Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 135 of 207
Found at i:41363790 original size:24 final size:24
Alignment explanation
Indices: 41363756--41363809 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
41363746 CGATATCTAT
* *
41363756 GGGATCTTCTTCTTCTTCTTTTTC
1 GGGATCATCTTCTTCTTCTTCTTC
41363780 GGGATCATCTTCTTCTTCTTCTTC
1 GGGATCATCTTCTTCTTCTTCTTC
41363804 GGGATC
1 GGGATC
41363810 CTCACTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.07, C:0.26, G:0.17, T:0.50
Consensus pattern (24 bp):
GGGATCATCTTCTTCTTCTTCTTC
Found at i:41364736 original size:25 final size:26
Alignment explanation
Indices: 41364700--41364752 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
41364690 TGATTAGTAT
*
41364700 AAAATATTAATAATTCAAT-AAATTG
1 AAAATATTAATAATTAAATAAAATTG
41364725 AAAAT-TTAAATAATTAAATAAAATTG
1 AAAATATT-AATAATTAAATAAAATTG
41364751 AA
1 AA
41364753 GTTAGGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 15 0.60
26 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATATTAATAATTAAATAAAATTG
Found at i:41372189 original size:19 final size:20
Alignment explanation
Indices: 41372153--41372190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41372143 ACCTAACACG
*
41372153 AATTAAATTTAAGCCATATT
1 AATTAAATTTAAGACATATT
*
41372173 AATTAATTTTAA-ACATAT
1 AATTAAATTTAAGACATAT
41372191 AAACATCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTAAATTTAAGACATATT
Found at i:41385089 original size:24 final size:24
Alignment explanation
Indices: 41385062--41385110 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
41385052 AGATCCGAAG
* *
41385062 GCATTTGTGCGAGATACTAATTCC
1 GCATTGGTGCGAGATACTAAATCC
*
41385086 GCATTGGTGCGAGTTACTAAATCC
1 GCATTGGTGCGAGATACTAAATCC
41385110 G
1 G
41385111 GGTTAAGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (24 bp):
GCATTGGTGCGAGATACTAAATCC
Found at i:41385141 original size:40 final size:40
Alignment explanation
Indices: 41385086--41385172 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
41385076 TACTAATTCC
* * *
41385086 GCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAG
1 GCATTTGTGCAAGTTACTATAA-CCGGGCTAAGTCCCGAAG
*
41385126 GCATTTGTGCAAGTTACTATAACCGGGCTATGTCCCGAAG
1 GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
41385166 GCATTTG
1 GCATTTG
41385173 AACGAGTAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
GCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAG
Found at i:41388692 original size:54 final size:54
Alignment explanation
Indices: 41388634--41388800 Score: 126
Period size: 54 Copynumber: 3.1 Consensus size: 54
41388624 TTATTACTTC
41388634 TATCATTTATATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCACT
1 TATCATTTATATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCACT
* * * * * *** * * ** * * *
41388688 TATCAATTAGGGAT-TTTAT-GTATTTTTATTTTAGTGTACACAAT--TTATTACTT
1 TATCATTTA--TATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCAC-T
*
41388741 CTATCATTTGTATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCACT
1 -TATCATTTATATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCACT
41388796 TATCA
1 TATCA
41388801 ATTAGGGAAA
Statistics
Matches: 74, Mismatches: 31, Indels: 16
0.61 0.26 0.13
Matches are distributed among these distances:
52 6 0.08
53 5 0.07
54 52 0.70
55 5 0.07
56 6 0.08
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (54 bp):
TATCATTTATATATCTATACTATTTATAAAGTCGTTTACTGAATAGGTGTCACT
Found at i:41388782 original size:108 final size:108
Alignment explanation
Indices: 41388593--41388808 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
41388583 TTTGATTTTT
41388593 TTTTATGTATTTTTATTTTAGTGTACACAATTTATTACTTCTATCATTTATATATCTATACTATT
1 TTTTATGTATTTTTATTTTAGTGTACACAATTTATTACTTCTATCATTTATATATCTATACTATT
41388658 TATAAAGTCGTTTACTGAATAGGTGTCACTTATCAATTAGGGA
66 TATAAAGTCGTTTACTGAATAGGTGTCACTTATCAATTAGGGA
*
41388701 TTTTATGTATTTTTATTTTAGTGTACACAATTTATTACTTCTATCATTTGTATATCTATACTATT
1 TTTTATGTATTTTTATTTTAGTGTACACAATTTATTACTTCTATCATTTATATATCTATACTATT
41388766 TATAAAGTCGTTTACTGAATAGGTGTCACTTATCAATTAGGGA
66 TATAAAGTCGTTTACTGAATAGGTGTCACTTATCAATTAGGGA
41388809 AACTATTTAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (108 bp):
TTTTATGTATTTTTATTTTAGTGTACACAATTTATTACTTCTATCATTTATATATCTATACTATT
TATAAAGTCGTTTACTGAATAGGTGTCACTTATCAATTAGGGA
Found at i:41390468 original size:21 final size:21
Alignment explanation
Indices: 41390419--41390468 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
41390409 ATAAATGCGA
*
41390419 AAACCCTACACTTGAGGCCCT
1 AAACCCTACACTCGAGGCCCT
* * * *
41390440 AGATCCTATACTCGAGGCCTT
1 AAACCCTACACTCGAGGCCCT
41390461 AAACCCTA
1 AAACCCTA
41390469 AACCCAAAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (21 bp):
AAACCCTACACTCGAGGCCCT
Found at i:41392494 original size:14 final size:14
Alignment explanation
Indices: 41392475--41392516 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
41392465 AGTAGTCTCG
41392475 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
*
41392489 TTTTTATTTATTTA
1 TTTTTATTTTTTTA
**
41392503 TTTACATTTTTTTA
1 TTTTTATTTTTTTA
41392517 AGAAACGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:41392721 original size:19 final size:20
Alignment explanation
Indices: 41392671--41392710 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41392661 GGCGGCGCCA
*
41392671 CTGCCGGCGGTCGGAGGCCG
1 CTGCCGGTGGTCGGAGGCCG
41392691 CTGCCGGTGGTCGGAGGCCG
1 CTGCCGGTGGTCGGAGGCCG
41392711 TCGCGGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.33, G:0.50, T:0.12
Consensus pattern (20 bp):
CTGCCGGTGGTCGGAGGCCG
Found at i:41393474 original size:3 final size:3
Alignment explanation
Indices: 41393461--41393544 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
41393451 TCACATTTTA
* * *
41393461 TAT TGT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * *
41393509 CAT TGC TAT TAT TAT TAG CAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41393545 ATATCAATTT
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:41395360 original size:16 final size:16
Alignment explanation
Indices: 41395335--41395368 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41395325 TGTGTTTTGC
* *
41395335 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
41395351 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
41395367 TT
1 TT
41395369 CATCTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:41407143 original size:24 final size:24
Alignment explanation
Indices: 41407089--41407146 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
41407079 ATGTCCCAAA
*
41407089 ATTACAATGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
41407113 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
41407137 ATTACAGTGG
1 ATTACAGTGG
41407147 GGGCAATCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTGAAG
Found at i:41407563 original size:51 final size:51
Alignment explanation
Indices: 41407429--41407711 Score: 334
Period size: 51 Copynumber: 5.7 Consensus size: 51
41407419 ACCGTTAAAG
** * * * *
41407429 TTGCAGTGGAGCAGATTAAAGCTGAAGGTAGCGAATCTTATTTCCCTGGCG
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* * *
41407480 TCGCA---G--TAGATTACAGCTGAAGGGAGCGAATCTCATTTCCTTGGCA
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* * * **
41407526 TTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTATTTCCTTGGTG
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
41407577 TTGCA---G--TAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* *
41407623 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGCG
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* *
41407674 TTGTAGTGGAATAGATTAAAGCTGAAGGCAGCGTATCT
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCT
41407712 TTTTTCCCTA
Statistics
Matches: 198, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
46 78 0.39
48 2 0.01
49 2 0.01
51 116 0.59
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (51 bp):
TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
Found at i:41407595 original size:97 final size:97
Alignment explanation
Indices: 41407429--41407711 Score: 395
Period size: 97 Copynumber: 2.9 Consensus size: 97
41407419 ACCGTTAAAG
** * * * * *
41407429 TTGCAGTGGAGCAGATTAAAGCTGAAGGTAGCGAATCTTATTTCCCTGGCGTCGCAGTAGATTAC
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGTGTTGCAGTAGATTAA
*
41407494 AGCTGAAGGGAGCGAATCTCATTTCCTTGGCA
66 AGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* *
41407526 TTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTATTTCCTTGGTGTTGCAGTAGATTAA
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGTGTTGCAGTAGATTAA
41407591 AGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
66 AGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
* * *
41407623 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGCGTTGTAGTGGAATAG
1 TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTT-G-G-TGT--TGCAGTAG
*
41407688 ATTAAAGCTGAAGGCAGCGTATCT
61 ATTAAAGCTGAAGGCAGCGAATCT
41407712 TTTTTCCCTA
Statistics
Matches: 165, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
97 131 0.79
98 1 0.01
99 1 0.01
100 3 0.02
102 29 0.18
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (97 bp):
TTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGTGTTGCAGTAGATTAA
AGCTGAAGGCAGCGAATCTCATTTCCTTGGCA
Found at i:41407718 original size:51 final size:51
Alignment explanation
Indices: 41407428--41407775 Score: 323
Period size: 51 Copynumber: 7.1 Consensus size: 51
41407418 TACCGTTAAA
** * * * *
41407428 GTTGCAGTGGAGCAGATTAAAGCTGAAGGTAGCGAATCTTATTTCCCTGGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
* * * *
41407479 GTCGCA---G--TAGATTACAGCTGAAGGGAGCGAATCTCATTTCCTTGGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
* * * * * *
41407525 ATTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTATTTCCTTGGT
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
*
41407576 GTTGCA---G--TAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
*
41407622 ATTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
* * ** *
41407673 GTTGTAGTGGAATAGATTAAAGCTGAAGGCAGCGTATCTTTTTTCCCTAGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
* * * * *
41407724 GTT--A---CACTAGATTAAAGCTGAAGGCAG-GAAAACTTATTTCCCTAGC
1 GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCG-AATCTCATTTCCTTAGC
41407770 GTTGCA
1 GTTGCA
41407776 ATGGTGTGAC
Statistics
Matches: 252, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.00
46 116 0.46
48 3 0.01
49 3 0.01
51 129 0.51
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (51 bp):
GTTGCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTAGC
Found at i:41407763 original size:148 final size:148
Alignment explanation
Indices: 41407441--41407764 Score: 399
Period size: 148 Copynumber: 2.2 Consensus size: 148
41407431 GCAGTGGAGC
* * * * * * *
41407441 AGATTAAAGCTGAAGGTAGCGAATCTTATTTCCCTGGCGTCGCA---G--TAGATTACAGCTGAA
1 AGATTAAAGCTGAAGGCAGCGAAACTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTGAA
* *
41407501 GGGAGCGAATCTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTA
66 GGCAGCGAATCTCATTTCCTTAGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTA
* * * * *
41407566 TTTCCTTGGTGTTGCAGT
131 TTTCCCTAGCGTTACACT
*
41407584 AGATTAAAGCTGAAGGCAGCGAATCTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTGAA
1 AGATTAAAGCTGAAGGCAGCGAAACTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTGAA
* * * ** *
41407649 GGCAGCGAATCTCATTTCCTTAGCGTTGTAGTGGAATAGATTAAAGCTGAAGGCAGCGTATCTTT
66 GGCAGCGAATCTCATTTCCTTAGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTA
41407714 TTTCCCTAGCGTTACACT
131 TTTCCCTAGCGTTACACT
*
41407732 AGATTAAAGCTGAAGGCAG-GAAAACTTATTTCC
1 AGATTAAAGCTGAAGGCAGCG-AAACTCATTTCC
41407765 CTAGCGTTGC
Statistics
Matches: 154, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
143 39 0.25
146 1 0.01
147 1 0.01
148 113 0.73
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (148 bp):
AGATTAAAGCTGAAGGCAGCGAAACTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTGAA
GGCAGCGAATCTCATTTCCTTAGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAACAAATCTTA
TTTCCCTAGCGTTACACT
Found at i:41410127 original size:47 final size:47
Alignment explanation
Indices: 41410061--41410720 Score: 1191
Period size: 47 Copynumber: 14.1 Consensus size: 47
41410051 GAAATGATAG
41410061 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41410108 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410155 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410202 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410249 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-A
41410297 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41410344 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410391 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410438 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410485 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41410532 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410579 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410626 TAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
** * * * * * *
41410672 -CGGGCCGAGTGGCCAACGTGATG-ATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41410717 TAAG
1 TAAG
41410721 TCCCGAAGGG
Statistics
Matches: 594, Mismatches: 16, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
45 25 0.04
46 48 0.08
47 474 0.80
48 47 0.08
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41410894 original size:36 final size:37
Alignment explanation
Indices: 41410839--41410916 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
41410829 CCGAGCTCTA
* *
41410839 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41410875 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41410912 AAGAC
1 AAGAC
41410917 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41418336 original size:24 final size:24
Alignment explanation
Indices: 41418309--41418366 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
41418299 ATGTCCCAAA
41418309 ATTACAATGGATTGAACCTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
*
41418333 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
41418357 ATTACAATGG
1 ATTACAATGG
41418367 GGGCAATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (24 bp):
ATTACAATGGATTGAACCTTGAAG
Found at i:41418818 original size:97 final size:97
Alignment explanation
Indices: 41418663--41419387 Score: 1038
Period size: 97 Copynumber: 7.5 Consensus size: 97
41418653 AGTGGAGCAA
* * * * *
41418663 ATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTCGCAATAGATTAAAGTTGAAGGTAGCG
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
*
41418728 AATCTCATTTCCTTGGCGTTGCAGTGGAATAG
66 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
* * * *
41418760 ATTCAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTG
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
*
41418825 AATCTCATTTCCTTGGCATTGCAGTGGAATAT
66 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
* * * *
41418857 ATTAAAGCTGAAGGTAGCAAATCTTATTTTCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCCAGC
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGG-CAGC
*
41418922 GAATCTCATTTCCTTGGCGTTGCAGTGGAATAG
65 GAATCTCATTTCCTTGGCATTGCAGTGGAATAG
** * * *
41418955 ATTAAAGTTGAAGATAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTACAGCTGAAAGCAGTG
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
41419020 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
66 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
* * *
41419052 ATTAAAGCTAAAGGTAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCCAGC
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGG-CAGC
*
41419117 TAATCTCATTTCCTTGGCATTGCAGTGGAATAG
65 GAATCTCATTTCCTTGGCATTGCAGTGGAATAG
* * * * *
41419150 ATTAATGTTGAAGGCAGCAAATCTTATTTCCCTGGCATTTCAGTAGATTACAGCTGAAGGCAGTG
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
* *
41419215 AATCTCGTTTCCTTGGCATTGCAGTGGAATAA
66 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
* * *
41419247 ATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTTGCAGTAGATTAAAGCTGAAGGTAGCG
1 ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
* * * * *
41419312 AATCTTATTTCCCTAGCGTTGCAGTGGAACAG
66 AATCTCATTTCCTTGGCATTGCAGTGGAATAG
* *
41419344 ATTAAAGCTT-AAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGT
1 ATTAAAG-TTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGT
41419388 GGAATAGATT
Statistics
Matches: 559, Mismatches: 66, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
97 382 0.68
98 177 0.32
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (97 bp):
ATTAAAGTTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGCG
AATCTCATTTCCTTGGCATTGCAGTGGAATAG
Found at i:41418983 original size:195 final size:194
Alignment explanation
Indices: 41418652--41419383 Score: 1135
Period size: 195 Copynumber: 3.8 Consensus size: 194
41418642 GCTAAAGTTA
** * * *
41418652 CAGTGGAGCAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTCGCAATAGATTAAAGT
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* *
41418717 TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTCAAGTTGAAGGCAGCAAAT
66 TGAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGTTGAAGGCAGCAAAT
41418782 CTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTG
131 CTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTG
* * * *
41418846 CAGTGGAATATATTAAAGCTGAAGGTAGCAAATCTTATTTTCCTAGCGTTGCAGTAGATTAAAGC
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
**
41418911 TGAAGGCCAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGTTGAAGATAGCAAA
66 TGAAGG-CAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGTTGAAGGCAGCAAA
* *
41418976 TCTTATTTCCCTGGCGTTGCAGTAGATTACAGCTGAAAGCAGTGAATCTCATTTCCTTGGCATTG
130 TCTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTG
* * *
41419041 CAGTGGAATAGATTAAAGCTAAAGGTAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* * *
41419106 TGAAGGCCAGCTAATCTCATTTCCTTGGCATTGCAGTGGAATAGATTAATGTTGAAGGCAGCAAA
66 TGAAGG-CAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGTTGAAGGCAGCAAA
* *
41419171 TCTTATTTCCCTGGCATT-TCAGTAGATTACAGCTGAAGGCAGTGAATCTCGTTTCCTTGGCATT
130 TCTTATTTCCCTGGCGTTGT-AGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATT
41419235 G
194 G
*
41419236 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTTGCAGTAGATTAAAGC
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* * * * * *
41419301 TGAAGGTAGCGAATCTTATTTCCCTAGCGTTGCAGTGGAACAGATTAAAGCTT-AAGGCAGCGAA
66 TGAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAG-TTGAAGGCAGCAAA
*
41419365 TCTTATTTCCCTAGCGTTG
130 TCTTATTTCCCTGGCGTTG
41419384 CAGTGGAATA
Statistics
Matches: 491, Mismatches: 43, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
194 124 0.25
195 367 0.75
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (194 bp):
CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
TGAAGGCAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGTTGAAGGCAGCAAAT
CTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTG
Found at i:41419220 original size:292 final size:292
Alignment explanation
Indices: 41418652--41419387 Score: 1080
Period size: 292 Copynumber: 2.5 Consensus size: 292
41418642 GCTAAAGTTA
** * * *
41418652 CAGTGGAGCAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTCGCAATAGATTAAAGT
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* * *
41418717 TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTCAAGTTGAAGGCAGCAAAT
66 TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAAGGCAGCAAAT
* *
41418782 CTTATTTCCCTGGCGTTGTAGTAGATTACAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTGC
131 CTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTGC
* * * *
41418847 AGTGGAATATATTAAAGCTGAAGGTAGCAAATCTTATTTTCCTAGCGTTGCAGTAGATTAAAGCT
196 AGTGGAATAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGCATTGCAGTAGATTAAAGCT
*
41418912 GAAGGCCAGCGAATCTCATTTCCTTGGCGTTG
261 GAAGGCCAGCGAATCTCATTTCCTTGGCATTG
* * ** *
41418944 CAGTGGAATAGATTAAAGTTGAAGATAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTACAGC
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* * * * *
41419009 TGAAAGCAGTGAATCTCATTTCCTTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAGCAAAT
66 TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAAGGCAGCAAAT
41419074 CTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCCAGCT-AATCTCATTTCCTTGGCATT
131 CTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGG-CAG-TGAATCTCATTTCCTTGGCATT
* * * * *
41419138 GCAGTGGAATAGATTAATGTTGAAGGCAGCAAATCTTATTTCCCTGGCATTTCAGTAGATTACAG
194 GCAGTGGAATAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGCATTGCAGTAGATTAAAG
* *
41419203 CTGAAGG-CAGTGAATCTCGTTTCCTTGGCATTG
259 CTGAAGGCCAGCGAATCTCATTTCCTTGGCATTG
*
41419236 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTTGCAGTAGATTAAAGC
1 CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
* * * * * *
41419301 TGAAGGTAGCGAATCTTATTTCCCTAGCGTTGCAGTGGAACAGATTAAAGCTTAAGGCAGCGAAT
66 TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAAGGCAGCAAAT
*
41419366 CTTATTTCCCTAGCGTTGCAGT
131 CTTATTTCCCTGGCGTTGCAGT
41419388 GGAATAGATT
Statistics
Matches: 392, Mismatches: 50, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
292 305 0.78
293 86 0.22
294 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (292 bp):
CAGTGGAATAAATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGCGTTGCAGTAGATTAAAGC
TGAAGGTAGCGAATCTCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTAAAGGCAGCAAAT
CTTATTTCCCTGGCGTTGCAGTAGATTAAAGCTGAAGGCAGTGAATCTCATTTCCTTGGCATTGC
AGTGGAATAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGCATTGCAGTAGATTAAAGCT
GAAGGCCAGCGAATCTCATTTCCTTGGCATTG
Found at i:41422100 original size:21 final size:20
Alignment explanation
Indices: 41422051--41422106 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
41422041 TTTTCATTTT
41422051 TTTAAA-TTTAAAAATATAA
1 TTTAAATTTTAAAAATATAA
* *
41422070 TCTT-ATTTTTAAAATATTTAA
1 T-TTAAATTTTAAAA-ATATAA
41422091 TTTAAATTTTGAAAAA
1 TTTAAATTTT-AAAAA
41422107 CGTTAAGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 12 0.41
22 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATTTTAAAAATATAA
Found at i:41436182 original size:31 final size:31
Alignment explanation
Indices: 41436144--41436211 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
41436134 AAGTATATAT
*
41436144 ATGTGATAGGGCCGAGTGGCCAATGTGATGA
1 ATGTGATAGGGCCGAGTGGCCAACGTGATGA
41436175 ATGTGATAGGGCCGAGTGGCCAACGTGATGA
1 ATGTGATAGGGCCGAGTGGCCAACGTGATGA
41436206 ATGTGA
1 ATGTGA
41436212 AAGTGTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.38, T:0.22
Consensus pattern (31 bp):
ATGTGATAGGGCCGAGTGGCCAACGTGATGA
Found at i:41436245 original size:47 final size:47
Alignment explanation
Indices: 41436175--41436419 Score: 364
Period size: 47 Copynumber: 5.2 Consensus size: 47
41436165 AATGTGATGA
* * *
41436175 ATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * * * *
41436222 ATGTGATAGGGTCGAGTGACCAACGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
*
41436269 ATGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* * *
41436316 ATGAGATAAGACCTAATGGCCAATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
* *
41436363 ATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATAA
1 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
41436410 ATGTGATAAG
1 ATGTGATAAG
41436420 TCCCGAAGGG
Statistics
Matches: 182, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 182 1.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATAT
Found at i:41440372 original size:28 final size:28
Alignment explanation
Indices: 41440340--41440395 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
41440330 ATGAAAAGTT
41440340 AGCAAAAGATATGTTAACATAATCATCA
1 AGCAAAAGATATGTTAACATAATCATCA
41440368 AGCAAAAGATATGTTAACATAATCATCA
1 AGCAAAAGATATGTTAACATAATCATCA
41440396 CCCCTCGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (28 bp):
AGCAAAAGATATGTTAACATAATCATCA
Found at i:41446068 original size:8 final size:9
Alignment explanation
Indices: 41446055--41446104 Score: 50
Period size: 8 Copynumber: 5.3 Consensus size: 9
41446045 GTAGTTAAAG
41446055 TAAGTTAA-
1 TAAGTTAAT
41446063 TAAGTTAAT
1 TAAGTTAAT
41446072 TAAGTATTAAAT
1 TAAG--TT-AAT
41446084 TAA-TTAAT
1 TAAGTTAAT
41446092 TAATGTTAAT
1 TAA-GTTAAT
41446102 TAA
1 TAA
41446105 ACTTAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 14 0.39
9 6 0.17
10 8 0.22
11 2 0.06
12 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
TAAGTTAAT
Found at i:41448198 original size:6 final size:6
Alignment explanation
Indices: 41448187--41448223 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
41448177 AGTTGGGATA
41448187 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T
41448224 GTCTCCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:41450574 original size:191 final size:190
Alignment explanation
Indices: 41450239--41450619 Score: 717
Period size: 191 Copynumber: 2.0 Consensus size: 190
41450229 TCTATTTCTA
41450239 TTTAGAGGCCTAAAAATGGGCCAAACCTGATGGGCCTTCTAGTATGGCTCAACTATGCAGTGACT
1 TTTAGAGGCCTAAAAATGGGCCAAACCTGATGGGCCTTCTAGTATGGCTCAACTATGCAGTGACT
*
41450304 ATGGTAGGCGCCATCCGGGCGAGTGCTGGAGGAGGTTGGGAGCATGTCTGCAATATAGGTCGATC
66 ATGGTAGGCGCCATCCGGGCGAGTGCTGGAGGAGGTTGGGAGCATGTCTACAATATAGGTCGATC
*
41450369 GAGTATCATATTAGAGAATGCCTACAACATTCTGATTAGATACAAGCTTCAGTTCTGGGT
131 GAGTATCATATTAGAGAATGCCTACAACATTCTGATCAGATACAAGCTTCAGTTCTGGGT
41450429 TTTAGAGGCCTAAAAAATGGGCCAAACCTGATGGGCCTTCTAGTATGGCTCAACTATGCAGTGAC
1 TTTAGAGGCCT-AAAAATGGGCCAAACCTGATGGGCCTTCTAGTATGGCTCAACTATGCAGTGAC
41450494 TATGGTAGGCGCCATCCGGGCGAGTGCTGGAGGAGGTTGGGAGCATGTCTACAATATAGGTCGAT
65 TATGGTAGGCGCCATCCGGGCGAGTGCTGGAGGAGGTTGGGAGCATGTCTACAATATAGGTCGAT
* *
41450559 CGAGTATCGTATTAGAGAATGCCTACAACATTCTGATCAGATACAAGCTTCGGTTCTGGGT
130 CGAGTATCATATTAGAGAATGCCTACAACATTCTGATCAGATACAAGCTTCAGTTCTGGGT
41450620 GTTATTTAGC
Statistics
Matches: 186, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
190 11 0.06
191 175 0.94
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (190 bp):
TTTAGAGGCCTAAAAATGGGCCAAACCTGATGGGCCTTCTAGTATGGCTCAACTATGCAGTGACT
ATGGTAGGCGCCATCCGGGCGAGTGCTGGAGGAGGTTGGGAGCATGTCTACAATATAGGTCGATC
GAGTATCATATTAGAGAATGCCTACAACATTCTGATCAGATACAAGCTTCAGTTCTGGGT
Found at i:41459654 original size:16 final size:16
Alignment explanation
Indices: 41459614--41459648 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41459604 ACAAAGGGTC
*
41459614 ATAATTATTCAAGTTG
1 ATAATTATTCAAGTAG
41459630 ATAATTATTCAAGTAG
1 ATAATTATTCAAGTAG
41459646 ATA
1 ATA
41459649 TCTATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (16 bp):
ATAATTATTCAAGTAG
Found at i:41460929 original size:21 final size:22
Alignment explanation
Indices: 41460881--41460933 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
41460871 CTTTCTTTTT
*
41460881 TATGATATATATTTACTTTGAGA
1 TATGATAT-TATTTACTTTGAAA
41460904 TATGATATTATTTA-TTT-AAA
1 TATGATATTATTTACTTTGAAA
41460924 TCATGATATT
1 T-ATGATATT
41460934 TGAAATCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 11 0.39
22 6 0.21
23 8 0.29
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGATATTATTTACTTTGAAA
Found at i:41468058 original size:25 final size:25
Alignment explanation
Indices: 41468030--41468090 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
41468020 TCACAGCTTA
* * *
41468030 TGTGAACATACCGATTTATAGCTCG
1 TGTGAGCATACCAATTTACAGCTCG
41468055 TGTGAGCATACCAATTTACAGCTCG
1 TGTGAGCATACCAATTTACAGCTCG
41468080 TGTGAGCATAC
1 TGTGAGCATAC
41468091 ATGTACAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (25 bp):
TGTGAGCATACCAATTTACAGCTCG
Found at i:41471042 original size:36 final size:36
Alignment explanation
Indices: 41470958--41471111 Score: 152
Period size: 35 Copynumber: 4.3 Consensus size: 36
41470948 CATCATCAGC
* * *
41470958 CCAACC-ATAACACATCAAATGCTCACACGAGCCAAT
1 CCAACCGA-AACACATCAAATGCTCACAAGAGCTAGT
** *
41470994 CCTTCCAAAACACATCAAATGCTCACAAGAGCTAGT
1 CCAACCGAAACACATCAAATGCTCACAAGAGCTAGT
* * *
41471030 CCAACCGTAACACA-CTAATGCTCATAAGAGCTAGT
1 CCAACCGAAACACATCAAATGCTCACAAGAGCTAGT
* * * * *
41471065 CCAAGCGAAACAC-GCCAATGCTCATAAAAGCTAGT
1 CCAACCGAAACACATCAAATGCTCACAAGAGCTAGT
41471100 CCAACCGAAACA
1 CCAACCGAAACA
41471112 TACCAAACAG
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
35 60 0.60
36 39 0.39
37 1 0.01
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (36 bp):
CCAACCGAAACACATCAAATGCTCACAAGAGCTAGT
Found at i:41478966 original size:62 final size:63
Alignment explanation
Indices: 41478843--41478967 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 63
41478833 TCAGGTGTCT
*
41478843 CAACTCCAGTGGGGGTACTGAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
1 CAACTCCAGTGGGGGTACTAAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
*
41478906 CAACTCCAGTGGGGGTACTAAAGTC-AAAAGGGAAAAATTAGTCATCAATAAAATAGTTAATA
1 CAACTCCAGTGGGGGTACTAAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
41478968 ATCCACTAAC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 36 0.60
63 24 0.40
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (63 bp):
CAACTCCAGTGGGGGTACTAAAGTCAAAAAGGAAAAAATTAGTCATCAATAAAATAGTTAATA
Found at i:41479164 original size:6 final size:6
Alignment explanation
Indices: 41479153--41479197 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
41479143 CTTCAATCTG
* * * *
41479153 CTCTTC CTCTTC CTCTTC TTCTTC TTCTTC TTCTTC CTCCTC CTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTC
41479198 CTCTTCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
CTCTTC
Found at i:41479174 original size:3 final size:3
Alignment explanation
Indices: 41479154--41479188 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
41479144 TTCAATCTGC
* *
41479154 TCT TCC TCT TCC TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
41479189 CTCCTCCTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:41480328 original size:14 final size:14
Alignment explanation
Indices: 41480309--41480341 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
41480299 AAAAACTGAA
41480309 AGACATTAATCATT
1 AGACATTAATCATT
41480323 AGACATTAATCATT
1 AGACATTAATCATT
41480337 AGACA
1 AGACA
41480342 CGAATCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (14 bp):
AGACATTAATCATT
Found at i:41480347 original size:14 final size:14
Alignment explanation
Indices: 41480316--41480350 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41480306 GAAAGACATT
**
41480316 AATCATTAGACATT
1 AATCATTAGACACG
41480330 AATCATTAGACACG
1 AATCATTAGACACG
41480344 AATCATT
1 AATCATT
41480351 CAAGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (14 bp):
AATCATTAGACACG
Found at i:41485531 original size:17 final size:17
Alignment explanation
Indices: 41485511--41485554 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41485501 TAATTTTATC
*
41485511 ATAATATTAAATTAAAA
1 ATAATAATAAATTAAAA
* *
41485528 ATAATTAATAATTTAAAT
1 ATAA-TAATAAATTAAAA
41485546 ATAATAATA
1 ATAATAATA
41485555 TCTAACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAATAAATTAAAA
Found at i:41488639 original size:18 final size:18
Alignment explanation
Indices: 41488618--41488680 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
41488608 GGTTGATAAC
41488618 GAAGAGGAAGTTGAGAAT
1 GAAGAGGAAGTTGAGAAT
** *
41488636 GAAGAGTGAA-AAGAGAAC
1 GAAGAG-GAAGTTGAGAAT
* *
41488654 AAAGAGGGAGTTGAGAAT
1 GAAGAGGAAGTTGAGAAT
41488672 GAAGAGGAA
1 GAAGAGGAA
41488681 TCTAAAACCG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 2 0.06
18 28 0.85
19 3 0.09
ACGTcount: A:0.49, C:0.02, G:0.38, T:0.11
Consensus pattern (18 bp):
GAAGAGGAAGTTGAGAAT
Found at i:41490669 original size:23 final size:24
Alignment explanation
Indices: 41490625--41490670 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
41490615 AAAATAGTTG
*
41490625 AGAGAATATGATCGAATGAGATTA
1 AGAGAATATGATCGAATAAGATTA
41490649 AGAGAAT-TGA-CAGAATAAGATT
1 AGAGAATATGATC-GAATAAGATT
41490671 GAATAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 12 0.60
24 7 0.35
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAGAATATGATCGAATAAGATTA
Found at i:41492887 original size:23 final size:23
Alignment explanation
Indices: 41492857--41492908 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
41492847 TAGATTTTTC
*
41492857 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
41492880 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
41492903 CAAAAT
1 CTAAAT
41492909 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:41498458 original size:22 final size:20
Alignment explanation
Indices: 41498426--41498467 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 20
41498416 CATTTTATCT
41498426 ATTTTACTTAAATAAAAAAA
1 ATTTTACTTAAATAAAAAAA
41498446 ATTTGTACGTTAAATCAAAAAA
1 ATTT-TAC-TTAAAT-AAAAAA
41498468 TACATTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 6 0.32
23 6 0.32
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTTACTTAAATAAAAAAA
Found at i:41502943 original size:21 final size:21
Alignment explanation
Indices: 41502917--41502958 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41502907 AATCAATACA
*
41502917 ATTTTTTTCTATTTTT-CTTTT
1 ATTTTTTTAT-TTTTTGCTTTT
41502938 ATTTTTTTATTTTTTGCTTTT
1 ATTTTTTTATTTTTTGCTTTT
41502959 CTCTGCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81
Consensus pattern (21 bp):
ATTTTTTTATTTTTTGCTTTT
Found at i:41503664 original size:87 final size:87
Alignment explanation
Indices: 41503529--41504035 Score: 734
Period size: 87 Copynumber: 5.8 Consensus size: 87
41503519 GCTTAAATTT
* * * * * * *
41503529 GTTTCCCTATTCCCGGGGAAGATGAGATTCACCATCTTGGATCTGCTCCACTATTGCTTAGGGAG
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
* ****
41503594 ATAGAACCCGTGG-CTTAAATCC
66 ATAGGATTAATGGTC-TAAATCC
* * *
41503616 GTTTCCCTACTTCTAGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCATTATTGCTTAAGGAG
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
41503681 ATAGGATTAATGGTCTAAATCC
66 ATAGGATTAATGGTCTAAATCC
* * *
41503703 ATTTCCCTACT-CTAGGGGAAGATGAGATTCGCCGTCTTGGATCCGCTCCACTATTACTTAAGGA
1 GTTTCCCTACTCCT-GGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGA
*
41503767 GATAGGATTAATGGTCTAAATCT
65 GATAGGATTAATGGTCTAAATCC
41503790 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTT-AGAGA
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAG-GA
41503854 GATAGGATTAATGG-CTTAAATCC
65 GATAGGATTAATGGTC-TAAATCC
***
41503877 GTTTCCCTACTCCTGGGGAAGATGAGATTTAACGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
41503942 ATAGGATTAATGGTCTAAATCC
66 ATAGGATTAATGGTCTAAATCC
* *
41503964 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGTTCCACTATTGCTTAGGGAG
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
41504029 ATAGGAT
66 ATAGGAT
41504036 CTGCCATCTT
Statistics
Matches: 380, Mismatches: 33, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
86 5 0.01
87 369 0.97
88 6 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (87 bp):
GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTATTGCTTAAGGAG
ATAGGATTAATGGTCTAAATCC
Found at i:41504010 original size:44 final size:44
Alignment explanation
Indices: 41503790--41504010 Score: 118
Period size: 44 Copynumber: 5.1 Consensus size: 44
41503780 GTCTAAATCT
**
41503790 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCC
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCAACGTCTTCGATCC
* * * ** * * **
41503834 G-CTCCACTATTGCT-TAGAGAGAT-AGGATT-AATGGCTTAAATCC
1 GTTTCC-CTACTCCTGGGGA-AGATGA-GATTCAACGTCTTCGATCC
*
41503877 GTTTCCCTACTCCTGGGGAAGATGAGATTTAACGTCTTCGATCC
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCAACGTCTTCGATCC
* * * ** * **
41503921 G-CTCCACTATTGCTTAAGG-AGAT-AGGATT-AATGGTC-TAAATCC
1 GTTTCC-CTACT-CCTGGGGAAGATGA-GATTCAA-CGTCTTCGATCC
**
41503964 GTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCC
1 GTTTCCCTACTCCTGGGGAAGATGAGATTCAACGTCTTCGATCC
41504008 GTT
1 GTT
41504011 CCACTATTGC
Statistics
Matches: 123, Mismatches: 38, Indels: 32
0.64 0.20 0.17
Matches are distributed among these distances:
42 4 0.03
43 56 0.46
44 59 0.48
45 4 0.03
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (44 bp):
GTTTCCCTACTCCTGGGGAAGATGAGATTCAACGTCTTCGATCC
Found at i:41517910 original size:15 final size:16
Alignment explanation
Indices: 41517882--41517911 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41517872 ATATCTTTCA
41517882 TCAATTGTATATAATT
1 TCAATTGTATATAATT
41517898 TCAATTG-ATATAAT
1 TCAATTGTATATAAT
41517912 AACAAATTTA
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:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
TCAATTGTATATAATT
Found at i:41518446 original size:29 final size:29
Alignment explanation
Indices: 41518414--41518497 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
41518404 AAACAAATAT
41518414 TAAAAAGTATAAAAAACTTATAAATTTTA
1 TAAAAAGTATAAAAAACTTATAAATTTTA
**
41518443 TAAAAACGTATAAAATTTCTTATAAATTTTA
1 TAAAAA-GTATAAAA-AACTTATAAATTTTA
* * *
41518474 -ATAAATTATAAAAAATATTATAAA
1 TAAAAAGTATAAAAAA-CTTATAAA
41518498 AATAAGGCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 20 0.44
30 12 0.27
31 13 0.29
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAAAAGTATAAAAAACTTATAAATTTTA
Found at i:41518468 original size:31 final size:30
Alignment explanation
Indices: 41518414--41518478 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
41518404 AAACAAATAT
41518414 TAAAAAGTATAAAAAACTTATAAATTTT-A
1 TAAAAAGTATAAAAAACTTATAAATTTTAA
**
41518443 TAAAAACGTATAAAATTTCTTATAAATTTTAA
1 TAAAAA-GTATAAAA-AACTTATAAATTTTAA
41518475 TAAA
1 TAAA
41518479 TTATAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.19
30 8 0.26
31 12 0.39
32 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAAAAGTATAAAAAACTTATAAATTTTAA
Found at i:41518670 original size:86 final size:87
Alignment explanation
Indices: 41518516--41518702 Score: 245
Period size: 86 Copynumber: 2.2 Consensus size: 87
41518506 TTAAGGGTCT
* * *
41518516 AAAAA-TCCTTCAAACTTTAAAAAAAAAGCAATTAAGCAGCTCCTTTTTTTGCACTTAATTGAGC
1 AAAAAGTCCTTCAAACTTTAAAAAAAAAGCAATTAAGCACCTCATTTTTTTGCACTCAATTGAGC
*
41518580 ACTTGAACTTTCAGAATGCATC
66 ACTTGAACTTTCAAAATGCATC
** * *
41518602 AAAAAGTCCTTCAAACTTCTTCAAAAAAAGCAATTAAGC-CCTTATTTTTTT-CACTCAATTGCG
1 AAAAAGTCCTTCAAACTT-TAAAAAAAAAGCAATTAAGCACCTCATTTTTTTGCACTCAATTGAG
*
41518665 TACTTGAACTTTCAAAATGCATC
65 CACTTGAACTTTCAAAATGCATC
* *
41518688 AAAAAGACCCTCAAA
1 AAAAAGTCCTTCAAA
41518703 AGTGACCTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
86 49 0.56
87 21 0.24
88 18 0.20
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (87 bp):
AAAAAGTCCTTCAAACTTTAAAAAAAAAGCAATTAAGCACCTCATTTTTTTGCACTCAATTGAGC
ACTTGAACTTTCAAAATGCATC
Found at i:41524761 original size:40 final size:42
Alignment explanation
Indices: 41524715--41524805 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 42
41524705 CCGATGTGAT
41524715 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTG
1 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCC-----G
41524762 ATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 --GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
41524806 ATGTGATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 1 0.02
49 41 0.98
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (42 bp):
GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
Found at i:41524767 original size:49 final size:47
Alignment explanation
Indices: 41524461--41524825 Score: 651
Period size: 47 Copynumber: 7.7 Consensus size: 47
41524451 ATGATAGTAT
41524461 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41524508 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
41524555 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41524602 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
41524649 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT-A
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
41524695 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
*
41524744 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
41524793 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
41524826 CCCGAAGGGC
Statistics
Matches: 311, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
46 34 0.11
47 184 0.59
48 12 0.04
49 77 0.25
50 4 0.01
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:41524999 original size:37 final size:37
Alignment explanation
Indices: 41524943--41525021 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41524933 CCGAGCTCTA
* * *
41524943 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
41524980 AAGACCTGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41525017 AAGAC
1 AAGAC
41525022 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41534028 original size:41 final size:41
Alignment explanation
Indices: 41533983--41534116 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 41
41533973 ACCAGCAATT
* ** *
41533983 AGCCTGCTAGACTTATCGTCTGAATTATTTCACCGGCACAA
1 AGCCTGCTAGACATAAAGTCCGAATTATTTCACCGGCACAA
*
41534024 AGCCTACTAGACATAAAGTCCGAATTATTTCACCGGCACAA
1 AGCCTGCTAGACATAAAGTCCGAATTATTTCACCGGCACAA
* * * *
41534065 AGCCTGCTAGACATAAAGTCCGAATAACTTCACTGGC-CTTA
1 AGCCTGCTAGACATAAAGTCCGAATTATTTCACCGGCAC-AA
41534106 AGCCTGCTAGA
1 AGCCTGCTAGA
41534117 TTTTAAACCT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 1 0.01
41 81 0.99
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCCGAATTATTTCACCGGCACAA
Found at i:41534787 original size:46 final size:46
Alignment explanation
Indices: 41534734--41534825 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
41534724 CCGAATATAA
41534734 GTGTACACATATAAGCCATCCATATATCAAACTTAATCAATCAAAG
1 GTGTACACATATAAGCCATCCATATATCAAACTTAATCAATCAAAG
41534780 GTGTACACATATAAGCCATCCATATATCAAACTTAATCAATCAAAG
1 GTGTACACATATAAGCCATCCATATATCAAACTTAATCAATCAAAG
41534826 TATTTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (46 bp):
GTGTACACATATAAGCCATCCATATATCAAACTTAATCAATCAAAG
Found at i:41539980 original size:25 final size:24
Alignment explanation
Indices: 41539929--41540142 Score: 121
Period size: 25 Copynumber: 8.6 Consensus size: 24
41539919 ACTCACCACA
* * * *
41539929 GCTCTTATGAGCATCCTGATATATG
1 GCTCTCATGAGCTTCC-CATATTTG
*
41539954 GCTCTCTTGAGCTTCCCATTATTTG
1 GCTCTCATGAGCTTCCCA-TATTTG
* ** *
41539979 GCTCTCACGAGCTTCTTGATAATTG
1 GCTCTCATGAGCTTC-CCATATTTG
*
41540004 GCTGTCATGAGCTTCCCATTATTTG
1 GCTCTCATGAGCTTCCCA-TATTTG
* * *
41540029 GCTCTCACGAGCTTCCTGATAATTG
1 GCTCTCATGAGCTTCC-CATATTTG
* *
41540054 GCTCTCATAAGCTTCCCGAT-TAATG
1 GCTCTCATGAGCTTCCC-ATAT-TTG
* *
41540079 GCTCTTC-GGAGCTTCTCGATATTTG
1 GCTC-TCATGAGCTTC-CCATATTTG
** *
41540104 GCTCTTTTGAGCTTCCCGT-TTATG
1 GCTCTCATGAGCTTCCCATATT-TG
41540128 GCTCGT-ATGAGCTTC
1 GCTC-TCATGAGCTTC
41540143 TCGATAATTG
Statistics
Matches: 144, Mismatches: 33, Indels: 25
0.71 0.16 0.12
Matches are distributed among these distances:
23 2 0.01
24 19 0.13
25 117 0.81
26 6 0.04
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (24 bp):
GCTCTCATGAGCTTCCCATATTTG
Found at i:41540006 original size:50 final size:51
Alignment explanation
Indices: 41539952--41540154 Score: 222
Period size: 50 Copynumber: 4.1 Consensus size: 51
41539942 TCCTGATATA
* * *
41539952 TGGCTCTCTTGAGCTTCCCATTATTTGGCTC-TCACGAGCTTCTTGATAAT
1 TGGCTCTCATGAGCTTCCCATTATATGGCTCGTCACGAGCTTCTCGATAAT
* *
41540002 TGGCTGTCATGAGCTTCCCATTATTTGGCTC-TCACGAGCTTC-CTGATAAT
1 TGGCTCTCATGAGCTTCCCATTATATGGCTCGTCACGAGCTTCTC-GATAAT
* * * *
41540052 TGGCTCTCATAAGCTTCCCGATTA-ATGGCTCTTC-GGAGCTTCTCGATATT
1 TGGCTCTCATGAGCTTCCC-ATTATATGGCTCGTCACGAGCTTCTCGATAAT
** * *
41540102 TGGCTCTTTTGAGCTTCCCGTT-TATGGCTCGT-ATGAGCTTCTCGATAAT
1 TGGCTCTCATGAGCTTCCCATTATATGGCTCGTCACGAGCTTCTCGATAAT
41540151 TGGC
1 TGGC
41540155 ACACAAGAGC
Statistics
Matches: 132, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
49 28 0.21
50 97 0.73
51 7 0.05
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (51 bp):
TGGCTCTCATGAGCTTCCCATTATATGGCTCGTCACGAGCTTCTCGATAAT
Found at i:41545056 original size:23 final size:24
Alignment explanation
Indices: 41545012--41545056 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41545002 CTTCTTATGT
*
41545012 GGAGCAATAAGGAAGGTGAGAGAA
1 GGAGAAATAAGGAAGGTGAGAGAA
*
41545036 GGAGAAATAAGG-CGGTGAGAG
1 GGAGAAATAAGGAAGGTGAGAG
41545057 GCTACGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.04, G:0.44, T:0.09
Consensus pattern (24 bp):
GGAGAAATAAGGAAGGTGAGAGAA
Found at i:41545306 original size:48 final size:48
Alignment explanation
Indices: 41545235--41545331 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
41545225 ATTATGTGTA
41545235 AGTATGAAAATGGCTAGTTATGTACCCCAAAACCAATCTTTGTACTAT
1 AGTATGAAAATGGCTAGTTATGTACCCCAAAACCAATCTTTGTACTAT
41545283 AGTATGAAAATGGCTAGTTATGTACCCCAAAACCAATCTTTGTACTAT
1 AGTATGAAAATGGCTAGTTATGTACCCCAAAACCAATCTTTGTACTAT
41545331 A
1 A
41545332 CTTGCTCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (48 bp):
AGTATGAAAATGGCTAGTTATGTACCCCAAAACCAATCTTTGTACTAT
Found at i:41547857 original size:20 final size:20
Alignment explanation
Indices: 41547832--41547869 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41547822 GGGAGCAGTT
*
41547832 TTTCAATCGATTTAAAAATA
1 TTTCAATCGAGTTAAAAATA
*
41547852 TTTCAATTGAGTTAAAAA
1 TTTCAATCGAGTTAAAAA
41547870 AGTTTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTCAATCGAGTTAAAAATA
Found at i:41557539 original size:29 final size:30
Alignment explanation
Indices: 41557499--41557564 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
41557489 TGGTTTAAAG
* *
41557499 TGCAATTGTATACATGAACA-TTGATTTTA
1 TGCAATTGTATACATGAAAATTTGATTTGA
*
41557528 TGCAATTTTATACATGAAAATTTGATTTGA
1 TGCAATTGTATACATGAAAATTTGATTTGA
*
41557558 TCCAATT
1 TGCAATT
41557565 CTTGTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (30 bp):
TGCAATTGTATACATGAAAATTTGATTTGA
Found at i:41557773 original size:29 final size:30
Alignment explanation
Indices: 41557701--41557786 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 30
41557691 TAAGTAAAAT
* * * *
41557701 TTAAAGTTTCAAGTATACATTTGAACCTCAA
1 TTAAAGTTTCATGTATACAATTGCACC-GAA
* * *
41557732 TTAGAGTTTCATGTGTATAATTGCACCGAA
1 TTAAAGTTTCATGTATACAATTGCACCGAA
41557762 TTAAAG-TTCATGTATACAATTGCAC
1 TTAAAGTTTCATGTATACAATTGCAC
41557787 AATAAATCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 17 0.38
30 7 0.16
31 21 0.47
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (30 bp):
TTAAAGTTTCATGTATACAATTGCACCGAA
Found at i:41559357 original size:7 final size:7
Alignment explanation
Indices: 41559345--41559405 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
41559335 AATATGTATT
41559345 ATTTTAA
1 ATTTTAA
41559352 ATTTTAA
1 ATTTTAA
*
41559359 A-TTTAT
1 ATTTTAA
41559365 ATTATT-A
1 ATT-TTAA
* *
41559372 ATCTATATT
1 AT-TTTA-A
41559381 ATTTTAA
1 ATTTTAA
41559388 ATTTTAA
1 ATTTTAA
41559395 ATTTTAA
1 ATTTTAA
41559402 ATTT
1 ATTT
41559406 ATGTTATACC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.12
7 30 0.70
8 6 0.14
9 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:41559523 original size:17 final size:18
Alignment explanation
Indices: 41559501--41559537 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41559491 TTTCCTCAAA
*
41559501 TCAAACCCTC-CATCCAT
1 TCAAACCCTCAAATCCAT
41559518 TCAAACCCTCAAATCCAT
1 TCAAACCCTCAAATCCAT
41559536 TC
1 TC
41559538 TTCTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.24
Consensus pattern (18 bp):
TCAAACCCTCAAATCCAT
Found at i:41560847 original size:28 final size:28
Alignment explanation
Indices: 41560796--41560849 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
41560786 AAAAATTCAG
*
41560796 AAAAACTATAAAAGAATTTGAAATATGT
1 AAAAACTATAAAAGAATTTAAAATATGT
*
41560824 AAAAAGTATAAAA-AATTTCAAAATAT
1 AAAAACTATAAAAGAATTT-AAAATAT
41560850 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAAACTATAAAAGAATTTAAAATATGT
Found at i:41565513 original size:9 final size:9
Alignment explanation
Indices: 41565499--41565523 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41565489 AAAATGTAAA
41565499 GCCCAAATG
1 GCCCAAATG
41565508 GCCCAAATG
1 GCCCAAATG
41565517 GCCCAAA
1 GCCCAAA
41565524 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.20, T:0.08
Consensus pattern (9 bp):
GCCCAAATG
Found at i:41570218 original size:50 final size:50
Alignment explanation
Indices: 41570150--41570711 Score: 378
Period size: 50 Copynumber: 11.2 Consensus size: 50
41570140 TAACTCGTAA
* * * * *
41570150 CTTTAATCTATTTAACTACAATGTCGGGGAAGTATGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * * ** * * * *
41570200 CTTCAATCTGTTCCACTACACCG-CTAGGGAGGTGAGATTCG-TCATTGTGG
1 CTTTAATCTGTTTCACTGCAATGTC-GGGGAAGTAAGATTCGCT-GTTGTGG
* * ** * ***
41570250 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCAATGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* ** * * *
41570300 CTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * * * * * *
41570350 CTTTAATCTTTTTAACTGCAATGTCGGGTAAGCAAGATTCACCGATGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* ** * * *
41570400 CTTTAATCTGTTGCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * * * * *
41570450 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGTTGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * ** * * * *
41570500 CTTTAATTTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * * * * *
41570550 CTTTAATCTTTTTAACTTCAATGTCGGGGAAGCAAGATTCACTGATGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
* * * *
41570600 CTTTAATCTGTTGCACTGC---GTCGCATGGGGAGTAAGATTCACTGTTGTAG
1 CTTTAATCTGTTTCACTGCAATGTCG---GGGAAGTAAGATTCGCTGTTGTGG
* * * * * * * * *
41570650 CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGGTTCACCGATGTGG
1 CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
41570700 CTTTAATCTGTT
1 CTTTAATCTGTT
41570712 CCAGTGCACC
Statistics
Matches: 381, Mismatches: 121, Indels: 20
0.73 0.23 0.04
Matches are distributed among these distances:
47 4 0.01
49 2 0.01
50 372 0.98
51 1 0.00
53 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (50 bp):
CTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCTGTTGTGG
Found at i:41570272 original size:100 final size:100
Alignment explanation
Indices: 41570150--41570735 Score: 807
Period size: 100 Copynumber: 5.9 Consensus size: 100
41570140 TAACTCGTAA
* * * * * * * * *
41570150 CTTTAATCTATTTAACTACAATGTCGGGGAAGTATGATTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * * * *
41570215 CTACACCGCTAGGGAGGTGAGATTCG-TCATTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCT-GTTGTAG
* *
41570250 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCAATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
41570315 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
* *
41570350 CTTTAATCTTTTTAACTGCAATGTCGGGTAAGCAAGATTCACCGATGTGGCTTTAATCTGTTGCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
41570415 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
* * *
41570450 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGTTGTGGCTTTAATTTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
41570515 CTGCACCGCCAGGGAAATAAGATTCGCTGTTGTAG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
* * *
41570550 CTTTAATCTTTTTAACTTCAATGTCGGGGAAGCAAGATTCACTGATGTGGCTTTAATCTGTTGCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
** * *
41570615 CTGCGTCG-CATGGGGAGTAAGATTCACTGTTGTAG
66 CTGCACCGCCA-GGGAAGTAAGATTCGCTGTTGTAG
* * *
41570650 CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGGTTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
41570715 GTGCACCGCCAGGGAAATAAG
66 CTGCACCGCCAGGGAAGTAAG
41570736 TTTTAATGCG
Statistics
Matches: 430, Mismatches: 53, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
99 2 0.00
100 425 0.99
101 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
Found at i:41570726 original size:50 final size:50
Alignment explanation
Indices: 41570244--41570730 Score: 404
Period size: 50 Copynumber: 9.7 Consensus size: 50
41570234 AGATTCGTCA
* * * * * * *
41570244 TTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCGAGATTCACCA
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * * * * *
41570294 ATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCTG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * * * *
41570344 TTGTAGCTTTAATCTTTTTAACTGCAATGTC-GGGTAAGCAAGATTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGG-AAGCAAGATTCACCG
* * * * *
41570394 ATGTGGCTTTAATCTGTTGCACTGCACCGCCAGGGAAGTAAGATTCGCCG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * * *
41570444 TTGTGGCTTTAATCTTTTTAACTGCAATGTC-GAGGAAGCAAGATTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAG-GGAAGCAAGATTCACCG
* * * ** * *
41570494 TTGTGGCTTTAATTTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * * * * * * *
41570544 TTGTAGCTTTAATCTTTTTAACTTCAATGTCGGGGAAGCAAGATTCACTG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * ** * * *
41570594 ATGTGGCTTTAATCTGTTGCACTGCGTCG-CATGGGGAGTAAGATTCACTG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCA-GGGAAGCAAGATTCACCG
* * * * *
41570644 TTGTAGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGGTTCACCG
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
* * * *
41570694 ATGTGGCTTTAATCTGTTCCAGTGCACCGCCAGGGAA
1 TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAA
41570731 ATAAGTTTTA
Statistics
Matches: 332, Mismatches: 99, Indels: 12
0.75 0.22 0.03
Matches are distributed among these distances:
49 5 0.02
50 321 0.97
51 6 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (50 bp):
TTGTGGCTTTAATCTGTTTCACTGCAACGCCAGGGAAGCAAGATTCACCG
Found at i:41572245 original size:14 final size:13
Alignment explanation
Indices: 41572226--41572274 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 13
41572216 TTAGCCTCTC
41572226 CATTTTTACTTTTT
1 CATTTTT-CTTTTT
41572240 CATTTTTCCATTTTT
1 CATTTTT-C-TTTTT
*
41572255 CATTTTTCATTTT
1 CATTTTTCTTTTT
41572268 CATTTTT
1 CATTTTT
41572275 TCATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 11 0.34
14 9 0.28
15 12 0.38
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTTCTTTTT
Found at i:41572283 original size:8 final size:7
Alignment explanation
Indices: 41572226--41572282 Score: 73
Period size: 7 Copynumber: 8.0 Consensus size: 7
41572216 TTAGCCTCTC
41572226 CATTTTT
1 CATTTTT
41572233 -ACTTTTT
1 CA-TTTTT
41572240 CATTTTT
1 CATTTTT
41572247 CCATTTTT
1 -CATTTTT
41572255 CATTTTT
1 CATTTTT
41572262 CA-TTTT
1 CATTTTT
41572268 CATTTTTT
1 CA-TTTTT
41572276 CATTTTT
1 CATTTTT
41572283 TTCTGACTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.16
7 24 0.53
8 14 0.31
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:41572285 original size:9 final size:8
Alignment explanation
Indices: 41572235--41572283 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
41572225 CCATTTTTAC
41572235 TTTTTCAT
1 TTTTTCAT
*
41572243 TTTTCCA-
1 TTTTTCAT
41572250 TTTTTCA-
1 TTTTTCAT
41572257 TTTTTCA-
1 TTTTTCAT
41572264 -TTTTCAT
1 TTTTTCAT
41572271 TTTTTCAT
1 TTTTTCAT
41572279 TTTTT
1 TTTTT
41572284 TCTGACTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 6 0.16
7 13 0.35
8 18 0.49
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:41578902 original size:15 final size:15
Alignment explanation
Indices: 41578884--41578938 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
41578874 TGGTTGTTTA
41578884 TATTGTCATTATTAT
1 TATTGTCATTATTAT
*
41578899 TATTGTCCCCTATATTAT
1 TATTGT--CAT-TATTAT
41578917 TATTTGT-ATTATTAT
1 TA-TTGTCATTATTAT
41578932 TATTGTC
1 TATTGTC
41578939 TTTGTCTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 1 0.03
17 2 0.06
18 8 0.24
19 4 0.12
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (15 bp):
TATTGTCATTATTAT
Found at i:41579295 original size:100 final size:100
Alignment explanation
Indices: 41579122--41579322 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
41579112 TATATCTTAT
41579122 AAAAATTTCTCTACCCTTTTACCCAAATTTGTAAAAAGGAAAGAAATCTCAAAATAAGGAAATGT
1 AAAAATTTCTCTACCCTTTTACCCAAATTTGTAAAAAGGAAAGAAATCTCAAAATAAGGAAATGT
41579187 TTCGCGATTTAGAAATTTGAGAAAATCGTACCCTA
66 TTCGCGATTTAGAAATTTGAGAAAATCGTACCCTA
*
41579222 AAAAATTTCTCTACCCTTTTACCCAAATTTGTAAAAAGGAAAGAAATCTCAAAATAAGGCAATGT
1 AAAAATTTCTCTACCCTTTTACCCAAATTTGTAAAAAGGAAAGAAATCTCAAAATAAGGAAATGT
41579287 TTCGCGATTTAGAAATTTGAGAAAATCGTACCCTA
66 TTCGCGATTTAGAAATTTGAGAAAATCGTACCCTA
41579322 A
1 A
41579323 CTTACGGGGT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (100 bp):
AAAAATTTCTCTACCCTTTTACCCAAATTTGTAAAAAGGAAAGAAATCTCAAAATAAGGAAATGT
TTCGCGATTTAGAAATTTGAGAAAATCGTACCCTA
Found at i:41582684 original size:19 final size:19
Alignment explanation
Indices: 41582660--41582703 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41582650 ATGCCTCTTT
*
41582660 TGCATT-CATCTCATGCATC
1 TGCATTGCATCTCAT-CATA
*
41582679 TGCATTGCATTTCATCATA
1 TGCATTGCATCTCATCATA
41582698 TGCATT
1 TGCATT
41582704 AAGTTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (19 bp):
TGCATTGCATCTCATCATA
Found at i:41590820 original size:44 final size:44
Alignment explanation
Indices: 41590759--41590862 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
41590749 CTGATCTCTC
* * *
41590759 TGAAGTTGCAATAGAGC-AGATCATAGCTACAAACCTTATCTCCT
1 TGAAGTTGCAGTGGAGCAAGATCA-AGCTACAAACCATATCTCCT
* * * * *
41590803 TGAAGTTGTAGTGGAGCAAGTTGAAGCTACTAATCATATCTCCT
1 TGAAGTTGCAGTGGAGCAAGATCAAGCTACAAACCATATCTCCT
41590847 TGAAGTTGCAGTGGAG
1 TGAAGTTGCAGTGGAG
41590863 TGGATTAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 46 0.92
45 4 0.08
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAAGATCAAGCTACAAACCATATCTCCT
Found at i:41591013 original size:45 final size:43
Alignment explanation
Indices: 41590939--41591265 Score: 178
Period size: 44 Copynumber: 7.3 Consensus size: 43
41590929 GTCTTATTTC
*
41590939 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTGTCTT
1 CCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CAAACCTTATC-T
* * **
41590984 CCTGAAGTTGCAGTGGAGCA-AGTTTAAGATACAAGTCTTATCT
1 CCTGAAGTTGCAGTGGAGCAGA-CTGAAGATACAAACCTTATCT
* * * *
41591027 CCTTGAAGTTGTAGTGGAACAGATTAAAGCTATA-AATATCAGATCTTATCT
1 CC-TGAAGTTGCAGTGGAGCAGACTGAAG--ATACAA-A-C----CTTATCT
* * * * *
41591078 CTCTGAAGTTGTAGTAGAGCAGA-T-CATAT-CAAACTTTATCT
1 C-CTGAAGTTGCAGTGGAGCAGACTGAAGATACAAACCTTATCT
* ** * * *
41591119 CCTTGAAGTTGCAGTGGAGCAGAATGGGGCTACAAATCTTACCT
1 CC-TGAAGTTGCAGTGGAGCAGACTGAAGATACAAACCTTATCT
* * * * * * *
41591163 CCCTGAAGTGGCAGCGGAGCAAATTGAAGACACTAATCTTATCT
1 -CCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAACCTTATCT
* * * *
41591207 CCCTGAAGATGCAGTGGAGCAGATTGAAGATACTAATCTTATCT
1 -CCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAACCTTATCT
*
41591251 CCCTAAAGTTGCAGT
1 -CCTGAAGTTGCAGT
41591266 AGAGTAAATT
Statistics
Matches: 223, Mismatches: 41, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
40 1 0.00
41 25 0.11
42 1 0.00
43 4 0.02
44 122 0.55
45 33 0.15
46 4 0.02
47 4 0.02
49 1 0.00
50 1 0.00
51 26 0.12
52 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
CCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAACCTTATCT
Found at i:41591265 original size:44 final size:44
Alignment explanation
Indices: 41591113--41591265 Score: 189
Period size: 44 Copynumber: 3.5 Consensus size: 44
41591103 ATATCAAACT
* * ** * *
41591113 TTATCTCCTTGAAGTTGCAGTGGAGCAGAATGGGGCTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
* * * * *
41591157 TTACCTCCCTGAAGTGGCAGCGGAGCAAATTGAAGACACTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
*
41591201 TTATCTCCCTGAAGATGCAGTGGAGCAGATTGAAGATACTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
*
41591245 TTATCTCCCTAAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGT
41591266 AGAGTAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 90 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
Found at i:41591275 original size:88 final size:88
Alignment explanation
Indices: 41591113--41591275 Score: 209
Period size: 88 Copynumber: 1.9 Consensus size: 88
41591103 ATATCAAACT
* * ** * *
41591113 TTATCTCCTTGAAGTTGCAGTGGAGCAGAATGGGGCTACAAATCTTACCTCCCTGAAGTGGCAGC
1 TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTACCTCCCTAAAGTGGCAGC
*
41591178 GGAGCAAATTGAAGACACTAATC
66 AGAGCAAATTGAAGACACTAATC
* * * * *
41591201 TTATCTCCCTGAAGATGCAGTGGAGCAGATTGAAGATACTAATCTTATCTCCCTAAAGTTGCAGT
1 TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTACCTCCCTAAAGTGGCAGC
*
41591266 AGAGTAAATT
66 AGAGCAAATT
41591276 TAAGCGACAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
88 62 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TTATCTCCCTGAAGATGCAGTGGAGCAGAATGAAGATACAAATCTTACCTCCCTAAAGTGGCAGC
AGAGCAAATTGAAGACACTAATC
Found at i:41592547 original size:30 final size:31
Alignment explanation
Indices: 41592503--41592561 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
41592493 TTCAATGTGG
* *
41592503 TTTTTTTTATATTTTTTATTTCGG-CCTTAAA
1 TTTTTCTTATATTTTTAATTT-GGTCCTTAAA
41592534 TTTTTCTTA-ATTTTTAATTTGGTCCTTA
1 TTTTTCTTATATTTTTAATTTGGTCCTTA
41592562 GACCATGCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 15 0.60
31 8 0.32
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTTTCTTATATTTTTAATTTGGTCCTTAAA
Found at i:41592902 original size:9 final size:9
Alignment explanation
Indices: 41592887--41592932 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
41592877 TTAAATTTCA
41592887 TTTTTTTAT
1 TTTTTTTAT
* *
41592896 ATTTTTTCT
1 TTTTTTTAT
41592905 TTTCGTTTTAT
1 TTT--TTTTAT
41592916 TTTTTTTAT
1 TTTTTTTAT
41592925 TTTTTTTA
1 TTTTTTTA
41592933 AAATTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 23 0.74
11 8 0.26
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:41592915 original size:20 final size:20
Alignment explanation
Indices: 41592890--41592927 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41592880 AATTTCATTT
*
41592890 TTTTATATTTTTTCTTTTCG
1 TTTTATATTTTTTATTTTCG
*
41592910 TTTTATTTTTTTTATTTT
1 TTTTATATTTTTTATTTT
41592928 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTATATTTTTTATTTTCG
Found at i:41594468 original size:31 final size:31
Alignment explanation
Indices: 41594428--41594603 Score: 187
Period size: 31 Copynumber: 5.7 Consensus size: 31
41594418 CTCTATAATA
* *
41594428 TATATTCATATACAAATCAATTTCAATAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* *
41594459 TATAATCATATACAAATTAATTTCAGCAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* * * *
41594490 AATAATCATATACGAATCAA-TTCGACAGCT-
1 TATAATCATATACAAATCAATTTCAACA-ATG
* *
41594520 TAT-ATCCTTATACAAATCAATTTCAATAATG
1 TATAAT-CATATACAAATCAATTTCAACAATG
*
41594551 TATAATCATATACAAATTAATTTCAACAATG
1 TATAATCATATACAAATCAATTTCAACAATG
* * *
41594582 AATAATCATATACGAATGAATT
1 TATAATCATATACAAATCAATT
41594604 CGACAGCTTA
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
29 2 0.02
30 20 0.17
31 94 0.80
32 2 0.02
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (31 bp):
TATAATCATATACAAATCAATTTCAACAATG
Found at i:41594696 original size:92 final size:92
Alignment explanation
Indices: 41594436--41594686 Score: 409
Period size: 92 Copynumber: 2.7 Consensus size: 92
41594426 TATATATTCA
41594436 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
1 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
41594501 ACGAATCAATTCGACAGCTTATATCCT
66 ACGAATCAATTCGACAGCTTATATCCT
*
41594528 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAACAATGAATAATCATAT
1 TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
*
41594593 ACGAATGAATTCGACAGCTTATATCCT
66 ACGAATCAATTCGACAGCTTATATCCT
* * *
41594620 TATACAAATCAAATTCAATAATG-AGTAA-CTATAAATAAATTAATTTCAGCAATGAAT-ATCGA
1 TATACAAATCAATTTCAATAATGTA-TAATC-ATATACAAATTAATTTCAGCAATGAATAATC-A
41594682 TATAC
63 TATAC
41594687 CCAACAATTC
Statistics
Matches: 150, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
91 5 0.03
92 145 0.97
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (92 bp):
TATACAAATCAATTTCAATAATGTATAATCATATACAAATTAATTTCAGCAATGAATAATCATAT
ACGAATCAATTCGACAGCTTATATCCT
Found at i:41595535 original size:11 final size:11
Alignment explanation
Indices: 41595519--41595543 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41595509 CCATGATGTA
41595519 AATATTAAAAT
1 AATATTAAAAT
41595530 AATATTAAAAT
1 AATATTAAAAT
41595541 AAT
1 AAT
41595544 TTTACGACCT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:41601235 original size:46 final size:45
Alignment explanation
Indices: 41601177--41601329 Score: 137
Period size: 46 Copynumber: 3.3 Consensus size: 45
41601167 AAAAAATTTA
* * *
41601177 AAAATATCTCAAGGCATATTTGAAAGCATCTTTGAGAGAGATTTTG
1 AAAACATCTCAAGG-ATATTTGAAAGCATCCTTGAGAGAGGTTTTG
* * * * *
41601223 AAAATATTTCAAGGGAGATATGAAAGTC-TCCTTAAGAGAGGTTTTG
1 AAAACATCTCAA-GGATATTTGAAAG-CATCCTTGAGAGAGGTTTTG
* * * *
41601269 AGAACATCTCAAGGATGATTTGAGAGCACCCTTGAGAGAGGGTTTTA
1 AAAACATCTCAAGGAT-ATTTGAAAGCATCCTTGAGAGA-GGTTTTG
*
41601316 AAAACATTTCAAGG
1 AAAACATCTCAAGG
41601330 GAGATCTCAT
Statistics
Matches: 85, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
45 4 0.05
46 60 0.71
47 21 0.25
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAACATCTCAAGGATATTTGAAAGCATCCTTGAGAGAGGTTTTG
Found at i:41603622 original size:5 final size:5
Alignment explanation
Indices: 41603612--41603660 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
41603602 AATTGATTGT
41603612 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
41603661 GTATGTCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:41611168 original size:28 final size:26
Alignment explanation
Indices: 41611122--41611173 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
41611112 ATTATAATGA
* *
41611122 AAAATTGACATGTAGTAAAGTATATT
1 AAAAGTGACATGTAGTAAAATATATT
41611148 AAAAGTGACATGTCATGTAAAATATA
1 AAAAGTGACATGT-A-GTAAAATATA
41611174 AAATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 1 0.05
28 9 0.41
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (26 bp):
AAAAGTGACATGTAGTAAAATATATT
Found at i:41618319 original size:24 final size:24
Alignment explanation
Indices: 41618292--41618350 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
41618282 CCCTAAACAC
* **
41618292 AAAAATCCTAAAATTAAAAATATT
1 AAAAACCCTAAAACAAAAAATATT
* *
41618316 AAAACCCCTAAACCAAAAAATATT
1 AAAAACCCTAAAACAAAAAATATT
41618340 AAAAACCCTAA
1 AAAAACCCTAA
41618351 CCCTAGGAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAAACCCTAAAACAAAAAATATT
Found at i:41624031 original size:37 final size:37
Alignment explanation
Indices: 41623990--41624129 Score: 147
Period size: 37 Copynumber: 3.8 Consensus size: 37
41623980 TAGCTTTTTG
*
41623990 GAGCAATTGGCATGTTATCGGGTGGATTAGCTCTTAT
1 GAGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTAT
* * * * * *
41624027 GAGCATTTGGTGTGTTTTCGGTTGGACTAGCTCTT-C
1 GAGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTAT
* *
41624063 GAAGAAATTGGCGTGTTATCGGGTGGATGAGCTCTTAT
1 G-AGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTAT
* * * *
41624101 GAGCATTTGGTGTGTTTTCGGATGGATTA
1 GAGCAATTGGCGTGTTATCGGGTGGATTA
41624130 CCGTACTCGT
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
36 1 0.01
37 78 0.98
38 1 0.01
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (37 bp):
GAGCAATTGGCGTGTTATCGGGTGGATTAGCTCTTAT
Found at i:41624085 original size:74 final size:74
Alignment explanation
Indices: 41623964--41624126 Score: 254
Period size: 74 Copynumber: 2.2 Consensus size: 74
41623954 CTGTTTTGAC
* * * * * *
41623964 GTGTTTTTGGTTGGACTAGCTTTTTGGAGCAATTGGCATGTTATCGGGTGGATTAGCTCTTATGA
1 GTGTTTTCGGTTGGACTAGCTCTTCGAAGAAATTGGCATGTTATCGGGTGGATGAGCTCTTATGA
41624029 GCATTTGGT
66 GCATTTGGT
*
41624038 GTGTTTTCGGTTGGACTAGCTCTTCGAAGAAATTGGCGTGTTATCGGGTGGATGAGCTCTTATGA
1 GTGTTTTCGGTTGGACTAGCTCTTCGAAGAAATTGGCATGTTATCGGGTGGATGAGCTCTTATGA
41624103 GCATTTGGT
66 GCATTTGGT
*
41624112 GTGTTTTCGGATGGA
1 GTGTTTTCGGTTGGA
41624127 TTACCGTACT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 81 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.39
Consensus pattern (74 bp):
GTGTTTTCGGTTGGACTAGCTCTTCGAAGAAATTGGCATGTTATCGGGTGGATGAGCTCTTATGA
GCATTTGGT
Found at i:41625308 original size:21 final size:20
Alignment explanation
Indices: 41625268--41625309 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
41625258 GACTCGAATT
*
41625268 GCCTCAAAGCTATTTTTAGG
1 GCCTCAAAGCTATATTTAGG
*
41625288 GCCTCAAAGGCTCTATTTAGG
1 GCCTCAAA-GCTATATTTAGG
41625309 G
1 G
41625310 ACGATATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
GCCTCAAAGCTATATTTAGG
Found at i:41627292 original size:37 final size:37
Alignment explanation
Indices: 41627234--41627449 Score: 351
Period size: 37 Copynumber: 5.8 Consensus size: 37
41627224 GCTCAGACGA
* * * *
41627234 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
41627271 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
* * *
41627308 AATCTCCACACATAGTCATCGGGTCTTGCCCGAACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
41627345 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
41627382 AATCTCCACACGTAGTCATCGGGTCTTATCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
41627419 AATCTCCACACGTATTCATCGGGTCTTACCC
1 AATCTCCACACGTAGTCATCGGGTCTTACCC
41627450 AGAATATATT
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 166 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:41627717 original size:47 final size:47
Alignment explanation
Indices: 41627659--41627900 Score: 331
Period size: 47 Copynumber: 5.1 Consensus size: 47
41627649 ACACGTTTTG
* * * *
41627659 CATTAGCCATTCGGCCTTACCACTTATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
41627706 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
41627753 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
41627800 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* * *
41627851 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
41627898 CAT
1 CAT
41627901 AAAATCCTAA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
47 127 0.74
49 6 0.03
51 39 0.23
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:41627787 original size:94 final size:96
Alignment explanation
Indices: 41627659--41627900 Score: 353
Period size: 98 Copynumber: 2.5 Consensus size: 96
41627649 ACACGTTTTG
* * ** **
41627659 CATTAGCCATTCGGCCTTACCACTTATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
41627724 AT-CTC-ATATATGCATGTTCACATTCATCA
66 ATACACAATATATACAGGTTCACATTCATCA
41627753 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
41627818 ATCACACATATATATACGGGTTCACATTCATCA
66 AT-ACACA-ATATATACAGGTTCACATTCATCA
*
41627851 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
41627901 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
94 61 0.46
96 2 0.02
98 70 0.53
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (96 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATACACAATATATACAGGTTCACATTCATCA
Found at i:41637860 original size:47 final size:47
Alignment explanation
Indices: 41637794--41638267 Score: 804
Period size: 47 Copynumber: 10.1 Consensus size: 47
41637784 GAAATGATAG
41637794 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41637841 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41637888 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41637935 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41637982 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41638029 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41638076 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41638123 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41638170 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
41638217 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41638264 TAAG
1 TAAG
41638268 TCCCGAAGGG
Statistics
Matches: 408, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 408 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41638442 original size:37 final size:37
Alignment explanation
Indices: 41638386--41638464 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
41638376 CCGAGCTCTA
* *
41638386 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
41638423 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41638460 AAGAC
1 AAGAC
41638465 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41640237 original size:33 final size:33
Alignment explanation
Indices: 41640200--41640265 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
41640190 TGTTTTTCAA
41640200 CTTGTTCTAACATGATTAGAAGGTTTCTAAACT
1 CTTGTTCTAACATGATTAGAAGGTTTCTAAACT
41640233 CTTGTTCTAACATGATTAGAAGGTTTCTAAACT
1 CTTGTTCTAACATGATTAGAAGGTTTCTAAACT
41640266 TACTTTAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (33 bp):
CTTGTTCTAACATGATTAGAAGGTTTCTAAACT
Found at i:41641999 original size:184 final size:186
Alignment explanation
Indices: 41641681--41642288 Score: 924
Period size: 186 Copynumber: 3.3 Consensus size: 186
41641671 TTTAACAAAA
* * *
41641681 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTT-TTCTTCAAAATACATGGTCGGCTCA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
*
41641745 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTCTGTAAATCC
66 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAA-CC
*
41641810 ACACCACACTTTCAGCTTAAAATCA-T-TTTTTTTCCCTCCACTGTCGGTTGCCATT
130 ACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCATT
* *
41641865 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTTAAAACATATGGTTGGCTCA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
*
41641930 TTTCATCTACAAGAATTTCCATTACCATGATTATAATCAT-CTTTTGTGTAATTTTTGTAAACGC
66 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAAC-C
* *
41641994 ACACCATACCTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCATT
130 ACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCATT
* * * *
41642051 TTTTCTCTTTTATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCGCA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
** * * *
41642116 TTTCATCTACAATAATTTCCACCACCATGATTGTAATCATGCTTTTATGCAATTTTTGTAAACCC
66 TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAA-CC
* * * *
41642181 ACACCACACTTTCAACTTAAAACCATTGTTTTTTTCCCT-CGCTGTCAGCTGCCA--
130 ACACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCATT
*
41642235 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACTATTTTTCTTCTTCAAAACACA
1 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACA
41642289 ACATCTAGTT
Statistics
Matches: 386, Mismatches: 32, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
183 1 0.00
184 132 0.34
185 61 0.16
186 136 0.35
187 55 0.14
188 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (186 bp):
TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGGTTGGCTCA
TTTCATCTACAATAATTTCCATTACCATGATTATAATCATGCTTTTGTGTAATTTTTGTAAACCA
CACCACACTTTCAGCTTAAAATCATTGTTTTTTTCCCTCCACTGTCGGCTGCCATT
Found at i:41642630 original size:14 final size:15
Alignment explanation
Indices: 41642603--41642631 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41642593 ACAGTTAGAG
41642603 GGGAAGAGAGAAAGA
1 GGGAAGAGAGAAAGA
41642618 GGGAAGA-AGAAAGA
1 GGGAAGAGAGAAAGA
41642632 AAATGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
GGGAAGAGAGAAAGA
Found at i:41646392 original size:39 final size:40
Alignment explanation
Indices: 41646241--41646406 Score: 226
Period size: 40 Copynumber: 4.2 Consensus size: 40
41646231 GGACTAAGAT
* * *
41646241 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
41646281 CCGAAGGCATTCGTGCGAGTTATTAAATTCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
41646321 CCGAAGGTATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * * *
41646361 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
41646400 CCGAAGG
1 CCGAAGG
41646407 TATTTGAACG
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 30 0.27
40 83 0.73
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:41649039 original size:61 final size:58
Alignment explanation
Indices: 41648950--41649082 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 58
41648940 TCTCAGAATA
* *
41648950 ATATTATTTTAATAGAATTAATATTAAATTAAAT-TAAATATTTATTTTATAGATAAATATT
1 ATATTAATTTAATAGAATTAATATTAAATTAAATCT-AATATTTA-TCT-T-GATAAATATT
* * * *
41649011 CTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAATTATT
1 ATATTAATTTAATAGAATTAATATTAAATTAAATCTAATATTTATCTTGATAAATATT
41649069 ATATTAATTTAATA
1 ATATTAATTTAATA
41649083 TTAAAGGGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 22 0.34
59 1 0.02
60 2 0.03
61 38 0.59
62 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (58 bp):
ATATTAATTTAATAGAATTAATATTAAATTAAATCTAATATTTATCTTGATAAATATT
Found at i:41649212 original size:13 final size:14
Alignment explanation
Indices: 41649193--41649225 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
41649183 TTGTAGAGAG
41649193 AAAATTATTT-AAA
1 AAAATTATTTCAAA
*
41649206 GAAATTATTTCAAA
1 AAAATTATTTCAAA
41649220 AAAATT
1 AAAATT
41649226 TTACAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
AAAATTATTTCAAA
Found at i:41651818 original size:51 final size:50
Alignment explanation
Indices: 41651692--41651840 Score: 147
Period size: 51 Copynumber: 2.9 Consensus size: 50
41651682 GCACTGAAGG
* * * * *
41651692 ACCATATCATGTAAGATCGTAACTGGGGGGTTATGACATTATATGGAAAGAAG
1 ACCATATC-TGTAAGATCATAACTGGTGGGTTAT-ACATCATAT-GAAAAAAA
* *
41651745 ATCATATTCTGTAAGACCATAACTGGTGGGTTATATCATCATAT-AAAAAAA
1 ACCATA-TCTGTAAGATCATAACTGGTGGGTTATA-CATCATATGAAAAAAA
* *
41651796 ACCATATCGTGTAAGATTATAACTGGTGGGTTTTAACATCATATG
1 ACCATATC-TGTAAGATCATAACTGGTGGGTTAT-ACATCATATG
41651841 GGGAAGTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
50 2 0.03
51 40 0.50
52 2 0.03
53 34 0.43
54 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (50 bp):
ACCATATCTGTAAGATCATAACTGGTGGGTTATACATCATATGAAAAAAA
Found at i:41652061 original size:60 final size:59
Alignment explanation
Indices: 41651967--41652303 Score: 334
Period size: 60 Copynumber: 5.6 Consensus size: 59
41651957 AAAGGACAGT
* * * * *
41651967 CTTTGTGGAAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGAATAC
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAG-ATGC
* ** * **
41652027 ATTTGTGGCAAAACTCTATACAGGAAAGTCTTTGTGGTGAGTGA-TGAATGTAAATGATGC
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGT-ACTGAATGTAAA-GATGC
* * *
41652087 CTTTGTGGAAAAAATCTTGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGC
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAA-GATGC
* * * **
41652147 CTTCGTGGCAAAACACTGGACAGAAAAGCCTTTGTGGCAAGTGTTGAATGTAAATGATGC
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAA-GATGC
* * * ** *
41652207 CTTTGTAGCCAAACTCTGGACAGAAAAGCCTTTGTGGTGAGTACTAAATGTAAAAGATGC
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAATGT-AAAGATGC
* * * * **
41652267 TTTTGTGGCAAACCTCTAGAAAGTTAAGCCTTTGTGG
1 CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGG
41652304 AAACCTTTGT
Statistics
Matches: 229, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.00
60 223 0.97
61 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (59 bp):
CTTTGTGGCAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGATGC
Found at i:41652180 original size:120 final size:120
Alignment explanation
Indices: 41651967--41652303 Score: 395
Period size: 120 Copynumber: 2.8 Consensus size: 120
41651957 AAAGGACAGT
* * * *
41651967 CTTTGTGGAAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGAATACATTTG
1 CTTTGTGGAAAAACTCTGGACAGGAAAGCCTTTGTGGAAAGTACTGAATGTAAAGGATGCATTTG
* * * * **
41652032 TGGCAAAACTCTATACAGGAAAGTCTTTGTGGTGAGTGATGAATGTAAATGATGC
66 TGGCAAAACACTAGACAGAAAAGCCTTTGTGGCAAGTGATGAATGTAAATGATGC
* * * * *
41652087 CTTTGTGGAAAAAATCTTGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGCCTTCG
1 CTTTGTGGAAAAACTCTGGACAGGAAAGCCTTTGTGGAAAGTACTGAATGTAAAGGATGCATTTG
* *
41652152 TGGCAAAACACTGGACAGAAAAGCCTTTGTGGCAAGTGTTGAATGTAAATGATGC
66 TGGCAAAACACTAGACAGAAAAGCCTTTGTGGCAAGTGATGAATGTAAATGATGC
* ** * ** * * *
41652207 CTTTGTAGCCAAACTCTGGACAGAAAAGCCTTTGTGGTGAGTACTAAATGTAAAAGATGCTTTTG
1 CTTTGTGGAAAAACTCTGGACAGGAAAGCCTTTGTGGAAAGTACTGAATGTAAAGGATGCATTTG
* * * **
41652272 TGGCAAACCTCTAGAAAGTTAAGCCTTTGTGG
66 TGGCAAAACACTAGACAGAAAAGCCTTTGTGG
41652304 AAACCTTTGT
Statistics
Matches: 182, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
120 182 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (120 bp):
CTTTGTGGAAAAACTCTGGACAGGAAAGCCTTTGTGGAAAGTACTGAATGTAAAGGATGCATTTG
TGGCAAAACACTAGACAGAAAAGCCTTTGTGGCAAGTGATGAATGTAAATGATGC
Found at i:41652298 original size:180 final size:180
Alignment explanation
Indices: 41651971--41652303 Score: 420
Period size: 180 Copynumber: 1.9 Consensus size: 180
41651961 GACAGTCTTT
* *
41651971 GTGGAAAAACTCTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGAATACATTTGTGGC
1 GTGGAAAAACACTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGAATACATTTGTAGC
* * * * *
41652036 AAAACTCTATACAGGAAAGTCTTTGTGGTGAGTGATGAATGTAAATGATGCCTTTGTGGAAAAAA
66 AAAACTCTAGACAGAAAAGCCTTTGTGGTGAGTGATAAATGTAAAAGATGCCTTTGTGGAAAAAA
* *
41652101 TCTTGACAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGCCTTC
131 TCTAGAAAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGCCTTC
* * * * *
41652151 GTGGCAAAACACTGGAC-AGAAAAGCCTTTGTGGCAAGTGTTGAATGTAAATG-ATGCCTTTGTA
1 GTGGAAAAACACTGGACAAG-AAAGCCTTTGTGGAAAGTATTGAATGTAAA-GAATACATTTGTA
* * * *
41652214 GCCAAACTCTGGACAGAAAAGCCTTTGTGGTGAGT-ACTAAATGTAAAAGATGCTTTTGTGGCAA
64 GCAAAACTCTAGACAGAAAAGCCTTTGTGGTGAGTGA-TAAATGTAAAAGATGCCTTTGTGGAAA
** **
41652278 ACCTCTAGAAAGTTAAGCCTTTGTGG
128 AAATCTAGAAAGGAAAGCCTTTGTGG
41652304 AAACCTTTGT
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
179 3 0.02
180 124 0.97
181 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (180 bp):
GTGGAAAAACACTGGACAAGAAAGCCTTTGTGGAAAGTATTGAATGTAAAGAATACATTTGTAGC
AAAACTCTAGACAGAAAAGCCTTTGTGGTGAGTGATAAATGTAAAAGATGCCTTTGTGGAAAAAA
TCTAGAAAGGAAAGCCTTTGTGGCAAGTACTGAATGTAAAGGATGCCTTC
Found at i:41654373 original size:148 final size:148
Alignment explanation
Indices: 41654038--41654356 Score: 381
Period size: 148 Copynumber: 2.2 Consensus size: 148
41654028 CGAATGCTTT
* * * * * * * * *
41654038 GGGAAATGAAATTTTCATT-AGATTCCACAATCCGGTATTGCTATGTGCAGACCATGATGTGCGA
1 GGGACATGAAA-TTCCATTAAGATACCACCATACGGTATTGCTAGGTGCAAACCATAATATGCGA
* * * * * * *
41654102 AGCTCCGGGCCTTATGGAGGGGTCATTGTGGTGTTTGAGCATCAATATTAGAAATGACGAAATGA
65 AGCTCCGGGCCTTAGGGAGGGGACATTGCGGTGTTCGAGCATCAAGATTAGAAATGACAAAAAGA
* *
41654167 AGGTATGGGCAGATGAATA
130 AGGTATGAGCAAATGAATA
* *
41654186 GGGACATGAAATTCCATTAAGATACCACCATACGGTATTGCTGGGTGCAAACCATAATATGTGAA
1 GGGACATGAAATTCCATTAAGATACCACCATACGGTATTGCTAGGTGCAAACCATAATATGCGAA
* * * *
41654251 GCTCTGGGCCTTAGGGAGGGGACATTGCGGTGTTCGAGTATCAAGGTTAGAAATGGCAAAACAG-
66 GCTCCGGGCCTTAGGGAGGGGACATTGCGGTGTTCGAGCATCAAGATTAGAAATGACAAAA-AGA
41654315 AGGTATGAGCAAATGAATA
130 AGGTATGAGCAAATGAATA
*
41654334 GGGACATGGAATTCCATTAAGAT
1 GGGACATGAAATTCCATTAAGAT
41654357 GCTGCTATAC
Statistics
Matches: 144, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
147 6 0.04
148 137 0.95
149 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (148 bp):
GGGACATGAAATTCCATTAAGATACCACCATACGGTATTGCTAGGTGCAAACCATAATATGCGAA
GCTCCGGGCCTTAGGGAGGGGACATTGCGGTGTTCGAGCATCAAGATTAGAAATGACAAAAAGAA
GGTATGAGCAAATGAATA
Found at i:41657853 original size:17 final size:17
Alignment explanation
Indices: 41657831--41657864 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41657821 ACCAACCTTT
41657831 TTCCATTACAAAAATTC
1 TTCCATTACAAAAATTC
41657848 TTCCATTACAAAAATTC
1 TTCCATTACAAAAATTC
41657865 ACTCCTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
TTCCATTACAAAAATTC
Found at i:41657874 original size:18 final size:17
Alignment explanation
Indices: 41657832--41657874 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
41657822 CCAACCTTTT
*
41657832 TCCATTACAAAAATTCT
1 TCCATTACAAAAATTCC
41657849 TCCATTACAAAAATTCAC
1 TCCATTACAAAAATTC-C
*
41657867 TCCTTTAC
1 TCCATTAC
41657875 TTCATTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (17 bp):
TCCATTACAAAAATTCC
Found at i:41658644 original size:3 final size:3
Alignment explanation
Indices: 41658636--41658675 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41658626 AACTATTTCC
41658636 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41658676 TACATAGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41660699 original size:18 final size:19
Alignment explanation
Indices: 41660670--41660705 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41660660 TGGTTGAAAA
*
41660670 AGATGTGTTGTGGTGTAAC
1 AGATGTGTTGTGGAGTAAC
41660689 AGATG-GTTGTGGAGTAA
1 AGATGTGTTGTGGAGTAA
41660706 AACGTATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (19 bp):
AGATGTGTTGTGGAGTAAC
Found at i:41670788 original size:15 final size:17
Alignment explanation
Indices: 41670754--41670790 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41670744 GTTTAATGGA
41670754 AAAATTATAAATAAATC
1 AAAATTATAAATAAATC
*
41670771 AAAATTA-AACTAAA-C
1 AAAATTATAAATAAATC
41670786 AAAAT
1 AAAAT
41670791 AAGACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTATAAATAAATC
Found at i:41681434 original size:49 final size:47
Alignment explanation
Indices: 41681374--41681828 Score: 703
Period size: 47 Copynumber: 9.6 Consensus size: 47
41681364 GATAATTGTG
* *
41681374 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41681421 ATGTGAAAGTGTATATATGTGACAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41681468 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41681515 ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41681564 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41681613 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41681662 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41681709 ATGTGAAAGTGTATATATGTGATGAGGCCTGATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
41681756 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41681803 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
41681829 TCCCGAAGGG
Statistics
Matches: 382, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 239 0.63
49 143 0.37
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41694787 original size:18 final size:18
Alignment explanation
Indices: 41694764--41694806 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41694754 TTTGGTTCGA
41694764 TTATTTTACTTAGTAGT-T
1 TTATTTTACTTAGT-GTAT
*
41694782 TTATTTAACTTAGTGTAT
1 TTATTTTACTTAGTGTAT
41694800 TTATTTT
1 TTATTTT
41694807 TTACAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.63
Consensus pattern (18 bp):
TTATTTTACTTAGTGTAT
Found at i:41696285 original size:85 final size:85
Alignment explanation
Indices: 41696142--41696320 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
41696132 GGCCGGCCAT
41696142 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
41696207 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
41696227 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
41696292 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
41696312 GGGCATGGG
1 GAGCATGGG
41696321 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:41697644 original size:47 final size:47
Alignment explanation
Indices: 41697590--41698222 Score: 871
Period size: 47 Copynumber: 13.6 Consensus size: 47
41697580 TATTTGAATA
41697590 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
41697637 AATGTGAAAGTGTATATATATGTGATGAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
* *
41697686 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
41697733 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTAATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
41697780 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
41697827 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
41697874 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
41697923 AATGTGAAAGTGTATATATGTG---A----TAA-GG-C--TGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
41697959 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
*
41698006 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
41698055 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
41698102 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
41698149 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
* * *
41698196 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
41698223 TCCCGAAGGG
Statistics
Matches: 548, Mismatches: 19, Indels: 38
0.91 0.03 0.06
Matches are distributed among these distances:
36 29 0.05
38 1 0.00
39 3 0.01
40 3 0.01
43 2 0.00
44 3 0.01
45 1 0.00
46 1 0.00
47 367 0.67
49 137 0.25
50 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
Found at i:41697943 original size:16 final size:16
Alignment explanation
Indices: 41697924--41697981 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
41697914 GATGTGATGA
41697924 ATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATAT
41697940 ATGTGATAAGGCTGTGATGA-
1 ATGTGA-AA-G-TGT-AT-AT
41697960 ATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATAT
41697976 ATGTGA
1 ATGTGA
41697982 TAAGGCCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 1 0.03
16 14 0.39
17 5 0.14
18 2 0.06
19 5 0.14
20 8 0.22
21 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.34
Consensus pattern (16 bp):
ATGTGAAAGTGTATAT
Found at i:41697957 original size:36 final size:36
Alignment explanation
Indices: 41697916--41697987 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
41697906 TAATGGCCGA
41697916 TGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
1 TGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
41697952 TGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
1 TGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
41697988 CGAATGGCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (36 bp):
TGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
Done.