTGAAAATTTAATTTTCCTTGATGCTTCAAAATTGCTTCTC
9942326 GGTTTTATGCTTTTAGTAGTGTCTGTTG
66 GGTTTTATGCTTTTAGTAGTGTCTGTTG
9942354 ATTCATAA-TTGGATAGTCTTAGGCTGAAAATTTAATTTTCCTTGATGCTTCAAAATTGCTTCTC
1 ATTCATAATTTGGATAGTCTTAGGCTGAAAATTTAATTTTCCTTGATGCTTCAAAATTGCTTCTC
9942418 GGTTTTATGCTTTTAGTAGTGTCTGTTG
66 GGTTTTATGCTTTTAGTAGTGTCTGTTG
9942446 A
1 A
9942447 GCCGTTTTTC
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 85 0.91
93 8 0.09
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
ATTCATAATTTGGATAGTCTTAGGCTGAAAATTTAATTTTCCTTGATGCTTCAAAATTGCTTCTC
GGTTTTATGCTTTTAGTAGTGTCTGTTG
Found at i:9943250 original size:14 final size:17
Alignment explanation
Indices: 9943220--9943259 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
9943210 ATATGCTTTC
9943220 CCTTTTTTTCTCATTTT
1 CCTTTTTTTCTCATTTT
9943237 -CTTTTTTT-TC-TTTT
1 CCTTTTTTTCTCATTTT
9943251 CCTTTTTTT
1 CCTTTTTTT
9943260 ATCACGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
CCTTTTTTTCTCATTTT
Found at i:9945468 original size:25 final size:24
Alignment explanation
Indices: 9945414--9945469 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
9945404 TTAATTAGTA
9945414 TAAAATATTAATAATTTAATAAAT
1 TAAAATATTAATAATTTAATAAAT
9945438 TGAAAA-ATTAAATAA-TTAATTAAAAT
1 T-AAAATATT-AATAATTTAA-T-AAAT
9945464 TAAAAT
1 TAAAAT
9945470 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
24 8 0.30
25 14 0.52
26 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATATTAATAATTTAATAAAT
Found at i:9949668 original size:15 final size:16
Alignment explanation
Indices: 9949648--9949677 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9949638 TTTAACTAAG
9949648 TAAAAT-AAATAAAAA
1 TAAAATAAAATAAAAA
9949663 TAAAATAAAATAAAA
1 TAAAATAAAATAAAA
9949678 TTTCCAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:9950361 original size:20 final size:18
Alignment explanation
Indices: 9950336--9950372 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
9950326 ACCTAACACG
9950336 AATTAAATTTAAACCATATT
1 AATTAAA-TTAAA-CATATT
9950356 AATTAAATTAAACATAT
1 AATTAAATTAAACATAT
9950373 CAACATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:9954703 original size:44 final size:44
Alignment explanation
Indices: 9954640--9954727 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
9954630 ACTGCAGAAG
* ** *
9954640 TCGTATATACAACGCACCAGCTTTTAGTTCTTTTTCTGTTCAAA
1 TCGTATATACAACACACCAGCTTCCAGTTCCTTTTCTGTTCAAA
* *
9954684 TCGTATATGCAACATACCAGCTTCCAGTTCCTTTTCTGTTCAAA
1 TCGTATATACAACACACCAGCTTCCAGTTCCTTTTCTGTTCAAA
9954728 CTCAGGCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (44 bp):
TCGTATATACAACACACCAGCTTCCAGTTCCTTTTCTGTTCAAA
Found at i:9956075 original size:41 final size:40
Alignment explanation
Indices: 9956018--9956107 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 40
9956008 AAATGTAATA
9956018 TTAGATTTTAATTGCATAACCAATTGATTGGGTTCTCTGTT
1 TTAGATTTTAATTGCATAACCAATTGATT-GGTTCTCTGTT
9956059 TTAGATTTTAATTGCATAACCAATTGATTGGTTCTCTGTT
1 TTAGATTTTAATTGCATAACCAATTGATTGGTTCTCTGTT
*
9956099 TTACATTTT
1 TTAGATTTT
9956108 TGGTTTTCAG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.40
41 29 0.60
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (40 bp):
TTAGATTTTAATTGCATAACCAATTGATTGGTTCTCTGTT
Found at i:9958622 original size:24 final size:24
Alignment explanation
Indices: 9958590--9958639 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
9958580 AATGCACAAG
9958590 TTAGTGCATACATACATAAATTAC
1 TTAGTGCATACATACATAAATTAC
9958614 TTAGTGCATACATACATAAATTAC
1 TTAGTGCATACATACATAAATTAC
9958638 TT
1 TT
9958640 GAATTAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (24 bp):
TTAGTGCATACATACATAAATTAC
Found at i:9961381 original size:12 final size:13
Alignment explanation
Indices: 9961364--9961394 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9961354 GTATTTCTTG
9961364 ATTTTTA-TTTTT
1 ATTTTTATTTTTT
9961376 ATTTTTATTTTTT
1 ATTTTTATTTTTT
9961389 ATTTTT
1 ATTTTT
9961395 TTGGTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:9961395 original size:7 final size:6
Alignment explanation
Indices: 9961364--9961394 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
9961354 GTATTTCTTG
9961364 ATTTTT ATTTTT ATTTTT ATTTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT
9961395 TTGGTACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
ATTTTT
Found at i:9963309 original size:8 final size:8
Alignment explanation
Indices: 9963310--9963338 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
9963300 TTTTTAAATT
9963310 TTTTAAAA
1 TTTTAAAA
9963318 TTTTAAAA
1 TTTTAAAA
9963326 TTTTAAAA
1 TTTTAAAA
9963334 TTTTA
1 TTTTA
9963339 TTAAACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTTAAAA
Found at i:9964768 original size:9 final size:9
Alignment explanation
Indices: 9964754--9964779 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9964744 TTAGAAGGAG
9964754 ATTAATTTA
1 ATTAATTTA
9964763 ATTAATTTA
1 ATTAATTTA
9964772 ATTAATTT
1 ATTAATTT
9964780 CAATATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:9965534 original size:20 final size:19
Alignment explanation
Indices: 9965500--9965540 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9965490 TGATTGGCAG
*
9965500 TTTTATTTTCTTTCTTTGT
1 TTTTATTTTCTTTCTCTGT
*
9965519 TTTTCTTTTCCTTTCTCTGT
1 TTTTATTTT-CTTTCTCTGT
9965539 TT
1 TT
9965541 CTTTTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTATTTTCTTTCTCTGT
Found at i:9965556 original size:17 final size:18
Alignment explanation
Indices: 9965520--9965563 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
9965510 TTTCTTTGTT
*
9965520 TTTCTTTTCCTTTCTCTG
1 TTTCTTTTCATTTCTCTG
9965538 TTTCTTTTCATTT-TCTG
1 TTTCTTTTCATTTCTCTG
*
9965555 TTTTTTTTC
1 TTTCTTTTC
9965564 TCTATAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (18 bp):
TTTCTTTTCATTTCTCTG
Found at i:9966569 original size:15 final size:15
Alignment explanation
Indices: 9966544--9966577 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9966534 TATACTAATT
9966544 TTTTGATTTATTTATA
1 TTTTGATTTATTT-TA
9966560 TTTT-ATTTATTTTA
1 TTTTGATTTATTTTA
9966574 TTTT
1 TTTT
9966578 CTTCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 8 0.44
16 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTGATTTATTTTA
Found at i:9974431 original size:43 final size:43
Alignment explanation
Indices: 9974383--9974468 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
9974373 AAGTCGGGTC
9974383 GGGTCGAATCAAGTGAAATTGTTCATGTTAGATTAAAAAATTA
1 GGGTCGAATCAAGTGAAATTGTTCATGTTAGATTAAAAAATTA
*
9974426 GGGTCGAATCGAGTGAAATTGTTCATGTTAGATTAAAAAATTA
1 GGGTCGAATCAAGTGAAATTGTTCATGTTAGATTAAAAAATTA
9974469 AACATGTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (43 bp):
GGGTCGAATCAAGTGAAATTGTTCATGTTAGATTAAAAAATTA
Found at i:9974681 original size:10 final size:10
Alignment explanation
Indices: 9974668--9974724 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
9974658 CTTTACATAT
9974668 TTTTTTGAAA
1 TTTTTTGAAA
9974678 TTTTTT-AAA
1 TTTTTTGAAA
* *
9974687 ATTTTTAAAA
1 TTTTTTGAAA
9974697 TTTTTAT-AAA
1 TTTTT-TGAAA
*
9974707 TATTTTG-AA
1 TTTTTTGAAA
9974716 -TTTTTGAAA
1 TTTTTTGAAA
9974725 ATTATTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 5 0.13
9 13 0.33
10 20 0.51
11 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:9974691 original size:9 final size:9
Alignment explanation
Indices: 9974669--9974727 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
9974659 TTTACATATT
*
9974669 TTTTTGAAAT
1 TTTTT-AAAA
9974679 TTTTTAAAA
1 TTTTTAAAA
9974688 TTTTTAAAA
1 TTTTTAAAA
9974697 TTTTTATAAA
1 TTTTTA-AAA
*
9974707 TATTTT-GAA
1 T-TTTTAAAA
9974716 TTTTTGAAAA
1 TTTTT-AAAA
9974726 TT
1 TT
9974728 ATTTTAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.10
9 21 0.50
10 13 0.31
11 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:9974717 original size:19 final size:19
Alignment explanation
Indices: 9974676--9974737 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
9974666 ATTTTTTTGA
* *
9974676 AATTTTTTAAAATT-TTTAA
1 AATTTTTGAAAATTATTT-T
9974695 AATTTTT-ATAAA-TATTTT
1 AATTTTTGA-AAATTATTTT
9974713 GAATTTTTGAAAATTATTTT
1 -AATTTTTGAAAATTATTTT
9974733 AATTT
1 AATTT
9974738 CTTTTTGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 2 0.05
19 28 0.76
20 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
AATTTTTGAAAATTATTTT
Found at i:9980614 original size:59 final size:62
Alignment explanation
Indices: 9980500--9980635 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 62
9980490 TTAAGGCCTA
* * *
9980500 TGTTTAGGGTTTTAGGGTTTGATTAGGGTTTAGGATAAATTAAATTAAAGTATTATGTTTTTAAT
1 TGTTTAGAGTTTTAGGGTTTGATTAAGGTTTAGG--AAA-TAAATTAAAGTATTATATTTTTAAT
*
9980565 TGTTTAGAGTTTTAGGGTTTTATTAAGGTTTAGG-AA-AAATT-AAGTATTATATTTTTAAT
1 TGTTTAGAGTTTTAGGGTTTGATTAAGGTTTAGGAAATAAATTAAAGTATTATATTTTTAAT
*
9980624 TGTTTAGTGTTT
1 TGTTTAGAGTTT
9980636 AGGAAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 28 0.42
60 5 0.08
62 2 0.03
65 31 0.47
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (62 bp):
TGTTTAGAGTTTTAGGGTTTGATTAAGGTTTAGGAAATAAATTAAAGTATTATATTTTTAAT
Found at i:9980748 original size:30 final size:30
Alignment explanation
Indices: 9980714--9980800 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 30
9980704 CTAAGTACTA
* *
9980714 TTCTGGGAAATATAATTTTGACGAGATGGG
1 TTCTGGAAAAAATAATTTTGACGAGATGGG
* * * *
9980744 TTCT-GAAAAAATAAATTTGTCGTGATGTG
1 TTCTGGAAAAAATAATTTTGACGAGATGGG
* *
9980773 TTCTGAAAAAAAT-ATTTTAACGAGATGG
1 TTCTGGAAAAAATAATTTTGACGAGATGG
9980801 ATTTTGTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (30 bp):
TTCTGGAAAAAATAATTTTGACGAGATGGG
Found at i:9982133 original size:41 final size:41
Alignment explanation
Indices: 9982063--9982376 Score: 391
Period size: 41 Copynumber: 7.6 Consensus size: 41
9982053 TTTTCAGGGA
* * * *
9982063 TTTAGCGGCGTTTCT-CAAGAAGCGCCGCTAGTGCT-TGGGGC
1 TTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAATGCTCT-GGTC
* * *
9982104 TTTAGCGGCGTTTTTGGAAATGCGTCGCTAATGTTCTGGTC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
*** * *
9982145 TTTAGCGGCGTTTTTGGAAGTTCGTCGGTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
* *
9982186 TTTAGCGGCGTTTTTTGGAAAAGCGCCGCTAATGCTCTAGCC
1 TTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
* *
9982228 TTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
*
9982269 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
*
9982310 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGTC
1 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
* *
9982351 TTTAACGGCGTTTTTGGAAAAACGCC
1 TTTAGCGGCGTTTTTGGAAAAGCGCC
9982377 ACAAAAAGTA
Statistics
Matches: 243, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
40 23 0.09
41 147 0.60
42 73 0.30
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
Found at i:9982237 original size:83 final size:82
Alignment explanation
Indices: 9982063--9982376 Score: 382
Period size: 83 Copynumber: 3.8 Consensus size: 82
9982053 TTTTCAGGGA
* * * * *
9982063 TTTAGCGGCGTTTCT-CAAGAAGCGCCGCTAGTGCT-TGGGGCTTTAGCGGCGTTTTTGGAAATG
1 TTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAATGCTCT-GGTCTTTAGCGGCGTTTTTGGAAAAG
* * *
9982126 CGTCGCTAATGTTCTGGTC
64 CGCCGCTAATGCTCTGGCC
*** * *
9982145 TTTAGCGGCGTTTTTGGAAGTTCGTCGGTAATGCTCTGGTCTTTAGCGGCGTTTTTTGGAAAAGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCG-TTTTTGGAAAAGC
*
9982210 GCCGCTAATGCTCTAGCC
65 GCCGCTAATGCTCTGGCC
* * *
9982228 TTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGCG
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAAAAGCG
*
9982293 CCGCTAATGCTCTGGTCT
66 CCGCTAATGCTCTGG-CC
* * *
9982311 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGTCTTTAACGGCGTTTTTGGAAAAACG
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAAAAGCG
9982375 CC
66 CC
9982377 ACAAAAAGTA
Statistics
Matches: 198, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
82 90 0.45
83 108 0.55
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTGGAAAAGCG
CCGCTAATGCTCTGGCC
Found at i:9982242 original size:124 final size:123
Alignment explanation
Indices: 9982063--9982371 Score: 386
Period size: 124 Copynumber: 2.5 Consensus size: 123
9982053 TTTTCAGGGA
* * * * ** * * *
9982063 TTTAGCGGCGTTTCTCAAGAAGCGCCGCTAGTGCTTGGGGCTTTAGCGGCGTTTTTGGAAATGCG
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TCAGCCTTTAGCGGCGTTTTTGGAAAAGCA
* * * * *** * *
9982128 TCGCTAATGTTCTGGTCTTTAGCGGCGTTTTTGGAAGTTCGTCGGTAATGCTCTGGTC-
65 CCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCT
*
9982186 TTTAGCGGCGTTTTTTGGAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGGAAAAGC
1 TTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGCTC-AGCCTTTAGCGGCGTTTTTGGAAAAGC
9982251 ACCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCT
64 ACCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCT
* * *
9982311 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGTCTTTAACGGCGTTTTTGGAAAA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGCCTTTAGCGGCGTTTTTGGAAAA
9982372 ACGCCACAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
123 33 0.21
124 117 0.73
125 10 0.06
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.33
Consensus pattern (123 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGCCTTTAGCGGCGTTTTTGGAAAAGCAC
CGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTCT
Found at i:9982893 original size:29 final size:29
Alignment explanation
Indices: 9982853--9982913 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
9982843 TTAAGAGTAC
* * *
9982853 TTAAGGATTAGGGGTTTATGATTTAGGGT
1 TTAAGGATTAGGGGCTAAGGATTTAGGGT
*
9982882 TTAAGAGA-TAGGGGCTAAGGGTTTAGGGT
1 TTAAG-GATTAGGGGCTAAGGATTTAGGGT
9982911 TTA
1 TTA
9982914 GATTAATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (29 bp):
TTAAGGATTAGGGGCTAAGGATTTAGGGT
Found at i:9985168 original size:12 final size:11
Alignment explanation
Indices: 9985151--9985192 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
9985141 AATTGTATAG
9985151 AAATAATATAAT
1 AAATAA-ATAAT
9985163 AAATAAATAAAT
1 AAATAAAT-AAT
9985175 AAATAAATAA-
1 AAATAAATAAT
9985185 AAATAAAT
1 AAATAAAT
9985193 CAATGACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 4 0.14
12 17 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:9985192 original size:4 final size:4
Alignment explanation
Indices: 9985151--9985185 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
9985141 AATTGTATAG
9985151 AAAT -AAT ATAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAA
9985186 AATAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:9987388 original size:9 final size:9
Alignment explanation
Indices: 9987371--9987407 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
9987361 TGAGTTTTCG
9987371 AATTCGAAT
1 AATTCGAAT
*
9987380 AACTCGAAT
1 AATTCGAAT
*
9987389 AATTCAAAT
1 AATTCGAAT
9987398 AATTCGAAT
1 AATTCGAAT
9987407 A
1 A
9987408 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:9990339 original size:43 final size:43
Alignment explanation
Indices: 9990272--9990358 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
9990262 CAATGATGTA
* *
9990272 CAAGATTTCCTTGATTAAATAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAATAAATGCATTATATCTTTTATTAC
* *
9990315 CAAGATTTACTTGATTAAGA-AAATGCATTGTATGTTTTATTAC
1 CAAGATTTACTTGATTAA-ATAAATGCATTATATCTTTTATTAC
9990358 C
1 C
9990359 TTGCATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 38 0.97
44 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAATAAATGCATTATATCTTTTATTAC
Found at i:9990726 original size:43 final size:43
Alignment explanation
Indices: 9990631--9990828 Score: 236
Period size: 43 Copynumber: 4.6 Consensus size: 43
9990621 TGTTTTTAGC
* * *
9990631 GGCGTTTGTGGGAAAAGCGTCGCTAAAGGTC-TGTTCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTATAGT
* * * *
9990673 GGCATTTGTGGGAAAAGCGTCGCTAAAAGTGATGATCTATCGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTATAGT
* * * *
9990716 GGTGTTTGTGGGAATAGCGCCGCTAAAAGTCATGAACTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTATAGT
* *
9990759 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTATAGT
* * * *
9990802 GACGTTTGTTGAAAAAGTGCCGCTAAA
1 GGCGTTTGTGGGAAAAGCGCCGCTAAA
9990829 GGCCTTGTTC
Statistics
Matches: 134, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 28 0.21
43 106 0.79
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTATAGT
Found at i:9990842 original size:86 final size:85
Alignment explanation
Indices: 9990625--9990848 Score: 259
Period size: 86 Copynumber: 2.6 Consensus size: 85
9990615 AAGATATGTT
* * *
9990625 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTGTTCTATAGTGGCATTTGTGGGAAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTGTGGGAAAAG
* *
9990690 CGTCGCTAAAAGTGATGATC
66 CGCCGCTAAAAGTCATGATC
* * * * * * **
9990710 TATCGTGGTGTTTGTGGGAATAGCGCCGCTAAAAGTCATGAACTATAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGTTCTATAGCGGCGTTTGTGGGAAAA
9990775 GCGCCGCTAAAAGTCATGATC
65 GCGCCGCTAAAAGTCATGATC
* * * * * *
9990796 TTTAGCGACGTTTGTTGAAAAAGTGCCGCTAAAGGCCTTGTTCTATAACGGCG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGTTCTATAGCGGCG
9990849 GTGTCAATAG
Statistics
Matches: 110, Mismatches: 28, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
85 30 0.27
86 80 0.73
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTGTGGGAAAAG
CGCCGCTAAAAGTCATGATC
Found at i:9991921 original size:32 final size:31
Alignment explanation
Indices: 9991884--9991955 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
9991874 GATCTACTGC
*
9991884 TATTATAAAAAAATTATAA-AAAATATTAATTA
1 TATTATAAAAAAATTA-AATAAAA-ATTAATAA
9991916 TATTAT--AAAAATTAAATAAAAATTAATAA
1 TATTATAAAAAAATTAAATAAAAATTAATAA
9991945 TATTA-AAAAAA
1 TATTATAAAAAA
9991956 TGAAATTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 14 0.39
30 16 0.44
32 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
TATTATAAAAAAATTAAATAAAAATTAATAA
Done.