Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 193 of 345
Found at i:54978326 original size:54 final size:54
Alignment explanation
Indices: 54978241--54978487 Score: 171
Period size: 54 Copynumber: 4.6 Consensus size: 54
54978231 ATTACTGTTT
* ***** *
54978241 TACCCTTAATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAA
* *
54978295 TACCCTTGATTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTCGATTTA-CAAAATTACCAAAA
* *** * *** *
54978349 TACCTCTAG-TTGGTAAAATTACCAAAATACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTTGATTTACAAAATTACCAAAATACC-CTCGATTTACAAAATTACCAAAA
** ** *
54978403 TACCCTCAATTTGTAAAATTACCAAAATACCC-CTGATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTC-GATTTACAAAATTACCA-AAA
* * **
54978457 TACCATTGGTTTACAAAATTACTGAAATACC
1 TACCCTTGATTTACAAAATTACCAAAATACC
54978488 TTTGGTTTGT
Statistics
Matches: 150, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
53 6 0.04
54 138 0.92
55 6 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
TACCCTTGATTTACAAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAA
Found at i:54978492 original size:27 final size:27
Alignment explanation
Indices: 54978417--54978495 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
54978407 CTCAATTTGT
** *
54978417 AAAATTACCA-AAATACCCCTGATTTAC
1 AAAATTA-CAGAAATACCATTGGTTTAC
*
54978444 AAAGTTACAGAAATACCATTGGTTTAC
1 AAAATTACAGAAATACCATTGGTTTAC
* *
54978471 AAAATTACTGAAATACCTTTGGTTT
1 AAAATTACAGAAATACCATTGGTTT
54978496 GTTGATTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.05
27 42 0.95
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACAGAAATACCATTGGTTTAC
Found at i:54978497 original size:81 final size:79
Alignment explanation
Indices: 54978270--54978487 Score: 233
Period size: 81 Copynumber: 2.7 Consensus size: 79
54978260 TACTGTTTTA
* * * **
54978270 CCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAAAATTACCAAAATACCCTCGATCAG
1 CCCT-GATTTAC-AAATTAC-AAAATACCATTGGTTTACAAAATTACCGAAATACCCTCGATTTG
54978335 TAAAATTACCAAAATAC
63 TAAAATTACCAAAATAC
* * *** *
54978352 CTCT-AGTTGGTA-AAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTT
1 CCCTGA-TT--TACAAATTA-CAAAATACCATTGGTTTACAAAATTACCGAAATACCCTCGATTT
54978415 GTAAAATTACCAAAATAC
62 GTAAAATTACCAAAATAC
*
54978433 CCCTGATTTACAAAGTTACAGAAATACCATTGGTTTACAAAATTACTGAAATACC
1 CCCTGATTTACAAA-TTACA-AAATACCATTGGTTTACAAAATTACCGAAATACC
54978488 TTTGGTTTGT
Statistics
Matches: 111, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
79 2 0.02
80 6 0.05
81 96 0.86
82 5 0.05
83 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (79 bp):
CCCTGATTTACAAATTACAAAATACCATTGGTTTACAAAATTACCGAAATACCCTCGATTTGTAA
AATTACCAAAATAC
Found at i:54978602 original size:27 final size:27
Alignment explanation
Indices: 54978547--54978609 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
54978537 ATGCCCCTAT
* * *
54978547 TAGGGTAAAGTGACCGTAAAGCTCTTG
1 TAGGGTAAAGTAACCGTAAAGCCCCTG
54978574 TAGGGTAAAGTAACCGTAATA-CCCCTG
1 TAGGGTAAAGTAACCGTAA-AGCCCCTG
*
54978601 TATGGTAAA
1 TAGGGTAAA
54978610 ATGACGAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
TAGGGTAAAGTAACCGTAAAGCCCCTG
Found at i:54979866 original size:9 final size:9
Alignment explanation
Indices: 54979854--54979930 Score: 73
Period size: 9 Copynumber: 7.9 Consensus size: 9
54979844 TTTGATAAAC
54979854 ATGATATGT
1 ATGATATGT
54979863 ATGATATGCAT
1 ATGATATG--T
54979874 ATGATATGT
1 ATGATATGT
*
54979883 ATGATATGCAC
1 ATGATATG--T
*
54979894 ATGACATGT
1 ATGATATGT
*
54979903 ATGATATGCAC
1 ATGATATG--T
54979914 ATGATATGT
1 ATGATATGT
54979923 ATGATATG
1 ATGATATG
54979931 CACACGAGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 32 0.57
11 24 0.43
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (9 bp):
ATGATATGT
Found at i:54979942 original size:20 final size:20
Alignment explanation
Indices: 54979852--54979934 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
54979842 ATTTTGATAA
54979852 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54979872 ATATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54979892 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
54979912 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54979932 ACA
1 ACA
54979935 CGAGATGTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:54980082 original size:23 final size:24
Alignment explanation
Indices: 54979989--54980130 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
54979979 AGGAAGTACA
54979989 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
54980013 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54980037 AAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54980061 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54980084 AAAAGGGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54980107 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54980131 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
23 39 0.36
24 62 0.57
25 7 0.06
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:54983120 original size:27 final size:27
Alignment explanation
Indices: 54983090--54983188 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
54983080 TTTAGTTTAC
*
54983090 TAAAATTACCGAAATACGCTTAG-CTTG
1 TAAAATTACCGAAATAC-CTTCGACTTG
* * * *
54983117 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCTTCGACTTG
*
54983144 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACCGAAATACCTTCGACTTG
54983171 TAAAATTACC-AAAGTACC
1 TAAAATTACCGAAA-TACC
54983189 CCCGATTTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
26 6 0.10
27 55 0.90
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (27 bp):
TAAAATTACCGAAATACCTTCGACTTG
Found at i:54983189 original size:54 final size:54
Alignment explanation
Indices: 54983090--54983196 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
54983080 TTTAGTTTAC
* *
54983090 TAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
* * *
54983144 TAAAATTACTGAAATAC-CTTCGACTTGTAAAATTAC-CAAAGTACCCCCGATTT
1 TAAAATTACCGAAATACGCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGATTT
54983197 ACAGAATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 7 0.15
54 39 0.85
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (54 bp):
TAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGATTTG
Found at i:54983204 original size:27 final size:27
Alignment explanation
Indices: 54983174--54983235 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
54983164 CGACTTGTAA
54983174 AATTACCAAAGTACCCCCGATTTACAG
1 AATTACCAAAGTACCCCCGATTTACAG
*** *
54983201 AATTACCATTTTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAG
54983228 AATTACCA
1 AATTACCA
54983236 TTTTACCGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAG
Found at i:54983205 original size:54 final size:54
Alignment explanation
Indices: 54983085--54983207 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
54983075 AATACTTTAG
* *
54983085 TTTACTAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTGAAATACCCTCGA
1 TTTAC-AAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGA
** * * *
54983140 TTTGTAAAATTACTGAAATAC-CTTCGACTTGTAAAATTAC-CAAAGTACCCCCGA
1 TTTACAAAATTACCGAAATACGCTTAG-CTTGTAAAAATACTCAAA-TACCCCCGA
*
54983194 TTTACAGAATTACC
1 TTTACAAAATTACC
54983208 ATTTTACCCC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
53 7 0.13
54 45 0.82
55 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (54 bp):
TTTACAAAATTACCGAAATACGCTTAGCTTGTAAAAATACTCAAATACCCCCGA
Found at i:54983251 original size:38 final size:38
Alignment explanation
Indices: 54983209--54983290 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
54983199 AGAATTACCA
* * *
54983209 TTTTACCCCCGATTTACATAATTACCATTTTACCGTCG
1 TTTTACCCCCGACTTACAGAATTACCATTTTACCCTCG
* *
54983247 TTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCG
1 TTTTACCCCCGACTTACAGAATTACCATTTTACCCTCG
*
54983285 ATTTAC
1 TTTTAC
54983291 AGAATTATCG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (38 bp):
TTTTACCCCCGACTTACAGAATTACCATTTTACCCTCG
Found at i:54983252 original size:27 final size:27
Alignment explanation
Indices: 54983185--54983242 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
54983175 ATTACCAAAG
54983185 TACCCCCGATTTACAGAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
*
54983212 TACCCCCGATTTACATAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
54983239 TACC
1 TACC
54983243 GTCGTTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.34
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCATTT
Found at i:54983289 original size:65 final size:65
Alignment explanation
Indices: 54983185--54983316 Score: 192
Period size: 65 Copynumber: 2.0 Consensus size: 65
54983175 ATTACCAAAG
* * *
54983185 TACCCCCGATTTACAGAATTACCATTTTACCCCCGATTTACATAATTACCATTTTACCGTCGTTT
1 TACCCCCGACTTACAGAATTACCATTTTACCCCCGATTTACAGAATTACCATTTTACCGTCGATT
* * * * *
54983250 TACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTATCGTTTTACCGTCGATT
1 TACCCCCGACTTACAGAATTACCATTTTACCCCCGATTTACAGAATTACCATTTTACCGTCGATT
54983315 TA
1 TA
54983317 TAGAATTACT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (65 bp):
TACCCCCGACTTACAGAATTACCATTTTACCCCCGATTTACAGAATTACCATTTTACCGTCGATT
Found at i:54983380 original size:27 final size:27
Alignment explanation
Indices: 54983246--54983380 Score: 182
Period size: 27 Copynumber: 5.0 Consensus size: 27
54983236 TTTTACCGTC
* *
54983246 GTTTTACCCTCGACTTACAGAATTACC
1 GTTTTACCCTCGATTTACAGAATTACT
54983273 GTTTTACCCTCGATTTACAGAATTA-T
1 GTTTTACCCTCGATTTACAGAATTACT
* *
54983299 CGTTTTACCGTCGATTTATAGAATTACT
1 -GTTTTACCCTCGATTTACAGAATTACT
** *
54983327 GTTTTACCCTTAATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
*
54983354 GTTTTACCCTCGATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
54983381 AAAATACCCT
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
27 94 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (27 bp):
GTTTTACCCTCGATTTACAGAATTACT
Found at i:54983388 original size:27 final size:27
Alignment explanation
Indices: 54983339--54983606 Score: 136
Period size: 27 Copynumber: 9.9 Consensus size: 27
54983329 TTTACCCTTA
****
54983339 ATTTACAAAATTACTGTTTTACCCTCG
1 ATTTACAAAATTACTAAAATACCCTCG
*
54983366 ATTTACAAAATTACTAAAATACCCTTG
1 ATTTACAAAATTACTAAAATACCCTCG
* *
54983393 GTTTACAAAATTACCAAAATACCCTCG
1 ATTTACAAAATTACTAAAATACCCTCG
* * * *
54983420 A-TCAGTAAAATTACCAAAATACCC-CT
1 ATTTA-CAAAATTACTAAAATACCCTCG
*** *
54983446 AGTTGGTAAAATTACCAAAATACCACT-G
1 A-TTTACAAAATTACTAAAATACC-CTCG
* *** * *
54983474 GTTTGTGAAATTACTGAAATACCCTCA
1 ATTTACAAAATTACTAAAATACCCTCG
** *
54983501 ATTTGTAAAATTACCAAAATACCC-CTG
1 ATTTACAAAATTACTAAAATACCCTC-G
* *
54983528 ATTTACAAAGTTAC-AGAAATACCCTTG
1 ATTTACAAAATTACTA-AAATACCCTCG
* *
54983555 ACTTT-CTAAAAATTA-TAGAAATACCATTG
1 A-TTTAC--AAAATTACTA-AAATACCCTCG
* *
54983584 GTTTACAAAATTACTGAAATACC
1 ATTTACAAAATTACTAAAATACC
54983607 TTTGGTTTGT
Statistics
Matches: 192, Mismatches: 34, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
26 8 0.04
27 156 0.81
28 9 0.05
29 19 0.10
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
ATTTACAAAATTACTAAAATACCCTCG
Found at i:54983389 original size:54 final size:55
Alignment explanation
Indices: 54983244--54983406 Score: 141
Period size: 54 Copynumber: 3.0 Consensus size: 55
54983234 CATTTTACCG
* * ***** ** *
54983244 TCGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTA-
1 TCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTAATTTACAAAATTAC
* * * ****
54983298 TCGTTTTACCGTCGATTTATAGAATTACTGTTTTACCCTTAATTTACAAAATTAC
1 TCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTAATTTACAAAATTAC
**
54983353 T-GTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTAC
1 TCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTAATTTACAAAATTAC
54983407 CAAAATACCC
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
54 91 0.99
55 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (55 bp):
TCGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTAATTTACAAAATTAC
Found at i:54983416 original size:54 final size:54
Alignment explanation
Indices: 54983358--54983615 Score: 177
Period size: 54 Copynumber: 4.7 Consensus size: 54
54983348 ATTACTGTTT
*
54983358 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGCAAAATTACCAAAA
* * * * * * *
54983412 TACCCTCGA-TCAGTAAAATTACCAAAATACCCCTAGTTGGTAAAATTACCAAAA
1 TACCCTCGATTTA-CAAAATTACTAAAATACCCTTGGTTTGCAAAATTACCAAAA
* *** * *** *
54983466 TACCACT-GGTTTGTGAAATTACTGAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACC-CTCGATTTACAAAATTACTAAAATACCCTTGGTTTGCAAAATTACCAAAA
* * *
54983520 TACCC-CTGATTTACAAAGTTAC-AGAAATACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAATACCCTTG-GTTTGC--AAAATTACCA-AAA
* * * * *
54983576 TACCATTGGTTTACAAAATTACTGAAATACCTTTGGTTTG
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTG
54983616 TTGATTTACC
Statistics
Matches: 155, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
53 3 0.02
54 105 0.68
55 10 0.06
56 37 0.24
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGCAAAATTACCAAAA
Found at i:54983443 original size:81 final size:79
Alignment explanation
Indices: 54983358--54983554 Score: 207
Period size: 81 Copynumber: 2.4 Consensus size: 79
54983348 ATTACTGTTT
*
54983358 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCC-CGATTTACAAAATTAC-AAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATC
54983423 AGTAAAATTACCAAAA
64 AGTAAAATTACCAAAA
* *** *** **
54983439 TACCCCTAGTTGGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACTGAAATACCCTCAAT
1 TACCCCGA-TTTACAAAATTA-CAAAATACC-CTTGGTTTACAAAATTACCAAAATACCCTCAAT
**
54983503 TTGTAAAATTACCAAAA
63 CAGTAAAATTACCAAAA
*
54983520 TACCCCTGATTTACAAAGTTACAGAAATACCCTTG
1 TACCCC-GATTTACAAAATTACA-AAATACCCTTG
54983555 ACTTTCTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
80 5 0.05
81 85 0.91
82 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (79 bp):
TACCCCGATTTACAAAATTACAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCAATCAG
TAAAATTACCAAAA
Found at i:54983611 original size:27 final size:27
Alignment explanation
Indices: 54983563--54983614 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
54983553 TGACTTTCTA
54983563 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
54983590 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
54983615 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:54983697 original size:27 final size:27
Alignment explanation
Indices: 54983666--54983733 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
54983656 ATGCCCCTAT
*
54983666 TAGGGTAAAGTGACCGTAA-AGCCCTTG
1 TAGGGTAAAGTGACCGTAATA-CCCCTG
*
54983693 TAGGGTAAAGTAACCGTAATACCCCTG
1 TAGGGTAAAGTGACCGTAATACCCCTG
* *
54983720 TATGGTAAAATGAC
1 TAGGGTAAAGTGAC
54983734 GAATATGCCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (27 bp):
TAGGGTAAAGTGACCGTAATACCCCTG
Found at i:54984918 original size:25 final size:25
Alignment explanation
Indices: 54984889--54984936 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54984879 TTATAATATG
* * *
54984889 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54984914 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54984937 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54984987 original size:9 final size:9
Alignment explanation
Indices: 54984975--54985051 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
54984965 TTTGATAAAC
54984975 ATGATATGT
1 ATGATATGT
*
54984984 ATGATATGCAC
1 ATGATATG--T
54984995 ATGATATGT
1 ATGATATGT
*
54985004 ATGATATGCAC
1 ATGATATG--T
*
54985015 ATGACATGT
1 ATGATATGT
*
54985024 ATGATATGCAC
1 ATGATATG--T
54985035 ATGATATGT
1 ATGATATGT
54985044 ATGATATG
1 ATGATATG
54985052 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:54985000 original size:11 final size:11
Alignment explanation
Indices: 54984984--54985055 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
54984974 CATGATATGT
54984984 ATGATATGCAC
1 ATGATATGCAC
*
54984995 ATGATATG--T
1 ATGATATGCAC
54985004 ATGATATGCAC
1 ATGATATGCAC
* *
54985015 ATGACATG--T
1 ATGATATGCAC
54985024 ATGATATGCAC
1 ATGATATGCAC
*
54985035 ATGATATG--T
1 ATGATATGCAC
54985044 ATGATATGCAC
1 ATGATATGCAC
54985055 A
1 A
54985056 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:54985063 original size:20 final size:20
Alignment explanation
Indices: 54984973--54985055 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
54984963 ATTTTGATAA
54984973 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54984993 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54985013 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
54985033 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54985053 ACA
1 ACA
54985056 CGAGATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:54985217 original size:23 final size:24
Alignment explanation
Indices: 54985109--54985298 Score: 244
Period size: 24 Copynumber: 8.0 Consensus size: 24
54985099 GAGGAAGTGC
*
54985109 AAAATGGGCTTATGCCCTAGTTATT
1 AAAA-GGGCTTATGCCCCAGTTATT
54985134 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54985158 AAAAGGGCTTATACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54985182 AAAAAGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
54985206 -AACGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54985229 AGAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
54985252 AAAAGAGCTT-TGCCCCAGTTGTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
54985275 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54985299 ATGATAAAGC
Statistics
Matches: 145, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
23 58 0.40
24 76 0.52
25 11 0.08
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:54985526 original size:31 final size:31
Alignment explanation
Indices: 54985491--54985554 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
54985481 CGTTTACAGT
* *
54985491 AAAGGCTTTGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
* **
54985522 AAAGGCTTCGGCCTAGTGTTATGAAAAATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
54985553 AA
1 AA
54985555 TATGAAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAAAATGA
Found at i:54988944 original size:16 final size:16
Alignment explanation
Indices: 54988923--54988954 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54988913 CATGTAACGC
54988923 CCCAAAAATCTCGAAA
1 CCCAAAAATCTCGAAA
*
54988939 CCCAAAAATCTTGAAA
1 CCCAAAAATCTCGAAA
54988955 TCCTAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (16 bp):
CCCAAAAATCTCGAAA
Found at i:54992024 original size:16 final size:16
Alignment explanation
Indices: 54992003--54992034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54991993 GTTGTAACGC
54992003 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
*
54992019 CCCAAAAGTCCCGAAA
1 CCCAAAAATCCCGAAA
54992035 TCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.38, G:0.09, T:0.06
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:54996592 original size:20 final size:21
Alignment explanation
Indices: 54996567--54996606 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54996557 CTCTTGAAAC
54996567 AGGGC-ACACACCCGTGTGGA
1 AGGGCAACACACCCGTGTGGA
*
54996587 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACACCCGTGTGG
54996607 TCATTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGGCAACACACCCGTGTGGA
Found at i:54998528 original size:46 final size:46
Alignment explanation
Indices: 54998478--54998699 Score: 297
Period size: 46 Copynumber: 4.8 Consensus size: 46
54998468 TGGTTGAGCA
54998478 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
54998524 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * *
54998570 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* * *
54998615 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
54998663 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54998700 GCGGGTTACA
Statistics
Matches: 155, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
43 6 0.04
45 4 0.03
46 108 0.70
47 28 0.18
48 4 0.03
50 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:55000682 original size:49 final size:50
Alignment explanation
Indices: 55000612--55000738 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
55000602 TCAAGTCGAT
** * **
55000612 GCCATGTCTTAAACATGGTCTTACACTGGCTATCGA-AT-TCGAGGCCGAC
1 GCCATGTCCCAAACATGGTCTTACACTGGCTATC-ACATATCCACACCGAC
* * * *
55000661 GCCATGTCCCAAACATAGTCTTACACTAGCTCTCACATATCCACACCGAT
1 GCCATGTCCCAAACATGGTCTTACACTGGCTATCACATATCCACACCGAC
*
55000711 GCCATGTCCCAGACATGGTCTTACACTG
1 GCCATGTCCCAAACATGGTCTTACACTG
55000739 ACACTTCTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.02
49 31 0.48
50 32 0.50
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAAACATGGTCTTACACTGGCTATCACATATCCACACCGAC
Found at i:55000732 original size:50 final size:49
Alignment explanation
Indices: 55000608--55000786 Score: 150
Period size: 48 Copynumber: 3.7 Consensus size: 49
55000598 TCCGTCAAGT
** * * *
55000608 CGATGCCATGTCTTAAACATGGTCTTACACTGGCTATCGA-AT-TCGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACT-GCTCTC-ACATATCCACGC
* * *
55000657 CGACGCCATGTCCCAAACATAGTCTTACACTAGCTCTCACATATCCACAC
1 CGATGCCATGTCCCAAACATGGTCTTACACT-GCTCTCACATATCCACGC
* * * * **
55000707 CGATGCCATGTCCCAGACATGGTCTTACACTGACACT-TC-TATACGTGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTG-CTCTCACATATCCACGC
* *
55000755 CGATGCCATGTCCCAGACAAGGTCTTACACTG
1 CGATGCCATGTCCCAAACATGGTCTTACACTG
55000787 ACACATCTCG
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
48 37 0.34
49 36 0.33
50 35 0.32
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (49 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGCTCTCACATATCCACGC
Found at i:55000771 original size:48 final size:46
Alignment explanation
Indices: 55000706--55000877 Score: 181
Period size: 48 Copynumber: 3.7 Consensus size: 46
55000696 CATATCCACA
55000706 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACTTCTATACGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACTTCT-T-CGTG
* *
55000754 CCGATGCCATGTCCCAGACAAGGTCTTACACTGACACATC-TCGTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGACACTTCTTCGT-G
* * * *
55000800 CTGATG-CATGTCCCAGACAT-GTCTTACACT-AGCTCTTGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTTCT-TC-GTG
***
55000846 TTAATGCCATGTCCCAGACATGGTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
55000878 AGCTCTAATG
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
43 1 0.01
44 13 0.12
45 16 0.15
46 14 0.13
47 15 0.14
48 48 0.45
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGACACTTCTTCGTG
Found at i:55000911 original size:34 final size:36
Alignment explanation
Indices: 55000847--55000914 Score: 113
Period size: 34 Copynumber: 1.9 Consensus size: 36
55000837 GTCTCAATGT
55000847 TAATGCCATGTCCCAGACATGGTCTTACACTAGCTC
1 TAATGCCATGTCCCAGACATGGTCTTACACTAGCTC
*
55000883 TAATG-CATGTCCCAGAGAT-GTCTTACACTAGC
1 TAATGCCATGTCCCAGACATGGTCTTACACTAGC
55000915 GTACAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 13 0.42
35 13 0.42
36 5 0.16
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (36 bp):
TAATGCCATGTCCCAGACATGGTCTTACACTAGCTC
Found at i:55001122 original size:71 final size:71
Alignment explanation
Indices: 55001034--55001165 Score: 264
Period size: 71 Copynumber: 1.9 Consensus size: 71
55001024 GCAATTTATG
55001034 CTATATCAATTCAAACACATATAATAACAATGTAGTTGTATTATTTACATACAACTTACCTTGAA
1 CTATATCAATTCAAACACATATAATAACAATGTAGTTGTATTATTTACATACAACTTACCTTGAA
55001099 TTAGAA
66 TTAGAA
55001105 CTATATCAATTCAAACACATATAATAACAATGTAGTTGTATTATTTACATACAACTTACCT
1 CTATATCAATTCAAACACATATAATAACAATGTAGTTGTATTATTTACATACAACTTACCT
55001166 CAGATTACAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (71 bp):
CTATATCAATTCAAACACATATAATAACAATGTAGTTGTATTATTTACATACAACTTACCTTGAA
TTAGAA
Found at i:55015943 original size:46 final size:46
Alignment explanation
Indices: 55015883--55016045 Score: 222
Period size: 46 Copynumber: 3.5 Consensus size: 46
55015873 TCGCCGATGC
*
55015883 CATGTCCCAAACATGTCTTACACTGGCTTACATCTCGAGTCCGATA
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGTCCGATA
* *
55015929 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAATA
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGTCCGATA
* * * *
55015975 CATGTCCCAGACATGTCTTACACTAGCTCT-CGTCTC-AATGCCGATGC
1 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAGT-CCGAT-A
55016022 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
55016046 AGCGCACAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 79 0.75
47 25 0.24
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGTCCGATA
Found at i:55028264 original size:2 final size:2
Alignment explanation
Indices: 55028257--55028286 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55028247 TTATTTTGGC
55028257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55028287 TCATGTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55034486 original size:28 final size:27
Alignment explanation
Indices: 55034423--55034492 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
55034413 ATAGTGAGTC
55034423 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
55034450 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
55034478 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55034493 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:55042671 original size:93 final size:93
Alignment explanation
Indices: 55042559--55042730 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55042549 GCCCATAAGT
* *
55042559 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55042624 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
55042652 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55042717 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
55042731 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:55042726 original size:46 final size:46
Alignment explanation
Indices: 55042551--55042726 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
55042541 TGTAACCCGC
* * *
55042551 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
55042597 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
55042647 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
55042690 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55042727 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:55045153 original size:30 final size:30
Alignment explanation
Indices: 55045109--55045197 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
55045099 CAAAGATAAC
55045109 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
55045138 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
55045168 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
55045198 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:55045157 original size:15 final size:15
Alignment explanation
Indices: 55045109--55045188 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
55045099 CAAAGATAAC
*
55045109 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
55045123 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
55045138 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
55045153 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
55045168 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
55045183 AAGAAA
1 AAGAAA
55045189 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55045197 original size:15 final size:15
Alignment explanation
Indices: 55045120--55045197 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
55045110 AGAAAACCGA
55045120 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
55045135 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
55045149 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
55045164 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
55045180 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
55045195 ATA
1 ATA
55045198 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:55048253 original size:93 final size:93
Alignment explanation
Indices: 55048141--55048312 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55048131 GCCCATAAGT
* *
55048141 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55048206 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
55048234 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55048299 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
55048313 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:55048308 original size:46 final size:46
Alignment explanation
Indices: 55048133--55048308 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
55048123 TGTAACCCGC
* * *
55048133 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
55048179 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
55048229 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
55048272 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55048309 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:55050860 original size:28 final size:27
Alignment explanation
Indices: 55050797--55050866 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
55050787 ATAGTGAGTC
55050797 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
55050824 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
55050852 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55050867 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:55061622 original size:49 final size:49
Alignment explanation
Indices: 55061569--55062035 Score: 723
Period size: 49 Copynumber: 9.7 Consensus size: 49
55061559 GATTTTATAC
* * *
55061569 GATGAATGTGAATGTGTATATATATGAGATAAGGCCGAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55061618 GATGAATGTGAAAGCGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* *
55061667 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55061716 GATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* *
55061765 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
55061814 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
55061863 GATGAATGTG-AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* * *
55061911 GATGAATGTG-AAG-GTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* * * * *
55061958 GATGAATGTGAAAGTG--TATATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55062005 GATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 GATGAATGTGAAAGTGTATATATATGTGATAAG
55062036 TCCCGAAGGG
Statistics
Matches: 393, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
47 93 0.24
48 55 0.14
49 245 0.62
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (49 bp):
GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
Found at i:55063513 original size:40 final size:40
Alignment explanation
Indices: 55063446--55063637 Score: 278
Period size: 40 Copynumber: 4.8 Consensus size: 40
55063436 GAGAATTGAG
* * *
55063446 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
**
55063486 AGTGATGTATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
55063526 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
55063566 AGTGATGTAACCAGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
55063606 AGTGATGTATCCGGGC-AAGGTCTCGAAGAGCA
1 AGTGATGTATCCGGACTAA-GTCCCGAAGAGCA
55063638 ATCATGCTGG
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
39 2 0.01
40 136 0.99
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
Found at i:55067577 original size:146 final size:144
Alignment explanation
Indices: 55067359--55067727 Score: 548
Period size: 146 Copynumber: 2.6 Consensus size: 144
55067349 GATTTTATGC
* * * *
55067359 GATGAATGTGAATGTGTATATATATGAGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAATG
1 GATGAATGTGAAAGTGTGTATATATGTGATAA-GCCGAATGGCCGATGTGATGAATGTGAAAGTG
55067424 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATACATATGTGATAA
65 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTATACATATGTGATAA
* *
55067489 GGCCTAATGGCCGATGT
128 GGCCGAATGGCCAATGT
*
55067506 GATGAATGTGAAAGTGTGTATATATGTGATAAGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 GATGAATGTGAAAGTGTGTATATATGTGATAAGCCGAATGGCCGATGTGATGAATGTGAAAGTGT
* *
55067571 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATGTGATAAGGC
66 ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTATACATATGTGATAAGGC
55067636 CGAATGGCCAATGT
131 CGAATGGCCAATGT
* * * * *
55067650 GATGAATGTGAAA--GTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 GATGAATGTGAAAGTGTGTATATATGTGATA-AGCCGAATGGCCGATGTGATGAATGTGAAAGTG
55067713 TATA-A-ATGTGATAAG
65 TATATATATGTGATAAG
55067728 TCCCGAAGGG
Statistics
Matches: 206, Mismatches: 15, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
141 10 0.05
142 17 0.08
143 31 0.15
144 43 0.21
145 3 0.01
146 73 0.35
147 29 0.14
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (144 bp):
GATGAATGTGAAAGTGTGTATATATGTGATAAGCCGAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTATACATATGTGATAAGGC
CGAATGGCCAATGT
Found at i:55067642 original size:47 final size:49
Alignment explanation
Indices: 55067359--55067727 Score: 545
Period size: 49 Copynumber: 7.7 Consensus size: 49
55067349 GATTTTATGC
* * *
55067359 GATGAATGTGAATGTGTATATATATGAGATAAGGCCGAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55067408 GATGAATGTGAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* *
55067457 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55067506 GATGAATGTGAAAGTGTGTATATATGTGATAA-GCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
55067554 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* * *
55067603 GATGAATGTG-AAG-GTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
* * * * *
55067650 GATGAATGTGAAAGTG--TATATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
*
55067697 GATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 GATGAATGTGAAAGTGTATATATATGTGATAAG
55067728 TCCCGAAGGG
Statistics
Matches: 296, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
47 93 0.31
48 54 0.18
49 149 0.50
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
Found at i:55068755 original size:48 final size:47
Alignment explanation
Indices: 55068695--55069155 Score: 397
Period size: 48 Copynumber: 9.6 Consensus size: 47
55068685 TATGTGCGCT
* *
55068695 AGTGTAAGACCATGTCTGGGACATGGCATCGGTCACAATATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATATGAGAGCC
* * * * * *
55068743 AGTGTAAGACCATGTTTGGAACATGGCATCGACGATGTTGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGATATGAGAGCC
* * * * * *
55068791 AGTGTAAGACCATGTTTGGGACATGGCATCGACATTGATATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGATATGAGAGCC
* *
55068839 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATTAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCACGATATGAGAGCC
* * * ** *
55068887 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGA-TATGAGAGCC
* * * *
55068935 AGTGTAAGGCCATGTCTGGGACATGG-ATCGGCATTGATATGTGCA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGATATGAG-AGCC
* *
55068982 AGTGTAAGACTATGTCTAGGACATGGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGA-TATGAGAGCC
* * * * * * *
55069030 AGTATAAAACCATGTCTGGGACTTGGCATCGGCATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGATATGAGAGCC
* * * * * * *
55069078 AGTGTAAGACCATGTCTGGGACATGGAATTAGCCTCGACATGTGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCA-TCGGCACGATATGAGAGCC
* * *
55069126 AGTGCAAGACCATGTTTGGAACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
55069156 AGTAATTCAC
Statistics
Matches: 333, Mismatches: 67, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
47 45 0.14
48 279 0.84
49 9 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATATGAGAGCC
Found at i:55068948 original size:144 final size:142
Alignment explanation
Indices: 55068684--55069157 Score: 576
Period size: 144 Copynumber: 3.3 Consensus size: 142
55068674 GCGGTGTTAC
* * *
55068684 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTCACAATATGAAAGCCAGTGTA
1 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC-ATATGAGAGCCAGTGTA
* * *
55068749 AGACCATGTTTGGAACATGGCATCGACGATGTTGTGAGAGCCAGTGTAAGACCATGTTTGGGACA
65 AGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCCAGTGTAAGACCATGTCTGGGACA
55068814 TGGCATCGACATTG
130 TGG-ATCGACATTG
* *
55068828 ATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATTAGAGCCAGTGTA
1 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC-ATATGAGAGCCAGTGTA
*
55068893 AGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCCAGTGTAAGGCCATGTCTGGGACA
65 AGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCCAGTGTAAGACCATGTCTGGGACA
*
55068958 TGGATCGGCATTG
130 TGGATCGACATTG
* * * * *
55068971 ATATGTGCACTAGTGTAAGACTATGTCTAGGACATGGCATCGGCCACATTATGAGAGCCAGTATA
1 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACA-TATGAGAGCCAGTGTA
* * * * * * * *
55069036 AAACCATGTCTGGGACTTGGCATCGGCATTGATATGT--GCGCTAGTGTAAGACCATGTCTGGGA
65 AGACCATGTTTGGAACATGGCATCGACAAT-AT-TGTGAGAGCCAGTGTAAGACCATGTCTGGGA
* * *
55069099 CATGGAAT-TAGCCTCG
128 CATGG-ATCGA-CATTG
* * * * *
55069115 ACATGTGAGCTAGTGCAAGACCATGTTTGGAACATGGCATCAG
1 ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAG
55069158 TAATTCACCC
Statistics
Matches: 285, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
142 1 0.00
143 117 0.41
144 164 0.58
145 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (142 bp):
ATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATATGAGAGCCAGTGTAA
GACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCCAGTGTAAGACCATGTCTGGGACAT
GGATCGACATTG
Found at i:55069137 original size:239 final size:239
Alignment explanation
Indices: 55068695--55069155 Score: 626
Period size: 239 Copynumber: 1.9 Consensus size: 239
55068685 TATGTGCGCT
*
55068695 AGTGTAAGACCATGTCTGGGACATGGCATCGGTCACAATATGAAAGCCAGTGTAAGACCATGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTCACAATATG-AAGCCAGTGTAAGACCATGTTA
* ** * * * *
55068760 GGAACATGGCATCGACGATGTTGTGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACA
65 GGAACATGGCATCGACCACATTATGAGAGCCAGTATAAAACCATGTCTGGGACATGGCATCGACA
* * *
55068825 TTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATTAGAGCCAGT
130 TTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGAATCAGCCACGACATTAGAGCCAGT
*
55068890 GTAAGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCC
195 GCAAGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCC
* ** * *
55068935 AGTGTAAGGCCATGTCTGGGACATGG-ATCGG-CATTGATATG-TGCACTAGTGTAAGACTATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTCA-CAATATGAAGC-C-AGTGTAAGACCATGT
* *
55068997 CTAGG-ACATGGCATCGGCCACATTATGAGAGCCAGTATAAAACCATGTCTGGGACTTGGCATCG
63 -TAGGAACATGGCATCGACCACATTATGAGAGCCAGTATAAAACCATGTCTGGGACATGGCATCG
* * *
55069061 GCATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGAATTAGCCTCGACATGT-GAGC
127 ACATTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGAATCAGCCACGACAT-TAGAGC
*
55069125 TAGTGCAAGACCATGTTTGGAACATGGCATC
191 CAGTGCAAGACCATGTTTGGAACATGGCATC
55069156 AGTAATTCAC
Statistics
Matches: 193, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
237 2 0.01
238 3 0.02
239 159 0.82
240 29 0.15
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (239 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGTCACAATATGAAGCCAGTGTAAGACCATGTTAG
GAACATGGCATCGACCACATTATGAGAGCCAGTATAAAACCATGTCTGGGACATGGCATCGACAT
TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGAATCAGCCACGACATTAGAGCCAGTG
CAAGACCATGTTTGGAACATGGCATCGACAATATTGTGAGAGCC
Found at i:55070917 original size:45 final size:45
Alignment explanation
Indices: 55070832--55070993 Score: 231
Period size: 45 Copynumber: 3.6 Consensus size: 45
55070822 CCGACATTTC
* *
55070832 GCCTGCTAGGCTCGAA-GCCCG-ATA-TCATTTCACCGGTATTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACCGGTATTATA
**
55070875 GCCTGCTAGGCTTGAAGGCCCGAATAGTATCTCACCGGTATTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
* * *
55070920 GCCTGCTAGGCTCAAAGGTCCGAATAGTATCTCACCGGCACTATA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
55070965 GCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 GCCTGCTAGGCTCAAAGGCCCGAATAGTA
55070994 CTGTACGATA
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 15 0.14
44 5 0.05
45 87 0.81
46 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (45 bp):
GCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGTATTATA
Found at i:55078886 original size:32 final size:33
Alignment explanation
Indices: 55078816--55078899 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 33
55078806 GAGTGTTCAG
55078816 AGATGAAGAAAAT-GACGGGGAAGAGGGGTTTGA
1 AGATGAAG-AAATCGACGGGGAAGAGGGGTTTGA
*
55078849 AGATGAAGAAATCGATGGGGAAG-GGGGTTTGA
1 AGATGAAGAAATCGACGGGGAAGAGGGGTTTGA
* *
55078881 CGATGAAGAAATCAACGGG
1 AGATGAAGAAATCGACGGG
55078900 AAAATGTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 29 0.63
33 17 0.37
ACGTcount: A:0.38, C:0.06, G:0.40, T:0.15
Consensus pattern (33 bp):
AGATGAAGAAATCGACGGGGAAGAGGGGTTTGA
Found at i:55082158 original size:28 final size:28
Alignment explanation
Indices: 55082118--55082179 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
55082108 GACATCCCAA
55082118 CACTTGGTTCGAACCCTAGCTCGGATAC
1 CACTTGGTTCGAACCCTAGCTCGGATAC
55082146 CACTTGGTTCGAACCCTAGCTCGGATAC
1 CACTTGGTTCGAACCCTAGCTCGGATAC
55082174 CACTTG
1 CACTTG
55082180 TCACTGGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (28 bp):
CACTTGGTTCGAACCCTAGCTCGGATAC
Found at i:55083515 original size:2 final size:2
Alignment explanation
Indices: 55083510--55083535 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55083500 ATATAGGAAT
55083510 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
55083536 CACACATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55084139 original size:15 final size:16
Alignment explanation
Indices: 55084121--55084150 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55084111 ATTACTGTTC
55084121 AAATTAAAA-TAATTT
1 AAATTAAAATTAATTT
55084136 AAATTAAAATTAATT
1 AAATTAAAATTAATT
55084151 AACATAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTAAAATTAATTT
Found at i:55084799 original size:17 final size:18
Alignment explanation
Indices: 55084777--55084810 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55084767 GAGTTCAAAT
55084777 TTTATT-ATCATCATATC
1 TTTATTAATCATCATATC
*
55084794 TTTATTAATCATTATAT
1 TTTATTAATCATCATAT
55084811 AAAAGGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATTAATCATCATATC
Found at i:55086430 original size:3 final size:3
Alignment explanation
Indices: 55086422--55086477 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
55086412 TGCAAAAACC
55086422 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55086470 AAT AAT AA
1 AAT AAT AA
55086478 CAAAAGCGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55088938 original size:28 final size:28
Alignment explanation
Indices: 55088898--55088955 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
55088888 CTTAAACATG
55088898 TTATATTAACTGCATTTAGATAATTATA
1 TTATATTAACTGCATTTAGATAATTATA
55088926 TTATATTAACTGCATTTAGATAATTATA
1 TTATATTAACTGCATTTAGATAATTATA
55088954 TT
1 TT
55088956 TATACATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (28 bp):
TTATATTAACTGCATTTAGATAATTATA
Found at i:55089825 original size:12 final size:12
Alignment explanation
Indices: 55089810--55089840 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55089800 AAAGAGTTAC
55089810 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
55089822 AAAAAAAGAAAA
1 AAAAAGAGAAAA
55089834 AAAAAGA
1 AAAAAGA
55089841 CAAAGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:55089953 original size:19 final size:20
Alignment explanation
Indices: 55089929--55089985 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
55089919 ATGCATTGAG
55089929 TTTAATTTCATAATATT-TA
1 TTTAATTTCATAATATTATA
*
55089948 TTTAA-TTAATAAATATTATA
1 TTTAATTTCAT-AATATTATA
55089968 TTATAATTATACATAATA
1 TT-TAATT-T-CATAATA
55089986 AAGGCCAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 4 0.13
21 3 0.10
22 1 0.03
23 5 0.17
24 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAATTTCATAATATTATA
Found at i:55090356 original size:2 final size:2
Alignment explanation
Indices: 55090349--55090382 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55090339 AATTATTTTC
55090349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55090383 ATTTGTATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55090669 original size:22 final size:22
Alignment explanation
Indices: 55090641--55090687 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55090631 TTGAGAGTAC
55090641 TTTTTATATTTAATATTTA-AAA
1 TTTTTAT-TTTAATATTTAGAAA
* *
55090663 TTTTTATTTTTATTTTTAGAAA
1 TTTTTATTTTAATATTTAGAAA
55090685 TTT
1 TTT
55090688 AATCCCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTTATTTTAATATTTAGAAA
Found at i:55093315 original size:49 final size:49
Alignment explanation
Indices: 55093243--55093431 Score: 216
Period size: 49 Copynumber: 3.8 Consensus size: 49
55093233 TGAGGTTACG
* *
55093243 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * * * * * * *
55093292 TGTGTAGTACTAAGTGCTGGCTACGATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCA
* * *
55093343 TGTGTAGTACTAAGTGCAGGATACTACGTGTACCGTATAATTTGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
* * *
55093392 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA
55093432 CCCTGTCTAC
Statistics
Matches: 112, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 72 0.64
50 4 0.04
51 36 0.32
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
Found at i:55093414 original size:100 final size:100
Alignment explanation
Indices: 55093240--55093432 Score: 314
Period size: 100 Copynumber: 1.9 Consensus size: 100
55093230 TTGTGAGGTT
* * *
55093240 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGTATGTGTAGTACTAA
1 ACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAA
* *
55093305 GTGCTGGCTACGATGCGTACCCGATAACTTCGATC
66 GTGCAGGCTACGATGCGTACCAGATAACTTCGATC
* *
55093340 ACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGTATAATTTGTCGCATGTGTAGTACTAA
1 ACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAA
*
55093405 GTGCAGGCTACTATGCGTACCAGATAAC
66 GTGCAGGCTACGATGCGTACCAGATAAC
55093433 CCTGTCTACA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (100 bp):
ACGTGTGTAGTACTAAGTGCAGGATACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAA
GTGCAGGCTACGATGCGTACCAGATAACTTCGATC
Found at i:55095548 original size:55 final size:56
Alignment explanation
Indices: 55095482--55095596 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 56
55095472 CAGCATGGCT
* *
55095482 ACCAGATACAGA-AAATGTGACTGAGTCACCAGATACAGATA-TGTTGTGGCAGT-GCC
1 ACCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAGT-TTGTGGCA-TAGCC
* * *
55095538 ACCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAGTTTGTGGCATAGCC
1 ACCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAGTTTGTGGCATAGCC
55095593 ACCA
1 ACCA
55095597 AGACGCTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 27 0.53
56 23 0.45
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (56 bp):
ACCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAGTTTGTGGCATAGCC
Found at i:55095560 original size:27 final size:27
Alignment explanation
Indices: 55095508--55095596 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
55095498 GTGACTGAGT
55095508 CACCAGATACAGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATAT-TTGTGGCAGTGC
* *
55095537 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
55095564 CACCAGAACAGATAGTTTGTGGCA-TAGC
1 CACCAGAACAGATA-TTTGTGGCAGT-GC
55095592 CACCA
1 CACCA
55095597 AGACGCTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 23 0.43
29 7 0.13
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:55095750 original size:28 final size:28
Alignment explanation
Indices: 55095703--55095794 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
55095693 AAATTAACCC
*
55095703 TAGGGGTATAGA-GGTTATTTTGCATACA
1 TAGGGGTATA-ATGGTAATTTTGCATACA
55095731 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55095759 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55095787 TAGGGGTA
1 TAGGGGTA
55095795 CTCTAGTACA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 1 0.02
28 61 0.98
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:55096080 original size:8 final size:8
Alignment explanation
Indices: 55096044--55096083 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
55096034 CCCAAAATAC
55096044 CGGCTTTT
1 CGGCTTTT
*
55096052 CGGCATTT
1 CGGCTTTT
*
55096060 CGGCATTT
1 CGGCTTTT
55096068 CGGCTTTT
1 CGGCTTTT
55096076 CGGCTTTT
1 CGGCTTTT
55096084 GCCGATCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.05, C:0.25, G:0.25, T:0.45
Consensus pattern (8 bp):
CGGCTTTT
Found at i:55101408 original size:40 final size:40
Alignment explanation
Indices: 55101308--55101485 Score: 144
Period size: 40 Copynumber: 4.5 Consensus size: 40
55101298 AAATTATAAT
* * * * **
55101308 CGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGCTATATC
1 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACTATATC
* *
55101348 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTATC
1 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACTATATC
* * *
55101388 CGGGCTAAGACCCGAAGGCATTTGTGC-AATC-GTGATATC
1 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACT-ATATC
* * * * * * * *
55101427 CGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTACCATATC
1 CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACTATATC
* *
55101467 CGGGCTATGTCCCGAAGGC
1 CGGGCTAAGACCCGAAGGC
55101486 GTTTGAACGA
Statistics
Matches: 110, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.26
40 80 0.73
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTCGTGCGAGTCACTATATC
Found at i:55109439 original size:40 final size:39
Alignment explanation
Indices: 55109351--55109534 Score: 140
Period size: 40 Copynumber: 4.6 Consensus size: 39
55109341 AAATTGAATG
* * * *
55109351 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGCAA-T-TG-TGCAAGTCGT
* * * *
55109391 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCG-T
* *
55109431 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTC-GT
* * *
55109471 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
* * *
55109510 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
55109535 CTTGGTGCGG
Statistics
Matches: 116, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.03
38 2 0.02
39 5 0.04
40 103 0.89
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGT
Found at i:55109515 original size:80 final size:80
Alignment explanation
Indices: 55109395--55109543 Score: 192
Period size: 80 Copynumber: 1.9 Consensus size: 80
55109385 GAAATTATAA
* * * *
55109395 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
55109460 TGCGAGTCATTCTAT
66 TGCGAGTCATTCTAT
* * * * * *
55109475 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ATATCCGGGCTAAGACCCGAAGGCATTC
55109539 GTGCG
65 GTGCG
55109544 GGTTACCATA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.02
80 57 0.98
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCATTCTAT
Found at i:55117309 original size:40 final size:40
Alignment explanation
Indices: 55117265--55117374 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
55117255 TTCACAATTT
* *
55117265 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
* * * *
55117305 GCACAATTGCCTTCGGGTCTTAACCCGAATGTAATTACCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
* * *
55117345 GCATAAATGTCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
55117375 ATCATTCAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATGTAATCACCA
Found at i:55126278 original size:55 final size:53
Alignment explanation
Indices: 55126191--55126420 Score: 202
Period size: 55 Copynumber: 4.3 Consensus size: 53
55126181 ATTAGGGTTT
* * *
55126191 AAGGATACCATGTAAGATCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * *
55126246 AAGGATATCATGTAAGGCCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * *
55126301 AAAGG-TCCCATGTAAGACCATGGCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* ** * * *
55126354 ATGGATACCATGTAAGATGATGTCGAGACATGGAAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
*
55126403 AAGGATACCACGTAAGAC
1 AAGGATACCATGTAAGAC
55126421 ATGAGATCAT
Statistics
Matches: 141, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
49 15 0.11
52 6 0.04
53 38 0.27
54 11 0.08
55 67 0.48
56 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:55126397 original size:108 final size:110
Alignment explanation
Indices: 55126198--55126398 Score: 264
Period size: 108 Copynumber: 1.8 Consensus size: 110
55126188 TTTAAGGATA
* * *
55126198 CCATGTAAGATCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
* *
55126263 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
* * *
55126308 CCATGTAAGACCATGGCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCATGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
** * *
55126370 ATGATGTCGAGACATGGAAATGGTAAGTT
65 ACCATGTCAAGACATGGAAATGATAAGTT
55126399 TCAAAAGGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
107 3 0.04
108 43 0.55
109 7 0.09
110 25 0.32
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:55134902 original size:4 final size:4
Alignment explanation
Indices: 55134874--55134916 Score: 50
Period size: 4 Copynumber: 9.8 Consensus size: 4
55134864 TACCCCAACT
55134874 TTTA TGTTA TTTCA GTTTCA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA T-TTA TTT-A -TTT-A TTTA TTTA TTTA TTTA TTTA TTT
55134917 CATATTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 23 0.64
5 8 0.22
6 5 0.14
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:55136466 original size:15 final size:15
Alignment explanation
Indices: 55136441--55136486 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
55136431 CTCTGAGTCC
55136441 ATTTATTTTATTTTTT
1 ATTT-TTTTATTTTTT
55136457 ATTTTTTTATTTTTGT
1 ATTTTTTTATTTTT-T
*
55136473 -TTTATTTATTTTTT
1 ATTTTTTTATTTTTT
55136487 GAGGACTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.79
16 5 0.18
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:55136467 original size:20 final size:20
Alignment explanation
Indices: 55136442--55136484 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
55136432 TCTGAGTCCA
*
55136442 TTTATTTTATTTTTTATTT-T
1 TTTATTTT-TGTTTTATTTAT
55136462 TTTATTTTTGTTTTATTTAT
1 TTTATTTTTGTTTTATTTAT
55136482 TTT
1 TTT
55136485 TTGAGGACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTATTTTTGTTTTATTTAT
Found at i:55139694 original size:19 final size:20
Alignment explanation
Indices: 55139659--55139705 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
55139649 TTTTCACTCG
55139659 TTTCTTTTTCAAGATCT-C-
1 TTTCTTTTTCAAGATCTCCT
55139677 TTTCTTTTTCCACA-ATCTCCT
1 TTTCTTTTT-CA-AGATCTCCT
55139698 TTTCTTTT
1 TTTCTTTT
55139706 AAAAGCTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 2 0.08
21 8 0.32
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTCTTTTTCAAGATCTCCT
Found at i:55139893 original size:36 final size:36
Alignment explanation
Indices: 55139802--55139894 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
55139792 ACAATCTTTC
*
55139802 TCTTTTTCATTTTCTTTTTC-ATTCATGTTTATTTT
1 TCTTTTTCAATTTCTTTTTCTATTCATGTTTATTTT
* * * *
55139837 TCTTTTTTCTATGTCATTTTCTA-TCAT-TTATTTTTT
1 TC-TTTTTCAATTTCTTTTTCTATTCATGTT-TATTTT
55139873 TCTTTTCTCAATTTCTTTTTCT
1 TCTTTT-TCAATTTCTTTTTCT
55139895 TGCTCCCTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
35 8 0.17
36 37 0.80
37 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (36 bp):
TCTTTTTCAATTTCTTTTTCTATTCATGTTTATTTT
Found at i:55142344 original size:55 final size:56
Alignment explanation
Indices: 55142279--55142393 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
55142269 ATCATGGCTG
* * *
55142279 CCAGATACAGA-AAATGTGATAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * * *
55142335 CCAGA-ACAGATATATGTGGCAGGGCCACTAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
55142390 CCAG
1 CCAG
55142394 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:55142356 original size:27 final size:27
Alignment explanation
Indices: 55142304--55142393 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
55142294 GTGATAGAGT
55142304 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
55142333 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
*
55142360 CACTAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
55142388 CACCAG
1 CACCAG
55142394 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 23 0.43
28 23 0.43
29 7 0.13
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:55142542 original size:28 final size:28
Alignment explanation
Indices: 55142499--55142587 Score: 151
Period size: 28 Copynumber: 3.2 Consensus size: 28
55142489 AAATTAACCC
*
55142499 TAGGGGTATAACGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
55142527 TTGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
*
55142555 TAAGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55142583 TAGGG
1 TAGGG
55142588 TATTCTAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:55144877 original size:40 final size:40
Alignment explanation
Indices: 55144780--55144958 Score: 141
Period size: 40 Copynumber: 4.5 Consensus size: 40
55144770 GAATCACGTA
* ** * *
55144780 CCTTCGGAACTTAA-CCGGATATAACGACTCGCTCAAATG
1 CCTTCGGGACTTAACCCGGATATAGTGACTCGCACGAATG
* *
55144819 CCTTCGGGAC-GAAGCCCGGTTATAGTGACTCGCACGAATG
1 CCTTCGGGACTTAA-CCCGGATATAGTGACTCGCACGAATG
* * * *
55144859 CCTTCGGGACTTAACCCGGGTTTAGTAACTTGCACGAATG
1 CCTTCGGGACTTAACCCGGATATAGTGACTCGCACGAATG
* ** * * *
55144899 CCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCAC-AAAG
1 CCTTCGGGA-CTTAACCCGGATATAGTGAC-TCGCACGAATG
*
55144939 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
55144959 CATCATTCGA
Statistics
Matches: 112, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.02
39 12 0.11
40 88 0.79
41 10 0.09
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGATATAGTGACTCGCACGAATG
Found at i:55154308 original size:28 final size:29
Alignment explanation
Indices: 55154260--55154322 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
55154250 GTGATAGAGT
*
55154260 CACCAGATACAGATATTTTGTGGCAGT-GC
1 CACCAGATACAGATAATTTGTGGCA-TAGC
55154289 CACCAGA-ACAGATAATTTGTGGCATAGC
1 CACCAGATACAGATAATTTGTGGCATAGC
55154317 CACCAG
1 CACCAG
55154323 GACGCTTCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (29 bp):
CACCAGATACAGATAATTTGTGGCATAGC
Found at i:55154461 original size:27 final size:27
Alignment explanation
Indices: 55154430--55154513 Score: 159
Period size: 27 Copynumber: 3.1 Consensus size: 27
55154420 TTAACCCTAG
*
55154430 GGGTATAACGGTAATTTTGCATACATA
1 GGGTATAATGGTAATTTTGCATACATA
55154457 GGGTATAATGGTAATTTTGCATACATA
1 GGGTATAATGGTAATTTTGCATACATA
55154484 GGGTATAATGGTAATTTTGCATACATA
1 GGGTATAATGGTAATTTTGCATACATA
55154511 GGG
1 GGG
55154514 GTATTCTAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (27 bp):
GGGTATAATGGTAATTTTGCATACATA
Found at i:55156847 original size:19 final size:19
Alignment explanation
Indices: 55156820--55156859 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
55156810 TTATTCTAGC
*
55156820 AACTAAATTAACTAAGATG
1 AACTAAATTAACTAACATG
*
55156839 AACTTAATTAACTAACATG
1 AACTAAATTAACTAACATG
55156858 AA
1 AA
55156860 TAGTTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (19 bp):
AACTAAATTAACTAACATG
Found at i:55162703 original size:24 final size:24
Alignment explanation
Indices: 55162669--55162718 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
55162659 AATGATGTAC
*
55162669 AATGTCTCCCTTATATGTAACCGA
1 AATGTCCCCCTTATATGTAACCGA
* * *
55162693 AATGTCCCCCTTGTTTGTAATCGA
1 AATGTCCCCCTTATATGTAACCGA
55162717 AA
1 AA
55162719 ATCACTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (24 bp):
AATGTCCCCCTTATATGTAACCGA
Found at i:55166487 original size:18 final size:19
Alignment explanation
Indices: 55166446--55166489 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
55166436 GGACACTTTC
55166446 TTTTCTTTCTTCAATCTCT
1 TTTTCTTTCTTCAATCTCT
*
55166465 CTTTCTTT-TTCAA-CTTCT
1 TTTTCTTTCTTCAATC-TCT
55166483 TTTTCTT
1 TTTTCTT
55166490 GCTCACATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 14 0.64
19 7 0.32
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTCTTTCTTCAATCTCT
Found at i:55168537 original size:24 final size:24
Alignment explanation
Indices: 55168503--55168552 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
55168493 AATGATGTAT
*
55168503 AATGTCTCCCTTGTATGTAACAGA
1 AATGTCCCCCTTGTATGTAACAGA
*
55168527 AATGTCCCCCTTGTATGTAACCGA
1 AATGTCCCCCTTGTATGTAACAGA
55168551 AA
1 AA
55168553 ATCACTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (24 bp):
AATGTCCCCCTTGTATGTAACAGA
Found at i:55179985 original size:30 final size:30
Alignment explanation
Indices: 55179949--55180049 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 30
55179939 GACAAGATTG
* * *
55179949 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
55179979 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
55180007 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
55180036 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55180050 GATTCACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 23 0.38
29 19 0.31
30 19 0.31
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:55180061 original size:29 final size:28
Alignment explanation
Indices: 55179978--55180053 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
55179968 AAAATTGTAC
* *
55179978 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
55180006 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
55180035 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
55180054 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:55184631 original size:42 final size:41
Alignment explanation
Indices: 55184513--55184679 Score: 133
Period size: 42 Copynumber: 3.9 Consensus size: 41
55184503 GGAACGTTGT
*
55184513 CATCGATCTGAGATATCGTGTAAGACCGTGTCTGGGACACAGG
1 CATCGATCTGAGAT-TCGTGTAAGACCATGTCTGGGACAC-GG
* * *
55184556 CCTCGAT-TAGAGATTTATGTGTAAGATCATGTCTGGGACATCGG
1 CATCGATCT-GAGA-TT-CGTGTAAGACCATGTCTGGGACA-CGG
* *
55184600 CATCGTATCTGA-ATTCGTGTAAGACCCTGTCTGGGACAGAGG
1 CATCG-ATCTGAGATTCGTGTAAGACCATGTCTGGGACA-CGG
* * * *
55184642 CATCGACACT-AAATTACATGTAAGACCACGTCTGGGAC
1 CATCGA-TCTGAGATT-CGTGTAAGACCATGTCTGGGAC
55184680 GTTGGCATTC
Statistics
Matches: 101, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
41 2 0.02
42 33 0.33
43 32 0.32
44 28 0.28
45 5 0.05
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (41 bp):
CATCGATCTGAGATTCGTGTAAGACCATGTCTGGGACACGG
Found at i:55186559 original size:42 final size:42
Alignment explanation
Indices: 55186474--55186562 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
55186464 TTAGGAATAT
* * * *
55186474 TTTTATTTTATCTTTTAGTCGTTTATTAGAGTTAGGAAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGAAACTA
* * *
55186516 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAGCTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGAAACTA
55186558 TTTTC
1 TTTTC
55186563 CCAATTAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.53
Consensus pattern (42 bp):
TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGGAAACTA
Found at i:55190162 original size:57 final size:57
Alignment explanation
Indices: 55190065--55190175 Score: 204
Period size: 57 Copynumber: 1.9 Consensus size: 57
55190055 TTCAAGCCCC
55190065 ACACATATCCTCATTACCCTTGTTAGTCATAGAATCCATAATAACATCACAAACCCT
1 ACACATATCCTCATTACCCTTGTTAGTCATAGAATCCATAATAACATCACAAACCCT
* *
55190122 ACACATATCCTCATTACCCTTGTTAGTCATATAATTCATAATAACATCACAAAC
1 ACACATATCCTCATTACCCTTGTTAGTCATAGAATCCATAATAACATCACAAAC
55190176 ATATATAGGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.30
Consensus pattern (57 bp):
ACACATATCCTCATTACCCTTGTTAGTCATAGAATCCATAATAACATCACAAACCCT
Found at i:55192239 original size:40 final size:40
Alignment explanation
Indices: 55192135--55192297 Score: 166
Period size: 40 Copynumber: 4.1 Consensus size: 40
55192125 GGAATTTAGT
** * * * *
55192135 CGGATATAACCGCAAGCACAATTGCCTTCGAGTCTTAACC
1 CGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCC
* *** *
55192175 CGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGCC
1 CGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCC
* *
55192215 CGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 CGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCC
* * *
55192255 TGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGCC
1 CGGATATAA-CAACTAGCACAAATGCCTTCGGGTCTTAGCC
55192295 CGG
1 CGG
55192298 GTATCATTCA
Statistics
Matches: 99, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
40 98 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCC
Found at i:55194827 original size:8 final size:8
Alignment explanation
Indices: 55194814--55194840 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
55194804 ATTCAGCATT
55194814 TTTCTCAA
1 TTTCTCAA
55194822 TTTCTCAA
1 TTTCTCAA
55194830 TTTCTCAA
1 TTTCTCAA
55194838 TTT
1 TTT
55194841 TACATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTCTCAA
Found at i:55208304 original size:14 final size:15
Alignment explanation
Indices: 55208280--55208308 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55208270 GTAGACCTTC
55208280 TATCTTTTTCCATAG
1 TATCTTTTTCCATAG
55208295 TATC-TTTTCCATAG
1 TATCTTTTTCCATAG
55208309 AATTCTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (15 bp):
TATCTTTTTCCATAG
Found at i:55216747 original size:93 final size:93
Alignment explanation
Indices: 55216588--55216760 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 93
55216578 CAGATATTTG
* * **
55216588 GGCATCCGAACTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTTGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCGAACTCATTGAG
55216653 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
55216681 GGCATCTGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATACGAACG-CCTGATCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCC-GAACTCATTGA
*
55216745 GTTGAGTCTGAGTTCG
65 GTTGAGTCCGAGTTCG
55216761 CTTATGGGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:55227324 original size:29 final size:29
Alignment explanation
Indices: 55227292--55227427 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
55227282 ATACCCTTCG
** * *
55227292 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
55227321 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
55227350 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
55227379 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
55227408 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
55227428 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:55227419 original size:58 final size:58
Alignment explanation
Indices: 55227267--55227426 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 58
55227257 AATTTAAGCC
* *** * * ** * *
55227267 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
* * * * *
55227325 TGCACACATAGTGTCATATTTTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
*
55227383 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
55227427 AATCTCGTCA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:55234090 original size:29 final size:29
Alignment explanation
Indices: 55234058--55234193 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
55234048 ATACCCTTCG
** * *
55234058 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
55234087 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
55234116 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
55234145 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
55234174 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
55234194 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:55234185 original size:58 final size:58
Alignment explanation
Indices: 55234033--55234192 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 58
55234023 AATTTAAGCC
* *** * * ** * *
55234033 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
* * * * *
55234091 TGCACACATAGTGTCATATTTTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
*
55234149 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
55234193 AATCTCGTCA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:55236202 original size:34 final size:34
Alignment explanation
Indices: 55236154--55236219 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
55236144 CTATTACTGT
55236154 TACTGAAATAGGCTAAGGACC-ACACTGATACTAA
1 TACTGAAATAGGCTAAGGACCTA-ACTGATACTAA
* * *
55236188 TACTGAAATGGGCTATGGCCCTAACTGATACT
1 TACTGAAATAGGCTAAGGACCTAACTGATACT
55236220 GGACTGTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (34 bp):
TACTGAAATAGGCTAAGGACCTAACTGATACTAA
Found at i:55238854 original size:31 final size:31
Alignment explanation
Indices: 55238812--55238913 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
55238802 CCTTTTCGTA
55238812 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
55238849 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
55238881 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
55238912 TT
1 TT
55238914 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:55238854 original size:38 final size:38
Alignment explanation
Indices: 55238789--55238896 Score: 180
Period size: 38 Copynumber: 2.8 Consensus size: 38
55238779 TCAATCATGC
* *
55238789 ACTGGGCCGTAGCCCTTTTCGTATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
55238828 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
55238866 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
55238897 ACTGGGCCGA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 54 0.83
39 11 0.17
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:55239151 original size:24 final size:24
Alignment explanation
Indices: 55239105--55239223 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
55239095 GCTTTATCAT
*
55239105 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
55239130 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
55239154 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
**
55239177 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTA
55239201 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
55239224 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 24 0.28
24 48 0.56
25 13 0.15
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:55239184 original size:47 final size:48
Alignment explanation
Indices: 55239105--55239223 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
55239095 GCTTTATCAT
*
55239105 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
*
55239154 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
55239201 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
55239224 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 2 0.03
47 43 0.65
48 9 0.14
49 12 0.18
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:55239299 original size:20 final size:20
Alignment explanation
Indices: 55239274--55239333 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
55239264 TATGATTACC
55239274 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
55239294 TCATGTGCGTATCATACATT
1 TCATGTGCATATCATACATA
55239314 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
55239334 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:55239408 original size:25 final size:25
Alignment explanation
Indices: 55239376--55239423 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55239366 ATACATAAAC
* * *
55239376 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
55239401 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
55239424 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:55247141 original size:31 final size:31
Alignment explanation
Indices: 55247099--55247200 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
55247089 CCTTTTCGTA
55247099 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
55247136 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
55247168 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
55247199 TT
1 TT
55247201 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:55247141 original size:38 final size:38
Alignment explanation
Indices: 55247076--55247183 Score: 180
Period size: 38 Copynumber: 2.8 Consensus size: 38
55247066 TCAATCATGC
* *
55247076 ACTGGGCCGTAGCCCTTTTCGTATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
55247115 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
55247153 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
55247184 ACTGGGCCGA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 54 0.83
39 11 0.17
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:55247438 original size:24 final size:24
Alignment explanation
Indices: 55247392--55247509 Score: 145
Period size: 23 Copynumber: 5.0 Consensus size: 24
55247382 GCTTTATCAT
*
55247392 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
55247417 ATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTTA
55247441 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
**
55247464 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTA
55247488 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
55247510 TCACTTCCTC
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
23 39 0.46
24 32 0.38
25 13 0.15
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:55247471 original size:47 final size:48
Alignment explanation
Indices: 55247392--55247509 Score: 163
Period size: 47 Copynumber: 2.5 Consensus size: 48
55247382 GCTTTATCAT
*
55247392 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
*
55247441 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
55247488 ATAACT-GGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
55247510 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
46 18 0.28
47 26 0.40
48 9 0.14
49 12 0.18
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:55247585 original size:20 final size:20
Alignment explanation
Indices: 55247560--55247619 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
55247550 TATGATTACC
55247560 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
55247580 TCATGTGCGTATCATACATT
1 TCATGTGCATATCATACATA
55247600 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
55247620 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:55247694 original size:25 final size:25
Alignment explanation
Indices: 55247662--55247709 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55247652 ATACATAAAC
* * *
55247662 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
55247687 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
55247710 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:55251974 original size:28 final size:28
Alignment explanation
Indices: 55251934--55251990 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55251924 ATAAGTATTA
55251934 CCATAACAATATTACCATCGCCTTTAAC
1 CCATAACAATATTACCATCGCCTTTAAC
55251962 CCATAACAATATTACCATCGCCTTTAAC
1 CCATAACAATATTACCATCGCCTTTAAC
55251990 C
1 C
55251991 TAGATTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (28 bp):
CCATAACAATATTACCATCGCCTTTAAC
Done.