Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 127 of 144
Found at i:39472286 original size:41 final size:41
Alignment explanation
Indices: 39472251--39472437 Score: 320
Period size: 41 Copynumber: 4.6 Consensus size: 41
39472241 GTGAAGTAAT
39472251 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
39472292 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
*
39472333 CCAGAAATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* *
39472374 CCAGACATTACGTCTAACAGGCTTGATGCCGGTAAAACATA
1 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
* * *
39472415 TCAGACTTTATGTCTAGCAGGCT
1 CCAGACATTACGTCTAGCAGGCT
39472438 AAGTGTCGGT
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (41 bp):
CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
Found at i:39472486 original size:123 final size:123
Alignment explanation
Indices: 39472251--39472490 Score: 279
Period size: 123 Copynumber: 2.0 Consensus size: 123
39472241 GTGAAGTAAT
* * *
39472251 CCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACCAGACATTACGTCTAGCAGGCTT
1 CCAGACATTACGTCTAACAGGCTTGATGCCGGTAAAACATACCAGACATTACGTCTAGCAGGCTA
* * * * *
39472316 GATGCCGGTGAAACATACCAGAAATTACGTCTAGCAGGCTTGATGCCGGTGAAACATA
66 GATGCCGGTGAAACAAAACAGAAATTAAGCCTAGCAGGCTAGATGCCGGTGAAACATA
* * *
39472374 CCAGACATTACGTCTAACAGGCTTGATGCCGGTAAAACATATCAGACTTTATGTCTAGCAGGCTA
1 CCAGACATTACGTCTAACAGGCTTGATGCCGGTAAAACATACCAGACATTACGTCTAGCAGGCTA
* * * ***
39472439 -AGTGTCGGTG-TACTAAAATAGGCTTTAAGCCTAGCAGGCTA-AGTGCCGGTGA
66 GA-TGCCGGTGAAAC-AAAACAGAAATTAAGCCTAGCAGGCTAGA-TGCCGGTGA
39472491 TATTGTTTAT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
122 4 0.04
123 93 0.96
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (123 bp):
CCAGACATTACGTCTAACAGGCTTGATGCCGGTAAAACATACCAGACATTACGTCTAGCAGGCTA
GATGCCGGTGAAACAAAACAGAAATTAAGCCTAGCAGGCTAGATGCCGGTGAAACATA
Found at i:39483720 original size:15 final size:16
Alignment explanation
Indices: 39483702--39483737 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
39483692 AATACGGGAA
39483702 AAAAAGGAAAT-AAGG
1 AAAAAGGAAATGAAGG
*
39483717 AAAAAGGAAATGAAGT
1 AAAAAGGAAATGAAGG
39483733 AAAAA
1 AAAAA
39483738 AAAGGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (16 bp):
AAAAAGGAAATGAAGG
Found at i:39487273 original size:7 final size:7
Alignment explanation
Indices: 39487261--39487285 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39487251 TTTAAGTTTC
39487261 ATTGTGG
1 ATTGTGG
39487268 ATTGTGG
1 ATTGTGG
39487275 ATTGTGG
1 ATTGTGG
39487282 ATTG
1 ATTG
39487286 AGTTTTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (7 bp):
ATTGTGG
Found at i:39499462 original size:7 final size:7
Alignment explanation
Indices: 39499450--39499477 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39499440 TTAAAACACA
39499450 AATTTAG
1 AATTTAG
39499457 AATTTAG
1 AATTTAG
39499464 AATTTAG
1 AATTTAG
39499471 AATTTAG
1 AATTTAG
39499478 TATAGTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (7 bp):
AATTTAG
Found at i:39500521 original size:20 final size:20
Alignment explanation
Indices: 39500496--39500536 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39500486 TATTTTTTAT
39500496 TAATTTTTAAATTTTAAAAA
1 TAATTTTTAAATTTTAAAAA
* *
39500516 TAATTTTTATATTTTTAAAA
1 TAATTTTTAAATTTTAAAAA
39500536 T
1 T
39500537 TTTAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTTAAATTTTAAAAA
Found at i:39514692 original size:31 final size:31
Alignment explanation
Indices: 39514651--39514719 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
39514641 AAAACTTAAC
* *
39514651 AGTTCGATAACTTAAATAAAAACTTTCAAAT
1 AGTTCAATAACTTAAATAAAAACTCTCAAAT
* *
39514682 AGTTCAATAACTTAAATGAAACCTCTCAAAT
1 AGTTCAATAACTTAAATAAAAACTCTCAAAT
39514713 AGTTCAA
1 AGTTCAA
39514720 GGATTATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (31 bp):
AGTTCAATAACTTAAATAAAAACTCTCAAAT
Found at i:39533194 original size:91 final size:92
Alignment explanation
Indices: 39533035--39533215 Score: 274
Period size: 91 Copynumber: 2.0 Consensus size: 92
39533025 TGGCAACTTC
* * *
39533035 CATCTACAAAAATCGTTGTGCATTCATAACTACTGGCAACGTATTAACCTACAAGCACGCGTGGT
1 CATCTACAAAAATCGTTGTGCATTCACAACTACTGACAACGTATTAACCTACAAGCACGCATGGT
*
39533100 TTATCCACAACTTATACTAGTAGCTTT
66 TTATACACAACTTATACTAGTAGCTTT
* * * *
39533127 CATCTGCAAAAATCGTTGTGTATTCACAACTA-TGACAACGTATTAACCTGCAAGCACTCATGGT
1 CATCTACAAAAATCGTTGTGCATTCACAACTACTGACAACGTATTAACCTACAAGCACGCATGGT
*
39533191 TTATACACAACTTATACTGGTAGCT
66 TTATACACAACTTATACTAGTAGCT
39533216 ATTATTTGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 51 0.64
92 29 0.36
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (92 bp):
CATCTACAAAAATCGTTGTGCATTCACAACTACTGACAACGTATTAACCTACAAGCACGCATGGT
TTATACACAACTTATACTAGTAGCTTT
Found at i:39533477 original size:92 final size:92
Alignment explanation
Indices: 39533359--39533588 Score: 293
Period size: 92 Copynumber: 2.5 Consensus size: 92
39533349 TAGCTTTTAG
* * *
39533359 CTGCAAAAATTGTTGTGTATTTACAACTATTGGCAGTGTATTAACCTGCAAGCACTCGTCGTTTA
1 CTGCAAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGAAAGCACTCGTCGTTTA
*
39533424 GCCACAACTTATATTGACAACT-TTCAT
66 GCCACAACTTATACTGACAACTATT-AT
** * *
39533451 CTGCAAAAATCGTTGTGTATTCACAACTACGGGCTGTGTATTAACCTGAAAGCACTCGTGGTTTA
1 CTGCAAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGAAAGCACTCGTCGTTTA
* *
39533516 TCCACAACTTATACTGGCAACTATTAT
66 GCCACAACTTATACTGACAACTATTAT
* ** * * *
39533543 CTAC-AAACCCATTGTGTATTCACAATTATTGGCAGCGTATTAACCT
1 CTGCAAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCT
39533589 AAAACAATAG
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
91 34 0.29
92 82 0.69
93 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (92 bp):
CTGCAAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGAAAGCACTCGTCGTTTA
GCCACAACTTATACTGACAACTATTAT
Found at i:39535478 original size:20 final size:21
Alignment explanation
Indices: 39535435--39535479 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39535425 ATACTATATA
* *
39535435 TTATAAAAATAATATATTTAT
1 TTATAAAAACAATATAATTAT
*
39535456 TTATAAAAACATTATAATT-T
1 TTATAAAAACAATATAATTAT
39535476 TTAT
1 TTAT
39535480 TACCATAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATAAAAACAATATAATTAT
Found at i:39543126 original size:24 final size:24
Alignment explanation
Indices: 39543063--39543114 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39543053 TTTCTAGAAG
* * *
39543063 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
39543087 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
39543111 ATTT
1 ATTT
39543115 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:39565673 original size:55 final size:53
Alignment explanation
Indices: 39565573--39565711 Score: 206
Period size: 54 Copynumber: 2.5 Consensus size: 53
39565563 CTTGTAAAAT
*
39565573 TAAATGAGATTTAATGAAAAAAGAAAGGTGTTAGATGTAGGAAAAAAATTTGAAA
1 TAAATGAGATTTAATG-AAAAA-AAAGGTGTTAGATGTAGAAAAAAAATTTGAAA
39565628 TAAATGAGATTTAATGAAAGAAAAAGGTGTTAGATGTAGAAAAAAAATTTGAAA
1 TAAATGAGATTTAATGAAA-AAAAAGGTGTTAGATGTAGAAAAAAAATTTGAAA
* * *
39565682 TTAATGAGACTGAATGAAAAAAAAGAGTGT
1 TAAATGAGATTTAATGAAAAAAAAG-GTGT
39565712 CAAATGGATT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
53 6 0.08
54 54 0.69
55 18 0.23
ACGTcount: A:0.53, C:0.01, G:0.22, T:0.25
Consensus pattern (53 bp):
TAAATGAGATTTAATGAAAAAAAAGGTGTTAGATGTAGAAAAAAAATTTGAAA
Found at i:39565862 original size:43 final size:43
Alignment explanation
Indices: 39565764--39565907 Score: 180
Period size: 44 Copynumber: 3.2 Consensus size: 43
39565754 TAGGAAAAAG
* * *
39565764 AAAGTGAGTCAATAAATGAGATTGAATTGAATTAAATGAAATTCTGA
1 AAAGTGAGTC-A-AAATGA-ATTGGATAGAAATAAATGAAATT-TGA
*
39565811 AAAGTGAGTCAAAATGAATTGGATAGAAACAAATGAAATTTGA
1 AAAGTGAGTCAAAATGAATTGGATAGAAATAAATGAAATTTGA
* *
39565854 AAAGTGAGTCAAAGATGGATGGGATAGAAATAAATGAAATTTGA
1 AAAGTGAGTCAAA-ATGAATTGGATAGAAATAAATGAAATTTGA
*
39565898 AAAGTTAGTC
1 AAAGTGAGTC
39565908 GGAACAATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
43 16 0.18
44 55 0.62
45 6 0.07
46 1 0.01
47 10 0.11
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (43 bp):
AAAGTGAGTCAAAATGAATTGGATAGAAATAAATGAAATTTGA
Found at i:39566118 original size:44 final size:43
Alignment explanation
Indices: 39566064--39566208 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 43
39566054 ATAATTATTC
*
39566064 TGACTAACTTTTCAAATTTCATTTATTTCTAT-CACATCCATCTT
1 TGACTCACTTTTCAAATTTCATTTATTTCTATCCA-ATCCAT-TT
* * * **
39566108 TGACTCACTTTTCAAATTTTATTTGTTTTTATCCAATTTATTT
1 TGACTCACTTTTCAAATTTCATTTATTTCTATCCAATCCATTT
* *
39566151 TGACTCACTTTTCAGAATTTCATTTAATTT-AATTCAATCTCATTTAT
1 TGACTCACTTTTCA-AATTTCATTT-ATTTCTATCCAATC-CA-TT-T
39566198 TGACTCACTTT
1 TGACTCACTTT
39566209 CTTTTTCCTA
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
43 16 0.19
44 47 0.57
45 6 0.07
46 2 0.02
47 12 0.14
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (43 bp):
TGACTCACTTTTCAAATTTCATTTATTTCTATCCAATCCATTT
Found at i:39566323 original size:52 final size:52
Alignment explanation
Indices: 39566267--39566397 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
39566257 TCTGACACTC
* *
39566267 TTTTTTTCATTCAGTCTCATTAATTTCAAATTTTTTCCTACATCTAACACCT
1 TTTTTTTCATTAAATCTCATTAATTTCAAATTTTTTCCTACATCTAACACCT
*
39566319 TTTTTTTCATTAAATCTCATTTATTTCAAATTTTTTCCTACATCTAACACCT
1 TTTTTTTCATTAAATCTCATTAATTTCAAATTTTTTCCTACATCTAACACCT
*
39566371 TGTTTTTCATTAAATCTCATTTAATTT
1 TTTTTTTCATTAAATCTCA-TTAATTT
39566398 TACAAGAATA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
52 67 0.92
53 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.02, T:0.53
Consensus pattern (52 bp):
TTTTTTTCATTAAATCTCATTAATTTCAAATTTTTTCCTACATCTAACACCT
Found at i:39569505 original size:115 final size:111
Alignment explanation
Indices: 39569275--39569761 Score: 552
Period size: 108 Copynumber: 4.5 Consensus size: 111
39569265 TGATAAATTT
* * * *
39569275 GGTGCCAGCCATTGACAGGCAAACACCC---AAAATTATTTTTTTACTGTTTTCGTATACTGATA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATT-TTTTTTTACTTTTTTCGTATACTGATA
* *
39569337 TCTGAGTCTGACGCG--AAAAAAAGAAATTTTTTTTAAAATTGTACTG
65 TCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTT-AAATTGTACTG
** * *
39569383 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAAAATTTTTATTTTTGTTTTTTTCGTATATTC
1 GGTGCCGGCCATTGACAGGCCAGCACCC--AAAAAAA-TTTT-TTTTTACTTTTTTCGTATACTG
*
39569448 ATATCTGATTTTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTACTG
62 ATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTACTG
39569498 GGTGCCGGCCATTGACAGGCCAGCACCC----AAATTTTTTTTTACTTTTTTCGTATACTGATAT
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTTTTACTTTTTTCGTATACTGATAT
* *
39569559 CTGATTCTGACACAAAAAAAAAAAGAAAATTTTTTTAAATTGTACTG
66 CTGATTCTGACAC-GAAAAAAAAAGAAATTTTTTTTAAATTGTACTG
*
39569606 GGTGCCGACCATTGACAGGCCAGCACCC---AAAATTTTTTTTTACTTTTTTCGTATACTGATAT
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTTTTACTTTTTTCGTATACTGATAT
* * * *
39569668 CTGATTCTGACATG--------A-AATTTTTTTTTAAATTGTATTA
66 CTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTACTG
* * *
39569705 GGTGCCGGTCATTGACAGGCCAGCACCC-AAAAATTTTGTTTTTTTC-TTTTTCGTATA
1 GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTT-TTTTTTACTTTTTTCGTATA
39569762 TCAGTATTAT
Statistics
Matches: 336, Mismatches: 29, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
99 44 0.13
100 1 0.00
101 17 0.05
102 7 0.02
107 34 0.10
108 87 0.26
109 48 0.14
113 6 0.02
114 34 0.10
115 39 0.12
116 19 0.06
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (111 bp):
GGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTTTTACTTTTTTCGTATACTGATAT
CTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTAAATTGTACTG
Found at i:39575127 original size:25 final size:24
Alignment explanation
Indices: 39575093--39575178 Score: 100
Period size: 25 Copynumber: 3.5 Consensus size: 24
39575083 TTTATGTGGT
* * *
39575093 GCCTTTGTGGTGAGTCACTTGTAAA
1 GCCTTTGTGGCGATTTA-TTGTAAA
*
39575118 GCCTTTGTGGCGATTTATTTTAGAA
1 GCCTTTGTGGCGATTTATTGTA-AA
*
39575143 GCCTTTGTGGCGATTTATTTGGAAA
1 GCCTTTGTGGCGATTTA-TTGTAAA
39575168 GCCTTTGTGGC
1 GCCTTTGTGGC
39575179 AGGTTACCTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
24 4 0.08
25 46 0.87
26 3 0.06
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (24 bp):
GCCTTTGTGGCGATTTATTGTAAA
Found at i:39575193 original size:25 final size:25
Alignment explanation
Indices: 39575165--39575229 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
39575155 ATTTATTTGG
*
39575165 AAAGCCTTTGTGGCAGGTTACCTGT
1 AAAGCCTTTGTGGCAGGTTACCTAT
* * *
39575190 AAAGTCTTTGAGGAAGGTTACCTAT
1 AAAGCCTTTGTGGCAGGTTACCTAT
* *
39575215 AAAGGCTATGTGGCA
1 AAAGCCTTTGTGGCA
39575230 TAATGACTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (25 bp):
AAAGCCTTTGTGGCAGGTTACCTAT
Found at i:39600560 original size:18 final size:18
Alignment explanation
Indices: 39600520--39600560 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39600510 GAAAAGGGCC
*
39600520 AAAGAA-AATTTTGAATT
1 AAAGAAGAATGTTGAATT
*
39600537 -AAGAAGAATGTTGATTT
1 AAAGAAGAATGTTGAATT
39600554 AAAGAAG
1 AAAGAAG
39600561 GGACTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 9 0.45
18 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (18 bp):
AAAGAAGAATGTTGAATT
Found at i:39603388 original size:22 final size:22
Alignment explanation
Indices: 39603362--39603403 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
39603352 ATTTATTCAC
39603362 TTGTGACGCTCATAATTTGGAA
1 TTGTGACGCTCATAATTTGGAA
39603384 TTGTGACGCTCATAATTTGG
1 TTGTGACGCTCATAATTTGG
39603404 CATACCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (22 bp):
TTGTGACGCTCATAATTTGGAA
Found at i:39605772 original size:20 final size:21
Alignment explanation
Indices: 39605740--39605778 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
39605730 ATCCAAGCTT
39605740 AATTTCTATCAATTTCACACC
1 AATTTCTATCAATTTCACACC
39605761 AATTTC-ATCAATTTCACA
1 AATTTCTATCAATTTCACA
39605779 ATCATGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTCTATCAATTTCACACC
Found at i:39606049 original size:21 final size:19
Alignment explanation
Indices: 39606022--39606070 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
39606012 TATTATTATA
* *
39606022 ACTTAATTAATTATGTTTTT
1 ACTTAATTAATCAT-ATTTT
39606042 ATCTTAATTAATCATATTTT
1 A-CTTAATTAATCATATTTT
39606062 ACTTAATTA
1 ACTTAATTA
39606071 CCAAAACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 6 0.23
21 12 0.46
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (19 bp):
ACTTAATTAATCATATTTT
Found at i:39616392 original size:38 final size:40
Alignment explanation
Indices: 39616327--39616413 Score: 124
Period size: 38 Copynumber: 2.2 Consensus size: 40
39616317 CATTAAAAAC
* *
39616327 ATATTAAAAAACACTACCATAAATATAATAAATGTTTTATT
1 ATATT-AAAAACACTACAATAAATATAATAAATATTTTATT
39616368 ATATTAAAAACAC-A-AATAAATATAATAAATATTTTATT
1 ATATTAAAAACACTACAATAAATATAATAAATATTTTATT
*
39616406 GTATTAAA
1 ATATTAAA
39616414 TATAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 29 0.67
39 1 0.02
40 8 0.19
41 5 0.12
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (40 bp):
ATATTAAAAACACTACAATAAATATAATAAATATTTTATT
Found at i:39616459 original size:13 final size:13
Alignment explanation
Indices: 39616441--39616465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39616431 TATATTTTGG
39616441 GTTGGGTAATTTA
1 GTTGGGTAATTTA
39616454 GTTGGGTAATTT
1 GTTGGGTAATTT
39616466 TTTTTTTTTA
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:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (13 bp):
GTTGGGTAATTTA
Found at i:39623542 original size:31 final size:31
Alignment explanation
Indices: 39623507--39623565 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
39623497 TTTAAAATGC
39623507 TCAAACATTTTCAAAAGTGATCAAATAAATA
1 TCAAACATTTTCAAAAGTGATCAAATAAATA
* * *
39623538 TCAAACATTTTTATAAGTGCTCAAATAA
1 TCAAACATTTTCAAAAGTGATCAAATAA
39623566 GGGTTTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (31 bp):
TCAAACATTTTCAAAAGTGATCAAATAAATA
Found at i:39625534 original size:6 final size:6
Alignment explanation
Indices: 39625523--39625549 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39625513 TCTGTTTATC
39625523 TATCTA TATCTA TATCTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TAT
39625550 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:39625538 original size:16 final size:16
Alignment explanation
Indices: 39625503--39625541 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
39625493 TTTATCATGT
* * *
39625503 TATCTATCTATCTGTT
1 TATCTATCTATATCTA
39625519 TATCTATCTATATCTA
1 TATCTATCTATATCTA
39625535 TATCTAT
1 TATCTAT
39625542 ATCTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (16 bp):
TATCTATCTATATCTA
Found at i:39625799 original size:6 final size:6
Alignment explanation
Indices: 39625790--39625821 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39625780 GTTTTTAAAG
39625790 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
39625822 ATATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:39629090 original size:16 final size:15
Alignment explanation
Indices: 39629069--39629126 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 15
39629059 AACGTTATAT
39629069 AAAATATAAAAATGAA
1 AAAATATAAAAAT-AA
39629085 AAAATATAAAAATAA
1 AAAATATAAAAATAA
*
39629100 AAAGTATTAAAAACTCAAA
1 AAAATA-TAAAAA-T--AA
39629119 AAAATATA
1 AAAATATA
39629127 TTTAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.19
16 19 0.53
17 1 0.03
18 2 0.06
19 7 0.19
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATATAAAAATAA
Found at i:39629189 original size:19 final size:19
Alignment explanation
Indices: 39629165--39629201 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39629155 AAATATATCA
39629165 ATTATATAAAATATAAAAC
1 ATTATATAAAATATAAAAC
*
39629184 ATTATATAAAGTATAAAA
1 ATTATATAAAATATAAAA
39629202 AATTGAAAAA
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:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
ATTATATAAAATATAAAAC
Found at i:39629241 original size:19 final size:18
Alignment explanation
Indices: 39629191--39629241 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
39629181 AACATTATAT
* *
39629191 AAAGTATAAAAAATTGAA
1 AAAGTATATAAAATTCAA
39629209 AAA--ATATAACAATTCAA
1 AAAGTATATAA-AATTCAA
39629226 AAAGTATATGAAAATT
1 AAAGTATAT-AAAATT
39629242 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 3 0.11
19 8 0.30
20 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAGTATATAAAATTCAA
Found at i:39629964 original size:40 final size:40
Alignment explanation
Indices: 39629895--39629971 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
39629885 CGTCCTAACC
*
39629895 TTGTAAGTTGTCTAAAAAGAAGGAAAAATAAAGGGGTGAG
1 TTGTAAGTTATCTAAAAAGAAGGAAAAATAAAGGGGTGAG
* * * *
39629935 TTGTGAGTTATCTCAAAAGAAGTAAAAATAAGGGGGT
1 TTGTAAGTTATCTAAAAAGAAGGAAAAATAAAGGGGT
39629972 AAGCTACGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.25
Consensus pattern (40 bp):
TTGTAAGTTATCTAAAAAGAAGGAAAAATAAAGGGGTGAG
Found at i:39634969 original size:284 final size:284
Alignment explanation
Indices: 39634452--39635018 Score: 1062
Period size: 284 Copynumber: 2.0 Consensus size: 284
39634442 TTCTCAGACT
*
39634452 TGGCCATAATAATCATGTTCATGCACATGTTTTCATATATATATATTCACGCATATGTATCATAA
1 TGGCCACAATAATCATGTTCATGCACATGTTTTCATATATATATATTCACGCATATGTATCATAA
*
39634517 CATAATTTTCTCGCTTTGTATGCACATAGTTTAAGTGATGCCATACATTTTCTAGTTCAAACAAA
66 CATAATTTTCTCGCTTTGTATGCACATAGTTTAAGTGATACCATACATTTTCTAGTTCAAACAAA
* * *
39634582 GTAAATCCTACCCCACCGCTACACACCATAATAGGAGTTCTTCAGACCTCCCTTTTTTAACACAC
131 ATAAATCCTACCCCACCGCTACACACCATAATAGGAGTTCTTCAGAACTCCCTTCTTTAACACAC
* *
39634647 CAGGATGTGAATTTACCACTATGGGTTTGCAAATAATAACTGCCATTTGGCTGTGAACATACAAC
196 CAAGATGTGAATTTACCACTACGGGTTTGCAAATAATAACTGCCATTTGGCTGTGAACATACAAC
*
39634712 AAGTTCCTGCATTTGGAATCTACA
261 AAGTTCCTGCAGTTGGAATCTACA
39634736 TGGCCACAATAATCATGTTCATGCACATGTTTTCATATATATATATTCACGCATATGTATCATAA
1 TGGCCACAATAATCATGTTCATGCACATGTTTTCATATATATATATTCACGCATATGTATCATAA
39634801 CATAATTTTCTCGCTTTGTATGCACATAGTTTAAGTGATACCATACATTTTCTAGTTCAAACAAA
66 CATAATTTTCTCGCTTTGTATGCACATAGTTTAAGTGATACCATACATTTTCTAGTTCAAACAAA
39634866 ATAAATCCTACCCCACCGCTACACACCATAATAGGAGTTCTTCAGAACTCCCTTCTTTAACACAC
131 ATAAATCCTACCCCACCGCTACACACCATAATAGGAGTTCTTCAGAACTCCCTTCTTTAACACAC
39634931 CAAGATGTGAATTTACCACTACGGGTTTGCAAATAATAACTGCCATTTGGCTGTGAACATACAAC
196 CAAGATGTGAATTTACCACTACGGGTTTGCAAATAATAACTGCCATTTGGCTGTGAACATACAAC
39634996 AAGTTCCTGCAGTTGGAATCTAC
261 AAGTTCCTGCAGTTGGAATCTAC
39635019 TTTCGTCTGT
Statistics
Matches: 275, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
284 275 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (284 bp):
TGGCCACAATAATCATGTTCATGCACATGTTTTCATATATATATATTCACGCATATGTATCATAA
CATAATTTTCTCGCTTTGTATGCACATAGTTTAAGTGATACCATACATTTTCTAGTTCAAACAAA
ATAAATCCTACCCCACCGCTACACACCATAATAGGAGTTCTTCAGAACTCCCTTCTTTAACACAC
CAAGATGTGAATTTACCACTACGGGTTTGCAAATAATAACTGCCATTTGGCTGTGAACATACAAC
AAGTTCCTGCAGTTGGAATCTACA
Found at i:39637874 original size:21 final size:21
Alignment explanation
Indices: 39637833--39637874 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39637823 CAATTTTTAT
**
39637833 TACTGGTAGTTTATCTGCAAA
1 TACTGGTAGTTTATCCACAAA
*
39637854 TACTGGTGGTTTATCCACAAA
1 TACTGGTAGTTTATCCACAAA
39637875 CCGGAGTGTT
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:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (21 bp):
TACTGGTAGTTTATCCACAAA
Found at i:39640764 original size:29 final size:29
Alignment explanation
Indices: 39640732--39640806 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
39640722 AGTTAATTAT
39640732 AAGTGGTTTTGAAAATTGAACAAATAGTC
1 AAGTGGTTTTGAAAATTGAACAAATAGTC
* *
39640761 AAGTAGTTTTGGAAATTGAACAAATAGTC
1 AAGTGGTTTTGAAAATTGAACAAATAGTC
39640790 AAGTGGTTTTGGAAAAT
1 AAGTGGTTTT-GAAAAT
39640807 GAGGTATCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 36 0.88
30 5 0.12
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (29 bp):
AAGTGGTTTTGAAAATTGAACAAATAGTC
Found at i:39643946 original size:23 final size:23
Alignment explanation
Indices: 39643903--39643977 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 23
39643893 TAAAATGACT
* *
39643903 ATATAAAAAATTTAATA--AAAA
1 ATATAAAATATTAAATATTAAAA
39643924 ATATAAAATATTAAATATT-AAA
1 ATATAAAATATTAAATATTAAAA
*
39643946 ATAATATAATA-TAAATATTTTAAAA
1 AT-ATAAAATATTAAATA--TTAAAA
39643971 A-ATAAAA
1 ATATAAAA
39643978 AATAATATGG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
21 15 0.34
22 11 0.25
23 12 0.27
24 2 0.05
25 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAAAATATTAAATATTAAAA
Found at i:39643960 original size:22 final size:22
Alignment explanation
Indices: 39643903--39643964 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
39643893 TAAAATGACT
* * *
39643903 ATATAAAAAATTTAATA-AAAA
1 ATATAAAATATTAAATATTAAA
39643924 ATATAAAATATTAAATATTAAA
1 ATATAAAATATTAAATATTAAA
*
39643946 ATAATATAATA-TAAATATT
1 AT-ATAAAATATTAAATATT
39643965 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 15 0.43
22 13 0.37
23 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAAAATATTAAATATTAAA
Found at i:39643982 original size:23 final size:21
Alignment explanation
Indices: 39643918--39643982 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 21
39643908 AAAAATTTAA
39643918 TAAAAAATATAAAATATTAAATAT
1 TAAAAAATA-AAAA-A-TAAATAT
* *
39643942 TAAAATAATATAATATAAATATTT
1 TAAAA-AATAAAAAATAAATA--T
39643966 TAAAAAATAAAAAATAA
1 TAAAAAATAAAAAATAA
39643983 TATGGGCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 6 0.18
23 11 0.32
24 13 0.38
25 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAAATAAAAAATAAATAT
Found at i:39644200 original size:22 final size:23
Alignment explanation
Indices: 39644164--39644211 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
39644154 AAAAAGTATG
*
39644164 AATATATTAAATTTATAACATAC
1 AATATATTAAATTTAAAACATAC
* *
39644187 AATAT-TTAATTTTAAAATATAC
1 AATATATTAAATTTAAAACATAC
39644209 AAT
1 AAT
39644212 TTCATTACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
AATATATTAAATTTAAAACATAC
Found at i:39650455 original size:39 final size:41
Alignment explanation
Indices: 39650411--39650488 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 41
39650401 CATATGTCAG
39650411 CCAAATATTCAATCATGCATTTTCA-T-AACCAACTATCAA
1 CCAAATATTCAATCATGCATTTTCATTAAACCAACTATCAA
*
39650450 CCAAATATTTAATCATGCATTTTCATTAAACCAACTATC
1 CCAAATATTCAATCATGCATTTTCATTAAACCAACTATC
39650489 CATACAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 24 0.67
40 1 0.03
41 11 0.31
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (41 bp):
CCAAATATTCAATCATGCATTTTCATTAAACCAACTATCAA
Found at i:39652637 original size:29 final size:29
Alignment explanation
Indices: 39652604--39652667 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
39652594 GGGATAAAGT
*
39652604 TGTGTAATAGGAGGATTCTGAGTAGTGAA
1 TGTGTAATAGGAAGATTCTGAGTAGTGAA
* *
39652633 TGTGTAGTGGGAAGATTCTGAGTAGTGAA
1 TGTGTAATAGGAAGATTCTGAGTAGTGAA
39652662 TGTGTA
1 TGTGTA
39652668 GTGGGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (29 bp):
TGTGTAATAGGAAGATTCTGAGTAGTGAA
Found at i:39652668 original size:29 final size:29
Alignment explanation
Indices: 39652617--39652674 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39652607 GTAATAGGAG
39652617 GATTCTGAGTAGTGAATGTGTAGTGGGAA
1 GATTCTGAGTAGTGAATGTGTAGTGGGAA
39652646 GATTCTGAGTAGTGAATGTGTAGTGGGAA
1 GATTCTGAGTAGTGAATGTGTAGTGGGAA
39652675 TTAGGGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (29 bp):
GATTCTGAGTAGTGAATGTGTAGTGGGAA
Found at i:39657548 original size:54 final size:53
Alignment explanation
Indices: 39657483--39657644 Score: 186
Period size: 54 Copynumber: 3.1 Consensus size: 53
39657473 ATTTTTATAC
* * ** *
39657483 AAATGATAAAAATAAAATTAAATATTTAACTAATTTAAATTCGATTTATTTAT
1 AAATTATAAAAATAAAATTAAATATTTAACTAACTTAAATTCGATTTAACTAA
** *
39657536 AAATTAT--AAA-AAAATTAAATATTTAAGCTAACTTAAATTTTACTTAACTAA
1 AAATTATAAAAATAAAATTAAATATTTAA-CTAACTTAAATTCGATTTAACTAA
* * *
39657587 AAATTATAAAAATAAAATTAAATATTTAAACTAACTTAAATCCGATTCAACTAT
1 AAATTATAAAAATAAAATTAAATATTT-AACTAACTTAAATTCGATTTAACTAA
39657641 AAAT
1 AAAT
39657645 GTGGATGAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
50 16 0.18
51 27 0.30
53 9 0.10
54 36 0.40
55 2 0.02
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (53 bp):
AAATTATAAAAATAAAATTAAATATTTAACTAACTTAAATTCGATTTAACTAA
Found at i:39657627 original size:18 final size:18
Alignment explanation
Indices: 39657550--39657627 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
39657540 TATAAAAAAA
*
39657550 TTAAATATTTAAGCTAAC
1 TTAAATATTTAAACTAAC
39657568 TTAAAT-TTT--ACTTAAC
1 TTAAATATTTAAAC-TAAC
* * *
39657584 -TAAAAATTATAAAAATAAAA
1 TTAAATATT-T-AAACT-AAC
39657604 TTAAATATTTAAACTAAC
1 TTAAATATTTAAACTAAC
39657622 TTAAAT
1 TTAAAT
39657628 CCGATTCAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.11
16 6 0.13
17 4 0.09
18 14 0.31
19 5 0.11
20 4 0.09
21 7 0.16
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (18 bp):
TTAAATATTTAAACTAAC
Found at i:39662138 original size:16 final size:17
Alignment explanation
Indices: 39662107--39662151 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
39662097 CCGATATAAT
* * *
39662107 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
39662124 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
39662140 AAATATTTTTAA
1 AAATATTTTTAA
39662152 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:39662149 original size:11 final size:11
Alignment explanation
Indices: 39662135--39662202 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
39662125 AATTTTTTAA
39662135 TTTTAAAATAT
1 TTTTAAAATAT
39662146 TTTTAAAATACT
1 TTTTAAAATA-T
** *
39662158 TTTTTTATTAT
1 TTTTAAAATAT
*
39662169 TTTT----TAA
1 TTTTAAAATAT
39662176 TTTTAAAATAT
1 TTTTAAAATAT
39662187 TTTTAAAATACT
1 TTTTAAAATA-T
39662199 TTTT
1 TTTT
39662203 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
7 6 0.13
11 27 0.59
12 13 0.28
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39662171 original size:41 final size:40
Alignment explanation
Indices: 39662118--39662211 Score: 163
Period size: 41 Copynumber: 2.4 Consensus size: 40
39662108 AATATATTTA
39662118 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
*
39662158 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTA-AATTTTTTAATTTTAAAATATTTTTAAAATACT
39662199 TTTTTT-AATTTTT
1 TTTTTTAAATTTTT
39662212 AAAATAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 6 0.12
40 7 0.14
41 38 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTTTAAATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:39662180 original size:30 final size:31
Alignment explanation
Indices: 39662144--39662217 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
39662134 ATTTTAAAAT
** *
39662144 ATTTTTAAAATACTTTTTTTATTA-TTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTA
39662175 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATAC-TTTTTTA
39662206 ATTTTTAAAATA
1 ATTTTTAAAATA
39662218 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 8 0.22
30 10 0.27
31 9 0.24
32 10 0.27
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:39662223 original size:21 final size:21
Alignment explanation
Indices: 39662185--39662224 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39662175 ATTTTAAAAT
**
39662185 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
39662206 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
39662225 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:39662231 original size:22 final size:20
Alignment explanation
Indices: 39662184--39662236 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
39662174 AATTTTAAAA
* *
39662184 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
39662204 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
39662227 TATTTATTAA
1 TATTT-TTAA
39662237 CAAAATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 11 0.41
22 10 0.37
23 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:39669218 original size:27 final size:27
Alignment explanation
Indices: 39669188--39669364 Score: 144
Period size: 27 Copynumber: 6.5 Consensus size: 27
39669178 ATATTGAGCC
* * *
39669188 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCCACATAATCAACT
* * *
39669215 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACATAATCAACT
* *
39669242 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACATAAT-CAACT
* ** *
39669270 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAATCAACT
* **
39669297 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CATAATCAACT
* *
39669324 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCCACATAA-TCA-ACT
39669351 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39669365 TGTACAATTT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.02
27 95 0.78
28 24 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAATCAACT
Found at i:39683410 original size:23 final size:23
Alignment explanation
Indices: 39683380--39683482 Score: 170
Period size: 23 Copynumber: 4.5 Consensus size: 23
39683370 ACATGTTATG
*
39683380 ATGCTGTCCAATTTGGTGTATAA
1 ATGCTGTCCAATTTGATGTATAA
39683403 ATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
39683426 ATGCTGTCCAATTTGGTGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
39683449 ATGTTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGATGTATAA
*
39683472 AAGCTGTCCAA
1 ATGCTGTCCAA
39683483 AACAGGGTAG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (23 bp):
ATGCTGTCCAATTTGATGTATAA
Found at i:39683432 original size:46 final size:46
Alignment explanation
Indices: 39683380--39683482 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
39683370 ACATGTTATG
39683380 ATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
*
39683426 ATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
*
39683472 AAGCTGTCCAA
1 ATGCTGTCCAA
39683483 AACAGGGTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (46 bp):
ATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
Found at i:39689879 original size:40 final size:40
Alignment explanation
Indices: 39689831--39689965 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 40
39689821 ACTATGTTTA
* *
39689831 GCACTTAGTATGTGATTCGAG-ATAGCTTCGGCTATTTATG
1 GCACTTAGTATGCGATT-GAGAATAGCTTCGGCTATATATG
* * *
39689871 GCATTTAGTGTGCGATTGGGAATAGCTTCGGCTATATATG
1 GCACTTAGTATGCGATTGAGAATAGCTTCGGCTATATATG
* * * * * *
39689911 GCACTTAGTGTGCGAAACTGAG-ATAACTTCAGCTATGTAAG
1 GCACTTAGTATGCG--ATTGAGAATAGCTTCGGCTATATATG
*
39689952 GCACTTAGTGTGCG
1 GCACTTAGTATGCG
39689966 GGATTGATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 45 0.56
41 29 0.36
42 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
GCACTTAGTATGCGATTGAGAATAGCTTCGGCTATATATG
Found at i:39690745 original size:23 final size:23
Alignment explanation
Indices: 39690717--39690789 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
39690707 TACATGTTAT
* *
39690717 AATGCTATCCAATTTGGTTTATA
1 AATGCTGTCCAATTTGGTGTATA
*
39690740 AATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATA
39690763 AATGCTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
39690786 AATG
1 AATG
39690790 TGTATAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (23 bp):
AATGCTGTCCAATTTGGTGTATA
Found at i:39690768 original size:46 final size:46
Alignment explanation
Indices: 39690717--39690945 Score: 269
Period size: 46 Copynumber: 4.8 Consensus size: 46
39690707 TACATGTTAT
* *
39690717 AATGCTATCCAATTTGGTTTATAAATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATA
39690763 AATGCTGTCCAATTTGGTGTATAAATGTGTATAAATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAA-TT--TG-------GTGTATAAATGCTGTCCAATTTGATGTATA
* * *
39690819 AATGCTGTCCAATTTAGTGTATAAATACTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATA
* * *
39690865 AATGCTGTCCAATTTGATGTATAAATGCTATCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATA
* * *
39690911 AATGTTGTCCAATTTGATGTATAAAAGCTGTCCAA
1 AATGCTGTCCAATTTGGTGTATAAATGCTGTCCAA
39690946 AACAGGGTAG
Statistics
Matches: 161, Mismatches: 12, Indels: 20
0.83 0.06 0.10
Matches are distributed among these distances:
46 113 0.70
47 2 0.01
49 2 0.01
53 1 0.01
55 2 0.01
56 41 0.25
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (46 bp):
AATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGATGTATA
Found at i:39690799 original size:33 final size:33
Alignment explanation
Indices: 39690757--39690822 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
39690747 TCCAATTTGA
*
39690757 TGTATAAATGCTGTCCAATTTGGTGTATAAATG
1 TGTATAAATGCTGTCCAATTTGATGTATAAATG
39690790 TGTATAAATGCTGTCCAATTTGATGTATAAATG
1 TGTATAAATGCTGTCCAATTTGATGTATAAATG
39690823 CTGTCCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (33 bp):
TGTATAAATGCTGTCCAATTTGATGTATAAATG
Found at i:39690819 original size:23 final size:23
Alignment explanation
Indices: 39690790--39690945 Score: 242
Period size: 23 Copynumber: 6.8 Consensus size: 23
39690780 TGTATAAATG
39690790 TGTATAAATGCTGTCCAATTTGA
1 TGTATAAATGCTGTCCAATTTGA
39690813 TGTATAAATGCTGTCCAATTT-A
1 TGTATAAATGCTGTCCAATTTGA
* *
39690835 GTGTATAAATACTGTCCAATTTGG
1 -TGTATAAATGCTGTCCAATTTGA
39690859 TGTATAAATGCTGTCCAATTTGA
1 TGTATAAATGCTGTCCAATTTGA
* *
39690882 TGTATAAATGCTATCCAATTTGG
1 TGTATAAATGCTGTCCAATTTGA
*
39690905 TGTATAAATGTTGTCCAATTTGA
1 TGTATAAATGCTGTCCAATTTGA
*
39690928 TGTATAAAAGCTGTCCAA
1 TGTATAAATGCTGTCCAA
39690946 AACAGGGTAG
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.01
23 119 0.99
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (23 bp):
TGTATAAATGCTGTCCAATTTGA
Found at i:39692216 original size:27 final size:27
Alignment explanation
Indices: 39692158--39692257 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
39692148 TTATCTTGGT
* * * *
39692158 GGACTCTCTCGTGTTTACTATCCCGAT
1 GGACTATCCCGTGTTTACTATCTCGAA
* *
39692185 GGACTATCCCGTGTTTGCTATCTCAGCA
1 GGACTATCCCGTGTTTACTATCTC-GAA
*
39692213 -GACTATCCCATGTTTACTATCTCGAA
1 GGACTATCCCGTGTTTACTATCTCGAA
*
39692239 GGACCATCCCGTGTTTACT
1 GGACTATCCCGTGTTTACT
39692258 GACTCCAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.03
27 57 0.95
28 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (27 bp):
GGACTATCCCGTGTTTACTATCTCGAA
Found at i:39698131 original size:12 final size:12
Alignment explanation
Indices: 39698114--39698138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39698104 TTAAAGTAAA
39698114 TTATTTGTAAGC
1 TTATTTGTAAGC
39698126 TTATTTGTAAGC
1 TTATTTGTAAGC
39698138 T
1 T
39698139 CAAATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATTTGTAAGC
Found at i:39708949 original size:22 final size:22
Alignment explanation
Indices: 39708919--39708976 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
39708909 ATTTCCTCTC
39708919 AATTCCTCTCAAATTCCTTCCAA
1 AATT-CTCTCAAATTCCTTCCAA
*
39708942 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAAATTCCTTCCAA
*
39708964 AATTCTTTCAAAT
1 AATTCTCTCAAAT
39708977 CTATATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTCTCTCAAATTCCTTCCAA
Found at i:39709022 original size:51 final size:51
Alignment explanation
Indices: 39708946--39709059 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
39708936 TTCCAAAATT
* *
39708946 CTCTCAATTTCCTTCCAAAATTCTTTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTTTCAAATCCATATTTAATTTCAATTTC
39708997 CTCTCAATTTCCTTCAAAAATTCTTTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTTTCAAATCCATATTTAATTTCAATTTC
*
39709048 TTCTCAATTTCC
1 CTCTCAATTTCC
39709060 CTTTTTAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTTTCAAATCCATATTTAATTTCAATTTC
Found at i:39710215 original size:7 final size:7
Alignment explanation
Indices: 39710203--39710228 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39710193 TATTTGATTG
39710203 GTATTTA
1 GTATTTA
39710210 GTATTTA
1 GTATTTA
39710217 GTATTTA
1 GTATTTA
39710224 GTATT
1 GTATT
39710229 ATGTATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:39715879 original size:18 final size:18
Alignment explanation
Indices: 39715853--39715887 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39715843 AGGTGCGTTT
*
39715853 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
39715871 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
39715888 TCCTTTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:39716359 original size:44 final size:45
Alignment explanation
Indices: 39716310--39716396 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
39716300 ATATTTTGAA
*
39716310 TATTTTGATATTATTTTATGTAAAAAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
* *
39716354 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGA
39716397 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAAAAAAATAGAAATTTATTTGAGT
Found at i:39716460 original size:29 final size:30
Alignment explanation
Indices: 39716422--39716485 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
39716412 AACCTAATTT
* *
39716422 AACCCTAAACCCTAACCTAAAATAA-TAAA
1 AACCCAAAACCATAACCTAAAATAATTAAA
**
39716451 AACCCAAAACCATAACCTAATTTAATTAAA
1 AACCCAAAACCATAACCTAAAATAATTAAA
39716481 AACCC
1 AACCC
39716486 TAGCCTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (30 bp):
AACCCAAAACCATAACCTAAAATAATTAAA
Found at i:39716574 original size:50 final size:51
Alignment explanation
Indices: 39716508--39716608 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 51
39716498 ATTAAAAACT
* *
39716508 CTAACCTAATTTAATTAAAAATCATAAACCCTTAA-TTAAAAACCCTAACC
1 CTAACCTAATTCAATTAAAAACCATAAACCCTTAACTTAAAAACCCTAACC
*
39716558 CTAACCTAATTCAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACC
1 CTAACCTAATTCAATTAAAAACCATAAACCCTTAACTTAAAAACCCTAACC
39716609 TAATTTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 32 0.68
51 15 0.32
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (51 bp):
CTAACCTAATTCAATTAAAAACCATAAACCCTTAACTTAAAAACCCTAACC
Found at i:39716611 original size:50 final size:49
Alignment explanation
Indices: 39716508--39717078 Score: 196
Period size: 45 Copynumber: 12.0 Consensus size: 49
39716498 ATTAAAAACT
* *
39716508 CTAACCTAATTTAATTAAAAATCATAAACCCTTAATTAAAAACCCTAACC
1 CTAACCTAA-TTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
39716558 CTAACCTAATTCAATTAAAAACCCTAAACCCTTAACTTAAAAACCCTAA-C
1 CTAACCTAATT-AATTAAAAACCCTAAACCCTTAA-TTAAAAACCCTAACC
* *
39716608 CTAA--T--TTAATTAAAAACCCT-AACCTAATTTAATTAAAAAACCTAAACC
1 CTAACCTAATTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCT-AACC
* * *
39716656 CT----TAATTAA-AAACCATAACCCT-AACCTAATTCAATTAAAAACTCT-A--
1 CTAACCTAATTAATTAA--A-AACCCTAAACC--CTT-AATTAAAAACCCTAACC
39716702 --AACCT--TTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAA----AACC
1 CTAACCTAATTAATTAAAAACCCTAAACCCT----TAA-TTAA--AAACCCTAACC
* * *
39716749 CTAGCCTAATTTAATTAAAAACCCT-AGCCTAATTTAATTAAAAACCCTAA-C
1 CTAACCTAA-TTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTAACC
* *
39716800 TTAA--T--TTAATTAAAAACCCT-AACCTAATTTAATTAAAAACCCTAA-C
1 CTAACCTAATTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTAACC
* * * *
39716846 CTAA--T--TTAATTAAAAATCCT--AGCC-TAATTTAATTAA----AATC
1 CTAACCTAATTAATTAAAAACCCTAAACCCTTAA-TTAA-AAACCCTAACC
39716886 CTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
1 CTAACCTAA-TTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
* * * *
39716936 ATAACCTAATTTAATTAAAAACCCT--AGCC-TAATTTAATTAA----AACT
1 CTAACCTAA-TTAATTAAAAACCCTAAACCCTTAA-TTAA-AAACCCTAACC
*
39716981 CTAACCTAATTTAATTAAAAACCCT-AA-CC-TAATTTAATTAAA--AT-A--
1 CTAACCTAA-TTAATTAAAAACCCTAAACCCTTAA-TTAA--AAACCCTAACC
39717026 CTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAAACC
1 CTAACCTAA-TTAATTAAAAACCCTAAACCCTTAATTAAAAACCCT-AACC
39717077 CT
1 CT
39717079 TAATTAAAAA
Statistics
Matches: 418, Mismatches: 33, Indels: 139
0.71 0.06 0.24
Matches are distributed among these distances:
39 2 0.00
40 5 0.01
41 3 0.01
42 6 0.01
43 2 0.00
44 14 0.03
45 98 0.23
46 88 0.21
47 28 0.07
48 29 0.07
49 14 0.03
50 87 0.21
51 21 0.05
52 20 0.05
55 1 0.00
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (49 bp):
CTAACCTAATTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACC
Found at i:39716611 original size:118 final size:116
Alignment explanation
Indices: 39716471--39717209 Score: 635
Period size: 118 Copynumber: 6.3 Consensus size: 116
39716461 CATAACCTAA
* * *
39716471 TTTAATTAAAAACCCTAGCCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAATCATAAA
1 TTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCT-AA
*
39716536 CCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAACC
65 CCCTTAATTAAAAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
* * *
39716588 CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAAACCTAA
1 TTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCT-A
*
39716653 ACCCTTAATTAAAAACCATAACCCTAACCTAATTCAATTAAAAACTCTAAACC
64 ACCCTTAATTAAAAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
* *
39716706 TTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAAC
1 TTTAATT--AAA----AACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAAC
* * * *
39716771 CCT-AGCC-TAATTTAATTAA--A-AACCCTAACTTAATTTAATTAAAAACCCT-AACC
60 CCTAACCCTTAA-TTAA-AAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
* *
39716824 TAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAA-TCCTAGCCTAATTTAATT-AAAATCC
1 ---TTTAATTAAAAACCCTAACCTAATTTAATTAAAAACT-CTAACCTAATTTAATTAAAAACCC
* *
39716887 TAA-CC-TAATTTAATTAA--A-AACCCTAAACC--CTT-AATTAAAAACCCTAACCATAACC
62 TAACCCTTAA-TTAA-AAACCATAACCCT-AACCTAATTCAATTAAAAACCCT----A-AACC
*
39716942 TAATTTAATTAAAAACCCTAGCCTAATTTAATT-AAAACTCTAACCTAATTTAATTAAAAACCCT
1 ---TTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCT
*
39717006 AA-CC-TAATTTAATTAAA--AT-A--CTAACCTAATTTAATTAAAAACCCTAAACC
63 AACCCTTAA-TTAA--AAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
* *
39717056 CTTAATTAAAAACCCTAAACC---CTTAATTAAAAACCCTAACCATAACCTAATTTAATTAAAAA
1 TTTAATTAAAAACCCT-AACCTAATTTAATTAAAAA--CT---C-TAACCTAATTTAATTAAAAA
* ** * *
39717118 CCCT-AGCC-TAATTTAATTA--A-AACTCTAACCTAATTTAATTAAAAACCCT-AACC
59 CCCTAACCCTTAA-TTAAAAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
*
39717171 TAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAAC
1 ---TTTAATTAAAAACCCTAACCTAATTTAATTAAAAAC
39717210 CTTAAACCCT
Statistics
Matches: 544, Mismatches: 32, Indels: 91
0.82 0.05 0.14
Matches are distributed among these distances:
109 6 0.01
110 4 0.01
111 15 0.03
112 18 0.03
113 2 0.00
114 35 0.06
115 52 0.10
116 63 0.12
117 30 0.06
118 188 0.35
119 50 0.09
120 15 0.03
121 14 0.03
122 2 0.00
123 50 0.09
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (116 bp):
TTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAAC
CCTTAATTAAAAACCATAACCCTAACCTAATTCAATTAAAAACCCTAAACC
Found at i:39716620 original size:28 final size:23
Alignment explanation
Indices: 39716456--39717210 Score: 768
Period size: 23 Copynumber: 32.3 Consensus size: 23
39716446 ATAAAAACCC
*
39716456 AAAACCATAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
*
39716479 AAAACCCTAGCCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
*
39716502 AAAACTCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
* *
39716525 AAAATCATAAACCCTTAA-TTAA--A
1 AAAACCCT-AA-CC-TAATTTAATTA
*
39716548 AACCCTAACCCTAACCTAATTCAATTA
1 AA----AACCCTAACCTAATTTAATTA
*
39716575 AAAACCCTAAACC---CTTAACTTA
1 AAAACCCT-AACCTAATTTAA-TTA
39716597 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39716620 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
* *
39716643 AAAAACCTAAACCCTTAA-TTAA-AA
1 AAAACCCT-AA-CC-TAATTTAATTA
*
39716667 ACCATAACCCTAACCTAATTCAATTA
1 A--A-AACCCTAACCTAATTTAATTA
*
39716693 AAAACTCTAAACC---TTTAATTAAA
1 AAAACCCT-AACCTAATTTAATT--A
39716716 AACCCTAACCCTAACCTAATTTAATTA
1 AA----AACCCTAACCTAATTTAATTA
*
39716743 AAAACCCTAGCCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
*
39716766 AAAACCCTAGCCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
*
39716789 AAAACCCTAACTTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39716812 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39716835 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
* *
39716858 AAAATCCTAGCCTAATTTAATT-
1 AAAACCCTAACCTAATTTAATTA
*
39716880 AAAATCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39716903 AAAACCCTAAACCCTTAA-TTAA--A
1 AAAACCCT-AA-CC-TAATTTAATTA
*
39716926 AACCCTAACCATAACCTAATTTAATTA
1 AA----AACCCTAACCTAATTTAATTA
*
39716953 AAAACCCTAGCCTAATTTAATT-
1 AAAACCCTAACCTAATTTAATTA
*
39716975 AAAACTCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39716998 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39717021 AAATA--CTAACCTAATTTAATTA
1 AAA-ACCCTAACCTAATTTAATTA
*
39717043 AAAACCCTAAACC---CTTAATTA
1 AAAACCCT-AACCTAATTTAATTA
39717064 AAAACCCTAAACCCTTAA-TTAA--A
1 AAAACCCT-AA-CC-TAATTTAATTA
*
39717087 AACCCTAACCATAACCTAATTTAATTA
1 AA----AACCCTAACCTAATTTAATTA
*
39717114 AAAACCCTAGCCTAATTTAATT-
1 AAAACCCTAACCTAATTTAATTA
*
39717136 AAAACTCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39717159 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
*
39717182 AAAACCCTAGCCTAATTTAATTA
1 AAAACCCTAACCTAATTTAATTA
39717205 AAAACC
1 AAAACC
39717211 TTAAACCCTT
Statistics
Matches: 627, Mismatches: 43, Indels: 124
0.79 0.05 0.16
Matches are distributed among these distances:
21 32 0.05
22 94 0.15
23 352 0.56
24 38 0.06
25 44 0.07
26 24 0.04
27 36 0.06
29 7 0.01
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (23 bp):
AAAACCCTAACCTAATTTAATTA
Found at i:39717062 original size:21 final size:21
Alignment explanation
Indices: 39717036--39717094 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
39717026 CTAACCTAAT
39717036 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAAACCC
39717057 TTAATTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAAACCC
39717078 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
39717095 CCATAACCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAATTAAAAACCCTAAACCC
Found at i:39717383 original size:116 final size:116
Alignment explanation
Indices: 39717246--39717463 Score: 382
Period size: 116 Copynumber: 1.9 Consensus size: 116
39717236 AACCTTAACG
* *
39717246 TAATGTTAGATTTGAAAAAATGTTTTGACTAGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATATTAGATTTGAAAAAATGTTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
39717311 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
* * * *
39717362 TAATATTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTGTATATAATTTGATA
1 TAATATTAGATTTGAAAAAATGTTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
39717427 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACTTAATA
39717464 CAATTTATCA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 96 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (116 bp):
TAATATTAGATTTGAAAAAATGTTTTGACTAGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTCACA
Found at i:39717480 original size:17 final size:18
Alignment explanation
Indices: 39717439--39717480 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39717429 TTTACTAACC
* *
39717439 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
39717457 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
39717474 ATTAATA
1 ATTAATA
39717481 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:39720236 original size:126 final size:123
Alignment explanation
Indices: 39719980--39720286 Score: 429
Period size: 126 Copynumber: 2.5 Consensus size: 123
39719970 TGACCGAGTG
*
39719980 TCTTCTCAAATAGCATCATGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATT
1 TCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATT
* *
39720045 ATTTCTTACATGACCTACTGTAGCAAAAGCGCGCTGACGAGGCTGCAATTTCACAAAT
66 ATTTCTTACATGACCTACTATAGCAAAAGCGCGCTCACGAGGCTGCAATTTCACAAAT
* * *
39720103 TCTTCTCAAATAGCATCCTGCTAGAAGTGATTTTATACTATTTGCTTAGAAACGTCAAAAAAATA
1 TCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTC--AAAAA-A
* * *
39720168 ATTATTTCTTCCGTGACCTACTATAGCAAAAGCGCG-TCCACGAGGGC-GCAATTTTACAAAT
63 ATTATTTCTTACATGACCTACTATAGCAAAAGCGCGCT-CACGA-GGCTGCAATTTCACAAAT
* * ** *
39720229 TCTTCTCAAATACCATCCTACTAGAAGCGATTTTATATTATTTTATCAGAAATGTCAA
1 TCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
39720287 CTCGAAATTA
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
123 52 0.32
124 2 0.01
125 6 0.04
126 99 0.61
127 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (123 bp):
TCTTCTCAAATAGCATCCTGCTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATT
ATTTCTTACATGACCTACTATAGCAAAAGCGCGCTCACGAGGCTGCAATTTCACAAAT
Found at i:39726812 original size:13 final size:13
Alignment explanation
Indices: 39726794--39726820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39726784 ACAAAAAAAG
39726794 TGAATTTTTTAAT
1 TGAATTTTTTAAT
39726807 TGAATTTTTTAAT
1 TGAATTTTTTAAT
39726820 T
1 T
39726821 ATAACAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TGAATTTTTTAAT
Found at i:39727727 original size:25 final size:26
Alignment explanation
Indices: 39727699--39727750 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
39727689 ATATACAATC
39727699 AAATCAA-AG-TATATTTATTTATTTA
1 AAATCAATAGCTATATTTATTT-TTTA
*
39727724 AAATCAATGGCTATATTTATTTTTTA
1 AAATCAATAGCTATATTTATTTTTTA
39727750 A
1 A
39727751 GGTTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 6 0.25
27 11 0.46
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (26 bp):
AAATCAATAGCTATATTTATTTTTTA
Found at i:39731206 original size:15 final size:16
Alignment explanation
Indices: 39731186--39731215 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39731176 GCCTTAGGTT
39731186 ATTTTTG-TTGGAAAA
1 ATTTTTGTTTGGAAAA
39731201 ATTTTTGTTTGGAAA
1 ATTTTTGTTTGGAAA
39731216 CAACTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
ATTTTTGTTTGGAAAA
Found at i:39736320 original size:9 final size:9
Alignment explanation
Indices: 39736306--39736331 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39736296 GAATGCTTTA
39736306 GAAACATTT
1 GAAACATTT
39736315 GAAACATTT
1 GAAACATTT
39736324 GAAACATT
1 GAAACATT
39736332 AAGGAAAAAG
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:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (9 bp):
GAAACATTT
Found at i:39748543 original size:16 final size:16
Alignment explanation
Indices: 39748510--39748549 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
39748500 GCATCTATGT
39748510 TTGTATATATAGTCGA
1 TTGTATATATAGTCGA
* * *
39748526 TTGTGTATATATTTGA
1 TTGTATATATAGTCGA
39748542 TTGTATAT
1 TTGTATAT
39748550 GAAGATTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (16 bp):
TTGTATATATAGTCGA
Found at i:39761549 original size:27 final size:28
Alignment explanation
Indices: 39761495--39761568 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
39761485 GTTTTGTTTG
*
39761495 ATTTTTCGTATTTCATAATTTAATTATA-A
1 ATTTTTC-TATTT-ATATTTTAATTATATA
*
39761524 ATTTTTCTATTTATATTTTATTTATATA
1 ATTTTTCTATTTATATTTTAATTATATA
* *
39761552 AATATT-TATTTATATTT
1 ATTTTTCTATTTATATTT
39761569 ATCTATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 23 0.57
28 10 0.25
29 7 0.17
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTTCTATTTATATTTTAATTATATA
Found at i:39761935 original size:88 final size:85
Alignment explanation
Indices: 39761765--39762268 Score: 303
Period size: 79 Copynumber: 6.0 Consensus size: 85
39761755 TTTTGTTTCC
* * * * *
39761765 AAATTAAAAGTAAATAAAATCCGTTTCGGGATTTATTTCCACCGTTCAATGGATTTTATTCCAAA
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGA-TTAATTCCGCCGTTCAA-AGATTTTATTCCAAA
* *
39761830 TTTTGGTTTTATGTCCAAACGGG
64 TTTT-GTTTTATTTCCAAACAGG
* *
39761853 AAATTAAAGGTAAAT-AAATCTGTTTCGGGATTAATTCCTGCCGTTCGACGAATTTTATT-CAAT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCC-GCCGTTCAAAG-ATTTTATTCCAA-
39761916 TATTTTGATTTTATTTCCAAACAGG
63 -ATTTTG-TTTTATTTCCAAACAGG
* * * * * *
39761941 ATATTACAGGTAAAATAAAATTTATTTCGAGATTGATTCCCGCCGTTCAAAGATTTTATTCCAAA
1 AAATTAAAGGT-AAATAAAATCTGTTTCGGGATTAATT-CCGCCGTTCAAAGATTTTATTCCAAA
39762006 TTTTGTTTTATTTCC--A-A--
64 TTTTGTTTTATTTCCAAACAGG
* ** * * * * * *
39762023 AAA--CAA-GTAAAATAAAATCCATTTTGGGATTGATTCCCGTCGTGCAACGATTTTATTCCAAT
1 AAATTAAAGGT-AAATAAAATCTGTTTCGGGATTAATT-CCGCCGTTCAAAGATTTTATTCCAAA
*
39762085 TTTTGTTTTATTT-C---TA--
64 TTTTGTTTTATTTCCAAACAGG
** * * * * *
39762101 AAA--ACGGGTAAAATAAAATCTGTTTCGGGATTTATTCTCGTCGTTCAACGAATTTATTAC-AA
1 AAATTAAAGGT-AAATAAAATCTGTTTCGGGATTAATTC-CGCCGTTCAAAGATTTTATTCCAAA
* * *
39762163 TTTTATTTTGTTTCCAAAAACAAG
64 TTTTGTTTTATTTCC--AAACAGG
** * * * **
39762187 AAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTTAACAAGATTTTATT--TT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATT-CCGCCG-TTCA-AAGATTTTATTCCAA
*
39762250 ATTTTATTTTATTTCCAAA
63 ATTTTGTTTTATTTCCAAA
39762269 TCAGAATTAA
Statistics
Matches: 338, Mismatches: 52, Indels: 54
0.76 0.12 0.12
Matches are distributed among these distances:
78 18 0.05
79 106 0.31
80 1 0.00
82 2 0.01
84 2 0.01
85 1 0.00
86 17 0.05
87 69 0.20
88 70 0.21
89 21 0.06
90 29 0.09
91 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (85 bp):
AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCGCCGTTCAAAGATTTTATTCCAAATT
TTGTTTTATTTCCAAACAGG
Found at i:39762038 original size:79 final size:79
Alignment explanation
Indices: 39761950--39762196 Score: 309
Period size: 79 Copynumber: 3.2 Consensus size: 79
39761940 GATATTACAG
* * * *
39761950 GTAAAATAAAATTTATTTCGAGATTGATTCCCGCCGTTCAAAGATTTTATTCCAAATTTTGTTTT
1 GTAAAATAAAATCTATTTCGGGATTGATTCCCGTCGTTCAACGATTTTATTCCAAATTTTGTTTT
39762015 ATTTCCAAAAACAA
66 ATTTCCAAAAACAA
* * * *
39762029 GTAAAATAAAATCCATTTTGGGATTGATTCCCGTCGTGCAACGATTTTATTCCAATTTTTGTTTT
1 GTAAAATAAAATCTATTTCGGGATTGATTCCCGTCGTTCAACGATTTTATTCCAAATTTTGTTTT
* **
39762094 ATTTCTAAAAACGG
66 ATTTCCAAAAACAA
* * * * * *
39762108 GTAAAATAAAATCTGTTTCGGGATTTATTCTCGTCGTTCAACGAATTTATTAC-AATTTTATTTT
1 GTAAAATAAAATCTATTTCGGGATTGATTCCCGTCGTTCAACGATTTTATTCCAAATTTTGTTTT
*
39762172 GTTTCCAAAAACAA
66 ATTTCCAAAAACAA
*
39762186 G-AAATTAAAAT
1 GTAAAATAAAAT
39762197 TAAATAAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
77 9 0.06
78 20 0.14
79 113 0.80
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (79 bp):
GTAAAATAAAATCTATTTCGGGATTGATTCCCGTCGTTCAACGATTTTATTCCAAATTTTGTTTT
ATTTCCAAAAACAA
Found at i:39762312 original size:84 final size:85
Alignment explanation
Indices: 39762162--39762370 Score: 244
Period size: 84 Copynumber: 2.4 Consensus size: 85
39762152 ATTTATTACA
* * ** *
39762162 ATTTTATTTTGTTTCCAAAAACAAGAAATTAAAATTAAA-TAA-AATCTGTTTTGGGATTTATTC
1 ATTTTATTTTATTTCC-AAATC-AG-AATTAAAATTAAATTAACAA--AATTTTAGGATTTATTC
* * ** *
39762225 CCGCCGTTTAACAAGATTTTATTTT
61 CCGCCGTTTAAAAAAAAATTATTTG
39762250 ATTTTATTTTATTTCCAAATCAGAATT-AAATTAAATTAACAAAATTTTAGGATTTATTCCCGCC
1 ATTTTATTTTATTTCCAAATCAGAATTAAAATTAAATTAACAAAATTTTAGGATTTATTCCCGCC
39762314 GTTTAAAAAAAAATTATTTG
66 GTTTAAAAAAAAATTATTTG
* *
39762334 ATTTTATTTTTTTTCCAAATTAGAATTAAAATTAAAT
1 ATTTTATTTTATTTCCAAATCAGAATTAAAATTAAAT
39762371 AAAATTTGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
84 67 0.63
85 16 0.15
86 4 0.04
87 4 0.04
88 15 0.14
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (85 bp):
ATTTTATTTTATTTCCAAATCAGAATTAAAATTAAATTAACAAAATTTTAGGATTTATTCCCGCC
GTTTAAAAAAAAATTATTTG
Found at i:39766310 original size:6 final size:6
Alignment explanation
Indices: 39766274--39766333 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
39766264 TAAATTATTC
* **
39766274 TATTTA TATTT- TAGTTA TATAAA TA-TT- TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
39766319 TATTTA TATTTA TAT
1 TATTTA TATTTA TAT
39766334 ATTTTATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 37 0.82
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:39766327 original size:28 final size:28
Alignment explanation
Indices: 39766262--39766340 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
39766252 AAAATTTAAT
39766262 TATAAATTATTCTATTTATATTT-TAGTTA
1 TATAAA-TATT-TATTTATATTTATAGTTA
*
39766291 TATAAATATTTATTTATATTTATATTTA
1 TATAAATATTTATTTATATTTATAGTTA
** *
39766319 TATTTATATTTATATAT-TTTAT
1 TATAAATATTTATTTATATTTAT
39766341 TTCACTAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.36
28 23 0.51
29 6 0.13
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (28 bp):
TATAAATATTTATTTATATTTATAGTTA
Found at i:39778080 original size:302 final size:302
Alignment explanation
Indices: 39777530--39778413 Score: 1687
Period size: 302 Copynumber: 2.9 Consensus size: 302
39777520 ATTGATACTC
* *
39777530 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATACAACTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
*
39777595 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATAGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
* *
39777660 GAAATAGAAGTAAAAAGAGAAAGAAAATTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
* *
39777725 AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACAGGTATCGTTAACAGAGACCACATC
196 AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
39777790 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
261 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
39777832 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
39777897 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
39777962 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
*
39778027 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
196 AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
*
39778092 GGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
261 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
39778134 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
39778199 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
39778264 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
39778329 AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
196 AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
39778394 AGGATAATTAGTTTCAGCAT
261 AGGATAATTAGTTTCAGCAT
39778414 GGTGGAGAAT
Statistics
Matches: 571, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
302 571 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (302 bp):
GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
AGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
Found at i:39789873 original size:2 final size:2
Alignment explanation
Indices: 39789866--39789895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39789856 TAGTCTATTC
39789866 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
39789896 TCCTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:39791765 original size:21 final size:19
Alignment explanation
Indices: 39791724--39791770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
39791714 CTATTAATTT
*
39791724 TAAAAAATATTTGAAATAA
1 TAAAAAACATTTGAAATAA
*
39791743 TAAAATAACATTTTAAAGTAA
1 TAAAA-AACATTTGAAA-TAA
39791764 TAAAAAA
1 TAAAAAA
39791771 AAAATGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 11 0.46
21 8 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAAAAACATTTGAAATAA
Found at i:39792360 original size:30 final size:28
Alignment explanation
Indices: 39792306--39792361 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
39792296 ATTGATAATA
39792306 AAAATATTATTAATAAAATAATAATTTT
1 AAAATATTATTAATAAAATAATAATTTT
* *
39792334 AAAATAATTATGTAATATAATTATAATT
1 AAAAT-ATTAT-TAATAAAATAATAATT
39792362 ATTATTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 5 0.21
30 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
AAAATATTATTAATAAAATAATAATTTT
Found at i:39797917 original size:3 final size:3
Alignment explanation
Indices: 39797909--39797946 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
39797899 ATTAATCTTG
*
39797909 TAT TAT TAT TAT TGAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
39797947 TATTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39805185 original size:3 final size:3
Alignment explanation
Indices: 39805177--39805214 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
39805167 ATTAATCTTG
*
39805177 TAT TAT TAT TAT TGAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
39805215 TATTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39809014 original size:20 final size:20
Alignment explanation
Indices: 39808989--39809029 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39808979 CCTCAATTTT
* *
39808989 AAAAATTTTATAAGTTTCTG
1 AAAAATTCTATAAATTTCTG
*
39809009 AAAAATTCTCTAAATTTCTG
1 AAAAATTCTATAAATTTCTG
39809029 A
1 A
39809030 TTTAGTCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAAATTCTATAAATTTCTG
Found at i:39815129 original size:12 final size:10
Alignment explanation
Indices: 39815100--39815133 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
39815090 TTTAGATGCC
39815100 TTAGAGAATT
1 TTAGAGAATT
39815110 TTAGAGAATT
1 TTAGAGAATT
39815120 TCTAAGAGAATT
1 T-T-AGAGAATT
39815132 TT
1 TT
39815134 CACTTTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (10 bp):
TTAGAGAATT
Found at i:39817387 original size:12 final size:12
Alignment explanation
Indices: 39817370--39817428 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
39817360 TATTTTAATG
39817370 AATTTAATATTA
1 AATTTAATATTA
*
39817382 AATTTAAT-CTA
1 AATTTAATATTA
39817393 AATATTAATA-TA
1 AAT-TTAATATTA
39817405 AGATATTAA-ATTA
1 A-AT-TTAATATTA
*
39817418 AATTAAATATT
1 AATTTAATATT
39817429 TATCTAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 8 0.20
12 22 0.55
13 10 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
AATTTAATATTA
Found at i:39817427 original size:30 final size:29
Alignment explanation
Indices: 39817376--39817489 Score: 95
Period size: 31 Copynumber: 3.8 Consensus size: 29
39817366 AATGAATTTA
39817376 ATATTAAATTTAATCTAAATATTAATATAAG
1 ATATTAAATTTAAT-TAAATATTAATAT-AG
* * *
39817407 ATATTAAATTAAATTAAATATTTATCTAG
1 ATATTAAATTTAATTAAATATTAATATAG
** * *
39817436 ATAGCATTTTA-TTAATTTAATATTAATATGAT
1 AT---ATTAAATTTAATTAAATATTAATAT-AG
*
39817468 ATATTAAATTTAATTTAATATT
1 ATATTAAATTTAATTAAATATT
39817490 TATCTAAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
29 8 0.12
30 24 0.36
31 27 0.41
32 7 0.11
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (29 bp):
ATATTAAATTTAATTAAATATTAATATAG
Found at i:39817458 original size:31 final size:30
Alignment explanation
Indices: 39817418--39817520 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 30
39817408 TATTAAATTA
* *
39817418 AATTAAATATTTATCTAGATAGCATTTTATT
1 AATTTAATATTTATCTAGATA-TATTTTATT
* * **
39817449 AATTTAATATTAATAT-GATATATTAAATTT
1 AATTTAATATTTATCTAGATATATTTTA-TT
*
39817479 AATTTAATATTTATCTAAATAATATTTTATT
1 AATTTAATATTTATCTAGAT-ATATTTTATT
*
39817510 AGTTTAATATT
1 AATTTAATATT
39817521 AATGTGGTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 4 0.07
30 20 0.35
31 27 0.47
32 6 0.11
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
AATTTAATATTTATCTAGATATATTTTATT
Found at i:39817463 original size:61 final size:61
Alignment explanation
Indices: 39817393--39817523 Score: 190
Period size: 61 Copynumber: 2.1 Consensus size: 61
39817383 ATTTAATCTA
* *
39817393 AATATTAATATAAGATATTAAATTAAATTAAATATTTATCTAGATAGCATTTTATTAATTT
1 AATATTAATATAAGATATTAAATTAAATTAAATATTTATCTAAATAACATTTTATTAATTT
* * * * * *
39817454 AATATTAATATGATATATTAAATTTAATTTAATATTTATCTAAATAATATTTTATTAGTTT
1 AATATTAATATAAGATATTAAATTAAATTAAATATTTATCTAAATAACATTTTATTAATTT
39817515 AATATTAAT
1 AATATTAAT
39817524 GTGGTTAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (61 bp):
AATATTAATATAAGATATTAAATTAAATTAAATATTTATCTAAATAACATTTTATTAATTT
Found at i:39818578 original size:19 final size:19
Alignment explanation
Indices: 39818554--39818592 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39818544 AGTGTTGACT
*
39818554 ACGAAATACATGACTTTGA
1 ACGAAATACATGAATTTGA
39818573 ACGAAATACATGAATTTGA
1 ACGAAATACATGAATTTGA
39818592 A
1 A
39818593 ATGGAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (19 bp):
ACGAAATACATGAATTTGA
Found at i:39820300 original size:37 final size:37
Alignment explanation
Indices: 39820235--39820326 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 37
39820225 ACAAGATCAA
* * * **
39820235 TTTCTTTGCAAAGAATTACTCATGTTCATCTTTGTCT
1 TTTCTTTGCAAGGAATCACTCATATTCATCTTCATCT
* *
39820272 TTTCTTTGCAGGGAATCACTCCTATTCATCTTCATCT
1 TTTCTTTGCAAGGAATCACTCATATTCATCTTCATCT
* *
39820309 TTTCCTTACAAGGAATCA
1 TTTCTTTGCAAGGAATCA
39820327 TTGATCTGCC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTCTTTGCAAGGAATCACTCATATTCATCTTCATCT
Found at i:39827393 original size:20 final size:20
Alignment explanation
Indices: 39827368--39827414 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 20
39827358 AGATTAATCC
39827368 ATATTTCATAATTT-TTTAAA
1 ATATTT-ATAATTTATTTAAA
39827388 ATATTTATAATTTAGTTTAAA
1 ATATTTATAATTTA-TTTAAA
39827409 ACTATT
1 A-TATT
39827415 AAATGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 7 0.29
22 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATTTATAATTTATTTAAA
Found at i:39828420 original size:11 final size:11
Alignment explanation
Indices: 39828405--39828434 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
39828395 AAAATTTAAA
39828405 AAAAAGTATTTT
1 AAAAA-TATTTT
39828417 AAAAATATTTT
1 AAAAATATTTT
39828428 AAAAATA
1 AAAAATA
39828435 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:39828437 original size:16 final size:16
Alignment explanation
Indices: 39828375--39828423 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
39828365 AAAACACAAA
39828375 AAAATTATTTTAAAAAT
1 AAAA-TATTTTAAAAAT
* *
39828392 AAAAAAATTTAAAAA-
1 AAAATATTTTAAAAAT
*
39828407 AAAGTATTTTAAAAAT
1 AAAATATTTTAAAAAT
39828423 A
1 A
39828424 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 12 0.46
16 10 0.38
17 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATATTTTAAAAAT
Found at i:39829025 original size:90 final size:90
Alignment explanation
Indices: 39828827--39829087 Score: 267
Period size: 90 Copynumber: 2.9 Consensus size: 90
39828817 ACTATTATTC
* * * * *
39828827 AAAATCTTCATATTATTTTTGTATCCGTAAATCAATTTTAGTCTATATTATTTGTTTGTTGAATT
1 AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
* * *
39828892 TCATATTTT-TGTATATTAATTTTGT
66 TTATATTTTCT-TATATCAATTTTCT
* * * * *
39828917 AAAATATTTGA-ATCATTTTTGGATCTGTAAA-AATATTTTAGTCTGTATTATTTGTCGGTCGAA
1 AAAAT-CTTCATATTATTTTTGTATCTGTAAATAA-ATTTTAGTCTGTATTATTTGTTGGTCGAA
39828980 TTTTATATTTTCTTATATCAATTTTCT
64 TTTTATATTTTCTTATATCAATTTTCT
* * * * * ** *
39829007 AAAATGTTCATATTATTTTTTTATTTGTAAATAAAATTTAGTATGTGCTATTTGTTGGTCAAATT
1 AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
* *
39829072 ATATATTTTCGTATAT
66 TTATATTTTCTTATAT
39829088 TAGTTTTATA
Statistics
Matches: 139, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
89 4 0.03
90 129 0.93
91 6 0.04
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (90 bp):
AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
TTATATTTTCTTATATCAATTTTCT
Found at i:39832668 original size:20 final size:20
Alignment explanation
Indices: 39832643--39832689 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 20
39832633 AGATTAATCC
39832643 ATATTTCATAATTT-TTTAAA
1 ATATTT-ATAATTTATTTAAA
39832663 ATATTTATAATTTAGTTTAAA
1 ATATTTATAATTTA-TTTAAA
39832684 ACTATT
1 A-TATT
39832690 AAATGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 7 0.29
22 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATTTATAATTTATTTAAA
Found at i:39833695 original size:11 final size:11
Alignment explanation
Indices: 39833680--39833709 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
39833670 AAAATTTAAA
39833680 AAAAAGTATTTT
1 AAAAA-TATTTT
39833692 AAAAATATTTT
1 AAAAATATTTT
39833703 AAAAATA
1 AAAAATA
39833710 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:39833712 original size:16 final size:16
Alignment explanation
Indices: 39833650--39833698 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
39833640 AAAACACAAA
39833650 AAAATTATTTTAAAAAT
1 AAAA-TATTTTAAAAAT
* *
39833667 AAAAAAATTTAAAAA-
1 AAAATATTTTAAAAAT
*
39833682 AAAGTATTTTAAAAAT
1 AAAATATTTTAAAAAT
39833698 A
1 A
39833699 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 12 0.46
16 10 0.38
17 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATATTTTAAAAAT
Found at i:39834300 original size:90 final size:90
Alignment explanation
Indices: 39834102--39834362 Score: 267
Period size: 90 Copynumber: 2.9 Consensus size: 90
39834092 ACTATTATTC
* * * * *
39834102 AAAATCTTCATATTATTTTTGTATCCGTAAATCAATTTTAGTCTATATTATTTGTTTGTTGAATT
1 AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
* * *
39834167 TCATATTTT-TGTATATTAATTTTGT
66 TTATATTTTCT-TATATCAATTTTCT
* * * * *
39834192 AAAATATTTGA-ATCATTTTTGGATCTGTAAA-AATATTTTAGTCTGTATTATTTGTCGGTCGAA
1 AAAAT-CTTCATATTATTTTTGTATCTGTAAATAA-ATTTTAGTCTGTATTATTTGTTGGTCGAA
39834255 TTTTATATTTTCTTATATCAATTTTCT
64 TTTTATATTTTCTTATATCAATTTTCT
* * * * * ** *
39834282 AAAATGTTCATATTATTTTTTTATTTGTAAATAAAATTTAGTATGTGCTATTTGTTGGTCAAATT
1 AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
* *
39834347 ATATATTTTCGTATAT
66 TTATATTTTCTTATAT
39834363 TAGTTTTATA
Statistics
Matches: 139, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
89 4 0.03
90 129 0.93
91 6 0.04
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (90 bp):
AAAATCTTCATATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTGTTGGTCGAATT
TTATATTTTCTTATATCAATTTTCT
Found at i:39841230 original size:109 final size:112
Alignment explanation
Indices: 39841048--39841251 Score: 261
Period size: 109 Copynumber: 1.8 Consensus size: 112
39841038 GTTGGTGTCA
* * * ** *
39841048 GCCATCTAGTTCCCTAAACCCAAATTTTTTTTTATCTAATAAAGTGGGTGTCAACCATTAGTGTG
1 GCCATCTAGTTCCCCAAACCCAAATATTTTTTTATCTAATAAAATGAATATCAACCATTAGTGTG
*
39841113 CCAGCACCAAAAAA-AA-TATCTTTTAATAAGAAAAAGGTAATGTTG
66 CCAACACCAAAAAACAATTATCTTTTAATAAGAAAAAGGTAATGTTG
* * * *
39841158 GCCATCTAGTTCCCCCAACCCAAA-ATTTTTTTATCTGATAAAATGAATATCGACTATTAGTGTG
1 GCCATCTAGTTCCCCAAACCCAAATATTTTTTTATCTAATAAAATGAATATCAACCATTAGTGTG
** *
39841222 TTAACACCAAAAAACAATTATTTTTTAATA
66 CCAACACCAAAAAACAATTATCTTTTAATA
39841252 TTAAAAAGTG
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
109 43 0.55
110 24 0.31
111 11 0.14
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (112 bp):
GCCATCTAGTTCCCCAAACCCAAATATTTTTTTATCTAATAAAATGAATATCAACCATTAGTGTG
CCAACACCAAAAAACAATTATCTTTTAATAAGAAAAAGGTAATGTTG
Found at i:39847515 original size:21 final size:18
Alignment explanation
Indices: 39847488--39847536 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
39847478 TTTTAGAAAA
39847488 TTTTTAAAATTTTAAAATT
1 TTTTTAAAATTTT-AAATT
*
39847507 ATATTTTAAAATTTTTAATT
1 -T-TTTTAAAATTTTAAATT
39847527 TTTTTAAAAT
1 TTTTTAAAAT
39847537 ATAATTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 5 0.19
21 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAAAATTTTAAATT
Found at i:39847535 original size:31 final size:30
Alignment explanation
Indices: 39847468--39847560 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 30
39847458 ATTTAGTTCC
39847468 AAAATTATTATTTTAGAAAATTTTTAAAATTTT
1 AAAATTA-TATTTT--AAAATTTTTAAAATTTT
**
39847501 AAAATTATATTTTAAAATTTTTAATTTTTTT
1 AAAATTATATTTTAAAATTTTTAA-AATTTT
**
39847532 AAAA-TATAATTTTTGAATTTTTGAAAATT
1 AAAATTAT-ATTTTAAAATTTTT-AAAATT
39847561 ATTTTAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 14 0.27
31 22 0.43
32 8 0.16
33 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
AAAATTATATTTTAAAATTTTTAAAATTTT
Found at i:39847564 original size:21 final size:23
Alignment explanation
Indices: 39847516--39847575 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
39847506 TATATTTTAA
*
39847516 AATTTTT-AATTTTTTTAAAATAT
1 AATTTTTGAA-TTTTTGAAAATAT
39847539 AATTTTTGAATTTTTGAAAAT-T
1 AATTTTTGAATTTTTGAAAATAT
* *
39847561 -ATTTTAGATTTTTTG
1 AATTTTTGAATTTTTG
39847576 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 13 0.39
22 1 0.03
23 17 0.52
24 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
AATTTTTGAATTTTTGAAAATAT
Found at i:39848055 original size:25 final size:23
Alignment explanation
Indices: 39848027--39848080 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
39848017 TTAGGTACAA
39848027 AATTTTGATATTTTAAACTAATTTT
1 AATTTTGATATTTT-AAC-AATTTT
* *
39848052 AATTTTTATATTTTAACCATTTT
1 AATTTTGATATTTTAACAATTTT
39848075 AATTTT
1 AATTTT
39848081 TCTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.41
24 3 0.11
25 13 0.48
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (23 bp):
AATTTTGATATTTTAACAATTTT
Found at i:39848077 original size:23 final size:24
Alignment explanation
Indices: 39848027--39848091 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
39848017 TTAGGTACAA
*
39848027 AATTTTGATATTTTAAACTAATTTT
1 AATTTTTATATTTT-AACTAATTTT
*
39848052 AATTTTTATATTTTAAC-CATTTT
1 AATTTTTATATTTTAACTAATTTT
*
39848075 AATTTTTCTATTATTAA
1 AATTTTTATATT-TTAA
39848092 ATTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.44
24 7 0.19
25 13 0.36
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTTTTATATTTTAACTAATTTT
Found at i:39851653 original size:29 final size:28
Alignment explanation
Indices: 39851607--39851679 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 28
39851597 TGTTGCAATG
39851607 GAAATTGTCTGCAGTTTTCAATGAAACTA
1 GAAATTGTCTGCA-TTTTCAATGAAACTA
*
39851636 GAAATTGTCTGCTATTTTCAATGAAACTG
1 GAAATTGTCTGC-ATTTTCAATGAAACTA
39851665 GAAATTGT-TGCATTT
1 GAAATTGTCTGCATTT
39851680 GTTTAGGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 4 0.10
28 3 0.07
29 34 0.81
30 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (28 bp):
GAAATTGTCTGCATTTTCAATGAAACTA
Found at i:39852177 original size:13 final size:13
Alignment explanation
Indices: 39852159--39852183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39852149 TTTATTAGTG
39852159 AAAGAGTACATAT
1 AAAGAGTACATAT
39852172 AAAGAGTACATA
1 AAAGAGTACATA
39852184 CAAATTTGAT
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAGAGTACATAT
Found at i:39852185 original size:51 final size:51
Alignment explanation
Indices: 39852088--39852190 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
39852078 AACTTTTTAC
* **
39852088 TAATATATAATTTATTAGTGAAAGCGTACATAAAAAAAATTGATACAAATT
1 TAATATATAATTTATTAGTGAAAGAGTACATAAAAAAAATACATACAAATT
* * *
39852139 TAATATATAATTTATTAGTGAAAGAGTACATATAAAGAGTACATACAAATT
1 TAATATATAATTTATTAGTGAAAGAGTACATAAAAAAAATACATACAAATT
39852190 T
1 T
39852191 GATACTAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.34
Consensus pattern (51 bp):
TAATATATAATTTATTAGTGAAAGAGTACATAAAAAAAATACATACAAATT
Found at i:39852416 original size:18 final size:17
Alignment explanation
Indices: 39852388--39852422 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39852378 TTTATTAAGA
*
39852388 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39852405 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39852423 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39852501 original size:66 final size:64
Alignment explanation
Indices: 39852425--39852622 Score: 184
Period size: 66 Copynumber: 3.2 Consensus size: 64
39852415 AAATATATTT
*
39852425 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATGTTAA-TTATATTTTATA-TATCATATATTATGATTTGAGTAAATTCATATAA
39852490 G
64 G
* * * * * **
39852491 AATATTAATTA--TTAA-GA-ATTTTAT-TA-AAT-TA-TAT-ATTTTAATTAAAAT-ATAT-TT
1 AATATTAATTATGTTAATTATATTTTATATATCATATATTATGA-TTTGAGTAAATTCATATAAG
* *
39852545 AATAATAATTATGTTAAATTATCTTTTATATTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATGTT-AATTATATTTTATA-TATCATATATTATGATTTGAGTAAATTCATATAA
39852610 G
64 G
39852611 AATATTAATTAT
1 AATATTAATTAT
39852623 TAAGAATTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 28
0.68 0.12 0.19
Matches are distributed among these distances:
54 10 0.10
55 5 0.05
56 14 0.14
57 4 0.04
58 3 0.03
59 8 0.08
61 9 0.09
62 3 0.03
63 2 0.02
64 16 0.16
65 5 0.05
66 21 0.21
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (64 bp):
AATATTAATTATGTTAATTATATTTTATATATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:39852536 original size:18 final size:17
Alignment explanation
Indices: 39852508--39852542 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39852498 ATTATTAAGA
*
39852508 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39852525 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39852543 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39852592 original size:120 final size:120
Alignment explanation
Indices: 39852379--39852684 Score: 567
Period size: 120 Copynumber: 2.5 Consensus size: 120
39852369 ATACTACTTT
*
39852379 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATT
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
39852444 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAA
66 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAA
39852499 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
* *
39852564 TATCTTTTATATTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAA
66 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAA
*
39852619 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAA
39852684 T
65 T
39852685 ATGATTAAAT
Statistics
Matches: 181, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 175 0.97
121 6 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAT
TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAA
Done.