Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 88 of 295
Found at i:27771058 original size:120 final size:121
Alignment explanation
Indices: 27770837--27771064 Score: 280
Period size: 120 Copynumber: 1.9 Consensus size: 121
27770827 GTTAATTATA
* * * *
27770837 CCTGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTGATTGAACATACGTGTCCCTT
1 CCTGAATTGCACATACGTGACCCTATTTCTACTTCGGTACCCTTGATTGAACATACGTGCCCCTG
* * * * * * *
27770902 TTTGTACTTCGATACCCTTGATTGCATATACGTGCCCTTGTTTGTACTTTAGTACC
66 TTTGTACATCGATACCCCTAATGGCACATACATGCCCCTGTTTGTACTTTAGTACC
* * * * *
27770958 CCTG-ATTGCACATATGTGACCTTTTTTCTACTTTGGTACCCTTGATTGCACATACG-GACCCCT
1 CCTGAATTGCACATACGTGACCCTATTTCTACTTCGGTACCCTTGATTGAACATACGTG-CCCCT
*
27771021 GTTTGTACATCGGTACCCCTAATGGCACATACATGCCCCTGTTT
65 GTTTGTACATCGATACCCCTAATGGCACATACATGCCCCTGTTT
27771065 ACACTTCGGA
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
119 1 0.01
120 84 0.94
121 4 0.04
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (121 bp):
CCTGAATTGCACATACGTGACCCTATTTCTACTTCGGTACCCTTGATTGAACATACGTGCCCCTG
TTTGTACATCGATACCCCTAATGGCACATACATGCCCCTGTTTGTACTTTAGTACC
Found at i:27771061 original size:40 final size:40
Alignment explanation
Indices: 27770842--27771073 Score: 241
Period size: 40 Copynumber: 5.8 Consensus size: 40
27770832 TTATACCTGA
*
27770842 ATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * * *
27770882 ATTGAACATACGTGTCCCTTTTTGTACTTCGATACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * ** *
27770922 ATTGCATATACGTGCCCTTGTTTGTACTTTAGTACCCCTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * * * * *
27770962 ATTGCACATATGTGACCTTTTTTCTACTTTGGTACCCTTG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
* * *
27771002 ATTGCACATACG-GACCCCTGTTTGTACATCGGTACCCCTA
1 ATTGCACATACGTG-CCCCTGTTTGTACTTCGGTACCCTTG
* * **
27771042 ATGGCACATACATGCCCCTGTTTACACTTCGG
1 ATTGCACATACGTGCCCCTGTTTGTACTTCGG
27771074 AAACTTCAAT
Statistics
Matches: 156, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 154 0.99
41 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (40 bp):
ATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
Found at i:27776351 original size:40 final size:39
Alignment explanation
Indices: 27776320--27776490 Score: 227
Period size: 39 Copynumber: 4.3 Consensus size: 39
27776310 GGACTAAGAT
27776320 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* *
27776359 CCGAAGGAATTTGTACGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* * *
27776398 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
* * * *
27776438 CTGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-C
27776478 CCGAAGGCATTTG
1 CCGAAGGCATTTG
27776491 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 71 0.61
40 46 0.39
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
Found at i:27776371 original size:39 final size:40
Alignment explanation
Indices: 27776267--27776490 Score: 237
Period size: 40 Copynumber: 5.7 Consensus size: 40
27776257 TTGAATGATG
* * *
27776267 TCCGGGCTAATTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
27776306 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27776347 TCCGGGCTAAG-CCCGAAGGAATTTGTACGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27776386 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
27776425 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
27776464 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
27776491 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
39 71 0.45
40 75 0.47
41 12 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:27776512 original size:79 final size:79
Alignment explanation
Indices: 27776320--27776513 Score: 207
Period size: 79 Copynumber: 2.5 Consensus size: 79
27776310 GGACTAAGAT
** * * * *
27776320 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGAATTTGTACGAGATACTA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCTGAAGGAATTTGTACGAGATACTA
*
27776384 ATTCCGGGCTAAGC
66 ATACCGGGCTAAGC
** * * *
27776398 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCTGAAGGAATTTGTACGAGATACTA
*
27776462 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
*
27776478 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAA
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAA
27776514 ATTCCGAAGG
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
78 37 0.37
79 38 0.38
80 25 0.25
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCTGAAGGAATTTGTACGAGATACTA
ATACCGGGCTAAGC
Found at i:27776523 original size:79 final size:78
Alignment explanation
Indices: 27776320--27776523 Score: 207
Period size: 78 Copynumber: 2.6 Consensus size: 78
27776310 GGACTAAGAT
** * * * *
27776320 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGAATTTGTACGAGATACTAA
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCGAAGGAATTTGTACGAGATACTAA
*
27776385 TTCCGGGCTAAGC
66 TACCGGGCTAAGC
** * * *
27776398 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCC-GAAGGAATTTGTACGAGATACTA
*
27776462 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
* *
27776478 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTT-AAGTCCGAAGG
27776524 TACGTGATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
78 39 0.36
79 39 0.36
80 30 0.28
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCGAAGGAATTTGTACGAGATACTAA
TACCGGGCTAAGC
Found at i:27785604 original size:29 final size:29
Alignment explanation
Indices: 27785567--27785698 Score: 203
Period size: 29 Copynumber: 4.6 Consensus size: 29
27785557 GTTGAGAGAT
27785567 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
27785596 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
27785625 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
* * * *
27785654 TGGCGCTAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTGAGTGTGCGAGCTTGAAA-TGCA
*
27785683 TGGCACTAAGTGTGCG
1 TGGCACTGAGTGTGCG
27785699 CGGTTGATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 5 0.05
29 92 0.95
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTGAGTGTGCGAGCTTGAAATGCA
Found at i:27793578 original size:29 final size:29
Alignment explanation
Indices: 27793541--27793643 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
27793531 GTTGAGAGAT
*
27793541 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
*
27793570 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* * *
27793599 TGGCGCTAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
27793628 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
27793644 CGGTTGATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
28 5 0.07
29 63 0.93
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:27800329 original size:29 final size:29
Alignment explanation
Indices: 27800296--27800456 Score: 211
Period size: 29 Copynumber: 5.6 Consensus size: 29
27800286 GTTGAGAGAT
27800296 TGGCACTGAATGTGCGAGCTTGAAATGCA
1 TGGCACTGAATGTGCGAGCTTGAAATGCA
*
27800325 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAATGTGCGAGCTTGAAATGCA
*
27800354 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAATGTGCGAGCTTGAAATGCA
* *
27800383 TGGCACTGAGTGTGCGAGCTTGAAATACA
1 TGGCACTGAATGTGCGAGCTTGAAATGCA
* * *
27800412 TGGCGCT-AAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTGAA-TGTGCGAGCTTGAAA-TGCA
27800441 TGGCACT-AAGTGTGCG
1 TGGCACTGAA-TGTGCG
27800457 CGGTTGATTA
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
28 6 0.05
29 118 0.95
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTGAATGTGCGAGCTTGAAATGCA
Found at i:27800368 original size:58 final size:58
Alignment explanation
Indices: 27800296--27800456 Score: 243
Period size: 58 Copynumber: 2.8 Consensus size: 58
27800286 GTTGAGAGAT
* *
27800296 TGGCACTGAATGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATACA
27800354 TGGCACTGAGTGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATACA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATACA
* * * * *
27800412 TGGCGCTAAGTGTGCGAG-TTTAAAGTACATGGCACTAAGTGTGCG
1 TGGCACTGAGTGTGCGAGCTTGAAA-TGCATGGCACTGAGTGTGCG
27800457 CGGTTGATTA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 5 0.05
58 90 0.95
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (58 bp):
TGGCACTGAGTGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATACA
Found at i:27800443 original size:87 final size:87
Alignment explanation
Indices: 27800296--27800456 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
27800286 GTTGAGAGAT
* * *
27800296 TGGCACTGAATGTGCGAGCTTGAAATGCATGGCACTGAGTGTGCGAGCTTGAAATGCATGGCACT
1 TGGCACTGAATGTGCGAGCTTGAAATACATGGCACTAAGTGTGCGAGCTTGAAATACATGGCACT
*
27800361 GAGTGTGCGAGCTTGAAATGCA
66 AAGTGTGCGAGCTTGAAATGCA
* * *
27800383 TGGCACTGAGTGTGCGAGCTTGAAATACATGGCGCTAAGTGTGCGAG-TTTAAAGTACATGGCAC
1 TGGCACTGAATGTGCGAGCTTGAAATACATGGCACTAAGTGTGCGAGCTTGAAA-TACATGGCAC
27800447 TAAGTGTGCG
65 TAAGTGTGCG
27800457 CGGTTGATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 5 0.08
87 61 0.92
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (87 bp):
TGGCACTGAATGTGCGAGCTTGAAATACATGGCACTAAGTGTGCGAGCTTGAAATACATGGCACT
AAGTGTGCGAGCTTGAAATGCA
Found at i:27803341 original size:12 final size:12
Alignment explanation
Indices: 27803326--27803355 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27803316 ATTGGTTGTT
27803326 ACACGGCCTAAC
1 ACACGGCCTAAC
*
27803338 ACACGGCCTGAC
1 ACACGGCCTAAC
27803350 ACACGG
1 ACACGG
27803356 GCGTTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:27804247 original size:16 final size:16
Alignment explanation
Indices: 27804226--27804271 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
27804216 GGATGTTATG
27804226 GATTTGGGGATTTCAC
1 GATTTGGGGATTTCAC
* *
27804242 GATTTGGGAAATTTGAC
1 GATTTGGG-GATTTCAC
*
27804259 GAGTTGGGGATTT
1 GATTTGGGGATTT
27804272 TAGAAATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.37
Consensus pattern (16 bp):
GATTTGGGGATTTCAC
Found at i:27805925 original size:20 final size:22
Alignment explanation
Indices: 27805900--27805946 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
27805890 CGTATGCTTC
*
27805900 ATTAAATACTTAATTA-TCT-A
1 ATTAAATAATTAATTACTCTCA
27805920 ATTAAATAATTAATTACTCTCA
1 ATTAAATAATTAATTACTCTCA
27805942 ATTAA
1 ATTAA
27805947 GTTATTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.62
21 3 0.12
22 6 0.25
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAATAATTAATTACTCTCA
Found at i:27810786 original size:40 final size:40
Alignment explanation
Indices: 27810597--27810822 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
27810587 TTGAATGATG
* * * *
27810597 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
27810637 TCCGGACTAAGAT-CCGAAGGAATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
27810677 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27810717 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27810757 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27810798 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
27810823 AACGAGGAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27810840 original size:80 final size:79
Alignment explanation
Indices: 27810608--27810855 Score: 227
Period size: 80 Copynumber: 3.1 Consensus size: 79
27810598 CCGGGCTAAG
* * * * * * ** *
27810608 TCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGAATTTGTGCGAGTT
1 TCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATTTGAACGAGTG
* *
27810671 ACTAAATTCGGACTAAGA
64 ACTAAATCCGG-TTAA-A
* ** *
27810689 T-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGAC
*
27810753 TAAATCCGGGTTAAG
66 TAAATCC-GGTTAAA
*
27810768 TCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GA
1 TCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA
*
27810831 GCTATATCCGGTTAAA
65 -CTAAATCCGGTTAAA
*
27810847 TTCCGAAGG
1 TCCCGAAGG
27810856 TACGTGATTT
Statistics
Matches: 143, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
79 17 0.12
80 114 0.80
81 12 0.08
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGAC
TAAATCCGGTTAAA
Found at i:27810840 original size:120 final size:120
Alignment explanation
Indices: 27810597--27810855 Score: 278
Period size: 120 Copynumber: 2.2 Consensus size: 120
27810587 TTGAATGATG
* *
27810597 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGAATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAATTT
* ** *
27810662 GTGCGAGTTACTAAATTCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTAAA
* * * ** *
27810717 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGAAT
* * *
27810780 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTGA-CTAAA
* *
27810837 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
27810856 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
119 17 0.15
120 91 0.78
121 9 0.08
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGAATTT
GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:27817138 original size:136 final size:137
Alignment explanation
Indices: 27816961--27817519 Score: 759
Period size: 136 Copynumber: 4.0 Consensus size: 137
27816951 ACATAGATAA
* * * * *
27816961 AATTAATAAATGAAATTGATTCATATAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATT-ATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
27817026 TGAATAATTATATTAATAAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
65 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
*
27817091 AAAAATAT
130 AAGAATAT
27817099 AATTA-ATATGAATTTGATTCATACAAAATATTAATTGTATACT-TTTTACCGAATTTATTAATA
1 AATTATATATGAATTTGATTCATACAAAATATTAATTGTATA-TATTTTACCGAATTTATTAATA
* ** *
27817162 TAAACAATTATATTAATTAATTTTGGTCAAAATATAAAATCCATGGAAATTAGTATTCTTTTGGA
65 TAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
27817227 AAGAATAT
130 AAGAATAT
* *
27817235 AATTAGTATATGAATTTAATTCATACAAAATATTATTTGTTTATATATTTTACCGAATTTATTAA
1 AATTA-TATATGAATTTGATTCATACAAAATATTAATTG--TATATATTTTACCGAATTTATTAA
* * *
27817300 TATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATAGAAATTAATATACTTTTT
63 TATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTC-TTTT
27817365 GGAAAGAATAT
127 GGAAAGAATAT
* **
27817376 AATTAACATATATGAATTTTATTCATA-AAAATTATTAATTGTATATATTTTACTAAATTTATTA
1 AATT---ATATATGAATTTGATTCATACAAAA-TATTAATTGTATATATTTTACCGAATTTATTA
*
27817440 ATATAAA-AAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-GATAATTAATATTCTT
62 ATATAAACAA-TTATATTAATTAATTTTGATCAAAATATAAAAGACATGGA-AATTAATATTCTT
*
27817503 TTAGAAAGAATAT
125 TTGGAAAGAATAT
27817516 AATT
1 AATT
27817520 CCTTTTTCTA
Statistics
Matches: 377, Mismatches: 31, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
136 120 0.32
137 2 0.01
138 34 0.09
139 1 0.00
140 96 0.25
141 93 0.25
142 4 0.01
143 26 0.07
144 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (137 bp):
AATTATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATAT
AAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAA
AGAATAT
Found at i:27817502 original size:281 final size:274
Alignment explanation
Indices: 27816961--27817519 Score: 784
Period size: 281 Copynumber: 2.0 Consensus size: 274
27816951 ACATAGATAA
* * *
27816961 AATTAATAAATGAAATTGATTCATATAAAAAATTAATTGTATATATTTTACTGAATTTATTAATA
1 AATTAATAAATGAAATTAATTCATACAAAAAATTAATTGTATATATTTTACCGAATTTATTAATA
* * * *
27817026 TGAATAATTATATTAATAAATTTCGATCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATAAATTTCGATCAAAATATAAAAGACATAGAAATTAATATACTTTTGGA
*
27817091 AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACCGAATTTA
131 AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACCAAATTTA
** *
27817156 TTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAATCCATGGAAATTAGTATTCT
196 TTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
*
27817221 TTTGGAAAGAATAT
261 TTTAGAAAGAATAT
* * * * *
27817235 AATTAGTATATGAATTTAATTCATACAAAATATTATTTGTTTATATATTTTACCGAATTTATTAA
1 AATTAATAAATGAAATTAATTCATACAAAAAATTAATTG--TATATATTTTACCGAATTTATTAA
* * *
27817300 TATAAACAGTTATATTAATTAATTTTGATCAAAATATAAAAGACATAGAAATTAATATACTTTTT
64 TATAAACAATTATATTAATAAATTTCGATCAAAATATAAAAGACATAGAAATTAATATAC-TTTT
* *
27817365 GGAAAGAATATAATTAACATATATGAATTTTATTCATA-AAAATTATTAATTGTATA-TATTTTA
128 GGAAAAAATATAATT---A-ATATGAATTTGATTCATACAAAA-TATTAATTGTATACT-TTTTA
*
27817428 CTAAATTTATTAATATAAA-AAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACAT-GATA
187 CCAAATTTATTAATATAAACAA-TTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGA-A
27817491 ATTAATATTCTTTTAGAAAGAATAT
250 ATTAATATTCTTTTAGAAAGAATAT
27817516 AATT
1 AATT
27817520 CCTTTTTCTA
Statistics
Matches: 251, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
274 32 0.13
276 76 0.30
277 18 0.07
280 10 0.04
281 115 0.46
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (274 bp):
AATTAATAAATGAAATTAATTCATACAAAAAATTAATTGTATATATTTTACCGAATTTATTAATA
TAAACAATTATATTAATAAATTTCGATCAAAATATAAAAGACATAGAAATTAATATACTTTTGGA
AAAAATATAATTAATATGAATTTGATTCATACAAAATATTAATTGTATACTTTTTACCAAATTTA
TTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
TTTAGAAAGAATAT
Found at i:27817622 original size:75 final size:75
Alignment explanation
Indices: 27817495--27817641 Score: 222
Period size: 75 Copynumber: 2.0 Consensus size: 75
27817485 ATGATAATTA
* * * * *
27817495 ATATTCTTTTAGAAAGAATATAATTCCTTTTTCTAACTTTTCATTTGTCTTCTCTATTAATAAGG
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
27817560 GAATAATCTT
66 GAATAATCTT
* * *
27817570 ATATTATTTTGGAAAGAATATAATTTATTTTTCTAACTTTCCATTTGCCTTCTCTATTAGTAAGA
1 ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
27817635 GAATAAT
66 GAATAAT
27817642 AATGGTTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (75 bp):
ATATTATTTTAGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGA
GAATAATCTT
Found at i:27822512 original size:30 final size:30
Alignment explanation
Indices: 27822478--27822676 Score: 163
Period size: 30 Copynumber: 6.7 Consensus size: 30
27822468 AGCCAAAGCT
*
27822478 ATCCCTTTCCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * *
27822508 ATCCCTTTCCATT-GTTGATGGTCCTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * * *
27822537 ATCCCTTTTCATAATTTGATAGCCG-AAGCTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-C-C
** * * *** *
27822568 -TCCCTTTTCACAATTCGATAG-CCAAAGTC
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* *
27822597 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
27822627 ATCCCTTTTCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* *
27822657 ATCCTTTTTCATAATTTGAT
1 ATCCCTTTTCATTATTTGAT
27822677 AGCCTAGGCT
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 28 0.20
30 107 0.78
31 3 0.02
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACC
Found at i:27822535 original size:29 final size:30
Alignment explanation
Indices: 27822478--27822544 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
27822468 AGCCAAAGCT
* *
27822478 ATCCCTTTCCATTATTTGATGGTCGTCACC
1 ATCCCTTTCCATTAGTTGATGGTCCTCACC
27822508 ATCCCTTTCCATT-GTTGATGGTCCTCACC
1 ATCCCTTTCCATTAGTTGATGGTCCTCACC
27822537 ATCCCTTT
1 ATCCCTTT
27822545 TCATAATTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.15, C:0.33, G:0.12, T:0.40
Consensus pattern (30 bp):
ATCCCTTTCCATTAGTTGATGGTCCTCACC
Found at i:27822663 original size:119 final size:120
Alignment explanation
Indices: 27822463--27822680 Score: 343
Period size: 119 Copynumber: 1.8 Consensus size: 120
27822453 TTTTCATAGC
*
27822463 TCGATAGCCAAAGCTATCCCTTTCCATTATTTGATGGTCGTCACCATCCCTTTCCATTGTTGATG
1 TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATTGTTGATG
27822528 GTCCTCACCATCCC-TTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
66 GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
* * * *
27822582 TCGATAGCCAAAG-TCATCCCTTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATTATTTGA
1 TCGATAGCCAAAGCT-ATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATT-GTTGA
*
27822646 TGGTCGTCACCAT-CCTTTTTCATAATTTGATAGCC
64 TGGTCCTCACCATCCCTTTTTCATAATTTGATAGCC
27822681 TAGGCTATCC
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
118 1 0.01
119 54 0.60
120 35 0.39
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (120 bp):
TCGATAGCCAAAGCTATCCCTTTCCATTATTCGATGGTCGTCACCATCCCTTTCCATTGTTGATG
GTCCTCACCATCCCTTTTTCATAATTTGATAGCCGAAGCTCTCCCTTTTCACAAT
Found at i:27822707 original size:31 final size:31
Alignment explanation
Indices: 27822663--27822732 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
27822653 CACCATCCTT
* *
27822663 TTTCA-TAATTTGATAGCCTAGGCTATCCCA
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
* * **
27822693 TTTCATTATTTTGATTGCCGAAGCTATCCTT
1 TTTCATTAATTTGATAGCCGAAGCTATCCCA
27822724 TTTCATTAA
1 TTTCATTAA
27822733 CCGATGATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTCATTAATTTGATAGCCGAAGCTATCCCA
Found at i:27824260 original size:6 final size:6
Alignment explanation
Indices: 27824251--27824281 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
27824241 CAATTTTTTG
*
27824251 CTTCCC CTTCCC CTTTCC CTTCCC CTTCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
27824282 CATCCTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTTCCC
Found at i:27827396 original size:19 final size:20
Alignment explanation
Indices: 27827372--27827413 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
27827362 CAAACACCAT
27827372 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
27827391 AAAAGTAAATCATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
27827411 AAA
1 AAA
27827414 TCATTTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:27827416 original size:14 final size:14
Alignment explanation
Indices: 27827397--27827434 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
27827387 CCAGAAAAGT
27827397 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
27827411 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
27827425 AAAACATTTT
1 AAATCATTTT
27827435 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:27836732 original size:20 final size:20
Alignment explanation
Indices: 27836707--27836748 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
27836697 AAGTTGTAGG
*
27836707 TTTGCTTACCAAAAATGTTA
1 TTTGCTTACCAAAAACGTTA
27836727 TTTGCTTACCAAAAACGTTA
1 TTTGCTTACCAAAAACGTTA
27836747 TT
1 TT
27836749 ATTTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTGCTTACCAAAAACGTTA
Found at i:27837553 original size:24 final size:24
Alignment explanation
Indices: 27837519--27837571 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
27837509 AAGTCTGTCA
* *
27837519 GGAGAGGATTTATGAGCTGATAAG
1 GGAGAGAATTTAGGAGCTGATAAG
*
27837543 GGAGAGAATTTAGGAGCTGATTAG
1 GGAGAGAATTTAGGAGCTGATAAG
27837567 GGAGA
1 GGAGA
27837572 ACAGTGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.23
Consensus pattern (24 bp):
GGAGAGAATTTAGGAGCTGATAAG
Found at i:27839060 original size:27 final size:26
Alignment explanation
Indices: 27838981--27839088 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 26
27838971 AAGCGTCCTA
* *
27838981 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCAC-ATTATCTGTTCTG
* * *
27839008 GTGGCTCTGCAACATATTTCTATTCTG
1 GTGGCTCTGCCACAT-TATCTGTTCTG
*
27839035 GTGGCTCTGCCGCGATTATCTGTTCTG
1 GTGGCTCTGCCAC-ATTATCTGTTCTG
* *
27839062 GTGACTCTGTCACATTATCTGTTCTG
1 GTGGCTCTGCCACATTATCTGTTCTG
27839088 G
1 G
27839089 CAGCCATACT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
26 16 0.24
27 49 0.73
28 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGTTCTG
Found at i:27845186 original size:11 final size:11
Alignment explanation
Indices: 27845170--27845194 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27845160 TCATACTGTA
27845170 AATAATAAAAT
1 AATAATAAAAT
27845181 AATAATAAAAT
1 AATAATAAAAT
27845192 AAT
1 AAT
27845195 TATTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:27859558 original size:28 final size:26
Alignment explanation
Indices: 27859502--27859559 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
27859492 AGCATGGCTG
**
27859502 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAACCA
*
27859528 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGACAGAACCA
27859556 CCAG
1 CCAG
27859560 GACGCTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 5 0.19
27 9 0.33
28 13 0.48
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAACCA
Found at i:27860988 original size:24 final size:24
Alignment explanation
Indices: 27860974--27861044 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
27860964 CTAGATTTTC
*
27860974 TCCCTTATCTACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
27860998 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
27861022 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
27861045 CTCCTGACAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:27862150 original size:54 final size:54
Alignment explanation
Indices: 27862083--27862244 Score: 306
Period size: 54 Copynumber: 3.0 Consensus size: 54
27862073 GCTACAGGTA
*
27862083 TGTATGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
27862137 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
*
27862191 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTGAGAATTTCATACTT
1 TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
27862245 ATTTAGTGAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (54 bp):
TGTACGGAAAACTATTCAAGTATTGAACTAATGGAAGTTAAGAATTTCATACTT
Found at i:27872670 original size:20 final size:18
Alignment explanation
Indices: 27872637--27872673 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27872627 TGTGATGTTG
27872637 ATATGATTAATTTAATTA
1 ATATGATTAATTTAATTA
27872655 ATATGACTTAAATTTAATT
1 ATATGA-TT-AATTTAATT
27872674 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATGATTAATTTAATTA
Found at i:27882551 original size:46 final size:45
Alignment explanation
Indices: 27882501--27882672 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
27882491 TGAGCATCCA
*
27882501 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
*** * *
27882547 AACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCCG
* * *
27882594 AGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
* *
27882640 AGCTCGTTGAGCTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27882673 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 62 0.60
47 31 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCCG
Found at i:27884059 original size:40 final size:39
Alignment explanation
Indices: 27883995--27884076 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
27883985 TTTATATATA
*
27883995 TAGCCAAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCAAAGCTATCTCAAACTGCACACCAAGTGCCA-TTT
* * * * *
27884035 TAGCCGAAGCTATTTCGAACTGCACACTAAGTGTCATTT
1 TAGCCAAAGCTATCTCAAACTGCACACCAAGTGCCATTT
27884074 TAG
1 TAG
27884077 ACGATAAGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 6 0.17
40 30 0.83
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (39 bp):
TAGCCAAAGCTATCTCAAACTGCACACCAAGTGCCATTT
Found at i:27889860 original size:22 final size:24
Alignment explanation
Indices: 27889815--27889862 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
27889805 TAATCTTTAA
27889815 TATATAATTATATCTATTATAATT
1 TATATAATTATATCTATTATAATT
27889839 TATAT-ATTA-ATCT-TTATCAATT
1 TATATAATTATATCTATTAT-AATT
27889861 TA
1 TA
27889863 GCATAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 4 0.17
24 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATAATTATATCTATTATAATT
Found at i:27895893 original size:18 final size:17
Alignment explanation
Indices: 27895866--27895899 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27895856 TCTTCTCTTC
*
27895866 TCTTCTCTCTTTCGCAAT
1 TCTTCCCTCTTT-GCAAT
27895884 TCTTCCCTCTTTGCAA
1 TCTTCCCTCTTTGCAA
27895900 CTTGTGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.35, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTTCCCTCTTTGCAAT
Found at i:27898530 original size:81 final size:84
Alignment explanation
Indices: 27898378--27898543 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 84
27898368 GAGTGTATCT
* * *
27898378 AACCTACATCGGTCTTTCAGATTCTGAGGCTTATTCTGTTAAGGATATCAGAAAGGTTAAAGACT
1 AACCTACATCGGTCTTTCAGATCCTGAGGCTTATTCTGTTAAGGATATCAGAAAGGTCAAACACT
27898443 TTCCAGATG-TTTTTCCCG
66 TTCCAGATGTTTTTTCCCG
* * *
27898461 AACCTAGATCGGTCTTTC-GATCCTGAGGCTTATTCTGTTAA-GCTCTCAGAAAGGTCAAACACT
1 AACCTACATCGGTCTTTCAGATCCTGAGGCTTATTCTGTTAAGGATATCAGAAAGGTCAAACACT
27898524 TTCCAGATGTTTTTTCCCG
66 TTCCAGATGTTTTTTCCCG
27898543 A
1 A
27898544 TTGAGCGACT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 27 0.36
82 32 0.42
83 17 0.22
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (84 bp):
AACCTACATCGGTCTTTCAGATCCTGAGGCTTATTCTGTTAAGGATATCAGAAAGGTCAAACACT
TTCCAGATGTTTTTTCCCG
Found at i:27903572 original size:49 final size:49
Alignment explanation
Indices: 27903498--27904047 Score: 727
Period size: 49 Copynumber: 11.1 Consensus size: 49
27903488 CCCTTCAGGA
* * * * *
27903498 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
27903545 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
27903594 CTTATCA-ACATATATACACTTTTCACATTCATACACGTTGGCCACTCGGCC
1 CTTATCACATATATATACAC-TTTCACATTCAT-CACATCGGCCATTAGG-C
* *
27903645 CTGTGTCACATATATATACACTTCCACATTCATTCACATCGGCCATTAGGC
1 CT-TATCACATATATATACACTTTCACATTCA-TCACATCGGCCATTAGGC
*
27903696 CTTATCACATATATACA-ACTTTCACATTCATCACATCGGCCATTAGGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTA-GGC
*
27903745 CCTATCACATATTAATATACACTTTTCACATTCATTCACATCGGCCATTAGGC
1 CTTATCACATA-T-ATATACAC-TTTCACATTCA-TCACATCGGCCATTAGGC
*
27903798 CTTTATCATATCATATA-ACACTTTCACATTCATCACAATCGGCCATTAGGC
1 C-TTATCACAT-ATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGC
* *
27903849 CTTATCACATATATATTACACTTTCACATTCATCACATGGGCCACTAGGC
1 CTTATCACATATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27903899 CTTATCACATATATACAAACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27903948 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27903997 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27904044 CTTA
1 CTTA
27904048 CTATTCATTT
Statistics
Matches: 445, Mismatches: 39, Indels: 38
0.85 0.07 0.07
Matches are distributed among these distances:
47 51 0.11
48 27 0.06
49 161 0.36
50 65 0.15
51 55 0.12
52 32 0.07
53 30 0.07
54 23 0.05
55 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27907591 original size:29 final size:29
Alignment explanation
Indices: 27907512--27907591 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
27907502 TTAATAAATC
*
27907512 AACCACGCACACTTAGTGCCATGTACTTTA
1 AACC-CGCACACTTAGTGCCATGCACTTTA
*
27907542 AACTCGCCACACTTAGTGCCATGCA-TTTCA
1 AACCCG-CACACTTAGTGCCATGCACTTT-A
*
27907572 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
27907592 AATCTCACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 19 0.43
30 25 0.57
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCACTTTA
Found at i:27907660 original size:45 final size:43
Alignment explanation
Indices: 27907573--27907766 Score: 284
Period size: 44 Copynumber: 4.4 Consensus size: 43
27907563 TGCATTTCAA
27907573 GCCCGCACACTTAGTGCCAAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCC-AATCTCACAACCGTGAACACTTATT
27907617 GCCGCGCACACTTAGTGCCAATCTCACAACCGTGAACACCTTATT
1 GCC-CGCACACTTAGTGCCAATCTCACAACCGTGAACA-CTTATT
*
27907662 GCCCGCACACTTAGTCGTCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGT-GCCAATCTCACAACCGTGAACACTTATT
* *
27907706 GCCCGCACACTTAAGTGCCAATTTCACAGA-CGTGAACAATTATT
1 GCCCGCACACTT-AGTGCCAATCTCACA-ACCGTGAACACTTATT
27907750 G-CCGCGACACTTAGTGC
1 GCCCGC-ACACTTAGTGC
27907767 TGAAAAACCA
Statistics
Matches: 140, Mismatches: 4, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
43 9 0.06
44 82 0.59
45 49 0.35
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:27907686 original size:89 final size:88
Alignment explanation
Indices: 27907573--27907766 Score: 288
Period size: 89 Copynumber: 2.2 Consensus size: 88
27907563 TGCATTTCAA
27907573 GCCCGCACACTTAGTGCCAAATCTCACAACCGTGAACACTTATTGCCGCGCACACTT-AGTGCCA
1 GCCCGCACACTTAGTGCCAAATCTCACAACCGTGAACACTTATTGCC-CGCACACTTAAGTGCCA
*
27907637 ATCTCACA-ACCGTGAACACCTTATT
65 ATCTCACAGA-CGTGAACA-ATTATT
*
27907662 GCCCGCACACTTAGTCGTC-AATCTCACAACCGTGAACACTTATTGCCCGCACACTTAAGTGCCA
1 GCCCGCACACTTAGT-GCCAAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAAGTGCCA
*
27907726 ATTTCACAGACGTGAACAATTATT
65 ATCTCACAGACGTGAACAATTATT
27907750 G-CCGCGACACTTAGTGC
1 GCCCGC-ACACTTAGTGC
27907767 TGAAAAACCA
Statistics
Matches: 97, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
87 5 0.05
88 24 0.25
89 65 0.67
90 3 0.03
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (88 bp):
GCCCGCACACTTAGTGCCAAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAAGTGCCAA
TCTCACAGACGTGAACAATTATT
Found at i:27910004 original size:97 final size:96
Alignment explanation
Indices: 27909838--27910376 Score: 834
Period size: 97 Copynumber: 5.5 Consensus size: 96
27909828 CCCTTCAGGA
* * * * * *
27909838 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGT-TCACATAT-TAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCT-TATCACATATATAT
*
27909901 ATCACTTTCACATTCATCACATCGGCCAATAGGC
64 A-CACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
27909935 CTTATCACATATATTACACTTTCCACATTCATCACGTTGGCCA-TCGCGCC-TGTCACATATATA
1 CTTATCACATATA-TACACTTT-CACATTCATCACATCGGCCATTAG-GCCTTATCACATATATA
27909998 TACACTTTCACATTCATCACATCGGCCATTAGGC
63 TACACTTTCACATTCATCACATCGGCCATTAGGC
27910032 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATATA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATATA
27910097 CACTTTCACATTCATCACATCGAGGCCATTAGGC
65 CACTTTCACATTCATCACATC--GGCCATTAGGC
*
27910131 CTTATCATTATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCA-CATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
27910196 CACTTTCACATTTCATCACATCGGCCATTAGGC
65 CACTTTCACA-TTCATCACATCGGCCATTAGGC
27910229 CTTATCACATATATACACTTTCACATTCATCACCATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCACATATATACACTTTCACATTCATCA-CATCGGCCATTAGGCCTTATCACATATATATA
27910294 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
27910326 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
27910377 CTAATCATTT
Statistics
Matches: 420, Mismatches: 9, Indels: 27
0.92 0.02 0.06
Matches are distributed among these distances:
95 21 0.05
96 35 0.08
97 172 0.41
98 77 0.18
99 57 0.14
100 58 0.14
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27910143 original size:147 final size:143
Alignment explanation
Indices: 27909838--27910376 Score: 775
Period size: 147 Copynumber: 3.7 Consensus size: 143
27909828 CCCTTCAGGA
* * * * * * *
27909838 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGT-TCACATATTATA
1 CTTATCATATATATACACTTTCACATTCATCACATCGGCCATTAGG-CCT-TATCACATA-TATA
*
27909902 TCACTTTCACATTCATCACATCGGCCAATAGGCCTTATCACATATAT-TACACTTTCCACATTCA
63 -CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTT-CACATTCA
* * *
27909966 TCACGTTGGCCA-TCGCGC
126 TCACATCGGCCATTAG-GC
27909984 CTGTCA-CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CT-T-ATCATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
27910048 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATATACACTTTCACATTCATC
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATATACACTTTCACATTCATC
27910113 ACATCGAGGCCATTAGGC
128 ACATC--GGCCATTAGGC
27910131 CTTATCATTATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
1 CTTATCA-TATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATA
27910196 CACTTTCACATTTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
63 CACTTTCACA-TTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
27910259 CACCATCGGCCATTAGGC
127 CA-CATCGGCCATTAGGC
27910277 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTAT--CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
27910342 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
27910377 CTAATCATTT
Statistics
Matches: 366, Mismatches: 11, Indels: 34
0.89 0.03 0.08
Matches are distributed among these distances:
144 65 0.18
145 42 0.11
146 39 0.11
147 164 0.45
148 9 0.02
149 17 0.05
150 30 0.08
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:27913797 original size:27 final size:27
Alignment explanation
Indices: 27913767--27913945 Score: 173
Period size: 27 Copynumber: 6.6 Consensus size: 27
27913757 ATATTGAGTC
* *
27913767 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
27913794 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
27913821 CGCACACCTTAGTGCTACATAGTCAAACT
1 CGCACA-CTTAGTGCTACATAATC-AACT
** ** *
27913850 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
**
27913877 CGCACACTTAGTGCATCACAT--TCATTT
1 CGCACACTTAGTGC-T-ACATAATCAACT
* * *
27913904 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
27913931 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27913946 GTACAATTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.03
27 83 0.65
28 29 0.23
29 12 0.09
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:27913928 original size:54 final size:54
Alignment explanation
Indices: 27913767--27913945 Score: 193
Period size: 54 Copynumber: 3.3 Consensus size: 54
27913757 ATATTGAGTC
* * * * *
27913767 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACAT-ATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
27913821 CGCACACCTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACA-CTTAGTGCTACATA-TCAAACTCGCACACTTAGTGCAACATAGTCAAAT
**
27913877 CGCACACTTAGTGCATCACAT-TC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGC-T-ACATATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
27913931 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27913946 GTACAATTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
53 1 0.01
54 46 0.43
55 23 0.22
56 32 0.30
57 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATATCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:27926409 original size:17 final size:17
Alignment explanation
Indices: 27926387--27926420 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27926377 TAGGGTTACG
*
27926387 GAGCATTACCGAACATA
1 GAGCATTACCAAACATA
27926404 GAGCATTACCAAACATA
1 GAGCATTACCAAACATA
27926421 TTATACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (17 bp):
GAGCATTACCAAACATA
Found at i:27940887 original size:43 final size:43
Alignment explanation
Indices: 27940839--27940973 Score: 161
Period size: 43 Copynumber: 3.2 Consensus size: 43
27940829 GATTTTGTGG
27940839 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
27940882 AAGACCATGTCTAGGACATTGGCATCG-TAT-ATGATTA-GTGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGA-GATTACGTGT
* ** * ** *
27940923 AAGATCC-TGTCTGGGACAAAGGCATCGATATGTGAAAACATGT
1 AAGA-CCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
27940966 AAGACCAT
1 AAGACCAT
27940974 ATCCGAGATA
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
41 26 0.33
42 18 0.23
43 35 0.44
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (43 bp):
AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACGTGT
Found at i:27943576 original size:20 final size:20
Alignment explanation
Indices: 27943547--27943591 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27943537 AGCACATGTA
* *
27943547 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
27943567 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
27943587 TTCAT
1 TTCAT
27943592 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:27945992 original size:39 final size:39
Alignment explanation
Indices: 27945943--27946071 Score: 161
Period size: 39 Copynumber: 3.3 Consensus size: 39
27945933 GGTAAACTAT
27945943 TGTACTGAATAATTGATAGTTAATGAATAACTAAATTAC
1 TGTACTGAATAATTGATAGTTAATGAATAACTAAATTAC
* * * * *
27945982 TGTATTGAATAATTGATAATTATTGAATTACTAAACTAC
1 TGTACTGAATAATTGATAGTTAATGAATAACTAAATTAC
* * * *
27946021 TGCACTGAAT-ATCTGATAGTTACTGAATGACTAAATTAT
1 TGTACTGAATAAT-TGATAGTTAATGAATAACTAAATTAC
27946060 TGTACTGAATAA
1 TGTACTGAATAA
27946072 CTAATTGTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
38 2 0.03
39 72 0.96
40 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (39 bp):
TGTACTGAATAATTGATAGTTAATGAATAACTAAATTAC
Found at i:27946082 original size:39 final size:39
Alignment explanation
Indices: 27945935--27946084 Score: 156
Period size: 39 Copynumber: 3.8 Consensus size: 39
27945925 TTAATAGGGG
* * *
27945935 TAAACTATTGTACTGAATAATTGATAGTTAATGAATAAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * * * *
27945974 TAAATTACTGTATTGAATAATTGATAATTATTGAATTAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * *
27946013 TAAACTACTGCACTGAATATCTGATAGTTACTGAATGAC
1 TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
* * * *
27946052 TAAATTATTGTACTGAATAACTAATTGTTACTG
1 TAAACTACTGTACTGAATAACTGATAGTTACTG
27946085 GTTAAATATG
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAACTGATAGTTACTGAATAAC
Found at i:27946715 original size:23 final size:23
Alignment explanation
Indices: 27946688--27946733 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
27946678 GGACTATCCG
27946688 AACAGGTCCCGATTCGATTCTAA
1 AACAGGTCCCGATTCGATTCTAA
27946711 AACAGGTCCCGATTCGATTCTAA
1 AACAGGTCCCGATTCGATTCTAA
27946734 CGTGTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (23 bp):
AACAGGTCCCGATTCGATTCTAA
Found at i:27958581 original size:23 final size:23
Alignment explanation
Indices: 27958555--27958600 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
27958545 TTCATGAATG
27958555 TTTGATAGTTACTGAATGACTAA
1 TTTGATAGTTACTGAATGACTAA
27958578 TTTGATAGTTACTGAATGACTAA
1 TTTGATAGTTACTGAATGACTAA
27958601 ATTACTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
TTTGATAGTTACTGAATGACTAA
Found at i:27964217 original size:40 final size:40
Alignment explanation
Indices: 27964147--27964364 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
27964137 AAGCCAGGTA
* * * *
27964147 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
27964186 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
27964226 CCTTCGGGACTTAGCCCGGATATAGTAACTCGAACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
27964266 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
27964306 CCTTCGGGACTTAGCCC-GAAACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
27964346 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
27964365 TTATCATCCG
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 143 0.90
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27972335 original size:39 final size:40
Alignment explanation
Indices: 27972188--27972403 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
27972178 CAAGCCAGTA
* * * *
27972188 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
27972227 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
27972267 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
27972307 CCTTCGGGACTTA-CCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
27972346 CCTT-GGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
27972385 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
27972404 TTATCATCCG
Statistics
Matches: 161, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
38 9 0.06
39 67 0.42
40 85 0.53
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27972397 original size:118 final size:119
Alignment explanation
Indices: 27972188--27972403 Score: 319
Period size: 118 Copynumber: 1.8 Consensus size: 119
27972178 CAAGCCAGTA
* * * **
27972188 CCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGATGTAGT
1 CCTTCGGGACTTAACCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGAACTAGT
*
27972253 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
66 AACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
27972307 CCTTCGGGACTTACCCGGATATAG-TAACTCGCACAAATGCCTT-GGGACTTAGCCCGGAACTAG
1 CCTTCGGGACTTAACCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGCCCGGAACTAG
* *
27972370 TCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
65 TAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
27972404 TTATCATCCG
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
118 49 0.57
119 37 0.43
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (119 bp):
CCTTCGGGACTTAACCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGAACTAGT
AACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:27974391 original size:25 final size:25
Alignment explanation
Indices: 27974363--27974427 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
27974353 TTCTTATGCA
*
27974363 TGTATGCTCATACGAGCTATGAATC
1 TGTATGCTCATACGAGCTATAAATC
*
27974388 TGTATGCTC-TAACGAGCTGTAAATC
1 TGTATGCTCAT-ACGAGCTATAAATC
*
27974413 GGTATGCTCATACGA
1 TGTATGCTCATACGA
27974428 ACTGAGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (25 bp):
TGTATGCTCATACGAGCTATAAATC
Found at i:27974447 original size:50 final size:49
Alignment explanation
Indices: 27974364--27974491 Score: 145
Period size: 50 Copynumber: 2.6 Consensus size: 49
27974354 TCTTATGCAT
* *
27974364 GTATGCTCATACGAGCT-ATGAATCTGTATGCTCTAACGAGCTGTAAATCG
1 GTATGCTCATACGAACTGA-GAATCTGTAAGCTCTAACGAGCTG-AAATCG
* *
27974414 GTATGCTCATACGAACTGAGAAT-TGATAAGCTCTCACGAGCTGCAATCG
1 GTATGCTCATACGAACTGAGAATCTG-TAAGCTCTAACGAGCTGAAATCG
* *
27974463 GTAAGCTCATAC-AAGCTGAGAATCGGTAA
1 GTATGCTCATACGAA-CTGAGAATCTGTAA
27974492 TCCCTAGTGA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
48 2 0.03
49 29 0.43
50 36 0.53
51 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (49 bp):
GTATGCTCATACGAACTGAGAATCTGTAAGCTCTAACGAGCTGAAATCG
Found at i:27974479 original size:24 final size:25
Alignment explanation
Indices: 27974409--27974491 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
27974399 ACGAGCTGTA
*
27974409 AATCGGTATGCTCATACGAA-CTGAG
1 AATCGGTAAGCTCATAC-AAGCTGAG
* * * *
27974434 AATTGATAAGCTC-TCACGAGCTG-C
1 AATCGGTAAGCTCAT-ACAAGCTGAG
27974458 AATCGGTAAGCTCATACAAGCTGAG
1 AATCGGTAAGCTCATACAAGCTGAG
27974483 AATCGGTAA
1 AATCGGTAA
27974492 TCCCTAGTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
24 20 0.44
25 25 0.56
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AATCGGTAAGCTCATACAAGCTGAG
Found at i:27978006 original size:41 final size:41
Alignment explanation
Indices: 27977931--27978012 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
27977921 TGATATCAGC
27977931 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
1 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
27977972 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
1 TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
27978013 AAGATTCAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.34, T:0.27
Consensus pattern (41 bp):
TCACACAGGAAGCATTAGTTGGTTGGATAGACGTTTGGAGG
Found at i:27984870 original size:25 final size:25
Alignment explanation
Indices: 27984842--27984895 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
27984832 ATTTTAATCC
* *
27984842 TTTTAATTTTTTTATA-ATTTATTTA
1 TTTTAAATATTTTATATA-TTATTTA
27984867 TTTTAAATATTTTATATATTATTTA
1 TTTTAAATATTTTATATATTATTTA
27984892 TTTT
1 TTTT
27984896 TACTATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTAAATATTTTATATATTATTTA
Found at i:27984943 original size:12 final size:12
Alignment explanation
Indices: 27984926--27985081 Score: 103
Period size: 12 Copynumber: 13.0 Consensus size: 12
27984916 TATGTAAAAA
27984926 ATTATTATATAT
1 ATTATTATATAT
* *
27984938 ATTATTTTTATTT
1 ATTA-TTATATAT
*
27984951 ATGTATTATTTAACAT
1 AT-TATTA--T-ATAT
27984967 ATTATT-TATAT
1 ATTATTATATAT
*
27984978 TTTATTATATAT
1 ATTATTATATAT
*
27984990 TTTATTATATAT
1 ATTATTATATAT
*
27985002 TTTATT-TATAT
1 ATTATTATATAT
27985013 ATT-TTAT-TAT
1 ATTATTATATAT
27985023 A-TATTATATCAT
1 ATTATTATAT-AT
* *
27985035 TTTACTATATAT
1 ATTATTATATAT
27985047 ATTATTCAT-TAT
1 ATTATT-ATATAT
*
27985059 ATTATT-TTTAT
1 ATTATTATATAT
27985070 -TCTATTATATAT
1 AT-TATTATATAT
27985082 TATATTATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
9 1 0.01
10 12 0.10
11 24 0.21
12 49 0.42
13 19 0.16
14 2 0.02
15 5 0.04
16 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:27984958 original size:29 final size:28
Alignment explanation
Indices: 27984926--27985029 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 28
27984916 TATGTAAAAA
27984926 ATTATTATATATATTATTTTTATTTATGT
1 ATTATTATATATATTATTTTTATTTAT-T
* *
27984955 ATTATT-TAACATATTATTTATATTTTATT
1 ATTATTAT-ATATATTATTTTTA-TTTATT
*
27984984 ATATATTTTAT-TA-TATATTTTATTTATAT
1 AT-TATTATATATATTAT-TTTTATTTAT-T
27985013 ATT-TTATTATATATTAT
1 ATTATTA-TATATATTAT
27985030 ATCATTTTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
27 2 0.03
28 13 0.21
29 32 0.52
30 13 0.21
31 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
ATTATTATATATATTATTTTTATTTATT
Found at i:27984959 original size:17 final size:18
Alignment explanation
Indices: 27984927--27985081 Score: 76
Period size: 19 Copynumber: 8.6 Consensus size: 18
27984917 ATGTAAAAAA
27984927 TTATTATATATATTATTT
1 TTATTATATATATTATTT
*
27984945 TTATT-TATGTATTA--T
1 TTATTATATATATTATTT
**
27984960 TTAACATAT-TATTTATATT
1 TTATTATATATA-TTAT-TT
*
27984979 TTATTATATATTTTATTAT
1 TTATTATATATATTATT-T
* * *
27984998 ATATTTTATTTA-TATATT
1 TTATTATATATATTAT-TT
27985016 TTATTATATAT-TATATCATT
1 TTATTATATATAT-TAT--TT
*
27985036 TTACTATATATATTA--T
1 TTATTATATATATTATTT
* *
27985052 TCATTATAT-TATTTTTAT
1 TTATTATATATATTATT-T
27985070 TCTATTATATAT
1 T-TATTATATAT
27985082 TATATTATTT
Statistics
Matches: 102, Mismatches: 18, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
15 10 0.10
16 14 0.14
17 8 0.08
18 20 0.20
19 32 0.31
20 17 0.17
21 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TTATTATATATATTATTT
Found at i:27984982 original size:23 final size:25
Alignment explanation
Indices: 27984973--27985087 Score: 88
Period size: 25 Copynumber: 4.9 Consensus size: 25
27984963 ACATATTATT
27984973 TATATTTTATTATATATTTTA-TTA
1 TATATTTTATTATATATTTTATTTA
27984997 TATATTTTATTTATATATTTTA-TTA
1 TATATTTTA-TTATATATTTTATTTA
* *
27985022 TATA--TTA-TAT-CATTTTA-CTA
1 TATATTTTATTATATATTTTATTTA
* *
27985042 TATATATTATTCAT-TATATTATTT-
1 TATATTTTATT-ATATATTTTATTTA
* *
27985066 T-TATTCTATTATATATTATATT
1 TATATTTTATTATATATTTTATT
27985088 ATTTTGTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
20 12 0.16
21 3 0.04
22 5 0.07
23 18 0.24
24 17 0.23
25 20 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTTTATTATATATTTTATTTA
Found at i:27984995 original size:35 final size:36
Alignment explanation
Indices: 27984939--27985027 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
27984929 ATTATATATA
* *
27984939 TTAT-TTTTATT-TATGTATTATT-TAACATATTA-T
1 TTATATTTTATTATATATTTTATTAT-ACATATTATT
* *
27984972 TTATATTTTATTATATATTTTATTATATATTTTATT
1 TTATATTTTATTATATATTTTATTATACATATTATT
27985008 TATATATTTTATTATATATT
1 T-TATATTTTATTATATATT
27985028 ATATCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 4 0.09
34 7 0.15
35 15 0.32
36 3 0.06
37 18 0.38
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (36 bp):
TTATATTTTATTATATATTTTATTATACATATTATT
Found at i:27985082 original size:12 final size:12
Alignment explanation
Indices: 27984968--27985089 Score: 114
Period size: 12 Copynumber: 10.6 Consensus size: 12
27984958 ATTTAACATA
27984968 TTATT-TATATT
1 TTATTATATATT
27984979 TTATTATATATT
1 TTATTATATATT
27984991 TTATTATATATT
1 TTATTATATATT
27985003 TTATTTATATATT
1 TTA-TTATATATT
27985016 TTATTATATA--
1 TTATTATATATT
*
27985026 TTA-TAT-CATT
1 TTATTATATATT
* *
27985036 TTACTATATATA
1 TTATTATATATT
*
27985048 TTATTCAT-TATA
1 TTATT-ATATATT
*
27985060 TTATT-TTTATT
1 TTATTATATATT
*
27985071 CTATTATATATT
1 TTATTATATATT
*
27985083 ATATTAT
1 TTATTAT
27985090 TTTGTTTTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
8 1 0.01
9 3 0.03
10 7 0.07
11 15 0.16
12 54 0.57
13 14 0.15
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATATATT
Found at i:27985527 original size:37 final size:40
Alignment explanation
Indices: 27985485--27985560 Score: 97
Period size: 43 Copynumber: 1.9 Consensus size: 40
27985475 TATTTTTATG
27985485 TTATTTA-TTGTT-TTTT-A-TATATTTGCATGGAAATTGA
1 TTATTTAGTTGTTATTTTAAGTATATTTGCAT-GAAATTGA
27985522 TTATTTATGTTGTTATTTTAAGTTATATTTGCATGAAAT
1 TTATTTA-GTTGTTATTTTAAG-TATATTTGCATGAAAT
27985561 ATTATTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
37 7 0.21
39 5 0.15
40 4 0.12
41 1 0.03
42 5 0.15
43 11 0.33
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.57
Consensus pattern (40 bp):
TTATTTAGTTGTTATTTTAAGTATATTTGCATGAAATTGA
Found at i:27986409 original size:18 final size:19
Alignment explanation
Indices: 27986386--27986423 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
27986376 TGGAAAGATA
*
27986386 AAAATTTGAAAGA-AAAGG
1 AAAATTAGAAAGATAAAGG
*
27986404 AAAATTAGAAGGATAAAGG
1 AAAATTAGAAAGATAAAGG
27986423 A
1 A
27986424 TAAGTGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (19 bp):
AAAATTAGAAAGATAAAGG
Found at i:27988390 original size:39 final size:39
Alignment explanation
Indices: 27988325--27988427 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 39
27988315 AATAGCACAC
* * *
27988325 CAGT-TTGTGGACAAGCCTCTAATAATACAGATAAACT-G
1 CAGTATTGTGGACAAG-CACTAGTAATACAAATAAACTAG
*
27988363 CGGTATTGTGGACAAGTCACTAGTAATACAAATAAACTAG
1 CAGTATTGTGGACAAG-CACTAGTAATACAAATAAACTAG
*
27988403 TAGTATTGTGGACAAGCTACTAGTA
1 CAGTATTGTGGACAAGC-ACTAGTA
27988428 TTGTAGATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.05
39 30 0.55
40 22 0.40
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (39 bp):
CAGTATTGTGGACAAGCACTAGTAATACAAATAAACTAG
Found at i:27989758 original size:5 final size:5
Alignment explanation
Indices: 27989720--27989790 Score: 87
Period size: 5 Copynumber: 14.6 Consensus size: 5
27989710 ATGTTTTAAA
*
27989720 TATAT TA-A- TATAT TAT-T TA-AT TATAAAA TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TAT--AT TATAT TATAT TATAT TATAT
27989768 TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TAT
27989791 TATGTAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
3 2 0.03
4 8 0.14
5 44 0.76
7 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:27989924 original size:21 final size:21
Alignment explanation
Indices: 27989890--27989930 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27989880 ATGTTTACTT
*
27989890 ATTATATAAGTATATTATTAA
1 ATTATATAAGTATAATATTAA
* *
27989911 ATTATATTATTATAATATTA
1 ATTATATAAGTATAATATTA
27989931 TTAATAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTATATAAGTATAATATTAA
Found at i:27991186 original size:24 final size:26
Alignment explanation
Indices: 27991146--27991194 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
27991136 GTAAAAGAAC
27991146 AAATTGCAATAGAATTGGTAT-TGAAT
1 AAATTGCAATAGAATT-GTATATGAAT
27991172 AAATTG-AAT-GAATTGTATATGAA
1 AAATTGCAATAGAATTGTATATGAA
27991195 ATGAAATGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 3 0.14
26 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (26 bp):
AAATTGCAATAGAATTGTATATGAAT
Found at i:27992152 original size:6 final size:6
Alignment explanation
Indices: 27992141--27992166 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27992131 CTAATAACAG
27992141 CCCTAA CCCTAA CCCTAA CCCTAA CC
1 CCCTAA CCCTAA CCCTAA CCCTAA CC
27992167 ATCGCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTAA
Found at i:28016680 original size:13 final size:13
Alignment explanation
Indices: 28016658--28016709 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
28016648 TTGGCTCACA
28016658 TGCCCATGTGTGT
1 TGCCCATGTGTGT
* *
28016671 TGCCCGTGTGTGACACA
1 TGCCCATGTGTG----T
28016688 TGCCCATGTGTGT
1 TGCCCATGTGTGT
28016701 TGCCCATGT
1 TGCCCATGT
28016710 ATGACACACG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 20 0.65
17 11 0.35
ACGTcount: A:0.12, C:0.27, G:0.29, T:0.33
Consensus pattern (13 bp):
TGCCCATGTGTGT
Found at i:28016688 original size:30 final size:30
Alignment explanation
Indices: 28016654--28016727 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
28016644 TAACTTGGCT
* *
28016654 CACATGCCCATGTGTGTTGCCCGTGTGTGA
1 CACATGCCCATGTGTGTTGCCCATGTATGA
28016684 CACATGCCCATGTGTGTTGCCCATGTATGA
1 CACATGCCCATGTGTGTTGCCCATGTATGA
*
28016714 CACACGCCCATGTG
1 CACATGCCCATGTG
28016728 GCCAAGCTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.27
Consensus pattern (30 bp):
CACATGCCCATGTGTGTTGCCCATGTATGA
Found at i:28016697 original size:17 final size:17
Alignment explanation
Indices: 28016671--28016727 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
28016661 CCATGTGTGT
*
28016671 TGCCCGTGTGTGACACA
1 TGCCCATGTGTGACACA
*
28016688 TGCCCATGTGTG----T
1 TGCCCATGTGTGACACA
*
28016701 TGCCCATGTATGACACA
1 TGCCCATGTGTGACACA
*
28016718 CGCCCATGTG
1 TGCCCATGTG
28016728 GCCAAGCTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
13 11 0.37
17 19 0.63
ACGTcount: A:0.18, C:0.30, G:0.26, T:0.26
Consensus pattern (17 bp):
TGCCCATGTGTGACACA
Found at i:28018230 original size:46 final size:45
Alignment explanation
Indices: 28018180--28018299 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 45
28018170 GAGAACTATT
*
28018180 GTAAGACATGTTTGGGACATGCATCGGCCT-CGAGATGTAAGCCAGG
1 GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGT--GCCAGG
** * * *
28018226 GTAAGACATGTCAAGGACATGCATTGG-CTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGTGCCAGG
*
28018270 GCAAGACCATGTCTGGGACATGGCATCGGC
1 GTAAGA-CATGTCTGGGACAT-GCATCGGC
28018300 ACGGATATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 9 0.15
45 14 0.23
46 37 0.62
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (45 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGTGCCAGG
Found at i:28018328 original size:50 final size:48
Alignment explanation
Indices: 28018267--28018395 Score: 136
Period size: 47 Copynumber: 2.7 Consensus size: 48
28018257 GAGATGTGTC
* *
28018267 AGTGCAAGACCATGTCTGGGACATGGCATCGGCAC-GGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-ACTGGAT-GGT-AGAGCT
* * * * *
28018317 AGTGTAAGACCATGTCTGGGATATGGAAT-TGACTTGATGGTTGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTGGATGGTAGAGCT
* *
28018364 AGTGTTAGACTATGTCTGGGACATGGCATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
28018396 TATTATACCT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
47 30 0.46
48 5 0.08
49 4 0.06
50 26 0.40
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGACTGGATGGTAGAGCT
Found at i:28019404 original size:28 final size:28
Alignment explanation
Indices: 28019364--28019418 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
28019354 CATGGGCTAA
28019364 GACACGAGC-GTGTCATGGCCGTGTGAGG
1 GACACGAGCGGTGTCA-GGCCGTGTGAGG
*
28019392 GACACGGGCGTGTGTCAGGCCGTGTGA
1 GACACGAGCG-GTGTCAGGCCGTGTGA
28019419 AAACCCCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 10 0.42
30 6 0.25
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (28 bp):
GACACGAGCGGTGTCAGGCCGTGTGAGG
Found at i:28025938 original size:46 final size:46
Alignment explanation
Indices: 28025777--28026083 Score: 191
Period size: 46 Copynumber: 6.5 Consensus size: 46
28025767 GATATTCATG
* * *
28025777 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCT
* * * * *
28025823 AGCGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCT
** *
28025871 AGTGTAATTCATGTTTGGGACATGCATCGGCCTCGAGATGTA-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCT
* * * * *
28025917 AGTGTAAGACATATCTAGGACATGTATCGG-CTACGAGATGTG-TC-
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCT
* * *
28025961 AGTGTAAGACCATGTCTGGGACATGGCATC-GACACG-TATAGAGATG-T
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGAT-GAGA-GCT
* * * * *
28026008 CAGTGTAAGGCCATGTCTGAGACATGGCATCAG-CACGAATATGTGAGAGCT
1 -AGTGTAA-GACATGTCTGGGACAT-GCATCGGCCTCG-AGA--TGAGAGCT
28026059 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
28026084 GCATTAGCAT
Statistics
Matches: 204, Mismatches: 35, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
44 11 0.05
45 20 0.10
46 62 0.30
47 26 0.13
48 51 0.25
49 5 0.02
50 23 0.11
51 5 0.02
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCT
Found at i:28026014 original size:48 final size:50
Alignment explanation
Indices: 28025957--28026092 Score: 174
Period size: 48 Copynumber: 2.8 Consensus size: 50
28025947 CTACGAGATG
28025957 TGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GACACG-TAT-AGAGA
1 TGTCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CACGATATGAGAGA
* * *
28026005 TGTCAGTGTAAGGCCATGTCTGAGACATGGCATCAGCACGAATATGTGAGA
1 TGTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACG-ATATGAGAGA
*
28026056 -G-CTAGTGTAAGACCATGTCTGGGACATGGCATTAGCA
1 TGTC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
28026093 TTATACCCCA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
48 36 0.47
49 2 0.03
50 35 0.45
51 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (50 bp):
TGTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGATATGAGAGA
Found at i:28026568 original size:46 final size:45
Alignment explanation
Indices: 28026518--28026637 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 45
28026508 GAGAACTATT
*
28026518 GTAAGACATGTTTGGGACATGCATCGGCCT-CGAGATGTAAGCCAGG
1 GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGT--GCCAGG
** * * *
28026564 GTAAGACATGTCAAGGACATGCATTGG-CTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGTGCCAGG
*
28026608 GCAAGACCATGTCTGGGACATGGCATCGGC
1 GTAAGA-CATGTCTGGGACAT-GCATCGGC
28026638 ACGGATATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
44 9 0.15
45 14 0.23
46 37 0.62
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (45 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTACGAGATGTGCCAGG
Found at i:28026666 original size:50 final size:48
Alignment explanation
Indices: 28026605--28026733 Score: 145
Period size: 47 Copynumber: 2.7 Consensus size: 48
28026595 GAGATGTGTC
* *
28026605 AGTGCAAGACCATGTCTGGGACATGGCATCGGCAC-GGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-ACTGGAT-GGT-AGAGCT
* * * *
28026655 AGTGTAAGACCATGTCTGGGATATGGCAT-TGACTTGATGGTTGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGACTGGATGGTAGAGCT
* *
28026702 AGTGTTAGACTATGTCTGGGACATGGCATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
28026734 TATTATACCT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 31 0.46
48 5 0.07
49 4 0.06
50 27 0.40
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGACTGGATGGTAGAGCT
Found at i:28027053 original size:643 final size:644
Alignment explanation
Indices: 28025819--28027112 Score: 2057
Period size: 643 Copynumber: 2.0 Consensus size: 644
28025809 ACATTATGAG
* * * **
28025819 AGCCAGCGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGAGCTAGTGTAATTCATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGACATCGGCATTGAGACGAGAACTAGTGTAAGACATG
* * * *
28025884 TTTGGGACATGCATCGGCCTCGAGATGTAAGCTAGTGTAAGACATATCTAGGACATGTATCGGCT
66 TTTGGGACATGCATCGGCCTCGAGATGTAAGCCAGGGTAAGACATATCAAGGACATGCATCGGCT
*
28025949 ACGAGATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGATGTCAGTGT
131 ACGAGATGTGTCAGTGCAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGATGTCAGTGT
* *
28026014 AAGGCCATGTCTGAGACATGGCATCAGCACGAATATGTGAGAGCTAGTGTAAGACCATGTCTGGG
196 AAGACCATGTCTGAGACATGGCATCAGCACGAATAGGTGAGAGCTAGTGTAAGACCATGTCTGGG
* * *
28026079 ACATGGCATTAGCATTATACCCCATGTTTGAGGTTTAATGAATATACGATAGCATTCCAAAAGGT
261 ACATGGCATCAGCATTATACCCCATATTTGAGGCTTAATGAATATACGATAGCATTCCAAAAGGT
28026144 TCAACGATGAGAGTTACAGTCTAAGTTAAAAGAGAAAAGTATAACTATGTTGTAAGTGGTACAAG
326 TCAACGATGAGAGTTACAGTCTAAGTTAAAAGAGAAAAGTATAACTATGTTGTAAGTGGTACAAG
* *
28026209 TACCTATTCGAAATTTATGAGATATGGGCTAAATATATGCCATATGAATTGTATTGGATGGTGAT
391 TACCTATTCGAAATGTATGAAATATGGGCTAAATATATGCCATATGAATTGTATTGGATGGTGAT
28026274 GGGTAAGTTGTGCTTATATCTACTTATGGTATTCATGAACAAGGTATGAAAAGTTATGAGCATAT
456 GGGTAAGTTGTGCTTATATCTACTTATGGTATTCATGAACAAGGTATGAAAAGTTATGAGCATAT
28026339 TATCCTATGACAATTAGTTAATGTTGTTTTCATGCAACTTACTAAGCTTTATGCTCACCTCATTT
521 TATCCTATGACAATTAGTTAATGTTGTTTTCATGCAACTTACTAAGCTTTATGCTCACCTCATTT
28026404 CCTTTCCATTTTCTTATAGTGTCGCCAAAGTAGCTCGAGGATCATCGCTATGTCGGAGA
586 CCTTTCCATTTTCTTATAGTGTCGCCAAAGTAGCTCGAGGATCATCGCTATGTCGGAGA
* * * *
28026463 AGCCAGTGTAAGACCATGTCTAGGATATTACATCGGCATTGAGATGAGAACTATTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGACATCGGCATTGAGACGAGAACTAGTGTAAGACATG
* *
28026528 TTTGGGACATGCATCGGCCTCGAGATGTAAGCCAGGGTAAGACATGTCAAGGACATGCATTGGCT
66 TTTGGGACATGCATCGGCCTCGAGATGTAAGCCAGGGTAAGACATATCAAGGACATGCATCGGCT
* *
28026593 ACGAGATGTGTCAGTGCAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTGAGA-G-CTA
131 ACGAGATGTGTCAGTGCAAGACCATGTCTGGGACATGGCATCGACAC-G-TAT-AGAGATGTC-A
* * * * * *
28026656 GTGTAAGACCATGTCTGGGATATGGCAT-TG-ACTTG-AT-GGT-TGAGCTAGTGTTAGACTATG
192 GTGTAAGACCATGTCTGAGACATGGCATCAGCAC--GAATAGGTGAGAGCTAGTGTAAGACCATG
* * ** * *
28026716 TCTGGGACATGGCATCGGTATTATACCTTATATTTGAGGCTTAATGAATATCCGATAGGATTCCA
255 TCTGGGACATGGCATCAGCATTATACCCCATATTTGAGGCTTAATGAATATACGATAGCATTCCA
* * * * *
28026781 AAAGGTTCAATGGTGAGAGTTACAGTTTAAGTTAAACA-AGTAAAGTATAA-TCATGTTGTGAGT
320 AAAGGTTCAACGATGAGAGTTACAGTCTAAGTTAAA-AGAGAAAAGTATAACT-ATGTTGTAAGT
* *
28026844 GGTACAGGTACCTATTTGAAATGTATGAAATATGGGCTAAATATATGCCATATGAATTGTATTGG
383 GGTACAAGTACCTATTCGAAATGTATGAAATATGGGCTAAATATATGCCATATGAATTGTATTGG
28026909 ATGGTGATGGGTAAGTTGTGCTTATATCTACTTATGGTATTCATGAACAAGGTATGAAAAGTTAT
448 ATGGTGATGGGTAAGTTGTGCTTATATCTACTTATGGTATTCATGAACAAGGTATGAAAAGTTAT
28026974 GAGCATATTATCCTATGACAATTAGTTAATGTTGTTTTCATGCAACTTACTAAGCTTTATGCTCA
513 GAGCATATTATCCTATGACAATTAGTTAATGTTGTTTTCATGCAACTTACTAAGCTTTATGCTCA
28027039 CCTCATTTCCTTTCCATTTTCTTATAGTGTCGCCAAAGTAGCTCGAGGATCATCGCTATGTCGGA
578 CCTCATTTCCTTTCCATTTTCTTATAGTGTCGCCAAAGTAGCTCGAGGATCATCGCTATGTCGGA
28027104 GA
643 GA
28027106 AGCCAGT
1 AGCCAGT
28027113 CACACTATCA
Statistics
Matches: 598, Mismatches: 44, Indels: 17
0.91 0.07 0.03
Matches are distributed among these distances:
642 1 0.00
643 392 0.66
644 165 0.28
645 5 0.01
646 31 0.05
647 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (644 bp):
AGCCAGTGTAAGACCATGTCTAGGACATGACATCGGCATTGAGACGAGAACTAGTGTAAGACATG
TTTGGGACATGCATCGGCCTCGAGATGTAAGCCAGGGTAAGACATATCAAGGACATGCATCGGCT
ACGAGATGTGTCAGTGCAAGACCATGTCTGGGACATGGCATCGACACGTATAGAGATGTCAGTGT
AAGACCATGTCTGAGACATGGCATCAGCACGAATAGGTGAGAGCTAGTGTAAGACCATGTCTGGG
ACATGGCATCAGCATTATACCCCATATTTGAGGCTTAATGAATATACGATAGCATTCCAAAAGGT
TCAACGATGAGAGTTACAGTCTAAGTTAAAAGAGAAAAGTATAACTATGTTGTAAGTGGTACAAG
TACCTATTCGAAATGTATGAAATATGGGCTAAATATATGCCATATGAATTGTATTGGATGGTGAT
GGGTAAGTTGTGCTTATATCTACTTATGGTATTCATGAACAAGGTATGAAAAGTTATGAGCATAT
TATCCTATGACAATTAGTTAATGTTGTTTTCATGCAACTTACTAAGCTTTATGCTCACCTCATTT
CCTTTCCATTTTCTTATAGTGTCGCCAAAGTAGCTCGAGGATCATCGCTATGTCGGAGA
Found at i:28027927 original size:20 final size:21
Alignment explanation
Indices: 28027889--28027927 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28027879 TCATAATGGT
28027889 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
28027910 CACACGGGCGTG-TGCCCT
1 CACACGGGCGTGTTGCCCT
28027928 ATTTCAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.31, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTC
Found at i:28032816 original size:20 final size:20
Alignment explanation
Indices: 28032793--28032830 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28032783 AATTTTTAAA
28032793 TTTTTATGAATTATTTATGT
1 TTTTTATGAATTATTTATGT
* *
28032813 TTTTTTTGAATTTTTTAT
1 TTTTTATGAATTATTTAT
28032831 TTCTTGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTTATGAATTATTTATGT
Found at i:28040809 original size:21 final size:21
Alignment explanation
Indices: 28040781--28040835 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
28040771 ACCGCTGTTT
28040781 CTAATCTCACCGCTACAGT-A
1 CTAATCTCACCGCTACAGTAA
*
28040801 TTCAATCTCACCGCTACAGTAA
1 CT-AATCTCACCGCTACAGTAA
28040823 CTAATCTCACCGC
1 CTAATCTCACCGC
28040836 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:28040981 original size:21 final size:21
Alignment explanation
Indices: 28040941--28040998 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
28040931 AAAATAGTGG
**
28040941 TAGCGGTGAGATTATTTACTA
1 TAGCGGTGAGATTAGATACTA
* *
28040962 TGGCGGTGAGATTGGATACTA
1 TAGCGGTGAGATTAGATACTA
*
28040983 TAACGGTGAGATTAGA
1 TAGCGGTGAGATTAGA
28040999 AATAGCGGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (21 bp):
TAGCGGTGAGATTAGATACTA
Found at i:28041089 original size:5 final size:5
Alignment explanation
Indices: 28041076--28041109 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
28041066 TATTAAAGAT
*
28041076 ATTAC ATTAA ATTAA ATTAA ATTAA ATTAA ATTA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTA
28041110 TATATGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:28042529 original size:17 final size:17
Alignment explanation
Indices: 28042509--28042571 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
28042499 AAGGTTAGGA
28042509 TTTTTAGTGGTTTATGG
1 TTTTTAGTGGTTTATGG
*
28042526 TTTTTGGTGGTTTATGG
1 TTTTTAGTGGTTTATGG
* *
28042543 TTTTTGGTGGTTTAGGG
1 TTTTTAGTGGTTTATGG
28042560 TTTTTAG-GGTTT
1 TTTTTAGTGGTTT
28042572 TTTAAGGGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
16 5 0.12
17 38 0.88
ACGTcount: A:0.08, C:0.00, G:0.33, T:0.59
Consensus pattern (17 bp):
TTTTTAGTGGTTTATGG
Found at i:28042858 original size:114 final size:115
Alignment explanation
Indices: 28042728--28042959 Score: 439
Period size: 114 Copynumber: 2.0 Consensus size: 115
28042718 GTTTTTTGTG
*
28042728 TTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAAT
1 TTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAAGGTTAATTAATTAAATTAACTATGAAAAT
*
28042793 AAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGTGTTTTTAGGGTT
66 AAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAGGGTT
28042843 TTTTAA-GGAAAAATTAATGAACACTTAGAGTTGAAGGTTAATTAATTAAATTAACTATGAAAAT
1 TTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAAGGTTAATTAATTAAATTAACTATGAAAAT
28042907 AAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAGGGTT
66 AAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAGGGTT
28042957 TTT
1 TTT
28042960 GATTATTTTA
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
114 109 0.95
115 6 0.05
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.36
Consensus pattern (115 bp):
TTTTAAGGGAAAAATTAATGAACACTTAGAGTTGAAGGTTAATTAATTAAATTAACTATGAAAAT
AAGAAAAAATCAATTAAATTAGGGCTTAGTGGTTTAGGGTTTTTAGGGTT
Found at i:28043081 original size:268 final size:264
Alignment explanation
Indices: 28042549--28043104 Score: 755
Period size: 268 Copynumber: 2.1 Consensus size: 264
28042539 ATGGTTTTTG
*
28042549 GTGGTTTAGGGTTTTTAGGGTTTTTTAAGGGAAAAAATAATAAACACTTAGAGTTGAGGGTTAAT
1 GTGGTTTAGGGTTTTTAGGGTTTTTTAAGGGAAAAAATAATAAACACTTAGAGTTGAAGGTTAAT
*
28042614 TAATTAAATTAACTATGAAAATAAAAAATCAATTAAATTAGGGTTTAGGGTTTTTAAGGTTAAGA
66 TAATTAAATTAACTATGAAAATAAAAAATCAATTAAATTAGGGCTTAGGG-TTTTAAGGTTAAGA
* * ** *
28042679 TTTTTTATTGTTTTAGGGTTAGGGTTTTAGCGATTTAGAGTTTTTTGTGTTTTAAGGGAAAAATT
130 TTTTTGATTATTTTAGGGTTAAAGTTTTAGCGATTTAGAGTTTTGTGTGTTTTAAGGGAAAAATT
28042744 AATGAACACTTAGAGTTGAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTA
195 AATGAACAC-------TGAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTA
*
28042809 AATTAGGGCTTA
253 AATTAAGGCTTA
* * *
28042821 GTGGTTTAGTGTTTTTAGGGTTTTTTAA-GGAAAAATTAATGAACACTTAGAGTTGAAGGTTAAT
1 GTGGTTTAGGGTTTTTAGGGTTTTTTAAGGGAAAAAATAATAAACACTTAGAGTTGAAGGTTAAT
*
28042885 TAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAGGGCTTAGTGG-TTTAGGGTTT
66 TAATTAAATTAACTATGAAAAT---AAAAAATCAATTAAATTAGGGCTTAG-GGTTTTAAGG---
* * * * *
28042949 TTAGGGTTTTTGATTATTTTAGGAGTTAAAGTTTTAGTGGTTTAGGGTTTTAGTGT-TATTTAAG
124 TTAAGATTTTTGATTATTTTAGG-GTTAAAGTTTTAGCGATTTAGAGTTTT-GTGTGT-TTTAAG
28043013 GGAAAAATTAATG-A-AC-GAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAAT
186 GGAAAAATTAATGAACACTGAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAAT
28043075 TAAATTAAGGCTTA
251 TAAATTAAGGCTTA
28043089 GTGGTTTAGGGTTTTT
1 GTGGTTTAGGGTTTTT
28043105 TGGTGGTTTA
Statistics
Matches: 256, Mismatches: 18, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
268 74 0.29
271 55 0.21
272 27 0.11
273 6 0.02
274 25 0.10
275 2 0.01
276 21 0.08
277 24 0.09
278 22 0.09
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (264 bp):
GTGGTTTAGGGTTTTTAGGGTTTTTTAAGGGAAAAAATAATAAACACTTAGAGTTGAAGGTTAAT
TAATTAAATTAACTATGAAAATAAAAAATCAATTAAATTAGGGCTTAGGGTTTTAAGGTTAAGAT
TTTTGATTATTTTAGGGTTAAAGTTTTAGCGATTTAGAGTTTTGTGTGTTTTAAGGGAAAAATTA
ATGAACACTGAGGGTTAATTAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAAGG
CTTA
Found at i:28043115 original size:122 final size:123
Alignment explanation
Indices: 28042980--28043221 Score: 289
Period size: 130 Copynumber: 2.0 Consensus size: 123
28042970 GGAGTTAAAG
* *
28042980 TTTTAGTGGTTTAGGG-TTTTAGTGTTATTTAAGGG-AAA-AA-TTAATGA-ACG-AGGGTTAAT
1 TTTTAGTGGTTTAGGGTTTTTAATATTATTTAAGGGAAAATAATTTAATGAGA-GTAGGGTTAAT
**
28043039 TAATTAAATTAACTATGAAAATAAGAAAAAATCAATTAAATTAAGGCTTAGTGGTTTAGGGTT
65 TAATTAAATTAACTACAAAAAT-A-AAAAAAT-AATTAAATTAAGGCTTAG-GGTTTAGGGTT
* * *
28043102 TTTTGGTGGTTTAGGGTTTTTAATATTTTTTAAGGGAAAATTAATTTAATTAGAGTTCAGGGTTA
1 TTTTAGTGGTTTAGGGTTTTTAATATTATTTAAGGGAAAA-TAATTTAATGAGAG-T-AGGGTTA
* *
28043167 ATTAATTAAATTAACTACAAAAATAAAAAAATAATTAAATTAGGGTTTAGGGTTT
63 ATTAATTAAATTAACTACAAAAATAAAAAAATAATTAAATTAAGGCTTAGGGTTT
28043222 TTTAGGATTT
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
122 15 0.15
123 16 0.16
124 3 0.03
126 7 0.07
127 23 0.23
128 8 0.08
129 1 0.01
130 29 0.28
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39
Consensus pattern (123 bp):
TTTTAGTGGTTTAGGGTTTTTAATATTATTTAAGGGAAAATAATTTAATGAGAGTAGGGTTAATT
AATTAAATTAACTACAAAAATAAAAAAATAATTAAATTAAGGCTTAGGGTTTAGGGTT
Found at i:28043648 original size:126 final size:126
Alignment explanation
Indices: 28043324--28043911 Score: 915
Period size: 126 Copynumber: 4.7 Consensus size: 126
28043314 TTGAGAAGAT
* ** *
28043324 TCAAAAACGCTTCAAGAAGGATGCACTTTTAGCAAAATTATAGGAAAAAGCTCCCACATGGACGC
1 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
* *
28043389 TCTTTTGCTATAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTTTGAACAAATAGTG
66 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
28043450 TCAAAAA-----C--GAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
1 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
28043508 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
66 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
* * * **
28043569 TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTACGGGAAAAATCTCCCACGTGGAAAC
1 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
28043634 TCTTTTGCTACAGTAGTATCTGATAAAATAA-TTTGAGAAGATGTTTCTGAACAAATAGTG
66 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
* * *
28043694 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGAGAAAAAGCTCCCATGTGGACAC
1 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
28043759 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
66 TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
* * * ** * *
28043820 TCAAAAACGCTTTAAGAATGATGCACTTTCAGCAAAATTATGAAAAAAAGCTCCCAAGTGGATGC
1 TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
*
28043885 TCTTTTGCTATAGTAGTATCTGA-AAAA
66 TCTTTTGCTACAGTAGTATCTGATAAAA
28043912 GCCTTAGACT
Statistics
Matches: 429, Mismatches: 25, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
119 112 0.26
121 1 0.00
125 123 0.29
126 193 0.45
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (126 bp):
TCAAAAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGC
TCTTTTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
Found at i:28043797 original size:251 final size:245
Alignment explanation
Indices: 28043324--28043911 Score: 928
Period size: 251 Copynumber: 2.4 Consensus size: 245
28043314 TTGAGAAGAT
* * * * * *
28043324 TCAAAAACGCTTCAAGAAGGATGCACTTTTAGCAAAATTATAGGAAAAAGCTCCCACATGGACGC
1 TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTATGGGAAAAAGCTCCCACGTGGAAGC
*
28043389 TCTTTTGCTATAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTTTGAACAAATAGTGTCAA
66 TCTTTTGCTATAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAA
* *
28043454 AAACGAAGGATGCACTTTCAGCAAAATTACGGGAAAAAGCTCCCACGTGGACGCTCTTTTGCTAC
131 AAACGAAGGATGCACTTTCAGCAAAATTACGAGAAAAAGCTCCCACGTGGACACTCTTTTGCTAC
28043519 AGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
196 AGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
* * *
28043569 TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTACGGGAAAAATCTCCCACGTGGAAAC
1 TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTATGGGAAAAAGCTCCCACGTGGAAGC
*
28043634 TCTTTTGCTACAGTAGTATCTGATAAAATAA-TTTGAGAAGATGTTTCTGAACAAATAGTGTCAA
66 TCTTTTGCTATAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAA
*
28043698 AAACGCTTCAAGAAGGATGCACTTTCAGCAAAATTACGAGAAAAAGCTCCCATGTGGACACTCTT
131 AAA-----C--GAAGGATGCACTTTCAGCAAAATTACGAGAAAAAGCTCCCACGTGGACACTCTT
28043763 TTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
189 TTGCTACAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
* ** * *
28043820 TCAAAAACGCTTTAAGAATGATGCACTTTCAGCAAAATTATGAAAAAAAGCTCCCAAGTGGATGC
1 TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTATGGGAAAAAGCTCCCACGTGGAAGC
28043885 TCTTTTGCTATAGTAGTATCTGA-AAAA
66 TCTTTTGCTATAGTAGTATCTGATAAAA
28043912 GCCTTAGACT
Statistics
Matches: 313, Mismatches: 23, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
244 35 0.11
245 86 0.27
249 1 0.00
250 4 0.01
251 187 0.60
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (245 bp):
TCAAAAACGCTTAAAGAATGATGCACTTTCAGCAAAATTATGGGAAAAAGCTCCCACGTGGAAGC
TCTTTTGCTATAGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAA
AAACGAAGGATGCACTTTCAGCAAAATTACGAGAAAAAGCTCCCACGTGGACACTCTTTTGCTAC
AGTAGTATCTGATAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTG
Found at i:28046968 original size:9 final size:9
Alignment explanation
Indices: 28046945--28046975 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28046935 ATTTATATTT
28046945 TATTAAAAA
1 TATTAAAAA
28046954 TA-TAAAAA
1 TATTAAAAA
28046962 TATTAAAAA
1 TATTAAAAA
28046971 TATTA
1 TATTA
28046976 CCGTAGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:28047248 original size:21 final size:21
Alignment explanation
Indices: 28047223--28047278 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 21
28047213 TGGTTCAGCT
28047223 TCCGGCGAGGG-TTGTGGTTGC
1 TCCGGCG-GGGATTGTGGTTGC
*
28047244 TCCGGTGGGGATTGTGGTTGC
1 TCCGGCGGGGATTGTGGTTGC
28047265 TCCGGCTGGGGATT
1 TCCGGC-GGGGATT
28047279 TAGTTGTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 3 0.10
21 21 0.68
22 7 0.23
ACGTcount: A:0.05, C:0.18, G:0.46, T:0.30
Consensus pattern (21 bp):
TCCGGCGGGGATTGTGGTTGC
Found at i:28047277 original size:22 final size:21
Alignment explanation
Indices: 28047234--28047278 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
28047224 CCGGCGAGGG
28047234 TTGTGGTTGCTCCGGTGGGGA
1 TTGTGGTTGCTCCGGTGGGGA
28047255 TTGTGGTTGCTCCGGCTGGGGA
1 TTGTGGTTGCTCCGG-TGGGGA
28047277 TT
1 TT
28047279 TAGTTGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.04, C:0.16, G:0.44, T:0.36
Consensus pattern (21 bp):
TTGTGGTTGCTCCGGTGGGGA
Found at i:28047284 original size:21 final size:21
Alignment explanation
Indices: 28047234--28047284 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
28047224 CCGGCGAGGG
*
28047234 TTGTGGTTGCTCCGGTGGGGA
1 TTGTAGTTGCTCCGGTGGGGA
*
28047255 TTGTGGTTGCTCCGGCTGGGGA
1 TTGTAGTTGCTCCGG-TGGGGA
28047277 TT-TAGTTG
1 TTGTAGTTG
28047285 TGGGTGTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.06, C:0.14, G:0.43, T:0.37
Consensus pattern (21 bp):
TTGTAGTTGCTCCGGTGGGGA
Found at i:28048199 original size:7 final size:7
Alignment explanation
Indices: 28048184--28048216 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
28048174 TTATATAGGT
28048184 AATACTA
1 AATACTA
*
28048191 AATAATA
1 AATACTA
28048198 AATACTA
1 AATACTA
28048205 AATACTA
1 AATACTA
28048212 AATAC
1 AATAC
28048217 GAAACGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:28051556 original size:89 final size:89
Alignment explanation
Indices: 28051445--28051622 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
28051435 CCAAGATTTC
*
28051445 AATCCTACTCAGGCTCAGATTAATAATAAGGAAACAGCGCTCAAAGGGTCCAATTCAGTAAGGCC
1 AATCCTACTCAGGCCCAGATTAATAATAAGGAAACAGCGCTCAAAGGGTCCAATTCAGTAAGGCC
28051510 AGTTGGGCTGATAAAGCATTGAAG
66 AGTTGGGCTGATAAAGCATTGAAG
*
28051534 AATCCTGCTCAGGCCCAGATTAATAATAAGGAAACAGCGCTCAAAGGGTCCAATTCAGTAAGGCC
1 AATCCTACTCAGGCCCAGATTAATAATAAGGAAACAGCGCTCAAAGGGTCCAATTCAGTAAGGCC
28051599 AGTTGGGCTGATAAAGCATTGAAG
66 AGTTGGGCTGATAAAGCATTGAAG
28051623 GGCCCAATTC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (89 bp):
AATCCTACTCAGGCCCAGATTAATAATAAGGAAACAGCGCTCAAAGGGTCCAATTCAGTAAGGCC
AGTTGGGCTGATAAAGCATTGAAG
Found at i:28057171 original size:20 final size:18
Alignment explanation
Indices: 28057134--28057176 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
28057124 CTATAACAAC
28057134 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
28057151 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
28057171 TTACAA
1 TCACAA
28057177 ACTTTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:28059929 original size:28 final size:28
Alignment explanation
Indices: 28059896--28059956 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
28059886 TCCATGGCCT
*
28059896 ATGTCCCTTACACGGCCTCGACACGCCC
1 ATGTCCCTCACACGGCCTCGACACGCCC
*
28059924 GTGTCCCTCACACGGCCTCGACACGCCC
1 ATGTCCCTCACACGGCCTCGACACGCCC
28059952 ATGTC
1 ATGTC
28059957 TTAGCCCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.16, C:0.46, G:0.20, T:0.18
Consensus pattern (28 bp):
ATGTCCCTCACACGGCCTCGACACGCCC
Found at i:28061938 original size:47 final size:47
Alignment explanation
Indices: 28061820--28061979 Score: 139
Period size: 45 Copynumber: 3.4 Consensus size: 47
28061810 ATTGACGGAT
** * * * *
28061820 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTA--AGGC
1 AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCACTAGAC
* * ** *
28061865 AAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCGGCACT-GATT
1 AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCACTAGA-C
** *
28061912 AAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCACATCAAGACATGGCATCGGCACT-AGAC
28061960 AAGGATACCATGTAAGACCA
1 AAGGATACCATGTAAGACCA
28061980 TGTTTGGAAC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
45 36 0.38
46 1 0.01
47 36 0.38
48 19 0.20
49 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (47 bp):
AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCACTAGAC
Found at i:28062041 original size:95 final size:91
Alignment explanation
Indices: 28061817--28062049 Score: 227
Period size: 95 Copynumber: 2.5 Consensus size: 91
28061807 GGAATTGACG
* * * * *
28061817 GATAAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGGCAAGGATCCCGTGTAAGA
1 GATAAGGATACCATGTAAGACCATGTCAAGATATGGCATTGGTAAGACAAGGATACCATGTAAGA
*
28061882 CCATGTCAAGACATGGCATCGGCACT
66 CCATGTCAAGACATGGCATCGGCACA
** *
28061908 GATTAAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGACAAGGATACCATG
1 GA-TAAGGA-TACCATGTAAGACCATGTCAAGATATGGCATTGG---TAAGACAAGGATACCATG
*** * *
28061972 TAAGACCATGTTTGGAACATGGCATTTGGTA-A
61 TAAGACCATGTCAAG-ACATGGCA-TCGGCACA
* * * *
28062004 GATAAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAG
1 GATAAGGATACCATGTAAGACCATGTCAAGATATGGCATTGGTAAG
28062050 TTCTATAAGG
Statistics
Matches: 113, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
91 2 0.02
92 37 0.33
93 1 0.01
94 1 0.01
95 58 0.51
96 10 0.09
97 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (91 bp):
GATAAGGATACCATGTAAGACCATGTCAAGATATGGCATTGGTAAGACAAGGATACCATGTAAGA
CCATGTCAAGACATGGCATCGGCACA
Found at i:28062071 original size:54 final size:54
Alignment explanation
Indices: 28062007--28062147 Score: 255
Period size: 54 Copynumber: 2.6 Consensus size: 54
28061997 TTGGTAAGAT
*
28062007 AAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
*
28062061 AAGGAAATCATGTAAGACCATGCCAAGATATGGCATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
*
28062115 AAGGAAATCATGTAAGACCATGCCAAGGCATGG
1 AAGGAAATCATGTAAGACCATGCCAAGGTATGG
28062148 AAATCATGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (54 bp):
AAGGAAATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGC
Found at i:28062143 original size:29 final size:29
Alignment explanation
Indices: 28062110--28062227 Score: 122
Period size: 29 Copynumber: 4.2 Consensus size: 29
28062100 TAAGTTCTAT
28062110 AAGGCAAGGAAATCATGTAAGACCATGCC
1 AAGGCAAGGAAATCATGTAAGACCATGCC
*
28062139 AAGGCATGGAAATCATGTAAGACCATGCC
1 AAGGCAAGGAAATCATGTAAGACCATGCC
* * * *
28062168 AAGGCATGG-CAT--TGATAAGTTCTAT---
1 AAGGCAAGGAAATCATG-TAAG-ACCATGCC
*
28062193 AAGGCAAGGAAATCATGTGAGACCATGCC
1 AAGGCAAGGAAATCATGTAAGACCATGCC
28062222 AAGGCA
1 AAGGCA
28062228 TGGCATTGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
25 8 0.11
26 7 0.10
27 7 0.10
28 7 0.10
29 43 0.60
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (29 bp):
AAGGCAAGGAAATCATGTAAGACCATGCC
Found at i:28062153 original size:83 final size:83
Alignment explanation
Indices: 28062056--28062230 Score: 314
Period size: 83 Copynumber: 2.1 Consensus size: 83
28062046 TAAGTTCTAT
* *
28062056 AAGGCAAGGAAATCATGTAAGACCATGCCAAGATATGGCATTGATAAGTTCTATAAGGCAAGGAA
1 AAGGCATGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAA
28062121 ATCATGTAAGACCATGCC
66 ATCATGTAAGACCATGCC
*
28062139 AAGGCATGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAA
1 AAGGCATGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAA
*
28062204 ATCATGTGAGACCATGCC
66 ATCATGTAAGACCATGCC
28062222 AAGGCATGG
1 AAGGCATGG
28062231 CATTGATAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 88 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (83 bp):
AAGGCATGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAA
ATCATGTAAGACCATGCC
Found at i:28062198 original size:54 final size:54
Alignment explanation
Indices: 28062139--28062386 Score: 320
Period size: 54 Copynumber: 4.6 Consensus size: 54
28062129 AGACCATGCC
*
28062139 AAGGCATGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
1 AAGGCAAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
*
28062193 AAGGCAAGGAAATCATGTGAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
1 AAGGCAAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
* * * * *
28062247 AAGGTAAGGAAATCATGTAAGACTATGTCAAGACATGGCATTGATGAGTTACTAT
1 AAGGCAAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTAT
*** * *
28062302 AAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-AT
1 AAGGC-AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
* * * *
28062355 AAGGCAAGGATACCACGTAAGACCATGTCAAG
1 AAGGCAAGGAAATCATGTAAGACCATGCCAAG
28062387 ACATAGAAAT
Statistics
Matches: 172, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
52 4 0.02
53 26 0.15
54 97 0.56
55 41 0.24
56 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGCAAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTAT
Found at i:28062259 original size:137 final size:137
Alignment explanation
Indices: 28062013--28062284 Score: 472
Period size: 137 Copynumber: 2.0 Consensus size: 137
28062003 AGATAAGGAT
*
28062013 ATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
1 ATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
* *
28062078 CCATGCCAAGATATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGCCAAGG
66 CCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGCCAAGA
28062143 CATGGAA
131 CATGGAA
*
28062150 ATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTGAGA
1 ATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
* * * *
28062215 CCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAAGGAAATCATGTAAGACTATGTCAAGA
66 CCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGCCAAGA
28062280 CATGG
131 CATGG
28062285 CATTGATGAG
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
137 127 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (137 bp):
ATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGA
CCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACCATGCCAAGA
CATGGAA
Found at i:28072175 original size:47 final size:48
Alignment explanation
Indices: 28072102--28072224 Score: 160
Period size: 47 Copynumber: 2.6 Consensus size: 48
28072092 TATAATACCA
*
28072102 ATGCCATGTCCCAGACATGGTCTTACAATGGCTCATC-AA-TCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACAATGGCT-ATCAAACTCAAGCCG
* * * *
28072149 ATGCCATGTCCCAGACATGGTATTACACTGGCTATCGAAACTGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACAATGGCTATC-AAACTCAAGCCG
*
28072198 ACGCCATGTCCCAGACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
28072225 CTAGCTCTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 3 0.05
47 31 0.47
48 2 0.03
49 30 0.45
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACAATGGCTATCAAACTCAAGCCG
Found at i:28072216 original size:49 final size:47
Alignment explanation
Indices: 28072104--28072231 Score: 159
Period size: 49 Copynumber: 2.7 Consensus size: 47
28072094 TAATACCAAT
* * *
28072104 GCCATGTCCCAGACATGGTCTTACAATGGCTCATCAATCAAGTCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCATCAATCAAGCCGAC
* * *
28072151 GCCATGTCCCAGACATGGTATTACACTGGCT-ATCGAAACTGAGGCCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGGCTCATC--AA-TCAAGCCGAC
*
28072200 GCCATGTCCCAGACATGGTCTTACACTAGCTC
1 GCCATGTCCCAGACATGGTCTTACACTGGCTC
28072232 TCATATATTC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 3 0.04
47 29 0.42
48 2 0.03
49 35 0.51
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCTCATCAATCAAGCCGAC
Found at i:28072267 original size:50 final size:49
Alignment explanation
Indices: 28072194--28072370 Score: 160
Period size: 48 Copynumber: 3.7 Consensus size: 49
28072184 CGAAACTGAG
* * *
28072194 GCCGACGCCATGTCCCAGACATGGTCTTACACTAG-C-TCTCATATATTCGT
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGACACCTC-TATA--CGT
* *
28072244 GCCGAT-CTCATGTCCTAGACATGGTCTCACAC-CGACACCTCTATACGT
1 GCCGATGC-CATGTCCTAGACATGGTCTTACACTAGACACCTCTATACGT
* *
28072292 GCCGATGCCATGTCTTAGACATGGTCTTACACT-GACACATCT-T--GT
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGACACCTCTATACGT
28072337 AGCCGATG-CATGTCCGTA-ACAT-GTCTTACACTAG
1 -GCCGATGCCATGTCC-TAGACATGGTCTTACACTAG
28072371 CTCTCACAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
44 10 0.09
45 13 0.12
46 9 0.08
47 1 0.01
48 39 0.35
49 3 0.03
50 32 0.29
51 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (49 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTAGACACCTCTATACGT
Found at i:28074058 original size:19 final size:19
Alignment explanation
Indices: 28074034--28074079 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
28074024 TGATTTATTC
28074034 TAAGATTTATCTA-CATAAA
1 TAAGATTTATCTATC-TAAA
28074053 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTATCTAAA
28074072 TAA-ATTTA
1 TAAGATTTA
28074080 AAATATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (19 bp):
TAAGATTTATCTATCTAAA
Found at i:28075780 original size:42 final size:40
Alignment explanation
Indices: 28075733--28075897 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 40
28075723 ATTAATGTTA
28075733 ATGAGACTAGATGTAAGACCATATCTGGGATATGGCATCATT
1 ATGAGACTAG-TGTAAGACCATATCTGGGATATGGCATCA-T
* * *
28075775 ATGAGACTACGTATAAGACCATATCTGGGATATGACATTGAT
1 ATGAGACTA-GTGTAAGACCATATCTGGGATATGGCA-TCAT
* * * * * *
28075817 ATAAGATTTCGTGTAAGACCATAGCTGGGCTATTAGCATCGAT
1 ATGAGA-CTAGTGTAAGACCATATCTGGGATA-TGGCATC-AT
* * * * *
28075860 ACGAGATTACATGTTAGACCATATTTGGGATATGGCAT
1 ATGAGACTA-GTGTAAGACCATATCTGGGATATGGCAT
28075898 TAGTATGGTA
Statistics
Matches: 96, Mismatches: 21, Indels: 12
0.74 0.16 0.09
Matches are distributed among these distances:
42 66 0.69
43 30 0.31
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (40 bp):
ATGAGACTAGTGTAAGACCATATCTGGGATATGGCATCAT
Found at i:28081478 original size:42 final size:42
Alignment explanation
Indices: 28081419--28081502 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
28081409 TAACCTAATT
* * *
28081419 GGGAAAATGATTCCCTTATTCTAGTAAACTACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCTAATAAACAACTAAAAGATAA
28081461 GGGAAAATAATTCCCTTATTCTAATAAACAACTAAAAGATAA
1 GGGAAAATAATTCCCTTATTCTAATAAACAACTAAAAGATAA
28081503 AATAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (42 bp):
GGGAAAATAATTCCCTTATTCTAATAAACAACTAAAAGATAA
Found at i:28081510 original size:42 final size:41
Alignment explanation
Indices: 28081421--28081515 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
28081411 ACCTAATTGG
* * **
28081421 GAAAATGATTCCCTTATTCTAGTAAACTACTAAAAGATAAGG
1 GAAAAT-ATTCCCTTATTCTAATAAACAACTAAAAGATAAAA
28081463 GAAAATAATTCCCTTATTCTAATAAACAACTAAAAGATAAAA
1 GAAAAT-ATTCCCTTATTCTAATAAACAACTAAAAGATAAAA
*
28081505 TAAAATATTCC
1 GAAAATATTCC
28081516 TAGAATATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 5 0.11
42 42 0.89
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (41 bp):
GAAAATATTCCCTTATTCTAATAAACAACTAAAAGATAAAA
Done.