Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 54 of 250
Found at i:17169143 original size:80 final size:80
Alignment explanation
Indices: 17168999--17169178 Score: 213
Period size: 81 Copynumber: 2.3 Consensus size: 80
17168989 AATCAAGCAT
* * * * *
17168999 CTTCGGG-TTTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAACCCGGATATGGTC
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAACCCAGATATAGTC
* *
17169062 ACT-AGCATAAATGC
66 ACTAAGCACAAAAGC
** * ** *
17169076 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGATCTTAGTCCAGATGTAGT
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCAC-AAGGCCTTCGGATCTTAACCCAGATATAGT
17169141 CACTAAGCACAAAAGC
65 CACTAAGCACAAAAGC
17169157 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17169179 CATTCGAGTA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 7 0.08
78 4 0.05
79 17 0.20
80 27 0.31
81 31 0.36
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAACCCAGATATAGTC
ACTAAGCACAAAAGC
Found at i:17174211 original size:45 final size:45
Alignment explanation
Indices: 17174158--17174278 Score: 188
Period size: 45 Copynumber: 2.7 Consensus size: 45
17174148 CGATGTCGAT
* * *
17174158 GTCCCAGACATGGTCTTACACGTAACCACATATATTGATGCCAAC
1 GTCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAAC
17174203 GTCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAAC
1 GTCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAAC
** *
17174248 GTCCCAGATGTGGTCTTACATGAAAACACAT
1 GTCCCAGACATGGTCTTACACGAAAACACAT
17174279 CAGAATCCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (45 bp):
GTCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAAC
Found at i:17182472 original size:47 final size:47
Alignment explanation
Indices: 17182419--17182549 Score: 174
Period size: 47 Copynumber: 2.8 Consensus size: 47
17182409 GTGCGAATAA
* * *
17182419 TACCTTGATTTGGCTATGGGCCATGCTATAGGTA-TTCAGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTC-GAGAGAAGT
* * *
17182466 TACCTTGATTTGGTTACGGGCCATGGTATAGGTACTTCGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGT
* *
17182513 TTCCTTGATTTGGCTACGAGCCATGGTATAGGTACTT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTT
17182550 ATCGATTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 71 0.96
48 3 0.04
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGT
Found at i:17184254 original size:21 final size:20
Alignment explanation
Indices: 17184206--17184246 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17184196 CTAAACCGAT
*
17184206 CACATATAAAAATTTCTGAA
1 CACATAGAAAAATTTCTGAA
*
17184226 CACTTAGAAAAATTTCATGAA
1 CACATAGAAAAATTTC-TGAA
17184247 ATCATAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (20 bp):
CACATAGAAAAATTTCTGAA
Found at i:17187210 original size:23 final size:23
Alignment explanation
Indices: 17187179--17187331 Score: 164
Period size: 23 Copynumber: 6.7 Consensus size: 23
17187169 GGAATCTATA
17187179 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* * * *
17187202 GGCTGCAATATAGTTGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
* *
17187225 GGCTAC-ATCTCAATGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
*
17187248 GGCTACAATACAGTGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
17187271 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* ** *
17187294 AGCTACGTTACAGTGATAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* * *
17187317 GACTATATTACAGTG
1 GGCTACAATACAGTG
17187332 TGGAAATTTG
Statistics
Matches: 106, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
22 2 0.02
23 102 0.96
24 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCTACAATACAGTGGTAGCTTC
Found at i:17187314 original size:69 final size:69
Alignment explanation
Indices: 17187179--17187331 Score: 182
Period size: 69 Copynumber: 2.2 Consensus size: 69
17187169 GGAATCTATA
* * * ** *
17187179 GGCTACAATACAGTGGTAGCTTCGGCTGCAATATAGTTGTAGCTTTGGCTACATCTCAATGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCTCAATGATAG
17187244 CTTC
66 CTTC
* * *
17187248 GGCTACAATACAGTGGTAGCTTTGGCTACAATACAGTGGTAGCTTCAGCTACGT-TACAGTGATA
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCT-CAATGATA
17187312 GCTTC
65 GCTTC
* * *
17187317 GACTATATTACAGTG
1 GGCTACAATACAGTG
17187332 TGGAAATTTG
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 1 0.01
69 70 0.99
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATACAGTGGTAGCTTCAGCTACATCTCAATGATAG
CTTC
Found at i:17189644 original size:27 final size:27
Alignment explanation
Indices: 17189614--17189694 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
17189604 AATCTCATAT
*
17189614 CTGTAGGCTAGTATTACTGAAATACCC
1 CTGTAGGCTAGAATTACTGAAATACCC
*
17189641 CTGTAGGCTAGAATTACTGAAATGCCC
1 CTGTAGGCTAGAATTACTGAAATACCC
*
17189668 CTGTAAGG-TAGAATTACTAAAATACCC
1 CTGT-AGGCTAGAATTACTGAAATACCC
17189695 TTGCTTTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 46 0.94
28 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (27 bp):
CTGTAGGCTAGAATTACTGAAATACCC
Found at i:17189709 original size:27 final size:27
Alignment explanation
Indices: 17189679--17189963 Score: 188
Period size: 27 Copynumber: 10.7 Consensus size: 27
17189669 TGTAAGGTAG
**
17189679 AATTACTAAAATACCCTTGCTTTACAA
1 AATTACTAAAATACCCTTAATTTACAA
* * * **
17189706 AATTACT-GAATAACTTTGGTTTACAA
1 AATTACTAAAATACCCTTAATTTACAA
*
17189732 AATTACTAAAATA-CCTTCGA-TTAGCAA
1 AATTACTAAAATACCCTT-AATTTA-CAA
* * * * **
17189759 AATTTCCAAAATACCCCT-GTTTGTAA
1 AATTACTAAAATACCCTTAATTTACAA
* * **
17189785 AATTACCAAAATACCCCTAATTTGTAA
1 AATTACTAAAATACCCTTAATTTACAA
* **
17189812 AATTACT-AAATACCCTTAACTTGTAA
1 AATTACTAAAATACCCTTAATTTACAA
* * **
17189838 AATTACTGAAATACCCTCAATTTTTAA
1 AATTACTAAAATACCCTTAATTTACAA
* * **
17189865 AATTACCAAAATACCCCTAATTTGGAA
1 AATTACTAAAATACCCTTAATTTACAA
* * *
17189892 AATTACCAAAATACCCTTGATTTAGAA
1 AATTACTAAAATACCCTTAATTTACAA
*
17189919 AATTAC-AGAAATACCCCTAATTTACAA
1 AATTACTA-AAATACCCTTAATTTACAA
17189946 AATTAC-AGAAATACCCTT
1 AATTACTA-AAATACCCTT
17189964 GACTTTCAAA
Statistics
Matches: 216, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
26 72 0.33
27 141 0.65
28 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (27 bp):
AATTACTAAAATACCCTTAATTTACAA
Found at i:17189717 original size:26 final size:27
Alignment explanation
Indices: 17189679--17189748 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
17189669 TGTAAGGTAG
*
17189679 AATTACTAAAATACCCTTGCTTTACAA
1 AATTACTAAAATAACCTTGCTTTACAA
* * *
17189706 AATTACT-GAATAACTTTGGTTTACAA
1 AATTACTAAAATAACCTTGCTTTACAA
17189732 AATTACTAAAAT-ACCTT
1 AATTACTAAAATAACCTT
17189749 CGATTAGCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 26 0.72
27 10 0.28
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (27 bp):
AATTACTAAAATAACCTTGCTTTACAA
Found at i:17189814 original size:80 final size:80
Alignment explanation
Indices: 17189730--17189961 Score: 242
Period size: 80 Copynumber: 2.9 Consensus size: 80
17189720 TTTGGTTTAC
*
17189730 AAAATTACTAAAATA-CCTTCGA-TTAGCAAAATTTCCAAAATACCCCTGTTTGTAAAATTACCA
1 AAAATTACTAAAATACCCTT-GACTTAG-AAAATTTCCAAAATACCCCTATTTGTAAAATTACCA
*
17189793 AAATACCCCTAATTTGT
64 AAATACCCCTAATTTGG
* * ** * *
17189810 AAAATTACT-AAATACCCTTAACTT-GTAAAATTACTGAAATACCCTCAATTTTTAAAATTACCA
1 AAAATTACTAAAATACCCTTGACTTAG-AAAATTTCCAAAATACCC-CTATTTGTAAAATTACCA
17189873 AAATACCCCTAATTTGG
64 AAATACCCCTAATTTGG
* * * **
17189890 AAAATTACCAAAATACCCTTGATTTAGAAAA-TTACAGAAATACCCCTAATTTACAAAATTA-CA
1 AAAATTACTAAAATACCCTTGACTTAGAAAATTTCCA-AAATACCCCT-ATTTGTAAAATTACCA
17189953 GAAATACCC
64 -AAATACCC
17189962 TTGACTTTCA
Statistics
Matches: 125, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
79 22 0.18
80 58 0.46
81 44 0.35
82 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.30
Consensus pattern (80 bp):
AAAATTACTAAAATACCCTTGACTTAGAAAATTTCCAAAATACCCCTATTTGTAAAATTACCAAA
ATACCCCTAATTTGG
Found at i:17189963 original size:54 final size:52
Alignment explanation
Indices: 17189679--17190023 Score: 214
Period size: 54 Copynumber: 6.4 Consensus size: 52
17189669 TGTAAGGTAG
* * ** * ** ** *
17189679 AATTACTAAAATACCCTTGCTTTACAAAATTACTGAATAACTTTGGTTTACAA
1 AATTAC-AAAATACCCTTGATTTAGAAAATTACAAAATACCCCTAATTTGCAA
* * *
17189732 AATTACTAAAATA-CCTTCGA-TTAGCAAAATTTCCAAAATACCCCT-GTTTGTAA
1 AATTAC-AAAATACCCTT-GATTTAG-AAAA-TTACAAAATACCCCTAATTTGCAA
* * * * * *
17189785 AATTACCAAAATACCCCTAATTT-GTAAAATTACTAAATACCCTTAACTTGTAA
1 AATTA-CAAAATACCCTTGATTTAG-AAAATTACAAAATACCCCTAATTTGCAA
* ** ** *
17189838 AATTACTGAAATACCCTCAATTTTTAAAATTACCAAAATACCCCTAATTTGGAA
1 AATTAC-AAAATACCCTTGATTTAGAAAATTA-CAAAATACCCCTAATTTGCAA
*
17189892 AATTACCAAAATACCCTTGATTTAGAAAATTACAGAAATACCCCTAATTTACAA
1 AATTA-CAAAATACCCTTGATTTAGAAAATTACA-AAATACCCCTAATTTGCAA
*** ** *
17189946 AATTACAGAAATACCCTTGACTTTCA-AAAATTACAGAAATACTATTGGTTTGAAA
1 AATTACA-AAATACCCTTGA-TTT-AGAAAATTACA-AAATACCCCTAATTTGCAA
*
17190001 AATTATCGAAATACCCTTGATTT
1 AATTA-CAAAATACCCTTGATTT
17190024 GTAAATTTAC
Statistics
Matches: 235, Mismatches: 41, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
52 20 0.09
53 76 0.32
54 94 0.40
55 43 0.18
56 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (52 bp):
AATTACAAAATACCCTTGATTTAGAAAATTACAAAATACCCCTAATTTGCAA
Found at i:17190043 original size:27 final size:27
Alignment explanation
Indices: 17189730--17190046 Score: 243
Period size: 27 Copynumber: 11.8 Consensus size: 27
17189720 TTTGGTTTAC
* * *
17189730 AAAATTACTAAAATA-CCTTCGATTAGC
1 AAAATTACCAAAATACCCTT-GATTTGT
* *
17189757 AAAATTTCCAAAATACCCCTG-TTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* *
17189783 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * *
17189810 AAAATTA-CTAAATACCCTTAACTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
** ** *
17189836 AAAATTACTGAAATACCCTCAATTTTT
1 AAAATTACCAAAATACCCTTGATTTGT
* * *
17189863 AAAATTACCAAAATACCCCTAATTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
17189890 AAAATTACCAAAATACCCTTGATTTAG-
1 AAAATTACCAAAATACCCTTGATTT-GT
* * **
17189917 AAAATTA-CAGAAATACCCCTAATTTAC
1 AAAATTACCA-AAATACCCTTGATTTGT
**
17189944 AAAATTA-CAGAAATACCCTTGACTTTCA
1 AAAATTACCA-AAATACCCTTGA-TTTGT
** * *
17189972 AAAATTA-CAGAAATACTATTGGTTTGA
1 AAAATTACCA-AAATACCCTTGATTTGT
* *
17189999 AAAATTATCGAAATACCCTTGATTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* *
17190026 AAATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
17190047 TAAGGTGAAA
Statistics
Matches: 239, Mismatches: 43, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
26 47 0.20
27 165 0.69
28 27 0.11
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGT
Found at i:17190329 original size:41 final size:41
Alignment explanation
Indices: 17190284--17190406 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
17190274 GGAGGAAGAA
*
17190284 ATTGAGGATCGCATGGTTGCTTGACAACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
17190325 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * * *
17190366 ATTAAGGATTGCATGGTTGCTTGATGATCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
17190407 GTGGCTTTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:17190600 original size:22 final size:22
Alignment explanation
Indices: 17190549--17190608 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
17190539 CCAATTATTT
* * *
17190549 TGATTATGGCTTTGCGCCAACC
1 TGATTATGGCTATGTGACAACC
* *
17190571 TCCA-TATGGCTCTGTGACAACC
1 T-GATTATGGCTATGTGACAACC
17190593 TGATTATGGCTATGTG
1 TGATTATGGCTATGTG
17190609 CCAAACGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (22 bp):
TGATTATGGCTATGTGACAACC
Found at i:17192632 original size:16 final size:16
Alignment explanation
Indices: 17192611--17192661 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
17192601 GCAAATCCTG
*
17192611 AAATGCTGAAAAGCCA
1 AAATGCCGAAAAGCCA
17192627 AAATGCCGAAAAGCCGA
1 AAATGCCGAAAAGCC-A
*
17192644 AAA-GCCGTAAAGCCA
1 AAATGCCGAAAAGCCA
17192659 AAA
1 AAA
17192662 GTTTGTCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 4 0.12
16 24 0.75
17 4 0.12
ACGTcount: A:0.51, C:0.22, G:0.20, T:0.08
Consensus pattern (16 bp):
AAATGCCGAAAAGCCA
Found at i:17192644 original size:8 final size:8
Alignment explanation
Indices: 17192618--17192662 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
17192608 CTGAAATGCT
17192618 GAAAAGCC
1 GAAAAGCC
17192626 -AAAATGCC
1 GAAAA-GCC
17192634 GAAAAGCC
1 GAAAAGCC
17192642 GAAAAGCC
1 GAAAAGCC
*
17192650 GTAAAGCC
1 GAAAAGCC
17192658 -AAAAG
1 GAAAAG
17192663 TTTGTCTACG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 8 0.24
8 21 0.64
9 4 0.12
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.04
Consensus pattern (8 bp):
GAAAAGCC
Found at i:17192914 original size:29 final size:29
Alignment explanation
Indices: 17192872--17192996 Score: 171
Period size: 29 Copynumber: 4.3 Consensus size: 29
17192862 GAAAGCACGT
17192872 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
17192901 ATATGAAAGTGATTTGGGCCTAATGAGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
17192930 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * * *
17192959 ATATGAATGAGA-TTAGGCCTAGTGGGTC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
17192987 ATATGCATGT
1 ATATGAATGT
17192997 ATGTAGACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 21 0.25
29 63 0.75
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:17194283 original size:27 final size:26
Alignment explanation
Indices: 17194253--17194344 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 26
17194243 ATTACCAAAG
* *
17194253 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTA-CGTTT
*
17194280 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTA-CGTTT
17194307 TACCCTC-AGTTTACAAAATTACTGTTT
1 TACCCTCGA-TTTACAAAATTAC-GTTT
17194334 TACCCTCGATT
1 TACCCTCGATT
17194345 GTGAAATTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.04
27 54 0.95
28 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (26 bp):
TACCCTCGATTTACAAAATTACGTTT
Found at i:17194298 original size:54 final size:54
Alignment explanation
Indices: 17194240--17194344 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 54
17194230 ATTGACTTGT
* *
17194240 AAAATTACCAAAGTACCCTC-GATTTATAGAATTA-TCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAGTACCCTCAG-TTTACAAAATTACT-GTTTTACCCTCGATTTAC
***
17194294 AAAATTACCATTTTACCCTCAGTTTACAAAATTACTGTTTTACCCTCGATT
1 AAAATTACCAAAGTACCCTCAGTTTACAAAATTACTGTTTTACCCTCGATT
17194345 GTGAAATTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (54 bp):
AAAATTACCAAAGTACCCTCAGTTTACAAAATTACTGTTTTACCCTCGATTTAC
Found at i:17194366 original size:27 final size:27
Alignment explanation
Indices: 17194336--17194525 Score: 135
Period size: 27 Copynumber: 7.1 Consensus size: 27
17194326 TACTGTTTTA
* * *
17194336 CCCTCGATTGTGAAATTACTAAAATAC
1 CCCTAGATTGTAAAATTACCAAAATAC
* * *
17194363 CCCTATA-GGATAGAATTACCAAAATAC
1 CCCTAGATTG-TAAAATTACCAAAATAC
* *
17194390 CCTTAGTTTGTAAAATTACCAAAA-AC
1 CCCTAGATTGTAAAATTACCAAAATAC
* *
17194416 CCCTAGTTTGTAAAATTACCGAAATAC
1 CCCTAGATTGTAAAATTACCAAAATAC
* * *
17194443 CACTAGTTTGTGAAATTA-CATAAATA-
1 CCCTAGATTGTAAAATTACCA-AAATAC
*
17194469 CCCTCA-ATTTGTAAAATTATCAAAATAC
1 CCCT-AGA-TTGTAAAATTACCAAAATAC
17194497 CCCT-GATT-TACAAAATTA-CAGAAATAC
1 CCCTAGATTGT--AAAATTACCA-AAATAC
17194524 CC
1 CC
17194526 TTGACTTTCT
Statistics
Matches: 132, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.01
26 33 0.25
27 91 0.69
28 7 0.05
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
CCCTAGATTGTAAAATTACCAAAATAC
Found at i:17194391 original size:53 final size:52
Alignment explanation
Indices: 17194334--17194498 Score: 147
Period size: 53 Copynumber: 3.1 Consensus size: 52
17194324 ATTACTGTTT
* * *
17194334 TACCCTCGATTGTGAAATTACTAAAATACCCCTA-TAGGATAGAATTACCAAAA
1 TACCCTAGTTTGTGAAATTAC-AAAATACCCCTAGTAGG-TAAAATTACCAAAA
* ** *
17194387 TACCCTTAGTTTGTAAAATTACCAAAA-ACCCCTAGTTTGTAAAATTACCGAAA
1 TACCC-TAGTTTGTGAAATTA-CAAAATACCCCTAGTAGGTAAAATTACCAAAA
* ** *
17194440 TACCACTAGTTTGTGAAATTACATAAATA-CCCTCAATTTGTAAAATTATCAAAA
1 TACC-CTAGTTTGTGAAATTACA-AAATACCCCT-AGTAGGTAAAATTACCAAAA
17194494 TACCC
1 TACCC
17194499 CTGATTTACA
Statistics
Matches: 94, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
52 2 0.02
53 50 0.53
54 41 0.44
55 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.30
Consensus pattern (52 bp):
TACCCTAGTTTGTGAAATTACAAAATACCCCTAGTAGGTAAAATTACCAAAA
Found at i:17194432 original size:80 final size:80
Alignment explanation
Indices: 17194343--17194525 Score: 178
Period size: 80 Copynumber: 2.3 Consensus size: 80
17194333 TTACCCTCGA
* * *
17194343 TTGTGAAATTACTAAAATACCCCTA-TAGGAT-AGAATTACCA-AAATACCCTTAGTTTGTAAAA
1 TTGTAAAATTAC-AAAATACCCCTAGTAGG-TGA-AATTA-CATAAATACCCTCAATTTGTAAAA
17194405 TTACCAAAA-ACCCCT-AGT
62 TTACCAAAATACCCCTGA-T
* * **
17194423 TTGTAAAATTACCGAAATACCACTAGTTTGTGAAATTACATAAATACCCTCAATTTGTAAAATTA
1 TTGTAAAATTA-CAAAATACCCCTAGTAGGTGAAATTACATAAATACCCTCAATTTGTAAAATTA
*
17194488 TCAAAATACCCCTGAT
65 CCAAAATACCCCTGAT
**
17194504 TTACAAAATTACAGAAATACCC
1 TTGTAAAATTACA-AAATACCC
17194526 TTGACTTTCT
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
79 2 0.02
80 54 0.64
81 27 0.32
82 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (80 bp):
TTGTAAAATTACAAAATACCCCTAGTAGGTGAAATTACATAAATACCCTCAATTTGTAAAATTAC
CAAAATACCCCTGAT
Found at i:17194563 original size:56 final size:55
Alignment explanation
Indices: 17194455--17194583 Score: 154
Period size: 56 Copynumber: 2.3 Consensus size: 55
17194445 CTAGTTTGTG
* * *
17194455 AAATTACATAAATACCC-TCAATTTGTAAAATTATCAAAATACCCCTGATTTACA
1 AAATTACAGAAATACCCTTCAATTTCTAAAATTATCAAAATACCACTGATTTACA
* * * *
17194509 AAATTACAGAAATACCCTTGACTTTCTAAAAATTAT-AGAAATACCATTGGTTTACA
1 AAATTACAGAAATACCCTTCAATTTCT-AAAATTATCA-AAATACCACTGATTTACA
*
17194565 AAATTACTGAAATACCCTT
1 AAATTACAGAAATACCCTT
17194584 AGTTTGTAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
54 16 0.25
55 7 0.11
56 41 0.64
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (55 bp):
AAATTACAGAAATACCCTTCAATTTCTAAAATTATCAAAATACCACTGATTTACA
Found at i:17194576 original size:27 final size:28
Alignment explanation
Indices: 17194503--17194580 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
17194493 ATACCCCTGA
* *
17194503 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCATTGAC
*
17194531 TTT-CTAAAAATTA-TAGAAATACCATTG-G
1 TTTAC--AAAATTACT-GAAATACCATTGAC
17194559 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
17194581 CTTAGTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 16 0.38
28 7 0.17
29 19 0.45
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (28 bp):
TTTACAAAATTACTGAAATACCATTGAC
Found at i:17194588 original size:27 final size:27
Alignment explanation
Indices: 17194384--17194591 Score: 149
Period size: 27 Copynumber: 7.7 Consensus size: 27
17194374 AGAATTACCA
*
17194384 AAATACCCTTAGTTTGTAAAATTAC-C
1 AAATACCCTTAGTTTGTAAAATTACTG
* * *
17194410 AAAAACCCCTAGTTTGTAAAATTACCG
1 AAATACCCTTAGTTTGTAAAATTACTG
*
17194437 AAATACCAC-TAGTTTGTGAAATTACAT-
1 AAATACC-CTTAGTTTGTAAAATTAC-TG
* * *
17194464 AAATACCCTCAATTTGTAAAATTA-TCA
1 AAATACCCTTAGTTTGTAAAATTACT-G
* ** *
17194491 AAATACCCCT-GATTTACAAAATTACAG
1 AAATACCCTTAG-TTTGTAAAATTACTG
* *
17194518 AAATACCCTTGACTTTCTAAAAATTA-TAG
1 AAATACCCTT-AGTTTGT-AAAATTACT-G
* * **
17194547 AAATACCATTGGTTTACAAAATTACTG
1 AAATACCCTTAGTTTGTAAAATTACTG
17194574 AAATACCCTTAGTTTGTA
1 AAATACCCTTAGTTTGTA
17194592 GATTTACCAA
Statistics
Matches: 139, Mismatches: 30, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
25 1 0.01
26 24 0.17
27 89 0.64
28 8 0.06
29 17 0.12
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATACCCTTAGTTTGTAAAATTACTG
Found at i:17194683 original size:27 final size:27
Alignment explanation
Indices: 17194641--17194706 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
17194631 TACCCCTAAT
* *
17194641 AGGTAAAAAGATCGTAA-AGCCCCTGTA
1 AGGTAAAATGACCGTAATA-CCCCTGTA
* *
17194668 AGGTAAAGTGACCGTAATACCCTTGTA
1 AGGTAAAATGACCGTAATACCCCTGTA
*
17194695 TGGTAAAATGAC
1 AGGTAAAATGAC
17194707 GAATATGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (27 bp):
AGGTAAAATGACCGTAATACCCCTGTA
Found at i:17195554 original size:25 final size:24
Alignment explanation
Indices: 17195516--17195585 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
17195506 AGGAAGTGCT
* *
17195516 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTCACC
* *
17195540 GAAAAAGGCTTTGCCCCAGTTCATC
1 -AAAAGGGCTTTGCCCCAGTTCACC
17195565 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
17195586 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTCACC
Found at i:17195792 original size:42 final size:42
Alignment explanation
Indices: 17195733--17195866 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
17195723 TAGTCTCCCC
17195733 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
17195775 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
* *
17195817 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
17195859 AAATGGGC
1 AAATGGGC
17195867 CTGAGGGCCA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:17195925 original size:31 final size:31
Alignment explanation
Indices: 17195890--17195995 Score: 151
Period size: 31 Copynumber: 3.4 Consensus size: 31
17195880 CGTTTACAGT
* *
17195890 AAAGGCTTCGGCCCAGTGATACGATTTATAA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
*
17195921 AAAGGCTTCAGCCCAGTGATAAGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
* *
17195952 AAAGGCTTCGGCCTAGTGATATA-ATTTATGG
1 AAAGGCTTCGGCCCAGTGATA-AGATTTATGA
17195983 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
17195996 AGGTATATGT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 67 0.99
32 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATAAGATTTATGA
Found at i:17201088 original size:17 final size:18
Alignment explanation
Indices: 17201055--17201088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17201045 TATAAGGAAG
17201055 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
17201073 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
17201089 CTTCAATGTG
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:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:17202882 original size:17 final size:17
Alignment explanation
Indices: 17202857--17202891 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17202847 GAGTTGTAAC
*
17202857 ACCCCAAAAATACCGAA
1 ACCCAAAAAATACCGAA
*
17202874 ACCCAAAAAATCCCGAA
1 ACCCAAAAAATACCGAA
17202891 A
1 A
17202892 TCTCAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.34, G:0.06, T:0.06
Consensus pattern (17 bp):
ACCCAAAAAATACCGAA
Found at i:17204151 original size:16 final size:16
Alignment explanation
Indices: 17204128--17204180 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
17204118 CGGTAAATCT
17204128 CGAAATGCCAAAAA-A
1 CGAAATGCCAAAAAGA
*
17204143 CGAAAATGCCAAAAAGT
1 CG-AAATGCCAAAAAGA
*
17204160 CGAAATGCCAAAAAGC
1 CGAAATGCCAAAAAGA
17204176 CGAAA
1 CGAAA
17204181 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 2 0.06
16 30 0.88
17 2 0.06
ACGTcount: A:0.55, C:0.21, G:0.17, T:0.08
Consensus pattern (16 bp):
CGAAATGCCAAAAAGA
Found at i:17204445 original size:28 final size:29
Alignment explanation
Indices: 17204394--17204449 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
17204384 AGCATGTATA
*
17204394 TGAATGTGATTTGGGCCTAATGGGCCATG
1 TGAATGAGATTTGGGCCTAATGGGCCATG
*
17204423 TGAATGAGA-TTGGGCCTAGTGGGCCAT
1 TGAATGAGATTTGGGCCTAATGGGCCAT
17204450 ATGCATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (29 bp):
TGAATGAGATTTGGGCCTAATGGGCCATG
Found at i:17213253 original size:93 final size:93
Alignment explanation
Indices: 17213124--17213295 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
17213114 GCCCATAAGT
*
17213124 GAACTAGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACTCAACGAGCTCAGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17213189 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * *
17213217 GAACTCGGACTCAACTCAATGAGTTC-GGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTAGGACTCAACTCAACGAGCTCAGG-CGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
17213281 ACGAGTTCGGATGCC
65 ACGAGCTCGGATGCC
17213296 CAAATATCCC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTAGGACTCAACTCAACGAGCTCAGGCGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:17213287 original size:46 final size:46
Alignment explanation
Indices: 17213116--17213291 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
17213106 TGTAACCTGC
* *
17213116 CCATAAGTGAACTAGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGACGCTCGCAT
* *
17213162 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCG---CAT
* * * *
17213212 -C-TCA-CGAACTCGGACTCAACTCAATGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
17213255 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
17213292 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 4 0.04
46 65 0.60
47 30 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:17213310 original size:46 final size:45
Alignment explanation
Indices: 17213167--17213310 Score: 130
Period size: 46 Copynumber: 3.1 Consensus size: 45
17213157 CGCATCCATA
* * *
17213167 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCC
* * * * * *
17213215 A-CGAACTCGGACTCAACTCAATGAGTTCGGACGCTC-GCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCC--C
*
17213260 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACATCCC
17213306 AGTGA
1 AGTGA
17213311 CATGTCACTT
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
43 4 0.05
45 1 0.01
46 36 0.48
47 29 0.39
48 5 0.07
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCCC
Found at i:17215722 original size:30 final size:30
Alignment explanation
Indices: 17215678--17215766 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
17215668 CAAAGATAAC
*
17215678 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
17215707 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
17215737 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
17215767 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:17215726 original size:15 final size:14
Alignment explanation
Indices: 17215678--17215760 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
17215668 CAAAGATAAC
*
17215678 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
17215692 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
17215707 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
17215722 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
17215737 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
17215752 AAGAAACCC
1 AAGAAACCC
17215761 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:17215766 original size:15 final size:15
Alignment explanation
Indices: 17215689--17215766 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
17215679 AGAAAACCGA
17215689 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
17215704 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
17215718 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
17215733 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
17215749 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
17215764 ATA
1 ATA
17215767 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:17217834 original size:40 final size:40
Alignment explanation
Indices: 17217740--17217884 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
17217730 TACTCGAATG
*
17217740 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
17217781 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
17217821 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
17217861 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
17217885 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:17225852 original size:40 final size:40
Alignment explanation
Indices: 17225758--17225902 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
17225748 TACTCGAATG
*
17225758 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
17225799 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
17225839 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
17225879 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
17225903 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:17230077 original size:93 final size:93
Alignment explanation
Indices: 17229918--17230089 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
17229908 GCCCATAAGT
* *
17229918 GAACTAGGACTCAACCCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACCCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17229983 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * *
17230011 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTAGGACTCAACCCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
17230076 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
17230090 CAAATATCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (93 bp):
GAACTAGGACTCAACCCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:17230085 original size:46 final size:46
Alignment explanation
Indices: 17229910--17230085 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
17229900 TGTAACCTGC
* * * *
17229910 CCATAAGTGAACTAGGACTCAACCCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* *
17229956 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCG---CAT
* * *
17230006 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
*
17230049 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
17230086 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 67 0.61
47 31 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:17240579 original size:68 final size:64
Alignment explanation
Indices: 17240387--17240594 Score: 192
Period size: 67 Copynumber: 3.2 Consensus size: 64
17240377 TCTTTTACAT
* * * *
17240387 ATGGTGTACACATAGTATCACCCATGTGACCTAGCCA-CTTTA-TCTCGTAGCTCTCTTGTTTAC
1 ATGGTGTACACATAGTATCA-CCATGAGACCTAGCTACCTCTATTCTCGTAGCTCTCTTGTCTAC
* * * * *
17240450 ATGGTGTCCTTCACCTAGAACCACACATGCA-ACCTAGCTACATCTA-TCTCGTAGCTCTCTTGT
1 ATGGTG---TACACATAGTATCAC-CATG-AGACCTAGCTACCTCTATTCTCGTAGCTCTCTTGT
17240513 CTAC
61 CTAC
17240517 ATGGTGTACACATAGTATCATCCATGAGACCTAGCTACCTCATAATGTCTCGTAGCTCTCTTGTA
1 ATGGTGTACACATAGTATCA-CCATGAGACCTAGCTACCTC-T-AT-TCTCGTAGCTCTCTTGT-
17240582 C-AC
61 CTAC
*
17240585 ATGGTATACA
1 ATGGTGTACA
17240595 TCCCGTATTA
Statistics
Matches: 117, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
63 7 0.06
64 26 0.22
65 3 0.03
66 23 0.20
67 29 0.25
68 28 0.24
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (64 bp):
ATGGTGTACACATAGTATCACCATGAGACCTAGCTACCTCTATTCTCGTAGCTCTCTTGTCTAC
Found at i:17244841 original size:24 final size:25
Alignment explanation
Indices: 17244814--17244868 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
17244804 GAAGTGCAAT
*
17244814 AGGGCTATGCCC-CAGTTACCGAAA
1 AGGGCTATGCCCTAAGTTACCGAAA
* * *
17244838 AGGGCTTTGCCCTAATTTATCGAAA
1 AGGGCTATGCCCTAAGTTACCGAAA
17244863 AGGGCT
1 AGGGCT
17244869 TTCACCCCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (25 bp):
AGGGCTATGCCCTAAGTTACCGAAA
Found at i:17244889 original size:26 final size:25
Alignment explanation
Indices: 17244814--17244906 Score: 89
Period size: 26 Copynumber: 3.7 Consensus size: 25
17244804 GAAGTGCAAT
* * *
17244814 AGGGCTATGCCCCAG-TTACCGAAA
1 AGGGCTTTGCCCCAGTTTATCAAAA
* * *
17244838 AGGGCTTTGCCCTAATTTATCGAAA
1 AGGGCTTTGCCCCAGTTTATCAAAA
*
17244863 AGGGCTTTCACCCCAGTTTATCAAAA
1 AGGGCTTT-GCCCCAGTTTATCAAAA
*
17244889 AAGGCTTTTGCCCCAGTT
1 AGGGC-TTTGCCCCAGTT
17244907 ATTAAAAGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 12 0.21
25 16 0.29
26 25 0.45
27 3 0.05
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (25 bp):
AGGGCTTTGCCCCAGTTTATCAAAA
Found at i:17244908 original size:25 final size:25
Alignment explanation
Indices: 17244821--17244919 Score: 74
Period size: 25 Copynumber: 3.9 Consensus size: 25
17244811 AATAGGGCTA
* * *
17244821 TGCCCCAGTTACCGAAAAGGGC-TT
1 TGCCCCAGTTATCAAAAAAGGCTTT
* * * *
17244845 TGCCCTAATTTATCGAAAAGGGCTTT
1 TGCCC-CAGTTATCAAAAAAGGCTTT
**
17244871 CACCCCAGTTTATCAAAAAAGGCTTT
1 TGCCCCAG-TTATCAAAAAAGGCTTT
* *
17244897 TGCCCCAGTTATTAAAAGAGGCT
1 TGCCCCAGTTATCAAAAAAGGCT
17244920 AGGCCTCCAG
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
24 5 0.08
25 28 0.47
26 26 0.44
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (25 bp):
TGCCCCAGTTATCAAAAAAGGCTTT
Found at i:17245165 original size:31 final size:31
Alignment explanation
Indices: 17245127--17245236 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
17245117 GTTTACAGTA
*
17245127 AAAGGCTTCAGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATGAATAATGC
*
17245158 AAAGGCTTCGGCCCAGTGACATGAACAATGC
1 AAAGGCTTCGGCCCAGTGACATGAATAATGC
* *
17245189 AAAGGCTTCGGCACAGTAACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATGAATAATGC
*
17245220 AAAGGCTTCGGCGCAGT
1 AAAGGCTTCGGCCCAGT
17245237 ATATGTTGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGACATGAATAATGC
Found at i:17247230 original size:12 final size:12
Alignment explanation
Indices: 17247213--17247237 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17247203 TATGTATGTT
17247213 TGAAAATTTTTA
1 TGAAAATTTTTA
17247225 TGAAAATTTTTA
1 TGAAAATTTTTA
17247237 T
1 T
17247238 TATTTGCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAAAATTTTTA
Found at i:17249433 original size:25 final size:25
Alignment explanation
Indices: 17249404--17249451 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17249394 TTATAATATG
** *
17249404 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCATTTTACCCCTAGGTA
17249429 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCCTAGG
17249452 GTTTAATTAT
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:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCCTAGGTA
Found at i:17249556 original size:20 final size:20
Alignment explanation
Indices: 17249533--17249574 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17249523 TATATGATTT
*
17249533 ATATATACGATATGCACATG
1 ATATATACGATAAGCACATG
* *
17249553 ATATGTATGATAAGCACATG
1 ATATATACGATAAGCACATG
17249573 AT
1 AT
17249575 GTATTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ATATATACGATAAGCACATG
Found at i:17249578 original size:18 final size:19
Alignment explanation
Indices: 17249541--17249578 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17249531 TTATATATAC
*
17249541 GATATGCACATGATATGTAT
1 GATAAGCACATGA-ATGTAT
17249561 GATAAGCACATG-ATGTAT
1 GATAAGCACATGAATGTAT
17249579 TCATTTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
GATAAGCACATGAATGTAT
Found at i:17249673 original size:25 final size:26
Alignment explanation
Indices: 17249621--17249716 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
17249611 GAGGAAGTGC
*
17249621 AAAAGGGC-TATGCCCCAG-TTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
17249645 AAAAGGGC-TTTGCCCCAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
* *
17249670 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCG
*
17249696 AAAAGGGCTTTTGCCCTAGTT
1 AAAAGGGCTTTTGCCCCAGTT
17249717 ATTAAAAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 17 0.26
25 14 0.21
26 35 0.53
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCG
Found at i:17249729 original size:25 final size:26
Alignment explanation
Indices: 17249631--17249729 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 26
17249621 AAAAGGGCTA
*
17249631 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
*
17249655 TGCCCCAGTTTACCGAAAAG-GGCTTT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
17249681 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
* *
17249707 TGCCCTAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
17249730 ATGTAACACC
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.12
25 30 0.45
26 29 0.43
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:17251305 original size:40 final size:40
Alignment explanation
Indices: 17251268--17251452 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
17251258 GCTACTCGTT
*
17251268 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
17251308 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
17251348 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAGCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
17251387 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
17251428 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17251453 CATCATTCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 78 0.63
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:17251379 original size:79 final size:81
Alignment explanation
Indices: 17251270--17251452 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 81
17251260 TACTCGTTCA
* *
17251270 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
17251333 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* * **
17251350 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAGCTTGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
17251413 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
17251429 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
17251453 CATCATTCGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 28 0.32
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:17253075 original size:30 final size:31
Alignment explanation
Indices: 17252994--17253076 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
17252984 TCAGTCTCGA
17252994 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
17253024 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
17253055 CATATCACT-GGCCAAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
17253077 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 17 0.33
31 34 0.67
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:17253321 original size:24 final size:25
Alignment explanation
Indices: 17253289--17253340 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
17253279 GCCTAGCATC
17253289 TTTTAAT-AACT-GGGCCAAAGCCCT
1 TTTTAATAAACTAGGG-CAAAGCCCT
*
17253313 TTTTGATAAACTAGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
17253338 TTT
1 TTT
17253341 CGGCAAACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 16 0.64
26 3 0.12
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:17253324 original size:25 final size:24
Alignment explanation
Indices: 17253296--17253365 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
17253286 ATCTTTTAAT
* *
17253296 AACTGGGCCAAAGCCCTTTTTGATA
1 AACTGGG-CAAAGCCCTTTTCGACA
*
17253321 AACTAGGGCAAAGCCCTTTTCGGCA
1 AACT-GGGCAAAGCCCTTTTCGACA
*
17253346 AACTGGGGCATAGCCCTTTT
1 AACT-GGGCAAAGCCCTTTT
17253366 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 36 0.92
26 3 0.08
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
AACTGGGCAAAGCCCTTTTCGACA
Found at i:17254221 original size:27 final size:27
Alignment explanation
Indices: 17254191--17254252 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
17254181 TTACCATACT
17254191 GGGGTATTACGGCCACTTTACCCTA-TA
1 GGGGTATTACGGCCACTTTA-CCTATTA
* **
17254218 GGGGCT-TTACGGTCTTTTTACCTATTA
1 GGGG-TATTACGGCCACTTTACCTATTA
17254245 GGGGTATT
1 GGGGTATT
17254253 TTACTCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 5 0.17
27 23 0.79
28 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (27 bp):
GGGGTATTACGGCCACTTTACCTATTA
Found at i:17254360 original size:56 final size:54
Alignment explanation
Indices: 17254270--17254471 Score: 183
Period size: 54 Copynumber: 3.7 Consensus size: 54
17254260 TTTCATCTTA
* * * *
17254270 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
* * * *
17254324 CAATGGTATTTCT-ATAATTTTTAGAAAGCCAAGGGTATTTCTGTAATTTTGTAAAT
1 CAAGGGTATTT-TGATAA-TTTTACAAA-CCAAGGGTATTTCAGTAATTTTGTAAAC
* ** * ***
17254380 CAGGGGTATTTTGATAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
* * * *
17254433 CTAGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTT
1 CAAG-GGTATTTTGATAATTTTACAAACCAAGGGTATTT
17254472 TGGTAATTCT
Statistics
Matches: 121, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
53 2 0.02
54 64 0.53
55 16 0.13
56 39 0.32
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (54 bp):
CAAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
Found at i:17254431 original size:27 final size:27
Alignment explanation
Indices: 17254271--17254479 Score: 147
Period size: 27 Copynumber: 7.7 Consensus size: 27
17254261 TTCATCTTAC
* * * *
17254271 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
** ** *
17254298 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTTTACAAACT
* * * *
17254325 AATGGTATTTCT-ATAATTTTTAGAAAGCC
1 AAGGGTATTT-TGGTAA-TTTTACAAA-CT
**
17254354 AAGGGTATTTCT-GTAATTTTGTAAA-T
1 AAGGGTATTT-TGGTAATTTTACAAACT
* * *
17254380 CAGGGGTATTTTGATAATTTTACAAATT
1 -AAGGGTATTTTGGTAATTTTACAAACT
* *
17254408 AAGGGTATTTCGGTAATTTCACAAACT
1 AAGGGTATTTTGGTAATTTTACAAACT
17254435 -AGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAACT
*
17254462 AGGGGTATTTTGGTAATT
1 AAGGGTATTTTGGTAATT
17254480 CTACCCTATA
Statistics
Matches: 145, Mismatches: 29, Indels: 16
0.76 0.15 0.08
Matches are distributed among these distances:
26 3 0.02
27 110 0.76
28 16 0.11
29 16 0.11
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAACT
Found at i:17254519 original size:27 final size:27
Alignment explanation
Indices: 17254356--17254519 Score: 136
Period size: 27 Copynumber: 6.1 Consensus size: 27
17254346 AGAAAGCCAA
*
17254356 GGGTATTTCTGTAATTTTGTA-AATC-AG
1 GGGTATTTCGGTAA-TTT-TACAATCTAG
* * *
17254383 GGGTATTTTGATAATTTTACAAAT-TAA
1 GGGTATTTCGGTAATTTTAC-AATCTAG
* *
17254410 GGGTATTTCGGTAATTTCACAAACTAG
1 GGGTATTTCGGTAATTTTACAATCTAG
* * *
17254437 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAATCTAG
* * ** *
17254464 GGGTATTTTGGTAATTCTACCCTATAG
1 GGGTATTTCGGTAATTTTACAATCTAG
* *
17254491 GGGTATTTCAGTAATTTTACAATCGAG
1 GGGTATTTCGGTAATTTTACAATCTAG
17254518 GG
1 GG
17254520 TAAAACTGTA
Statistics
Matches: 108, Mismatches: 25, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
25 2 0.02
26 5 0.05
27 101 0.94
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAATCTAG
Found at i:17254530 original size:26 final size:26
Alignment explanation
Indices: 17254500--17254601 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 26
17254490 GGGGTATTTC
17254500 AGTAATTT-TACAATCGAGGGTAAAACT
1 AGTAATTTATA-AATCGAGGGTAAAA-T
*
17254527 -GTAATTTCA-CAATCGAGGGTAAAAT
1 AGTAATTT-ATAAATCGAGGGTAAAAT
* *
17254552 AGTAATTTTGTAAATCAAGGGTAAAAT
1 AGTAA-TTTATAAATCGAGGGTAAAAT
17254579 AGTAATTCTATAAATCGAGGGTA
1 AGTAATT-TATAAATCGAGGGTA
17254602 CTTTGGTAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
25 1 0.02
26 27 0.43
27 35 0.56
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (26 bp):
AGTAATTTATAAATCGAGGGTAAAAT
Found at i:17255211 original size:54 final size:54
Alignment explanation
Indices: 17255129--17255239 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
17255119 TGTTGTCGCC
17255129 CCCTGTTAGCAAAATAAATGCTCCTTGCTTGCCATGGGATTCGAACCCATGCCT
1 CCCTGTTAGCAAAATAAATGCTCCTTGCTTGCCATGGGATTCGAACCCATGCCT
17255183 CCCTGTTAGCAAAATAAATGCTCCTTGCTTGCCATGGGATTCGAACCCATGCCT
1 CCCTGTTAGCAAAATAAATGCTCCTTGCTTGCCATGGGATTCGAACCCATGCCT
17255237 CCC
1 CCC
17255240 CTCAAATGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (54 bp):
CCCTGTTAGCAAAATAAATGCTCCTTGCTTGCCATGGGATTCGAACCCATGCCT
Found at i:17255933 original size:31 final size:31
Alignment explanation
Indices: 17255898--17255977 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
17255888 CGTTTACAGT
*
17255898 AAAAGGCTTCGGCCCAGTGAGATGAATAATG
1 AAAAGGCTTCGGCCCAGTGACATGAATAATG
*
17255929 AAAAGGCTTCAGCCCAGTGACATGAATAATG
1 AAAAGGCTTCGGCCCAGTGACATGAATAATG
*
17255960 CAAAGGCTTCGGCCCAGT
1 AAAAGGCTTCGGCCCAGT
17255978 ATATGTTGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGACATGAATAATG
Found at i:17257003 original size:30 final size:30
Alignment explanation
Indices: 17256969--17257029 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
17256959 TTCCTGAGCC
17256969 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
17256999 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
17257029 T
1 T
17257030 GAGTTAACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:17257645 original size:64 final size:64
Alignment explanation
Indices: 17257520--17257751 Score: 286
Period size: 64 Copynumber: 3.5 Consensus size: 64
17257510 TAATACGGGA
* *
17257520 TGTATACCATGT-GTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATAC
1 TGTACACCATGTAG-ACAAGAGAGCTACGAG--A-TAT-ATGTAGCTAGGTTGCATGGGTGATAC
17257584 TATG
61 TATG
* *
17257588 TGTACACCATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGGGTGATACTATG
1 TGTACACCATGTAGACAAGAGAGCTACGAGATATATGTAGCTAGGTTGCATGGGTGATACTATG
* * * *
17257652 TGTACACCATGTAGACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCTAGGT
1 TGTACACCATGTAGACAAGAGAGCTACGAGATATATGTAGCTAGGTTGCATGGGTGATACTA--T
17257717 G
64 G
* * *
17257718 AAGGACACCATGTAAACAAGAGAGCTACGAGATA
1 -TGTACACCATGTAGACAAGAGAGCTACGAGATA
17257752 AAGTGGCTAA
Statistics
Matches: 147, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
64 84 0.57
65 3 0.02
66 3 0.02
67 30 0.20
68 26 0.18
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (64 bp):
TGTACACCATGTAGACAAGAGAGCTACGAGATATATGTAGCTAGGTTGCATGGGTGATACTATG
Found at i:17261528 original size:30 final size:30
Alignment explanation
Indices: 17261494--17261554 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
17261484 TTCTCGAGCC
17261494 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
17261524 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
17261554 T
1 T
17261555 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:17265245 original size:33 final size:33
Alignment explanation
Indices: 17265208--17265307 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
17265198 GTTTCAATTA
17265208 GGATTTAGCCTGGACTGGTAATCCTAATTGACT
1 GGATTTAGCCTGGACTGGTAATCCTAATTGACT
* * *
17265241 GGATTTAGCCTGGACTGGAAATCCTAATCGATT
1 GGATTTAGCCTGGACTGGTAATCCTAATTGACT
* * *
17265274 GAATTTAGCCTGGACTAGTAATCCATATTTGACT
1 GGATTTAGCCTGGACTGGTAATCC-TAATTGACT
17265308 TTGTAGGGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
33 51 0.89
34 6 0.11
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (33 bp):
GGATTTAGCCTGGACTGGTAATCCTAATTGACT
Found at i:17276931 original size:21 final size:21
Alignment explanation
Indices: 17276889--17276929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17276879 CAACTTTAGC
*
17276889 CTCTCTCCTAATCCCTTAAAT
1 CTCTCCCCTAATCCCTTAAAT
*
17276910 CTCTCCCCTTATCTCCTTAA
1 CTCTCCCCTAATC-CCTTAA
17276930 TCCAAGCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (21 bp):
CTCTCCCCTAATCCCTTAAAT
Found at i:17278982 original size:21 final size:20
Alignment explanation
Indices: 17278954--17278993 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
17278944 CAAAACTTAT
17278954 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
17278974 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
17278994 AAAGCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:17287655 original size:40 final size:40
Alignment explanation
Indices: 17287577--17287760 Score: 230
Period size: 40 Copynumber: 4.5 Consensus size: 40
17287567 ACCCAAGTAT
* *
17287577 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
17287616 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
**
17287656 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
17287696 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGC
17287739 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17287761 CATCCGAATA
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 12 0.09
40 87 0.67
41 1 0.01
43 29 0.22
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:17289726 original size:50 final size:49
Alignment explanation
Indices: 17289624--17289745 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 49
17289614 CATAGTAACT
* * ** *
17289624 TGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 TGCACTTAGTACTACACACGTGACCAACCATCCGATACACGTAGTAGCC
*
17289673 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCC
1 TGCACTTAGTACTACACACGTGACC-AACCATCCGATACACGTAGTAGCC
17289723 TGCACTTAGTACTACACACGTGA
1 TGCACTTAGTACTACACACGTGA
17289746 TCAAAGTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
49 23 0.35
50 43 0.65
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (49 bp):
TGCACTTAGTACTACACACGTGACCAACCATCCGATACACGTAGTAGCC
Found at i:17290809 original size:27 final size:27
Alignment explanation
Indices: 17290789--17290911 Score: 158
Period size: 27 Copynumber: 4.6 Consensus size: 27
17290779 TAGACTTTCT
*
17290789 GTTTTACCCTCGATTTATAGAATTACC
1 GTTTTACCCTCAATTTATAGAATTACC
* *
17290816 ATTTTACCCTCAATTTACAGAATTACC
1 GTTTTACCCTCAATTTATAGAATTACC
* * *
17290843 GTTTTACCCTCAATTTACAAAATTACA
1 GTTTTACCCTCAATTTATAGAATTACC
*
17290870 ATTTTACCCTCAATTTA-AGAAATTACC
1 GTTTTACCCTCAATTTATAG-AATTACC
*
17290897 GTTTTACCCTTAATT
1 GTTTTACCCTCAATT
17290912 GTGAAATTAC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 83 0.99
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (27 bp):
GTTTTACCCTCAATTTATAGAATTACC
Found at i:17290847 original size:54 final size:54
Alignment explanation
Indices: 17290789--17290911 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
17290779 TAGACTTTCT
* * * *
17290789 GTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAG-AATTACC
1 GTTTTACCCTCAATTTACAAAATTACAATTTTACCCTCAATTTA-AGAAATTACC
17290843 GTTTTACCCTCAATTTACAAAATTACAATTTTACCCTCAATTTAAGAAATTACC
1 GTTTTACCCTCAATTTACAAAATTACAATTTTACCCTCAATTTAAGAAATTACC
*
17290897 GTTTTACCCTTAATT
1 GTTTTACCCTCAATT
17290912 GTGAAATTAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 2 0.03
54 61 0.97
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (54 bp):
GTTTTACCCTCAATTTACAAAATTACAATTTTACCCTCAATTTAAGAAATTACC
Found at i:17290970 original size:27 final size:27
Alignment explanation
Indices: 17290940--17291205 Score: 241
Period size: 27 Copynumber: 9.8 Consensus size: 27
17290930 CCCTATAGGA
17290940 TAAAATTACCAAAATACCCTTAGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
17290967 TAAAATTACCAAAATACCAC-TAGTTTG
1 TAAAATTACCAAAATACC-CTTAGTTTG
* *
17290994 TAAATTTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
*
17291021 TAAAATTACCAAAATACCAC-TGGTTTG
1 TAAAATTACCAAAATACC-CTTAGTTTG
* * * *
17291048 TGAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
* * * *
17291075 TAAAATTACCAAAACACCCCTAATTTA
1 TAAAATTACCAAAATACCCTTAGTTTG
* * * *
17291102 CAAAATTACAAAAATACCCTTGACTTTC
1 TAAAATTACCAAAATACCCTT-AGTTTG
* * * *
17291130 TAAAAATTA-TAGAAATACCATTGGTTTA
1 T-AAAATTACCA-AAATACCCTTAGTTTG
** *
17291158 TAAAATTACTGAAATACCCTTGGTTTG
1 TAAAATTACCAAAATACCCTTAGTTTG
* * *
17291185 TAGATTTACCAAAACACCCTT
1 TAAAATTACCAAAATACCCTT
17291206 GTAGGATGAA
Statistics
Matches: 197, Mismatches: 34, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.01
27 167 0.85
28 12 0.06
29 16 0.08
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTTAGTTTG
Found at i:17291003 original size:54 final size:54
Alignment explanation
Indices: 17290939--17291198 Score: 270
Period size: 54 Copynumber: 4.8 Consensus size: 54
17290929 CCCCTATAGG
17290939 ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTAGTTT
1 ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTAGTTT
* * * *
17290993 GTAAATTTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTT
1 ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTAGTTT
* * * * * * * *
17291047 GTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAACACCCCTAATTT
1 ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTAGTTT
* * * * * * *
17291101 ACAAAATTACAAAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTT
1 ATAAAATTACCAAAATACCCTT-AGTTTGT-AAAATTACCA-AAATACCACTAGTTT
** * * *
17291157 ATAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAA
1 ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
17291199 CACCCTTGTA
Statistics
Matches: 165, Mismatches: 37, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
54 118 0.72
55 11 0.07
56 36 0.22
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (54 bp):
ATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTAGTTT
Found at i:17292132 original size:24 final size:23
Alignment explanation
Indices: 17292096--17292162 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
17292086 AGGAAGTGCT
*
17292096 AAAA-GGCTATGCCCAGTTTACC
1 AAAAGGGCTTTGCCCAGTTTACC
*
17292118 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTG-CCCAGTTTACC
17292143 AAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTTGCCC-AGTT
17292163 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.18
24 22 0.56
25 10 0.26
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCAGTTTACC
Found at i:17292175 original size:24 final size:24
Alignment explanation
Indices: 17292107--17292175 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
17292097 AAAGGCTATG
*
17292107 CCCAGTTTACCGAAAAGGGCTTTGC
1 CCCAGTTTATC-AAAAGGGCTTTGC
17292132 CCCAGTTTATCAAAAGGGCTTTGC
1 CCCAGTTTATCAAAAGGGCTTTGC
* *
17292156 CCTAG-TTATTAAAAGAGGCT
1 CCCAGTTTATCAAAAG-GGCT
17292176 AGGCCTCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 9 0.22
24 21 0.52
25 10 0.25
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
CCCAGTTTATCAAAAGGGCTTTGC
Found at i:17292369 original size:42 final size:42
Alignment explanation
Indices: 17292310--17292401 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
17292300 TAGTCTCCCC
* *
17292310 AAATGGGCTTTCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
17292352 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
17292394 AAATGGGC
1 AAATGGGC
17292402 CTATGGGCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:17292460 original size:31 final size:31
Alignment explanation
Indices: 17292425--17292503 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
17292415 CGTTTACAAT
17292425 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
* *
17292456 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATAAGATTTATGA
17292487 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
17292504 ATATGTCGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATAAGATTTATGA
Found at i:17294836 original size:27 final size:27
Alignment explanation
Indices: 17294806--17294948 Score: 166
Period size: 27 Copynumber: 5.3 Consensus size: 27
17294796 TACTGAAATG
** * *
17294806 CCCTCGATTTGTAGAATTGCCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
17294833 CCCTCGATTT-CTAGAATTACCATTTTA
1 CCCTCGATTTAC-AGAATTACCATTTTA
*
17294860 CCCTCGATTTACAGAATTACTATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
17294887 CCCTTGATTTACAAAATTACCA-TTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
17294913 CCCTC-AGTTTACAAAATTACCGTTTTA
1 CCCTCGA-TTTACAGAATTACCATTTTA
17294940 CCCTCGATT
1 CCCTCGATT
17294949 ATGAAATTAC
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
25 1 0.01
26 22 0.22
27 77 0.75
28 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:17294982 original size:27 final size:27
Alignment explanation
Indices: 17294977--17295157 Score: 204
Period size: 27 Copynumber: 6.7 Consensus size: 27
17294967 CCCTGTAGGA
17294977 TAAAATTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
17295004 TAAAATTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
** *
17295031 TAAAATTATGAAAATACCCTTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
* * * *
17295058 TAAAATTATCGAAATACCACTGGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
* * *
17295085 TGAAATTACCGAAATA-CCCTCAATTTG
1 TAAAATTACCAAAATACCCCT-AGTTTG
* * *
17295112 TAAAATTACCAAAACACCCCTAATTTA
1 TAAAATTACCAAAATACCCCTAGTTTG
*
17295139 CAAAATTA-CAGAAATACCC
1 TAAAATTACCA-AAATACCC
17295158 TTGACTTTCT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.04
27 123 0.93
28 4 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTAGTTTG
Found at i:17296177 original size:25 final size:25
Alignment explanation
Indices: 17296143--17296271 Score: 138
Period size: 25 Copynumber: 5.2 Consensus size: 25
17296133 AGGAAGTGCT
*
17296143 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTATGCCCCAGTTTATCG
* *
17296168 AAAAGGGCTATGCCCTAGTTTATTG
1 AAAAGGGCTATGCCCCAGTTTATCG
* *
17296193 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTATCG
* *
17296218 AAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAGGGCTATGCCCCAGTTTATCG
*
17296241 AAAAGAGGCTAGGCCTCCAGTTATAT-G
1 AAAAG-GGCTATGCC-CCAGTT-TATCG
17296268 AAAA
1 AAAA
17296272 AGTAGCTATG
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 5 0.06
24 11 0.12
25 65 0.73
26 1 0.01
27 7 0.08
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTATGCCCCAGTTTATCG
Found at i:17296222 original size:50 final size:48
Alignment explanation
Indices: 17296142--17296282 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 48
17296132 GAGGAAGTGC
* * *
17296142 TAAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTATGCCCTAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTATCAAAAAGGGCTATGCCCCAG-TTAT
* *
17296191 TGAAAAGGGCTTTGCCCCAGTTTATCAAAAAGGGCTTTGCCCCAGTTAT
1 T-AAAAGGGCTATGCCCCAGTTTATCAAAAAGGGCTATGCCCCAGTTAT
* * *
17296240 TAAAAGAGGCTAGGCCTCCAGTTATATGAAAAAGTAGCTATGC
1 TAAAAG-GGCTATGCC-CCAGTT-TATCAAAAAG-GGCTATGC
17296283 TGCGAGTGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
48 5 0.06
49 13 0.17
50 44 0.57
51 9 0.12
52 6 0.08
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (48 bp):
TAAAAGGGCTATGCCCCAGTTTATCAAAAAGGGCTATGCCCCAGTTAT
Found at i:17296444 original size:42 final size:42
Alignment explanation
Indices: 17296385--17296476 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
17296375 TAGTCTCCCT
*
17296385 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
17296427 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
17296469 AAATGGGC
1 AAATGGGC
17296477 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:17296536 original size:31 final size:31
Alignment explanation
Indices: 17296500--17296583 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
17296490 CGTTTACAAT
*
17296500 AAAGGCTTTGGCCTAGTGATATGATTTATGA
1 AAAGGCTTTGGCCCAGTGATATGATTTATGA
17296531 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTTGGCCCAGTGATATGATTTATGA
*
17296562 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTTGGCCCAGTGATATG
17296584 TCGAGATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGATTTATGA
Found at i:17297727 original size:27 final size:27
Alignment explanation
Indices: 17297687--17297740 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
17297677 AAGTACAACC
* *
17297687 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
17297714 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
17297741 TCACATGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:17300067 original size:12 final size:12
Alignment explanation
Indices: 17300050--17300077 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17300040 CAAATCCTTA
17300050 CACGAGCAATCG
1 CACGAGCAATCG
17300062 CACGAGCAATCG
1 CACGAGCAATCG
17300074 CACG
1 CACG
17300078 CTCGTCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.25, T:0.07
Consensus pattern (12 bp):
CACGAGCAATCG
Found at i:17305658 original size:44 final size:45
Alignment explanation
Indices: 17305593--17305700 Score: 200
Period size: 44 Copynumber: 2.4 Consensus size: 45
17305583 GAATTAGACG
*
17305593 ACATTTGAAAATGTCAGGATTAGGGTCTATTTACTATATAAAAAC
1 ACATTTGAAAATGTCAGGATTAGGGTCCATTTACTATATAAAAAC
17305638 A-ATTTGAAAATGTCAGGATTAGGGTCCATTTACTATATAAAAAC
1 ACATTTGAAAATGTCAGGATTAGGGTCCATTTACTATATAAAAAC
17305682 ACATTTGAAAATGTCAGGA
1 ACATTTGAAAATGTCAGGA
17305701 GTCATCACAC
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
44 43 0.70
45 18 0.30
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (45 bp):
ACATTTGAAAATGTCAGGATTAGGGTCCATTTACTATATAAAAAC
Found at i:17316033 original size:21 final size:22
Alignment explanation
Indices: 17315988--17316046 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
17315978 TGAAAGGCTC
*
17315988 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGACCAAGGG
**
17316010 ACACGCCCGTGT-GACCCTGGG
1 ACACGCCCGTGTGGACCAAGGG
*
17316031 ACACACCCGTGCTGGA
1 ACACGCCCGTG-TGGA
17316047 GCCCGTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 16 0.52
22 13 0.42
23 2 0.06
ACGTcount: A:0.19, C:0.36, G:0.32, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGGACCAAGGG
Found at i:17319947 original size:16 final size:16
Alignment explanation
Indices: 17319926--17319991 Score: 114
Period size: 16 Copynumber: 4.1 Consensus size: 16
17319916 TGGTTCGCTA
17319926 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
*
17319942 TATTGGATTAGAAGTG
1 TATTGGATTAGAGGTG
17319958 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
*
17319974 TATTAGATTAGAGGTG
1 TATTGGATTAGAGGTG
17319990 TA
1 TA
17319992 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (16 bp):
TATTGGATTAGAGGTG
Found at i:17320315 original size:157 final size:157
Alignment explanation
Indices: 17320121--17320430 Score: 539
Period size: 157 Copynumber: 2.0 Consensus size: 157
17320111 CCCTTAGCAT
*
17320121 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
17320186 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
17320251 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * *
17320278 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* * *
17320343 TAATAAATAATTTCATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
17320408 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
17320431 ATATTCTTAT
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 144 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:17321328 original size:13 final size:13
Alignment explanation
Indices: 17321307--17321336 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17321297 CAATCAGCTA
*
17321307 AATTTAGAAAAAC
1 AATTCAGAAAAAC
17321320 AATTCAGAAAAAC
1 AATTCAGAAAAAC
17321333 AATT
1 AATT
17321337 ACATGACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:17324764 original size:25 final size:25
Alignment explanation
Indices: 17324735--17324782 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17324725 TTATAACATG
* *
17324735 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
17324760 AAAATGACTATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
17324783 GTTTATGTAT
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:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:17324964 original size:47 final size:47
Alignment explanation
Indices: 17324895--17325041 Score: 206
Period size: 47 Copynumber: 3.1 Consensus size: 47
17324885 GAGGAAGTGA
* *
17324895 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAATTAT
* *
17324941 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAATTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAATTAT
* * *
17324989 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAACTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAATTA-T
17325037 AAAAG
1 AAAAG
17325042 AGGCAAGGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
47 64 0.72
48 25 0.28
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAATTAT
Found at i:17325011 original size:71 final size:71
Alignment explanation
Indices: 17324895--17325030 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
17324885 GAGGAAGTGA
* * *
17324895 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
17324960 GTTATC
66 GTTATC
*
17324966 AAAAGGGCTTACGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
17325031 ACTATTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAATTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:17325040 original size:24 final size:24
Alignment explanation
Indices: 17324895--17325041 Score: 208
Period size: 24 Copynumber: 6.2 Consensus size: 24
17324885 GAGGAAGTGA
17324895 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
17324919 -AAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
17324942 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
17324966 AAAAGGGCTTACGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
17324990 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
* **
17325013 AAAAGGGCTTTTGCCCCAACTATT
1 AAAAGGGCTTATGCCCCAGTTATT
17325037 AAAAG
1 AAAAG
17325042 AGGCAAGGCC
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
23 42 0.38
24 68 0.62
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:17325289 original size:31 final size:31
Alignment explanation
Indices: 17325254--17325317 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
17325244 CATTTACAGT
*
17325254 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
17325285 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
17325316 AA
1 AA
17325318 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:17329827 original size:19 final size:20
Alignment explanation
Indices: 17329790--17329827 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17329780 ATAAGGTGGT
17329790 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
17329810 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
17329828 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:17338452 original size:12 final size:12
Alignment explanation
Indices: 17338435--17338461 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17338425 CGCGTATAAC
17338435 AGTTACCAAGCA
1 AGTTACCAAGCA
17338447 AGTTACCAAGCA
1 AGTTACCAAGCA
17338459 AGT
1 AGT
17338462 ATTCAGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (12 bp):
AGTTACCAAGCA
Found at i:17340967 original size:11 final size:11
Alignment explanation
Indices: 17340931--17340986 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
17340921 CATGGTATGT
17340931 ATGATATGCAC
1 ATGATATGCAC
* *
17340942 ATGACATG--T
1 ATGATATGCAC
17340951 ATGATATGCAC
1 ATGATATGCAC
*
17340962 ATGATATG--T
1 ATGATATGCAC
17340971 ATGATATGCAC
1 ATGATATGCAC
17340982 ATGAT
1 ATGAT
17340987 TTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:17340986 original size:20 final size:20
Alignment explanation
Indices: 17340920--17340986 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
17340910 ATTTTGATAA
*
17340920 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
17340940 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
17340960 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
17340980 ACATGAT
1 ACATGAT
17340987 TTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:17341092 original size:24 final size:23
Alignment explanation
Indices: 17341036--17341182 Score: 213
Period size: 24 Copynumber: 6.2 Consensus size: 23
17341026 GAGGAAGTGA
17341036 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
17341059 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
17341082 CAAAAGGGCTTATGCCCTAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
17341106 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
17341130 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
17341153 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
17341178 AAAAG
1 AAAAG
17341183 AGGCAAGGCC
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
23 43 0.38
24 68 0.61
25 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:17341105 original size:47 final size:47
Alignment explanation
Indices: 17341036--17341182 Score: 215
Period size: 47 Copynumber: 3.1 Consensus size: 47
17341026 GAGGAAGTGA
*
17341036 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* * *
17341082 CAAAAGGGCTTATGCCCTAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
17341130 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTA-T
17341178 AAAAG
1 AAAAG
17341183 AGGCAAGGCC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
47 63 0.71
48 26 0.29
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
Found at i:17341152 original size:71 final size:71
Alignment explanation
Indices: 17341036--17341182 Score: 249
Period size: 71 Copynumber: 2.1 Consensus size: 71
17341026 GAGGAAGTGA
* * *
17341036 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCTA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
17341101 GTTATC
66 GTTATC
*
17341107 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
17341172 GTTATT
66 GTTATC
17341178 AAAAG
1 AAAAG
17341183 AGGCAAGGCC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:17341430 original size:31 final size:31
Alignment explanation
Indices: 17341395--17341458 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
17341385 CGTTTACAGT
* * *
17341395 AAAGGCTTCTGCCTAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
17341426 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
17341457 AA
1 AA
17341459 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:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:17342325 original size:22 final size:23
Alignment explanation
Indices: 17342278--17342378 Score: 73
Period size: 22 Copynumber: 4.4 Consensus size: 23
17342268 CTGATGAACT
*
17342278 GTAAGCTCTATTGAGTTGAAAATA
1 GTAAGCTCTATTGAGCT-AAAATA
*
17342302 GTAAGCTTTATTGAGCT-AAATA
1 GTAAGCTCTATTGAGCTAAAATA
* * *
17342324 GTATGCTCT-TTCGAGCT-GAATCG
1 GTAAGCTCTATT-GAGCTAAAAT-A
* * *
17342347 GTAAGATCCAATGAGCTAAAATA
1 GTAAGCTCTATTGAGCTAAAATA
*
17342370 ATAAGCTCT
1 GTAAGCTCT
17342379 TACGAGCTGA
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
21 2 0.03
22 20 0.34
23 17 0.29
24 19 0.33
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTAAAATA
Found at i:17342351 original size:45 final size:46
Alignment explanation
Indices: 17342313--17342400 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
17342303 TAAGCTTTAT
* * * *
17342313 TGAGCT-AAATAGTATGCTCTTTCGAGCTGAATCGGTAAGATCCAA
1 TGAGCTAAAATAATAAGCTCTTACGAGCTGAATCGGTAAGCTCCAA
*
17342358 TGAGCTAAAATAATAAGCTCTTACGAGCTGAATGGGTAAGCTC
1 TGAGCTAAAATAATAAGCTCTTACGAGCTGAATCGGTAAGCTC
17342401 ATACGAGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
TGAGCTAAAATAATAAGCTCTTACGAGCTGAATCGGTAAGCTCCAA
Found at i:17342419 original size:23 final size:23
Alignment explanation
Indices: 17342371--17342423 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
17342361 GCTAAAATAA
* **
17342371 TAAGCTCTTACGAGCTGAATGGG
1 TAAGCTCATACGAGCTGAATCAG
17342394 TAAGCTCATACGAGCTG-ATACAG
1 TAAGCTCATACGAGCTGAAT-CAG
17342417 TAAGCTC
1 TAAGCTC
17342424 TTATGAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (23 bp):
TAAGCTCATACGAGCTGAATCAG
Found at i:17343921 original size:19 final size:19
Alignment explanation
Indices: 17343886--17343923 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17343876 GAGTGGGGCC
*
17343886 CACGAGCCCATTGGGCCCA
1 CACGAGCCCATTCGGCCCA
17343905 CACGA-CCCATTTCGGCCCA
1 CACGAGCCCA-TTCGGCCCA
17343924 AAATCAGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (19 bp):
CACGAGCCCATTCGGCCCA
Found at i:17345772 original size:30 final size:30
Alignment explanation
Indices: 17345733--17345789 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17345723 TTTTATAAGT
17345733 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
17345763 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
17345790 AATAACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:17345863 original size:47 final size:49
Alignment explanation
Indices: 17345757--17345863 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 49
17345747 ACTTAAAAAT
* *
17345757 ATTTAAAATTTATATTTCATATATTAAAATATTAATAACAAATTATAATA
1 ATTT-AAATTTATATTTCATATACTAAAATATTAACAACAAATTATAATA
*
17345807 ATTT--TTTTATA-TTC-T-TACTAAAATATTAACAACAAATTATAATA
1 ATTTAAATTTATATTTCATATACTAAAATATTAACAACAAATTATAATA
17345851 ATTTCAAATTTAT
1 ATTT-AAATTTAT
17345864 TTAAATGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
44 31 0.62
45 1 0.02
46 3 0.06
47 11 0.22
50 4 0.08
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (49 bp):
ATTTAAATTTATATTTCATATACTAAAATATTAACAACAAATTATAATA
Found at i:17348902 original size:13 final size:13
Alignment explanation
Indices: 17348886--17348915 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
17348876 ACATTTCCAC
17348886 AGCACTTTTCAAA
1 AGCACTTTTCAAA
17348899 AGCACTTTTCAAA
1 AGCACTTTTCAAA
17348912 AGCA
1 AGCA
17348916 TTGCTAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (13 bp):
AGCACTTTTCAAA
Found at i:17354922 original size:21 final size:21
Alignment explanation
Indices: 17354897--17354957 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
17354887 ATATTGTTAT
*
17354897 ACATGATATGGCATGGTATGC
1 ACATGATATGGCATGATATGC
**
17354918 ACATGATATGTTATGATATGC
1 ACATGATATGGCATGATATGC
17354939 ACATGATAT-GCTATGATAT
1 ACATGATATGGC-ATGATAT
17354958 ACTCATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (21 bp):
ACATGATATGGCATGATATGC
Found at i:17354927 original size:11 final size:11
Alignment explanation
Indices: 17354897--17354949 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
17354887 ATATTGTTAT
17354897 ACATGATATG-
1 ACATGATATGC
* *
17354907 GCATGGTATGC
1 ACATGATATGC
17354918 ACATGATATG-
1 ACATGATATGC
**
17354928 TTATGATATGC
1 ACATGATATGC
17354939 ACATGATATGC
1 ACATGATATGC
17354950 TATGATATAC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (11 bp):
ACATGATATGC
Found at i:17362998 original size:21 final size:21
Alignment explanation
Indices: 17362958--17363007 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17362948 ATATTGTTAT
*
17362958 ACATGATATGGCATGGTATGC
1 ACATGATATGGCATGATATGC
**
17362979 ACATGATATGTTATGATATGC
1 ACATGATATGGCATGATATGC
*
17363000 -TATGATAT
1 ACATGATAT
17363008 ACTCATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (21 bp):
ACATGATATGGCATGATATGC
Found at i:17366000 original size:20 final size:20
Alignment explanation
Indices: 17365972--17366017 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
17365962 TGGGATTCTC
17365972 TTTTT-AGATAGACATTAGG
1 TTTTTGAGATAGACATTAGG
17365991 TTTTTGAGATAGACATTAGG
1 TTTTTGAGATAGACATTAGG
17366011 TTCTTTG
1 TT-TTTG
17366018 TTTAACCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTTTGAGATAGACATTAGG
Found at i:17367195 original size:39 final size:40
Alignment explanation
Indices: 17366997--17367210 Score: 231
Period size: 40 Copynumber: 5.4 Consensus size: 40
17366987 CGGATGCTAA
* * * *
17366997 CGGGTTAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
* *
17367037 CGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TC
* *
17367077 CAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
* *
17367117 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
* * * **
17367157 CGGGCTAAGACCCGACGGC-CTTGTGCGAGTGGTTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
*
17367196 C--GCTAAATCCCGAAG
1 CGGGCTAAGTCCCGAAG
17367211 ATACTTGGGT
Statistics
Matches: 151, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
37 11 0.07
39 16 0.11
40 123 0.81
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATC
Done.