Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 135 of 211
Found at i:39756978 original size:200 final size:201
Alignment explanation
Indices: 39756559--39757080 Score: 780
Period size: 200 Copynumber: 2.6 Consensus size: 201
39756549 AATAATTCAA
* * * *
39756559 TTTCTCAAATCACATATATATAATCTATTCAATTAAATACATACATTTAAATACTCAATTTGCAT
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* * ** * *
39756624 ACCTTCTCAAATCACATATATATAATTGATTTAATTAAATACATACATTTAAATACTCAATTCGC
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
* * *
39756689 ATACTTTCTCAAATCATATACCTATAATCAATTCAATTAAATACATACATTTAATTACTAAATTC
131 ATACTTTCTCAAATCACATACCTACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
39756754 GCATAC
196 GCATAC
* * * *
39756760 TTTCT-TAATCACATACATACAATCGATTTAATTAAATACATACATTTAAATACTCAATTCGCAT
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* *
39756824 ACTTTCTCAAATCATATACATATAATCAATTCAATTAAATACATACATTTAATTACTAAATTCGC
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
* * * *
39756889 ATACTTTCTC-AATCACATACCTACAATCGATTTAGTTAAATACATACATTTAAATACTCAATTC
131 ATACTTTCTCAAATCACATACCTACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
39756953 GCATAC
196 GCATAC
* *
39756959 TTTCTCAAATCATATACATATAATCAATTAAATTAAATACATACATTTAATTACTCAATTCGC-T
1 TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
* *
39757023 ACTTTCTCAAATCACATACATATAATCAATTGAATTAAATACATACATTTAAAAACTA
66 ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTA
39757081 TTGCAATTGT
Statistics
Matches: 289, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
199 113 0.39
200 171 0.59
201 5 0.02
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (201 bp):
TTTCTCAAATCACATACATATAATCAATTAAATTAAATACATACATTTAAATACTCAATTCGCAT
ACTTTCTCAAATCACATACATATAATCAATTCAATTAAATACATACATTTAAATACTAAATTCGC
ATACTTTCTCAAATCACATACCTACAATCAATTCAATTAAATACATACATTTAAATACTAAATTC
GCATAC
Found at i:39759994 original size:28 final size:28
Alignment explanation
Indices: 39759927--39760058 Score: 203
Period size: 28 Copynumber: 4.8 Consensus size: 28
39759917 AACAGTAGAG
*
39759927 TGTGGGCCTTAGCCCAATACAGT-ACAG
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
39759954 TGTGGGCCTTAGCCCAATACAATAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
* *
39759982 TGTGGGCCTTAGCCCAATGCAGTAATAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
39760010 TGTGGGTCTTAGCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAATACAGTAACAA
*
39760038 TGTGGGCCTTCGCCCAATACA
1 TGTGGGCCTTAGCCCAATACA
39760059 ATATCGGTAC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
27 22 0.23
28 72 0.77
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATACAGTAACAA
Found at i:39760199 original size:26 final size:26
Alignment explanation
Indices: 39760169--39760269 Score: 157
Period size: 26 Copynumber: 3.9 Consensus size: 26
39760159 AACACACCAA
* * *
39760169 TATCGCAGAAAAGCTGCCAATAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
39760195 TATCGCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
39760221 TATCTCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
39760247 TATCGCAGCAAAGCTGCCAGTAA
1 TATCGCAGCAAAGCTGCCAGTAA
39760270 TAGTGTACTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 68 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:39760503 original size:27 final size:27
Alignment explanation
Indices: 39760439--39760724 Score: 257
Period size: 27 Copynumber: 10.3 Consensus size: 27
39760429 GGGTATAATA
* *
39760439 GTCATATTACCCTATAGGGGGTATTTCA
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
39760467 ATCATTTTACCCTATGGGAGTAATTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
39760494 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
39760521 GTCATTTTACCTTATGGGTGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
39760548 ATCATTTTACTCTACGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
39760575 GTCATTTTACCCTACGAGGCTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
**** **
39760602 GTCATTTACCCTAAACCCTACAAAGGTATTTTA
1 GTCATTT----T--ACCCTATGGGGGTATTTCG
*
39760635 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
39760662 GTTATTTTACACTACGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
39760689 GTCATTTTACCCTATGGGAGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
39760716 GTCATTTTA
1 GTCATTTTA
39760725 TTCTACAGGG
Statistics
Matches: 210, Mismatches: 42, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
27 173 0.82
28 13 0.06
29 1 0.00
31 1 0.00
33 22 0.10
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:39760713 original size:114 final size:114
Alignment explanation
Indices: 39760512--39760722 Score: 282
Period size: 114 Copynumber: 1.9 Consensus size: 114
39760502 ACCCTATGGG
* * *
39760512 GGTATTTCGGTCATTTTACCTTATGGGTGTATTTCGATCATTTTACTCTACGGGGGTATTTCAGT
1 GGTATTTCAGTCATTTTACCCTATGGGTGTATTTCGATCATTTTACACTACGGGGGTATTTCAGT
**
39760577 CATTTTACCCTACGAGGCTATTTTGGTCATTTACCCTAAACCCTACAAA
66 CATTTTACCCTACGAGGCTATTTCAGTCATTTACCCTAAACCCTACAAA
* * * **
39760626 GGTATTTTAGTCATTTTACCCTATAGGG-GTATTTCGGTTATTTTACACTACGGGGGTATTTTGG
1 GGTATTTCAGTCATTTTACCCTAT-GGGTGTATTTCGATCATTTTACACTACGGGGGTATTTCAG
* *
39760690 TCATTTTACCCTATG-GGAGTATTTCAGTCATTT
65 TCATTTTACCCTACGAGG-CTATTTCAGTCATTT
39760723 TATTCTACAG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 2 0.02
114 78 0.94
115 3 0.04
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (114 bp):
GGTATTTCAGTCATTTTACCCTATGGGTGTATTTCGATCATTTTACACTACGGGGGTATTTCAGT
CATTTTACCCTACGAGGCTATTTCAGTCATTTACCCTAAACCCTACAAA
Found at i:39778106 original size:79 final size:81
Alignment explanation
Indices: 39777970--39778154 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39777960 TTGAATGATG
*
39777970 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39778034 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39778049 TTCCGGGCTAAG-CCCGAAGGCATTTGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39778111 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39778129 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39778155 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.64
80 32 0.35
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39778168 original size:40 final size:40
Alignment explanation
Indices: 39777971--39778154 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
39777961 TGAATGATGT
* * * *
39777971 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39778011 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
39778051 CCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39778089 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39778130 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39778155 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39778176 original size:79 final size:79
Alignment explanation
Indices: 39778023--39778187 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
39778013 GGACTAAGAT
* ***
39778023 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39778088 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39778102 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39778165 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39778181 CCGAAGG
1 CCGAAGG
39778188 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39785881 original size:23 final size:26
Alignment explanation
Indices: 39785835--39785881 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
39785825 GAAAATGAAA
*
39785835 TAGAATGATGGCATTGATTTTATTGT
1 TAGAATGATGGCATTGATTATATTGT
39785861 TAGAATG-T-GCA-TGATTATATT
1 TAGAATGATGGCATTGATTATATT
39785882 TGAATGCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 1 0.05
26 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (26 bp):
TAGAATGATGGCATTGATTATATTGT
Found at i:39790987 original size:27 final size:27
Alignment explanation
Indices: 39790953--39791129 Score: 194
Period size: 27 Copynumber: 6.6 Consensus size: 27
39790943 TTAATTGTAC
*
39790953 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39790980 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39791006 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39791034 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39791061 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * * *
39791088 AGCAGTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39791115 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39791130 GACTCAATAT
Statistics
Matches: 126, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39791014 original size:54 final size:55
Alignment explanation
Indices: 39790953--39791129 Score: 216
Period size: 54 Copynumber: 3.3 Consensus size: 55
39790943 TTAATTGTAC
* **
39790953 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * ** *
39791008 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
39791061 AGCACTAAGTGTGCGATTTGATTACGTAGCAGTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
*
39791115 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39791130 GACTCAATAT
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 103 0.99
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:39791097 original size:81 final size:81
Alignment explanation
Indices: 39790954--39791108 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 81
39790944 TAATTGTACA
* * *
39790954 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
39791019 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** * *
39791035 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAGTAAGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTG
*
39791099 TGCGAGTTGA
65 TGCGAATTGA
39791109 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
80 1 0.02
81 64 0.98
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39791120 original size:81 final size:81
Alignment explanation
Indices: 39790950--39791129 Score: 218
Period size: 81 Copynumber: 2.2 Consensus size: 81
39790940 GGATTAATTG
* * *
39790950 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39791015 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** * *
39791031 TGCGGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAGTA
1 TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTA
* **
39791095 AGTGTGCGAGTTGATTA
65 AGTGTGCGAATTGACCA
* *
39791112 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39791130 GACTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 1 0.01
81 81 0.99
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39802149 original size:28 final size:28
Alignment explanation
Indices: 39802107--39802201 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
39802097 ATACAACATG
* * * *
39802107 CAGTAGCAGTCTGGGCCTGAGCCCTATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
*
39802135 CAGCAACAGTATGGGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
* * * *
39802163 TAGTAACAATGTGAGCCTTAGCCCAATA
1 CAGTAACAGTATGGGCCTTAGCCCAATA
39802191 CAGTAACAGTA
1 CAGTAACAGTA
39802202 CAATGCAGTA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (28 bp):
CAGTAACAGTATGGGCCTTAGCCCAATA
Found at i:39802366 original size:26 final size:26
Alignment explanation
Indices: 39802307--39802382 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
39802297 CACCAATATT
* * * *
39802307 GCAGCAAGGCTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAACAGTAAC
39802333 GCAGCAAAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAGTAACAGTAAC
* * *
39802359 GCATCAAAGTTTCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
39802383 TATGTGGCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAC
Found at i:39802633 original size:27 final size:27
Alignment explanation
Indices: 39802562--39802636 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
39802552 TATAACAGTT
* * *
39802562 ATTTTACTCTTCAGGGGCATTTCGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
* *
39802589 ATTTTACCCTTCGAGGGTATTTTGGTC
1 ATTTTACCCTTCGGGGGTATTTCGGTC
39802616 ATTTTACCCTTCGGGGGTATT
1 ATTTTACCCTTCGGGGGTATT
39802637 GAGATGCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGGTC
Found at i:39802686 original size:23 final size:23
Alignment explanation
Indices: 39802648--39802698 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39802638 AGATGCATAT
* *
39802648 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
39802671 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
39802694 AGTAA
1 TGTAA
39802699 GAAAGTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:39805770 original size:50 final size:54
Alignment explanation
Indices: 39805668--39805784 Score: 152
Period size: 56 Copynumber: 2.2 Consensus size: 54
39805658 TGTGAGCCAG
* ** *
39805668 TGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGTTTATGAGAGGTCCTA
1 TGTAAGACCATATTTGGGACATGGCATTGGCATCACCGAG--TATGAGAGGTCCCA
39805724 TGTAAGACCATATTTGGGACATGGCATT-G-A-CACCGAG-ATGAGAGGTCCCA
1 TGTAAGACCATATTTGGGACATGGCATTGGCATCACCGAGTATGAGAGGTCCCA
39805774 TGTAAGACCAT
1 TGTAAGACCAT
39805785 GTCTGTGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 23 0.40
53 5 0.09
54 1 0.02
55 1 0.02
56 27 0.47
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (54 bp):
TGTAAGACCATATTTGGGACATGGCATTGGCATCACCGAGTATGAGAGGTCCCA
Found at i:39812987 original size:25 final size:25
Alignment explanation
Indices: 39812941--39812990 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
39812931 AAAAAAATTC
39812941 CTATTATTATTATTATTTATTTTTA
1 CTATTATTATTATTATTTATTTTTA
39812966 CTATT-TTATT-TTATTTTCATTTTTA
1 CTATTATTATTATTA-TTT-ATTTTTA
39812991 TTTTTGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
CTATTATTATTATTATTTATTTTTA
Found at i:39812993 original size:6 final size:6
Alignment explanation
Indices: 39812944--39812995 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
39812934 AAAATTCCTA
* *
39812944 TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT TCATTT TTATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
39812994 TT
1 TT
39812996 GCAGGAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 23 0.59
7 6 0.15
8 5 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:39815487 original size:50 final size:50
Alignment explanation
Indices: 39815406--39815875 Score: 568
Period size: 50 Copynumber: 9.4 Consensus size: 50
39815396 ACACCCATCA
39815406 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
39815456 GTCTGGGACATGGCATTGGCACTGAGGTGAGAGGTCCCATGTAAGACTAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* *
39815506 GTCTAGGACATGGCCTTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * *
39815556 GTCCGGGACATGGCGTTGGCATCAAGATGAGAGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* *
39815606 GTCTGGGACATGGCATTTGCACCGAGATGAGCGGTCCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * *
39815656 GTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTTCCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * **
39815706 GTCTAGGACATGG-AGTTGGCACCGGGATGAGAGGCCCCCCGTAAGACCAT
1 GTCTGGGACATGGCA-TTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * ** * *
39815756 GTTTGGGACATGGCATGGGCACCGATATGAGAACTCTCATATAAGACCAT
1 GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
* * * * * * ** *
39815806 ATCTAGGATATGGCATTGGCA--GTACAGGAAACATCTCATGTAAGACCAT
1 GTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCCCATGTAAGACCAT
* *
39815855 GTTTGGGACATGGCTTTGGCA
1 GTCTGGGACATGGCATTGGCA
39815876 TGTTATTATC
Statistics
Matches: 357, Mismatches: 60, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
48 1 0.00
49 36 0.10
50 319 0.89
51 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
GTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
Found at i:39817390 original size:23 final size:23
Alignment explanation
Indices: 39817352--39817402 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39817342 GGGGGAGAAA
* *
39817352 TGTAATATCCCTAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
39817375 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
39817398 AGTAA
1 TGTAA
39817403 GAAAGTAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:39822905 original size:16 final size:17
Alignment explanation
Indices: 39822878--39822912 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39822868 ATACCCCTTT
39822878 CACCTATTCATTCAACA
1 CACCTATTCATTCAACA
*
39822895 CACCT-TTCATTCCACA
1 CACCTATTCATTCAACA
39822911 CA
1 CA
39822913 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCTATTCATTCAACA
Found at i:39847720 original size:12 final size:13
Alignment explanation
Indices: 39847696--39847724 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39847686 GGGCTATAAC
39847696 TATTGCATTTATT
1 TATTGCATTTATT
39847709 TATTGC-TTTATT
1 TATTGCATTTATT
39847721 TATT
1 TATT
39847725 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:39856800 original size:22 final size:21
Alignment explanation
Indices: 39856775--39856818 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39856765 TGATAAACTT
39856775 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
39856797 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
39856818 T
1 T
39856819 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:39861176 original size:50 final size:51
Alignment explanation
Indices: 39861113--39861289 Score: 205
Period size: 50 Copynumber: 3.4 Consensus size: 51
39861103 CAATGTCATA
* **
39861113 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
** * *
39861163 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG-CCAACTCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
** *
39861213 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TCGGTG-T-CCAATTCCATG
39861269 TCCCAGACATGGTCTTACATG
1 TCCCAGACATGGTCTTACATG
39861290 AGATCTCTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 70 0.66
53 4 0.04
56 30 0.28
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (51 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGTCCAATTCCATG
Found at i:39896196 original size:50 final size:50
Alignment explanation
Indices: 39896090--39896335 Score: 235
Period size: 50 Copynumber: 4.8 Consensus size: 50
39896080 TTTGGGTGAT
* * *
39896090 GAGGTCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGAGGTTATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGA
39896146 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
** * * * *
39896196 GAGGTCCCCCGTAAGACCGTGTCTGGGACATGGCATGGGAACCGATATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
** * * * * *
39896246 GAAATCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGA
* ** *
39896295 AACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39896336 TGTTATTATC
Statistics
Matches: 162, Mismatches: 27, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 79 0.49
52 1 0.01
53 2 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
Found at i:39897880 original size:32 final size:32
Alignment explanation
Indices: 39897839--39897955 Score: 164
Period size: 32 Copynumber: 3.7 Consensus size: 32
39897829 GTGATGCTAA
39897839 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATAGTACCGTTAC
**
39897871 TGATGGCTTTGTGTTGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
*
39897903 TGATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
* * *
39897935 CGATGGCTGTGTGTCGATCAT
1 TGATGGCTTTGTGCCGATCAT
39897956 TTCACTATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
32 75 0.99
33 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATAGTACCGTTAC
Found at i:39898017 original size:32 final size:31
Alignment explanation
Indices: 39897839--39898019 Score: 157
Period size: 32 Copynumber: 5.7 Consensus size: 31
39897829 GTGATGCTAA
39897839 TGATGGCTTTGTGCC-AGTCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGA-TCATA-TACCGTTAC
**
39897871 TGATGGCTTTGTGTTGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
39897903 TGATGGCTTTGTGCCGATCATATTACCGTTAC
1 TGATGGCTTTGTGCCGATCATA-TACCGTTAC
* * * * **
39897935 CGATGGCTGTGTGTCGATCATTTCACTATTAC
1 TGATGGCTTTGTGCCGATCATAT-ACCGTTAC
* * * * * * *
39897967 AGATTGCTGTGTGTCGGTCATATCACTGCTAC
1 TGATGGCTTTGTGCCGATCATAT-ACCGTTAC
*
39897999 TGATGGCTTTGTGCCGGTCAT
1 TGATGGCTTTGTGCCGATCAT
39898020 GATTCCTAAC
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 1 0.01
32 124 0.98
33 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (31 bp):
TGATGGCTTTGTGCCGATCATATACCGTTAC
Found at i:39910078 original size:29 final size:29
Alignment explanation
Indices: 39910045--39910229 Score: 106
Period size: 29 Copynumber: 6.4 Consensus size: 29
39910035 TGGTCGACCA
* * *
39910045 ATGAAAAGGGATAGCTTTGGTTCTCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
**
39910074 ATGAAAACAGATAGCTTCGATTATCGATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
* * ** * *
39910103 ATGAAAAGGGAT-GGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGATTATCGATT
* * ** ** *
39910132 ATGAAAATGGAT-GGTAAT-GACCATAAAAT
1 ATGAAAAGGGATAGCT--TCGATTATCGATT
*
39910161 ATGAAAAGGGATAGCTTCGATTATCAATT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
* * ** *
39910190 ATGAAAAGGGATGGTTTCGACCATCGAAT
1 ATGAAAAGGGATAGCTTCGATTATCGATT
39910219 ATGAAAAGGGA
1 ATGAAAAGGGA
39910230 CAGTTACTAC
Statistics
Matches: 122, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.02
29 117 0.96
30 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGATTATCGATT
Found at i:39910164 original size:58 final size:58
Alignment explanation
Indices: 39910102--39910244 Score: 146
Period size: 58 Copynumber: 2.5 Consensus size: 58
39910092 GATTATCGAT
* *
39910102 TATGAAAAGGGAT-GGTGACGACCATCAACTATGAAAATGGATGGTAAT-GACCATAAAA
1 TATGAAAAGGGATAGCT-ACGACCATCAACTATGAAAAGGGATGGT-ATCGACCATAAAA
* ** * * **
39910160 TATGAAAAGGGATAGCTTCGATTATCAATTATGAAAAGGGATGGTTTCGACCATCGAA
1 TATGAAAAGGGATAGCTACGACCATCAACTATGAAAAGGGATGGTATCGACCATAAAA
* * *
39910218 TATGAAAAGGGACAGTTACTACCATCA
1 TATGAAAAGGGATAGCTACGACCATCA
39910245 TTTAGAACAC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 1 0.01
58 65 0.96
59 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (58 bp):
TATGAAAAGGGATAGCTACGACCATCAACTATGAAAAGGGATGGTATCGACCATAAAA
Found at i:39917521 original size:51 final size:51
Alignment explanation
Indices: 39917391--39917575 Score: 178
Period size: 51 Copynumber: 3.6 Consensus size: 51
39917381 AGTTGCTAGG
* * * * * *
39917391 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATG-ATA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATGAAAATGA
* ***
39917441 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAAT-GA
* * * * * * *
39917492 TCACGTGTGTAGTATTTTGTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
39917543 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
39917576 TGAACCGGGT
Statistics
Matches: 107, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 2 0.02
50 36 0.34
51 67 0.63
52 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
Found at i:39917583 original size:102 final size:101
Alignment explanation
Indices: 39917391--39917583 Score: 291
Period size: 102 Copynumber: 1.9 Consensus size: 101
39917381 AGTTGCTAGG
* *
39917391 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAAAGGTCACATGTGTAGTAC
*
39917456 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
* *
39917492 TCACGTGTGTAGTATTTTGTGCAGGCTACTACGTGTA-TCGG-ATGAAAATGGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACT-GGAATG-AAA-GGTCACATGTGTAG
*
39917555 TACTATGTGCAGGCTACTATGTGAACCGG
63 TACTATGTGCAGGCTACTATGCGAACCGG
39917584 GTATCATTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
100 4 0.05
101 39 0.47
102 40 0.48
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTGGAATGAAAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:39922253 original size:39 final size:40
Alignment explanation
Indices: 39922148--39922393 Score: 250
Period size: 39 Copynumber: 6.2 Consensus size: 40
39922138 AAAATGAAGA
* * * * *
39922148 AGTGCCCCTGAATGCACATATGTGCCCCTGTTTGCACTTT
1 AGTGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
* * * *
39922188 GGTGCCTCTAAACGCACATCTATGCCCCTATTTACACTTC
1 AGTGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
* * *
39922228 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTC
1 AGTGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
* * *
39922267 -GATGCCCCTGAATGCACATCTATG-CCTTGTTTGCACTTC
1 AG-TGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
* * *
39922306 AGTGCCCCTAAATGCACATTTGTGCCCCTATTTTCACTTC
1 AGTGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
* *
39922346 -GCTGCCCCTGAATGCACATCTATG-CCTTATTTGCACTTC
1 AG-TGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
*
39922385 GGTGCCCCT
1 AGTGCCCCT
39922394 GATCGCACAT
Statistics
Matches: 169, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.01
39 85 0.50
40 83 0.49
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.33
Consensus pattern (40 bp):
AGTGCCCCTAAATGCACATCTATGCCCCTATTTGCACTTC
Found at i:39922262 original size:20 final size:20
Alignment explanation
Indices: 39922239--39922434 Score: 77
Period size: 20 Copynumber: 9.9 Consensus size: 20
39922229 GTGCCCTAAA
*
39922239 TGCACATTTGTGCCCCTGTT
1 TGCACATTTGTGCCCCTGAT
* *
39922259 TGCAC-TTCGATGCCCCTGAA
1 TGCACATTTG-TGCCCCTGAT
* * * *
39922279 TGCACATCTATG-CCTTGTT
1 TGCACATTTGTGCCCCTGAT
* * *
39922298 TGCAC-TTCAGTGCCCCTAAA
1 TGCACATT-TGTGCCCCTGAT
39922318 TGCACATTTGTGCCCCT-ATT
1 TGCACATTTGTGCCCCTGA-T
* * *
39922338 TTCAC-TTCGCTGCCCCTGAA
1 TGCACATTTG-TGCCCCTGAT
* * *
39922358 TGCACATCTATG--CCTTATT
1 TGCACATTTGTGCCCCTGA-T
*
39922377 TGCAC-TTCGGTGCCCCTGAT
1 TGCACATT-TGTGCCCCTGAT
* ** *
39922397 CGCACATTCATGCTCCTGAT
1 TGCACATTTGTGCCCCTGAT
39922417 TGCA-ATTTGGTGCCCCTG
1 TGCACATTT-GTGCCCCTG
39922435 TTAAGCATCT
Statistics
Matches: 122, Mismatches: 39, Indels: 30
0.64 0.20 0.16
Matches are distributed among these distances:
18 6 0.05
19 28 0.23
20 77 0.63
21 11 0.09
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (20 bp):
TGCACATTTGTGCCCCTGAT
Found at i:39922394 original size:39 final size:40
Alignment explanation
Indices: 39922149--39922434 Score: 269
Period size: 40 Copynumber: 7.2 Consensus size: 40
39922139 AAATGAAGAA
* * * *
39922149 GTGCCCCTGAATGCACATATGTGCCCCTGTTTGCACTTTG
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* * * * *
39922189 GTGCCTCTAAACGCACATCTATGCCCCTATTTACACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* * * *
39922229 GTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* * * *
39922268 ATGCCCCTGAATGCACATCTATG-CCTTGTTTGCACTTCA
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* * * *
39922307 GTGCCCCTAAATGCACATTTGTGCCCCTATTTTCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* *
39922347 CTGCCCCTGAATGCACATCTATG-CCTTATTTGCACTTCG
1 GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
* * *
39922386 GTGCCCCTG-ATCGCACAT-TCATGCTCCTGA-TTGCAATTTG
1 GTGCCCCTGAAT-GCACATCT-ATGCCCCT-ATTTGCACTTCG
39922426 GTGCCCCTG
1 GTGCCCCTG
39922435 TTAAGCATCT
Statistics
Matches: 199, Mismatches: 41, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
38 3 0.02
39 95 0.48
40 100 0.50
41 1 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGAATGCACATCTATGCCCCTATTTGCACTTCG
Found at i:39922404 original size:79 final size:79
Alignment explanation
Indices: 39922148--39922393 Score: 350
Period size: 79 Copynumber: 3.1 Consensus size: 79
39922138 AAAATGAAGA
* * * * * * *
39922148 AGTGCCCCTGAATGCACATATGTGCCCCTGTTTGCACTTTGGTGCCTCTAAACGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATG-
* *
39922213 CCCTATTTACACTTC
65 CCTTATTTGCACTTC
39922228 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
*
39922292 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* * *
39922306 AGTGCCCCTAAATGCACATTTGTGCCCCTATTTTCACTTCGCTGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
39922371 CTTATTTGCACTTC
66 CTTATTTGCACTTC
*
39922385 GGTGCCCCT
1 AGTGCCCCT
39922394 GATCGCACAT
Statistics
Matches: 150, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 16 0.11
79 130 0.87
80 4 0.03
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:39922431 original size:79 final size:79
Alignment explanation
Indices: 39922148--39922434 Score: 337
Period size: 79 Copynumber: 3.6 Consensus size: 79
39922138 AAAATGAAGA
* * * * * * *
39922148 AGTGCCCCTGAATGCACATATGTGCCCCTGTTTGCACTTTGGTGCCTCTAAACGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGATTGCACTTCGGTGCCCCTGAATGCACATCTATG-
* *
39922213 CCCTATTTACACTTC
65 CCTTATTTGCACTTC
* *
39922228 AGTG-CCCTAAATGCACATTTGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATCTATGC
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGATTGCACTTCGGTGCCCCTGAATGCACATCTATGC
*
39922292 CTTGTTTGCACTTC
66 CTTATTTGCACTTC
* *
39922306 AGTGCCCCTAAATGCACATTTGTGCCCCT-ATTTTCACTTCGCTGCCCCTGAATGCACATCTATG
1 AGTGCCCCTAAATGCACATTTGTGCCCCTGA-TTGCACTTCGGTGCCCCTGAATGCACATCTATG
39922370 CCTTATTTGCACTTC
65 CCTTATTTGCACTTC
* * ** * * *
39922385 GGTGCCCCT-GATCGCACATTCATGCTCCTGATTGCAATTTGGTGCCCCTG
1 AGTGCCCCTAAAT-GCACATTTGTGCCCCTGATTGCACTTCGGTGCCCCTG
39922435 TTAAGCATCT
Statistics
Matches: 180, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
78 18 0.10
79 157 0.87
80 5 0.03
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (79 bp):
AGTGCCCCTAAATGCACATTTGTGCCCCTGATTGCACTTCGGTGCCCCTGAATGCACATCTATGC
CTTATTTGCACTTC
Found at i:39928000 original size:13 final size:13
Alignment explanation
Indices: 39927978--39928008 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39927968 TTGAACATCA
39927978 TTAA-TATGTGTT
1 TTAATTATGTGTT
39927990 TTAATTATGTGTT
1 TTAATTATGTGTT
39928003 TTAATT
1 TTAATT
39928009 TTTACATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (13 bp):
TTAATTATGTGTT
Found at i:39945163 original size:50 final size:50
Alignment explanation
Indices: 39944999--39945170 Score: 193
Period size: 50 Copynumber: 3.4 Consensus size: 50
39944989 GGGAATGAGA
** *
39944999 TCCCATGTAAGACCAAGTCTGGGACATGGCGTAGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCTTGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
* * *
39945049 TCCCATGTAAGA-CTATGTCTGGGACATGGCGTTGGCACCAAGATAAGAGG
1 TCCCATGTAAGACCT-TGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
** * * * **
39945099 TCCCCCGTAAGACCTTGTCTGGGACATGGCATAGGCTCCGATATGAGAAC
1 TCCCATGTAAGACCTTGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
* *
39945149 TCCCATGTATGACCTTATCTGG
1 TCCCATGTAAGACCTTGTCTGG
39945171 AATATCGCAC
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 1 0.01
50 97 0.97
51 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCTTGTCTGGGACATGGCGTAGGCACCGAGATGAGAGG
Found at i:39945659 original size:34 final size:34
Alignment explanation
Indices: 39945616--39945682 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
39945606 TCACCAAGTT
*
39945616 AGTTCGAGGATCACAAGGATGTTGGAGTTCGTCC
1 AGTTCGAGGATCACAAGGATATTGGAGTTCGTCC
39945650 AGTTCGAGGATCACAAGGATATTGGAGTTCGTC
1 AGTTCGAGGATCACAAGGATATTGGAGTTCGTC
39945683 TCACACTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (34 bp):
AGTTCGAGGATCACAAGGATATTGGAGTTCGTCC
Found at i:39947229 original size:50 final size:49
Alignment explanation
Indices: 39947071--39947346 Score: 277
Period size: 50 Copynumber: 5.6 Consensus size: 49
39947061 AAAGCCAAAA
* * ** * *
39947071 CCATGTGCCAGACATGGTCTTACATGGGA--TGTTTTCTGTATTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTG--GTGCCAACG
* * * ** ** * * *
39947120 CCATATCCTAGATATGGTCTTACATAAGATTTCTCATATCGGTGCCCATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-GGTGCCAACG
* * ** * *
39947170 CTATCTCCCAGACATGGTCTTACGGGGGACCTCTCATCTGGATGCGAACA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTGG-TGCCAACG
39947220 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-GGTGCCAACG
*
39947270 CCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTTGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC-TGGTGCCAACG
39947320 CCATGTCCCAGACATGGTCTTACATGG
1 CCATGTCCCAGACATGGTCTTACATGG
39947347 CTTACATATT
Statistics
Matches: 186, Mismatches: 35, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
49 25 0.13
50 153 0.82
51 7 0.04
52 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTGGTGCCAACG
Found at i:39951718 original size:50 final size:50
Alignment explanation
Indices: 39951654--39952223 Score: 798
Period size: 50 Copynumber: 11.4 Consensus size: 50
39951644 ATGCCATATT
* ** * * * * *
39951654 CCAGATATGGTCTTACATGGGAGTTCCCATATCAGTGCCCATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
** ** * *
39951704 AAAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAATGCCACGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * *
39951754 CCAAACATAGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
39951804 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* *
39951854 CCAGACATGGTCTTACATGGGACCTCTCATCTCAGCGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * *
39951904 CCAGACATGGTCTTACATGAGACCTCTCATCTCAGTGCCAATGCCATATC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * * **
39951954 CCAAACATGCTCTTACATGGGACCTCTCATCTCGATGCCAACGCTGTGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* *
39952004 CCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACTCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * *
39952054 CCAGACATGGTCTTACGTGGGACCTCTCATCTCGGTGCCAACGCTATATC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
* * *
39952104 GCAGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
*
39952154 CCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTC
1 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
39952204 CCAGACATGGTCTTACATGG
1 CCAGACATGGTCTTACATGG
39952224 CTCACATATT
Statistics
Matches: 461, Mismatches: 59, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 461 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (50 bp):
CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
Found at i:39951792 original size:100 final size:100
Alignment explanation
Indices: 39951590--39952223 Score: 808
Period size: 100 Copynumber: 6.3 Consensus size: 100
39951580 GATAATAACA
* * ** * * *
39951590 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATTTCCAATGCCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG--GTGCCAATGCCATG
* * ** * * *
39951652 TTCCAGATATGGTCTTACATGGGAGTTCCCATATCAG
64 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** ** *
39951689 TGCCCATGCCATGTCAAAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAATGCCACGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
* * *
39951754 CCAAACATAGTCTTACATGAGACCTCTCATCTCGG
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
39951789 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
*
39951854 CCAGACATGGTCTTACATGGGACCTCTCATCTCAG
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
39951889 CGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCAGTGCCAATGCCATATC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
* * *
39951954 CCAAACATGCTCTTACATGGGACCTCTCATCTCGA
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
39951989 TGCCAACGCTGTGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACT-CCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAA-TGCCATGT
*
39952053 CCCAGACATGGTCTTACGTGGGACCTCTCATCTCGG
65 CCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * *
39952089 TGCCAACGCTATATCGCAGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
*
39952154 CCAGACATGGTCTTACATGGGACCTCTCATCTCAG
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
39952189 TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
39952224 CTCACATATT
Statistics
Matches: 462, Mismatches: 68, Indels: 9
0.86 0.13 0.02
Matches are distributed among these distances:
99 31 0.07
100 424 0.92
101 6 0.01
102 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (100 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTC
CCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39951825 original size:150 final size:150
Alignment explanation
Indices: 39951590--39952222 Score: 824
Period size: 150 Copynumber: 4.2 Consensus size: 150
39951580 GATAATAACA
* * * ** * *
39951590 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTATTTCCAATGCCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCG--GTGCCAATGCCATA
* * ** * * * * * *
39951652 TTCCAGATATGGTCTTACATGGGAGTTCCCATATCAGTGCCCATGCCATGTCAAAGACATGGTCT
64 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGACATGGTCT
** *
39951717 TACGGGGGACCTCTCATCTCGG
129 TACATGGGACCTCTCATCTCAG
* * * * *
39951739 TGCCAATGCCACGTCCCAAACATAGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATATC
*
39951804 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTA
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGACATGGTCTTA
39951869 CATGGGACCTCTCATCTCAG
131 CATGGGACCTCTCATCTCAG
* *
39951889 CGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCAGTGCCAATGCCATATC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATATC
* * * **
39951954 CCAAACATGCTCTTACATGGGACCTCTCATCTCGATGCCAACGCTGTGTCCCAA-ACATGGTCTT
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGT-CCAAGACATGGTCTT
*
39952018 ACATGGGACCTCTCATCTCGG
130 ACATGGGACCTCTCATCTCAG
* * * * *
39952039 TGCCAACTCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCGGTGCCAACGCTATATC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATATC
* * * *
39952104 GCAGACATGATCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAGTCCCAGACATGGTCTTA
66 CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGACATGGTCTTA
39952169 CATGGGACCTCTCATCTCAG
131 CATGGGACCTCTCATCTCAG
39952189 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
39952223 GCTCACATAT
Statistics
Matches: 422, Mismatches: 57, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
149 35 0.08
150 378 0.90
151 8 0.02
152 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (150 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAATGCCATATC
CCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCAAGACATGGTCTTA
CATGGGACCTCTCATCTCAG
Found at i:39954714 original size:8 final size:8
Alignment explanation
Indices: 39954701--39954725 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39954691 ATATATACTA
39954701 AATAAAAT
1 AATAAAAT
39954709 AATAAAAT
1 AATAAAAT
39954717 AATAAAAT
1 AATAAAAT
39954725 A
1 A
39954726 TGTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:39961346 original size:58 final size:53
Alignment explanation
Indices: 39961233--39961428 Score: 194
Period size: 50 Copynumber: 3.8 Consensus size: 53
39961223 GACATTAAGG
* *
39961233 GAATGAGA--TCCCATGTAAGACCATGTCTGGGACATGG-ATTGACATCACTATTGA
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-C-A-TGA
* *
39961287 GATTATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGGCGTTGGCACC--GA
1 GA--ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
* *
39961340 G-ATGAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGAACC--GA
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
** *
39961390 G-ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGC
1 GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
39961429 ATGAGCACCG
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
50 80 0.64
53 3 0.02
54 2 0.02
56 6 0.05
57 1 0.01
58 28 0.22
59 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (53 bp):
GAATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCATGA
Found at i:39961472 original size:50 final size:50
Alignment explanation
Indices: 39961291--39961464 Score: 233
Period size: 50 Copynumber: 3.5 Consensus size: 50
39961281 TATTGAGATT
* *
39961291 ATGAGAGGTCCCATGTAAGACCATGTCTAGGATATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* *
39961341 ATGAGAGGTCCCATGTAAGACTATGTCTGGGACATGGCGTTGGAACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * *
39961391 ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGC-ATGAGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTG-GCACCGAG
**
39961441 ATGAGAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
39961465 ATTTGGGATA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 2 0.02
50 106 0.98
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:39961748 original size:12 final size:12
Alignment explanation
Indices: 39961731--39961769 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39961721 ATGAGTTATT
39961731 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
39961743 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
39961755 TAAGTGAGTAAG
1 TAAGTAAGCAAG
39961767 TAA
1 TAA
39961770 AAAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:39968686 original size:362 final size:362
Alignment explanation
Indices: 39968021--39968744 Score: 1394
Period size: 362 Copynumber: 2.0 Consensus size: 362
39968011 ACGAGCATGA
*
39968021 ATTTACAAGAATATGGTAAGTGTTCTATATAAACCAAGACATGTATGTATGAAACACTTTGAAAT
1 ATTTACAAGAATATGGTAAGTGTTCTATATAAACCAAGACATGTATGTATGAAAAACTTTGAAAT
39968086 GGTGAACTACATGGAAAATATGTTATGTTGAGATGGATGATATATCCAATTGAATTATTCTCAAG
66 GGTGAACTACATGGAAAATATGTTATGTTGAGATGGATGATATATCCAATTGAATTATTCTCAAG
39968151 TACAATGGTTATCCATGTCAAATTCATATAAATCATGTTTAACTGAACTAACAAGTGTTATTGAT
131 TACAATGGTTATCCATGTCAAATTCATATAAATCATGTTTAACTGAACTAACAAGTGTTATTGAT
*
39968216 GTGCTTAGGCTTATGCTAAGCTTGTGGATATGAGTTATATTTGTGATTATGCTTGTACTATGCAT
196 GTGCTTAGGCTTATGCCAAGCTTGTGGATATGAGTTATATTTGTGATTATGCTTGTACTATGCAT
*
39968281 ATGAAACGGGTAAGAAAAGAGAATGAAATGGTAAGTACAAAATTGGGATGTATTATAATGTAATT
261 ATGAAACGGGTAAGAAAAGAGAATGAAATGGTAAGTACAAAATTGGGATGTATTATAATGTAATA
39968346 AAAGGTTTTATGTGATAAATGATGTATTTATATGTAT
326 AAAGGTTTTATGTGATAAATGATGTATTTATATGTAT
39968383 ATTTACAAGAATATGGTAAGTGTTCTATATAAACCAAGACATGTATGTATGAAAAACTTTGAAAT
1 ATTTACAAGAATATGGTAAGTGTTCTATATAAACCAAGACATGTATGTATGAAAAACTTTGAAAT
*
39968448 GGTGAACTACATGGAAAATATGTTATGTTGAGATGGATGATATATCCAATTGAATTATTCTTAAG
66 GGTGAACTACATGGAAAATATGTTATGTTGAGATGGATGATATATCCAATTGAATTATTCTCAAG
*
39968513 TACAATGGTTATCCATGTCAAATTCATATAAATCATGTTTAACTGAACTAACAAGTGTTGTTGAT
131 TACAATGGTTATCCATGTCAAATTCATATAAATCATGTTTAACTGAACTAACAAGTGTTATTGAT
39968578 GTGCTTAGGCTTATGCCAAGCTTGTGGATATGAGTTATATTTGTGATTATGCTTGTACTATGCAT
196 GTGCTTAGGCTTATGCCAAGCTTGTGGATATGAGTTATATTTGTGATTATGCTTGTACTATGCAT
*
39968643 ATGAAATGGGTAAGAAAAGAGAATGAAATGGTAAGTACAAAATTGGGATGTATTATAATGTAATA
261 ATGAAACGGGTAAGAAAAGAGAATGAAATGGTAAGTACAAAATTGGGATGTATTATAATGTAATA
39968708 AAAGGTTTTATGTGATAAATGATGTATTTATATGTAT
326 AAAGGTTTTATGTGATAAATGATGTATTTATATGTAT
39968745 GCAAACTGCT
Statistics
Matches: 356, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
362 356 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (362 bp):
ATTTACAAGAATATGGTAAGTGTTCTATATAAACCAAGACATGTATGTATGAAAAACTTTGAAAT
GGTGAACTACATGGAAAATATGTTATGTTGAGATGGATGATATATCCAATTGAATTATTCTCAAG
TACAATGGTTATCCATGTCAAATTCATATAAATCATGTTTAACTGAACTAACAAGTGTTATTGAT
GTGCTTAGGCTTATGCCAAGCTTGTGGATATGAGTTATATTTGTGATTATGCTTGTACTATGCAT
ATGAAACGGGTAAGAAAAGAGAATGAAATGGTAAGTACAAAATTGGGATGTATTATAATGTAATA
AAAGGTTTTATGTGATAAATGATGTATTTATATGTAT
Found at i:39972831 original size:37 final size:37
Alignment explanation
Indices: 39972701--39972832 Score: 104
Period size: 37 Copynumber: 3.6 Consensus size: 37
39972691 AGCACAGTAA
* * * * *
39972701 TCCATCCAAAGACACGCCAAATGCTCAGAAGATCTCA-
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCT-AG
* * * * *
39972738 TCCACCCGATAACACACCAATTGCTCCGAAAAGCTAG
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
* * *
39972775 TCCAACCAAAAACATGCCAAATGCTGCGAAGAGCTAG
1 TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
* * *
39972812 TCCAATCGAAAGCACGCCAAA
1 TCCAACCAAAAACACGCCAAA
39972833 ATAGGGAGTA
Statistics
Matches: 73, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 1 0.01
37 72 0.99
ACGTcount: A:0.39, C:0.32, G:0.15, T:0.14
Consensus pattern (37 bp):
TCCAACCAAAAACACGCCAAATGCTCCGAAAAGCTAG
Found at i:39974717 original size:16 final size:16
Alignment explanation
Indices: 39974696--39974726 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39974686 TGAAGAAATA
39974696 TTTAAAATTATTATTT
1 TTTAAAATTATTATTT
39974712 TTTAAAATTATTATT
1 TTTAAAATTATTATT
39974727 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTATTATTT
Found at i:39974780 original size:59 final size:59
Alignment explanation
Indices: 39974717--39974828 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
39974707 TATTTTTTAA
*
39974717 AATTATTATTAAA-A-TAA-AATTGAAATATTAAATACTTTATTAAAATTATAAATTATATT
1 AATTA-TATTAAATATTAATAATT-AAATAATAAATA-TTTATTAAAATTATAAATTATATT
*
39974776 AATTATATTAAATATTAATAATTTAATAATAAATATTTATTAAAATTATAAAT
1 AATTATATTAAATATTAATAATTAAATAATAAATATTTATTAAAATTATAAAT
39974829 AAATTCAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
58 7 0.15
59 24 0.50
60 13 0.27
61 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (59 bp):
AATTATATTAAATATTAATAATTAAATAATAAATATTTATTAAAATTATAAATTATATT
Found at i:39974792 original size:21 final size:20
Alignment explanation
Indices: 39974741--39974818 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
39974731 TAAAATTGAA
39974741 ATATTAAATACTTTATTAA--
1 ATATTAAATA-TTTATTAATT
39974760 A-ATTATAA-ATTATATTAATT
1 ATATTA-AATATT-TATTAATT
*
39974780 ATATTAAATA-TTAATAATTT
1 ATATTAAATATTTATTAA-TT
*
39974800 AATAATAAATATTTATTAA
1 -ATATTAAATATTTATTAA
39974819 AATTATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
19 8 0.17
20 6 0.13
21 14 0.30
22 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAAATATTTATTAATT
Found at i:39978258 original size:60 final size:60
Alignment explanation
Indices: 39978053--39978300 Score: 210
Period size: 60 Copynumber: 4.2 Consensus size: 60
39978043 ATGTGTAGTC
* * * * * * ** *
39978053 AGGGGCACCAAAGTGCGAACAGGGGCACGA-CATGCAAACAGGGATACTGAAGTTTATAT
1 AGGGGCACCAAAGTACGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
* ** * ** * * * *
39978112 AGGTGCGTCGAAGTGTGAACAAAGGCACAATCGTGCAAATAGGGACACTAAGGTGTACAT
1 AGGGGCACCAAAGTACGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
* *
39978172 AGGGGCACCAAAGTGCGAACAAGGGCACAATCATGCAAATAGGGACACCAAAGTGTATAT
1 AGGGGCACCAAAGTACGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
* * * * * * ** * *
39978232 AGGGGTACCAGAGTACGAACAGGGGCACAGTTGTGCAAACAATGACACCGAAGTGTATAC
1 AGGGGCACCAAAGTACGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
39978292 AGGGGCACC
1 AGGGGCACC
39978301 GAAGAGCAAA
Statistics
Matches: 150, Mismatches: 38, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
59 22 0.15
60 128 0.85
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (60 bp):
AGGGGCACCAAAGTACGAACAAGGGCACAATCGTGCAAATAGGGACACCAAAGTGTATAT
Found at i:39978279 original size:120 final size:119
Alignment explanation
Indices: 39978052--39978319 Score: 272
Period size: 120 Copynumber: 2.2 Consensus size: 119
39978042 TATGTGTAGT
* * ** *
39978052 CAGGGGCACCAAAGTGCGAACAGGGGCACGACATGCAAACAGGGATACTGAAGTTTATATAGGTG
1 CAGGGGCACCAAAGTGCGAACAGGGGCACAACATGCAAACAGGGACACCAAAGTGTATATAGGTG
* ** * * *
39978117 CGTCGAAGTGTGAACAAAGGCACAATCGTGCAAATAGGGACA-CTAAGGTGTACA
66 CGTCCAAGTACGAACAAAGGCACAATCGTGCAAACAAGGACACCGAA-GTGTACA
* * *
39978171 TAGGGGCACCAAAGTGCGAACAAGGGCACAATCATGCAAATAGGGACACCAAAGTGTATATAGG-
1 CAGGGGCACCAAAGTGCGAACAGGGGCACAA-CATGCAAACAGGGACACCAAAGTGTATATAGGT
** * * * *
39978235 G-GTACCAGAGTACGAACAGGGGCACAGTTGTGCAAACAATGACACCGAAGTGTATA
65 GCGT-CCA-AGTACGAACAAAGGCACAATCGTGCAAACAAGGACACCGAAGTGTACA
* * *
39978291 CAGGGGCACCGAAGAGCAAACAGGGGCAC
1 CAGGGGCACCAAAGTGCGAACAGGGGCAC
39978320 TTCTTCATTT
Statistics
Matches: 120, Mismatches: 25, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
118 2 0.02
119 31 0.26
120 84 0.70
121 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14
Consensus pattern (119 bp):
CAGGGGCACCAAAGTGCGAACAGGGGCACAACATGCAAACAGGGACACCAAAGTGTATATAGGTG
CGTCCAAGTACGAACAAAGGCACAATCGTGCAAACAAGGACACCGAAGTGTACA
Found at i:39982200 original size:15 final size:16
Alignment explanation
Indices: 39982171--39982200 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39982161 CAAACATGCT
39982171 TTAACACATTATCAAA
1 TTAACACATTATCAAA
39982187 TTAACACA-TATCAA
1 TTAACACATTATCAA
39982201 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:39983153 original size:30 final size:29
Alignment explanation
Indices: 39983094--39983154 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
39983084 CAATTGATTA
* *
39983094 ATTTTCATATACATGTATCATCCAATTCC
1 ATTTTCATATACATGTAACATACAATTCC
*
39983123 ATTTTCCATATACCATGTAACA-ACATTTCC
1 ATTTT-CATATA-CATGTAACATACAATTCC
39983153 AT
1 AT
39983155 GAAATTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.52
31 8 0.30
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTTTCATATACATGTAACATACAATTCC
Found at i:39983363 original size:25 final size:26
Alignment explanation
Indices: 39983335--39983389 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
39983325 GAATCAATAT
39983335 GCTCTG-ATGAGCT-ATAAATCGGTAA
1 GCTCTGTATGAGCTGA-AAATCGGTAA
*
39983360 GCTC-GTATGAGCTGAGAATCGGTAA
1 GCTCTGTATGAGCTGAAAATCGGTAA
39983385 GCTCT
1 GCTCT
39983390 CACGCGCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 1 0.04
25 24 0.92
26 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (26 bp):
GCTCTGTATGAGCTGAAAATCGGTAA
Found at i:39983398 original size:25 final size:24
Alignment explanation
Indices: 39983351--39983411 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
39983341 ATGAGCTATA
* *
39983351 AATCGGTAAGCTCGTATGAGCTGAG
1 AATCGGTAAGCTCGTACGAGCTG-C
*
39983376 AATCGGTAAGCTC-TCACGCGCTGC
1 AATCGGTAAGCTCGT-ACGAGCTGC
*
39983400 AATCGATAAGCT
1 AATCGGTAAGCT
39983412 AATACAAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCGTACGAGCTGC
Found at i:39985808 original size:27 final size:27
Alignment explanation
Indices: 39985770--39985832 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
39985760 GTAATGGGCC
39985770 TAAAATGACCAAAATACCCTC-AAAGGG
1 TAAAATGACCAAAATACCCTCGAAA-GG
39985797 TAAAATGACCAAAATACCCTCGAAAGG
1 TAAAATGACCAAAATACCCTCGAAAGG
39985824 TAAAATGAC
1 TAAAATGAC
39985833 TATTGTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (27 bp):
TAAAATGACCAAAATACCCTCGAAAGG
Found at i:39986100 original size:27 final size:27
Alignment explanation
Indices: 39986069--39986369 Score: 257
Period size: 27 Copynumber: 11.1 Consensus size: 27
39986059 AACAGCAAAA
39986069 GCCCCTATAGGGTAAAATAACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* * *
39986096 GCCCCGATAGGGTAAAATGACCGTATT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* *
39986123 ACCCC-AGTAGGGTAAAATGACTC-TAAT
1 GCCCCTA-TAGGGTAAAATAAC-CGTAAT
* * *
39986150 ACCCCTATAGAGTAAAATAACTGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* *
39986177 GCCCCTGTAGGGTAAAATGACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* * * * **
39986204 ACCCCTGTAGGATGAAATAACTATAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* ** * *
39986231 ACCTTTGTAGGGTAAAATGACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* *
39986258 GCCCC-AGTATGGTAAAATAACCATAAT
1 GCCCCTA-TAGGGTAAAATAACCGTAAT
* * * *
39986285 GGCCCTGTAAGGTAAAATGACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
* * * ** *
39986312 ACCCGTGTATTGTAAAATTACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
39986339 GCCCCTATAGGGTAAAATAACCGTAAT
1 GCCCCTATAGGGTAAAATAACCGTAAT
39986366 GCCC
1 GCCC
39986370 TGGTGGGTAA
Statistics
Matches: 218, Mismatches: 50, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.00
27 215 0.99
28 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
GCCCCTATAGGGTAAAATAACCGTAAT
Found at i:39986207 original size:81 final size:81
Alignment explanation
Indices: 39986070--39986385 Score: 327
Period size: 81 Copynumber: 3.9 Consensus size: 81
39986060 ACAGCAAAAG
* * *
39986070 CCCCTATAGGGTAAAATAACCGTAATGCCCC-GATAGGGTAAAATGACCGTATTACCCCAGTAGG
1 CCCCTATAGGGTAAAATAACCGTAATGCCCCTG-TAGGGTAAAATAACCGTAATACCCCTGTAGG
39986134 GTAAAATGACTCTAATA
65 GTAAAATGACTCTAATA
* * * *
39986151 CCCCTATAGAGTAAAATAACTGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGA
1 CCCCTATAGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGG
* * *
39986216 TGAAATAACTATAATA
66 TAAAATGACTCTAATA
** * * * * * ** *
39986232 CCTTTGTAGGGTAAAATGACCGTAATGCCCCAGTATGGTAAAATAACCATAATGGCCCTGTAAGG
1 CCCCTATAGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGG
39986297 TAAAATGAC-CGTAATA
66 TAAAATGACTC-TAATA
* * ** * * *
39986313 CCCGTGTATTGTAAAATTACCGTAATGCCCCTATAGGGTAAAATAACCGTAAT-GCCCTGGT-GG
1 CCCCTATAGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCCCT-GTAGG
39986376 GT-AAATGACT
65 GTAAAATGACT
39986386 ATTTTTGCCC
Statistics
Matches: 196, Mismatches: 35, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
79 7 0.04
80 8 0.04
81 180 0.92
82 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (81 bp):
CCCCTATAGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATAACCGTAATACCCCTGTAGGG
TAAAATGACTCTAATA
Found at i:39986462 original size:24 final size:24
Alignment explanation
Indices: 39986429--39986487 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
39986419 TCTGTGGTTA
*
39986429 AATGACTGATTTGTCTGTG-TTTG
1 AATGACTGATTTGTCTATGATTTG
*
39986452 CTATGACTGATTTGTCTATGATTTG
1 -AATGACTGATTTGTCTATGATTTG
39986477 AATGACTGATT
1 AATGACTGATT
39986488 CTAAACATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (24 bp):
AATGACTGATTTGTCTATGATTTG
Found at i:39986618 original size:26 final size:26
Alignment explanation
Indices: 39986589--39986659 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
39986579 ACTACTACTG
*
39986589 GCAGCTTTGCTACGATACTGTTGCTC
1 GCAGCTTTGCTGCGATACTGTTGCTC
* *
39986615 GCAGCTTTGCTGCGATATTGTTGCTG
1 GCAGCTTTGCTGCGATACTGTTGCTC
39986641 GCAGCTTTGCTGCGATACT
1 GCAGCTTTGCTGCGATACT
39986660 ACTGATGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (26 bp):
GCAGCTTTGCTGCGATACTGTTGCTC
Found at i:39986668 original size:26 final size:26
Alignment explanation
Indices: 39986577--39986668 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
39986567 TTGGCCACAT
*
39986577 ATACTACT-ACTGGCAGCTTTGCTACG
1 ATACTACTGA-TGGCAGCTTTGCTGCG
** * *
39986603 ATACTGTTGCTCGCAGCTTTGCTGCG
1 ATACTACTGATGGCAGCTTTGCTGCG
* ** *
39986629 ATATTGTTGCTGGCAGCTTTGCTGCG
1 ATACTACTGATGGCAGCTTTGCTGCG
39986655 ATACTACTGATGGC
1 ATACTACTGATGGC
39986669 TTTGTACCGA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (26 bp):
ATACTACTGATGGCAGCTTTGCTGCG
Found at i:39986826 original size:32 final size:32
Alignment explanation
Indices: 39986658--39986900 Score: 170
Period size: 32 Copynumber: 7.6 Consensus size: 32
39986648 TGCTGCGATA
* * *
39986658 CTACTGATGGCTTTGTACCGATCACAGT-ACCG
1 CTACTGATGGCTTTGTGCCGATCATA-TCACTG
* *
39986690 TTACTGATGGCTTTGTGCCGATCATAGT-ACCG
1 CTACTGATGGCTTTGTGCCGATCATA-TCACTG
* * * * *
39986722 TTACTGATGGCTTTGTACTGATCATATTATTG
1 CTACTGATGGCTTTGTGCCGATCATATCACTG
* * * * * *
39986754 TTACCGATGGATGTGTGCCAATCATTTCACTG
1 CTACTGATGGCTTTGTGCCGATCATATCACTG
* * * *
39986786 TTATTGATGGCTGTGTGCCGATCATATCACTA
1 CTACTGATGGCTTTGTGCCGATCATATCACTG
* * * * *
39986818 CTACTGATGGTTTTGTGTCGATAATGTTA-TCG
1 CTACTGATGGCTTTGTGCCGATCATATCACT-G
* *
39986850 TTACTGATGG-TTGTGTGCCGATCATATCACTA
1 CTACTGATGGCTT-TGTGCCGATCATATCACTG
*
39986882 CTACTGATGGCTTTCTGCC
1 CTACTGATGGCTTTGTGCC
39986901 ACTCAGATTA
Statistics
Matches: 167, Mismatches: 39, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
31 4 0.02
32 160 0.96
33 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (32 bp):
CTACTGATGGCTTTGTGCCGATCATATCACTG
Found at i:39986833 original size:96 final size:96
Alignment explanation
Indices: 39986689--39986893 Score: 234
Period size: 96 Copynumber: 2.1 Consensus size: 96
39986679 TCACAGTACC
* ** * *
39986689 GTTACTGATGGCTTTGTGCCGATCATAGTACCGTTACTGATGGCTTTGTACT-GATCATATTATT
1 GTTACTGATGGCTGTGTGCCGATCATAGTACCACTACTGATGGCTTTGT-CTCGATAATATTATC
*
39986753 GTTACCGATGGATGTGTGCCAATCATTTCACT
65 GTTACCGATGGATGTGTGCCAATCATATCACT
* * * * *
39986785 GTTATTGATGGCTGTGTGCCGATCATA-TCACTACTACTGATGGTTTTGTGTCGATAATGTTATC
1 GTTACTGATGGCTGTGTGCCGATCATAGT-ACCACTACTGATGGCTTTGTCTCGATAATATTATC
* * *
39986849 GTTACTGATGGTTGTGTGCCGATCATATCACT
65 GTTACCGATGGATGTGTGCCAATCATATCACT
**
39986881 ACTACTGATGGCT
1 GTTACTGATGGCT
39986894 TTCTGCCACT
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
95 2 0.02
96 88 0.98
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (96 bp):
GTTACTGATGGCTGTGTGCCGATCATAGTACCACTACTGATGGCTTTGTCTCGATAATATTATCG
TTACCGATGGATGTGTGCCAATCATATCACT
Found at i:39987004 original size:26 final size:26
Alignment explanation
Indices: 39986975--39987027 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39986965 AGCTCTTAGC
* *
39986975 CATTCTGACTACTGGCAGCTCTGCTG
1 CATTATGACTACTGGCAGCTATGCTG
*
39987001 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGGCAGCTATGCTG
39987027 C
1 C
39987028 GATATTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATGCTG
Found at i:39990304 original size:24 final size:27
Alignment explanation
Indices: 39990261--39990311 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 27
39990251 TACATCGATC
39990261 CATTCACATTATAAATAACA-TAATAA
1 CATTCACATTATAAATAACATTAATAA
39990287 CATTCA-ATT-TAAATAACATTAATAA
1 CATTCACATTATAAATAACATTAATAA
39990312 GATAACCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 9 0.38
26 6 0.25
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (27 bp):
CATTCACATTATAAATAACATTAATAA
Found at i:40003173 original size:73 final size:75
Alignment explanation
Indices: 40003029--40003174 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 75
40003019 AAGGAAAACA
40003029 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
1 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
40003094 AAAAGAATCT
66 AAAAGAATCT
* * * * *
40003104 AGGATTATTCCTTTATTAAT-GAGAAGGCAAATGGAAAGTTAGAAAAA-GAATTATATTTTTTCC
1 AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
40003167 AAAAGAAT
66 AAAAGAAT
40003175 ATTAATTTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 23 0.35
74 25 0.38
75 18 0.27
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (75 bp):
AGGATTATTCCCTTACTAATAGAGAAGGCAAATGAAAAATTAGAAAAATGAATTATATTCTTTCC
AAAAGAATCT
Found at i:40003332 original size:138 final size:138
Alignment explanation
Indices: 40003152--40003422 Score: 413
Period size: 138 Copynumber: 2.0 Consensus size: 138
40003142 TTAGAAAAAG
* * **
40003152 AATTATATTTTTTCCAAAAGAATATTAATTTCCATATTTTTTATATTTT-ACCTA-AAGTTAATT
1 AATTATATTATTTCCAAAAGAATATAAATTTCCATACCTTTTATATTTTGACC-AGAA-TTAATT
* *
40003215 AATATAACTATTTATATTAATAAATTCGGTAGAATATATACACTTAATATTTTGTATGAATCAAA
64 AATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA
40003280 TTCATATATT
129 TTCATATATT
*
40003290 AATTATATTATTTCCAAAAGAATATAAATTTTCA-AGCCTTTTATATTTTGACCAGAATTAATTA
1 AATTATATTATTTCCAAAAGAATATAAATTTCCATA-CCTTTTATATTTTGACCAGAATTAATTA
* *
40003354 ATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
40003419 TCAT
130 TCAT
40003423 GTTTGCATTG
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
137 1 0.01
138 115 0.95
139 5 0.04
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATAAATTTCCATACCTTTTATATTTTGACCAGAATTAATTAA
TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:40003516 original size:25 final size:25
Alignment explanation
Indices: 40003487--40003535 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
40003477 GTGTTTAATA
40003487 TTTAACTATCAAATTAAATTAATTG
1 TTTAACTATCAAATTAAATTAATTG
40003512 TTTAACTATCAAATTAAATTAATT
1 TTTAACTATCAAATTAAATTAATT
40003536 AATGTGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTAACTATCAAATTAAATTAATTG
Found at i:40007384 original size:23 final size:18
Alignment explanation
Indices: 40007339--40007379 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
40007329 ATATGTTGTT
40007339 GTTCTCAAATTTGTTTGA
1 GTTCTCAAATTTGTTTGA
40007357 GTTCTCAAATTTGTTTGA
1 GTTCTCAAATTTGTTTGA
40007375 GTTCT
1 GTTCT
40007380 ATTCTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (18 bp):
GTTCTCAAATTTGTTTGA
Found at i:40007739 original size:15 final size:15
Alignment explanation
Indices: 40007719--40007748 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40007709 AAGAAGATCA
40007719 ACATGACTCATCATT
1 ACATGACTCATCATT
40007734 ACATGACTCATCATT
1 ACATGACTCATCATT
40007749 GATCGAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
ACATGACTCATCATT
Found at i:40013463 original size:20 final size:20
Alignment explanation
Indices: 40013433--40013501 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
40013423 GTTAAAAAAA
*
40013433 AAAAGGAATTACATACTTTTT
1 AAAA-GAATTATATACTTTTT
40013454 AAAAGAATTATATACTTTTT
1 AAAAGAATTATATACTTTTT
*
40013474 AAAAGAATTATATTCTTTTT
1 AAAAGAATTATATACTTTTT
40013494 AAAAGAAT
1 AAAAGAAT
40013502 ATAGGATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 42 0.91
21 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAAGAATTATATACTTTTT
Found at i:40013748 original size:138 final size:138
Alignment explanation
Indices: 40013540--40013823 Score: 489
Period size: 138 Copynumber: 2.1 Consensus size: 138
40013530 TTAGGAAAAG
* * *
40013540 AATTATATTCTTTTCAAAAGAATATTAATTTTTATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
40013605 TATAACTGTTTATATTAATAAATTTGG-AAAACTATATACAATTAATATTTTGTATGAATAAAAT
66 TATAACTGTTTATATTAATAAATTTGGTAAAA-TATATACAATTAATATTTTGTATGAATAAAAT
40013669 TCATATATT
130 TCATATATT
* * *
40013678 AATTATATTCTTTCCAAAATAATATTAATTTTCATGTCTTTTCTATATTGGCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
*
40013743 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATAAAATT
40013808 CATATATT
131 CATATATT
40013816 AATTATAT
1 AATTATAT
40013824 CTATTTTATA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
138 134 0.97
139 4 0.03
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATATTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATAAAATT
CATATATT
Found at i:40020311 original size:22 final size:22
Alignment explanation
Indices: 40020283--40020324 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
40020273 ATTTGAGTTA
40020283 TCGTCAATAGGTATAGTACGCC
1 TCGTCAATAGGTATAGTACGCC
40020305 TCGTCAATAGGTATAGTACG
1 TCGTCAATAGGTATAGTACG
40020325 TCGAGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
TCGTCAATAGGTATAGTACGCC
Found at i:40021807 original size:13 final size:13
Alignment explanation
Indices: 40021789--40021814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40021779 CAGCTAAATA
40021789 AGCTTATTGGGTC
1 AGCTTATTGGGTC
40021802 AGCTTATTGGGTC
1 AGCTTATTGGGTC
40021815 GGTTTTGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
AGCTTATTGGGTC
Found at i:40028355 original size:41 final size:43
Alignment explanation
Indices: 40028310--40028427 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
40028300 GTTACTCGGT
* * *
40028310 GGAATCAGCACTTAGCAACCACCTT-ATATTC-AGTGATA-TGA
1 GGAATCAGCACTTAGCAACCACCTTCACAATCAAG-GATACGGA
* *
40028351 GGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGGT
1 GGAATCAGCACTTAGCAACCACC-TTCACAATCAAGGATACGGA
* * *
40028394 GGAATCAGTACTTAGCAACCACCTTTAGAATCAA
1 GGAATCAGCACTTAGCAACCACCTTCACAATCAA
40028428 TAATTTAGGG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.03
41 21 0.33
42 8 0.13
43 30 0.48
44 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (43 bp):
GGAATCAGCACTTAGCAACCACCTTCACAATCAAGGATACGGA
Found at i:40028555 original size:41 final size:41
Alignment explanation
Indices: 40028458--40028608 Score: 169
Period size: 41 Copynumber: 3.7 Consensus size: 41
40028448 TAGCAACCCC
* * * *
40028458 TCGGGAAATCTTCACTCAGCAACCTCTTTTTTTATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACC-CCTTTTTTATCAGAGTT
* * *
40028500 TCGGGAAATTTGCACTTAGCAACCCCTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTTATCAGAGTT
* * * *
40028541 TTGGGGAATCTGCACTTAGCAA-CCCTTTTTTATTAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTTATCAGAGTT
* *
40028581 TCAGGGAATTTGCACTTAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
40028609 ACATTCAATG
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
40 33 0.35
41 39 0.42
42 21 0.23
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTTATCAGAGTT
Found at i:40028567 original size:40 final size:40
Alignment explanation
Indices: 40028458--40028605 Score: 161
Period size: 40 Copynumber: 3.6 Consensus size: 40
40028448 TAGCAACCCC
* * *
40028458 TCGGGAAATCTTCACTCAGCAACCTCTTTTTTTATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACC-C-TTTTTTATCAGAGTT
* * *
40028500 TCGGGAAATTTGCACTTAGCAACCCCTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAA-CCCTTTTTTATCAGAGTT
* * * *
40028541 TTGGGGAATCTGCACTTAGCAACCCTTTTTTATTAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCTTTTTTATCAGAGTT
* *
40028581 TCAGGGAATTTGCACTTAGCAACCC
1 TCGGGGAATCTGCACTTAGCAACCC
40028606 CTTACATTCA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 36 0.40
41 33 0.36
42 20 0.22
43 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (40 bp):
TCGGGGAATCTGCACTTAGCAACCCTTTTTTATCAGAGTT
Found at i:40035847 original size:43 final size:42
Alignment explanation
Indices: 40035731--40035876 Score: 145
Period size: 43 Copynumber: 3.5 Consensus size: 42
40035721 GTTACTTGGT
* * *
40035731 GGAATCAGCACTTAGCAACCACC-TTATATTC-AGTGATACGG
1 GGAATCAGCACTTAACAACCACCTTTACAATCAAG-GATACGG
*
40035772 GGAATCAGCACATAACAACC-CCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAACAACCACCTTT-ACAATCAAGGATACGG
* * * ** *
40035814 TGGAATCAACACTTAAAAACCACCTTTAGAATCAATAATTCGG
1 -GGAATCAGCACTTAACAACCACCTTTACAATCAAGGATACGG
*
40035857 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAACAACC
40035877 CCTCGTGGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.02
41 20 0.23
42 28 0.33
43 31 0.36
44 5 0.06
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAACAACCACCTTTACAATCAAGGATACGG
Found at i:40035928 original size:41 final size:41
Alignment explanation
Indices: 40035883--40036029 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
40035873 AACCCCTCGT
*
40035883 GGAATCTACACTTAGCAACCACTTTTTTATTAGAGTTTCGG
1 GGAATCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGG
* * *
40035924 GGAATCTACATTTAGCAACCCCTTTTTTATCACAGTTTCGG
1 GGAATCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGG
* * * * *
40035965 GGAATCTGCACTTAGCAACCCCTTTTTGATTAGTGATTCAG
1 GGAATCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGG
40036006 GGAATCTACACTTAGCAACCCCTT
1 GGAATCTACACTTAGCAACCCCTT
40036030 ACATTCAATG
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (41 bp):
GGAATCTACACTTAGCAACCCCTTTTTTATTAGAGTTTCGG
Found at i:40036877 original size:12 final size:12
Alignment explanation
Indices: 40036860--40036890 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40036850 AAAAATTGGC
40036860 TTTTAATTTTGT
1 TTTTAATTTTGT
40036872 TTTTAATTTTGT
1 TTTTAATTTTGT
40036884 TTTTAAT
1 TTTTAAT
40036891 GAAAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTAATTTTGT
Found at i:40038273 original size:19 final size:19
Alignment explanation
Indices: 40038249--40038289 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40038239 AATACTAAAA
40038249 AAATATCAAACAAAACCAT
1 AAATATCAAACAAAACCAT
40038268 AAATATCAAACAAAACCAT
1 AAATATCAAACAAAACCAT
40038287 AAA
1 AAA
40038290 ATGCTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATATCAAACAAAACCAT
Found at i:40054648 original size:29 final size:29
Alignment explanation
Indices: 40054613--40054668 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
40054603 TTCCATAATT
*
40054613 TTGATGGTCGTCACTATCCCTTTTCATTG
1 TTGATGGTCGTCACCATCCCTTTTCATTG
40054642 TTGATGGTCGTCACCATCCCTTTTCAT
1 TTGATGGTCGTCACCATCCCTTTTCAT
40054669 AATTTGATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (29 bp):
TTGATGGTCGTCACCATCCCTTTTCATTG
Found at i:40054691 original size:30 final size:30
Alignment explanation
Indices: 40054537--40054733 Score: 114
Period size: 30 Copynumber: 6.6 Consensus size: 30
40054527 TGGTTGGCAC
* * *
40054537 ATCCCTTTCCATAATTCGATAGCCAAAGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCT
* * * * *
40054567 ATCCTTTTTCATGATTCGGTAGCTGAAGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCT
* * * * *
40054597 ATCCCATTCCATAATTTTGATGGTCGTCA-CT
1 ATCCCTTTTCATAA-TTTGATAGCCG-AAGCT
* * * *
40054628 ATCCCTTTTCAT--TGTTGATGGTCGTCA-CC
1 ATCCCTTTTCATAAT-TTGATAGCCG-AAGCT
*
40054657 ATCCCTTTTCATAATTTGATAGCCGAGGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCT
* * ** *
40054687 ATCCCTTTTAATGATTCAATAGCTGAAGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGCT
*
40054717 ATCCATTTTCATAATTT
1 ATCCCTTTTCATAATTT
40054734 TGATGCTCAT
Statistics
Matches: 127, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
28 1 0.01
29 26 0.20
30 80 0.63
31 19 0.15
32 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATAGCCGAAGCT
Found at i:40054752 original size:120 final size:119
Alignment explanation
Indices: 40054536--40054814 Score: 382
Period size: 120 Copynumber: 2.3 Consensus size: 119
40054526 ATGGTTGGCA
* * * * * **
40054536 CATCCCTTTCCATAATTCGATAGCCAAAGCTATCCTTTTTCATGATTCGGTAGCTGAAGCTATCC
1 CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGCTGAAGCTATCC
* * *
40054601 CATTCCATAATTTTGATGGTCGTCACTATCCCTTTTCATTGTTGATGGTCGTCAC
66 CATTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGT-AC
*
40054656 CATCCCTTTTCATAATTTGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGCTGAAGCTAT-C
1 CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGCTGAAGCTATCC
*
40054720 CATTTTCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
66 CA-TTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
** *
40054775 CATCCCTTTTCATAGCTCGATAGTCG-GAGCTATCCCTTTT
1 CATCCCTTTTCATAATTCGATAGCCGAG-GCTATCCCTTTT
40054815 CATTAGTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
118 1 0.01
119 39 0.28
120 101 0.72
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (119 bp):
CATCCCTTTTCATAATTCGATAGCCGAGGCTATCCCTTTTAATGATTCAATAGCTGAAGCTATCC
CATTCCATAATTTTGATGCTCATCACCATCCCTTTTCATTGTTGATGGTCGTAC
Found at i:40054757 original size:31 final size:29
Alignment explanation
Indices: 40054717--40054788 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
40054707 AGCTGAAGCT
* *
40054717 ATCCATTTTCATAATTTTGATGCTCATCACC
1 ATCCCTTTTCAT-ATGTTGATGCTCAT-ACC
* *
40054748 ATCCCTTTTCAT-TGTTGATGGTCGTACC
1 ATCCCTTTTCATATGTTGATGCTCATACC
40054776 ATCCCTTTTCATA
1 ATCCCTTTTCATA
40054789 GCTCGATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.42
29 10 0.28
31 11 0.31
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATATGTTGATGCTCATACC
Found at i:40056941 original size:37 final size:37
Alignment explanation
Indices: 40056891--40056969 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40056881 TTATTACGAA
* *
40056891 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
40056928 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
40056965 GTCTT
1 GTCTT
40056970 TAGAGCTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:40057166 original size:47 final size:47
Alignment explanation
Indices: 40057088--40057534 Score: 696
Period size: 47 Copynumber: 9.5 Consensus size: 47
40057078 CCCTTCGGGA
* * * * * * *
40057088 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
40057135 CCTGTCACATATATACACTTTCACATTCATCACATCGGCAACTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40057182 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40057229 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40057276 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40057323 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40057370 CTTATCACATATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40057419 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40057466 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40057513 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
40057535 TTGGCTGAAT
Statistics
Matches: 373, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 329 0.88
49 44 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40057442 original size:190 final size:188
Alignment explanation
Indices: 40057088--40057534 Score: 732
Period size: 190 Copynumber: 2.4 Consensus size: 188
40057078 CCCTTCGGGA
** * * * * * * * *
40057088 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
40057153 TTTCACATTCATCACATCGGCAACTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCAACTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
40057218 GGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
40057276 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
40057341 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCAACTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
40057406 TCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
129 TCGACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
40057466 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
40057531 TTTC
66 TTTC
40057535 TTGGCTGAAT
Statistics
Matches: 239, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
188 88 0.37
190 151 0.63
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCAACTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GACCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:40062898 original size:37 final size:35
Alignment explanation
Indices: 40062845--40062937 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 35
40062835 TATTCCAAAC
*
40062845 ATAATATTATTTTAATAGT-TTTATATAAAATTTAAT
1 ATAATATTATCTTAATAGTATTT-TAT-AAATTTAAT
*
40062881 ATAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 ATAATA-TTATCTTAATAGTATTTTATAAATTTAAT
40062917 ATTAAAGTGATTATCTTAATA
1 A-T-AA-T-ATTATCTTAATA
40062938 TTAAATTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
36 15 0.31
37 16 0.33
38 5 0.10
39 12 0.24
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (35 bp):
ATAATATTATCTTAATAGTATTTTATAAATTTAAT
Found at i:40067975 original size:22 final size:21
Alignment explanation
Indices: 40067949--40067990 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40067939 TAACACATCA
40067949 TGGATAAACCACCACATAATTG
1 TGGAT-AACCACCACATAATTG
* *
40067971 TGGATAACGATCACATAATT
1 TGGATAACCACCACATAATT
40067991 ATAGTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (21 bp):
TGGATAACCACCACATAATTG
Found at i:40070160 original size:39 final size:40
Alignment explanation
Indices: 40070115--40070339 Score: 215
Period size: 40 Copynumber: 5.7 Consensus size: 40
40070105 GCTCCTCGTT
* * * * *
40070115 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
40070155 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
40070194 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
40070234 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCA
** * * * *
40070274 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
40070315 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40070340 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:40070348 original size:41 final size:41
Alignment explanation
Indices: 40070271--40070348 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40070261 CTTGTATCTC
* * *
40070271 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40070312 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40070349 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40077640 original size:78 final size:78
Alignment explanation
Indices: 40077538--40077761 Score: 236
Period size: 78 Copynumber: 2.8 Consensus size: 78
40077528 GCTCCTCGTT
* * * *
40077538 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGGA
40077603 -TTAATAACTCGCA
66 CTT-ATAACTCGCA
* * * * * *
40077616 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACAAAGGCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGG-
* *
40077681 ACTTGTATCTCGCA
65 ACTTATAACTCGCA
* * * * * *
40077695 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAATAACTCA-CACAAAGCCTTCGGGACTTAACCCG
40077759 GAC
64 GAC
40077762 AGCATTCAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
78 57 0.48
79 36 0.31
80 25 0.21
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAAAGCCTTCGGGACTTAACCCGGA
CTTATAACTCGCA
Found at i:40077680 original size:39 final size:38
Alignment explanation
Indices: 40077538--40077760 Score: 173
Period size: 39 Copynumber: 5.7 Consensus size: 38
40077528 GCTCCTCGTT
* * * * * *
40077538 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAA-GCCTTCGGGACTTAACCCGG-ATTAATATCTCGCA
* *
40077578 CAATGCCTTCGGGACTTAACCCGGATTAATAACTCGCA
1 CAAAGCCTTCGGGACTTAACCCGGATTAATATCTCGCA
*
40077616 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 C-AAAGCCTTCGGGACTTAACCCGGA-TTAATATCTCGCA
* * *
40077656 CAAAGGCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAAGCCTTCGGGACTTAACCCGG-A-TTAATATCTCGCA
** * *
40077695 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCA
1 CAAA-GCCTTCGGGA-CTTAACCCGGAT-TAAT-ATC-TCGCA
*
40077736 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAACCCGGA
40077761 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
38 13 0.08
39 79 0.51
40 50 0.32
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (38 bp):
CAAAGCCTTCGGGACTTAACCCGGATTAATATCTCGCA
Found at i:40077769 original size:41 final size:41
Alignment explanation
Indices: 40077692--40077769 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40077682 CTTGTATCTC
* * *
40077692 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40077733 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40077770 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40081432 original size:75 final size:75
Alignment explanation
Indices: 40081309--40081460 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
40081299 GGCACACTTA
* * * *
40081309 TCTTGGTCATTAGCTACCATTCTTGAGATGCGAATGTGTCAATTTGGGTTCCTTGACCCGATTAC
1 TCTTGGTCATTAGCTACCATTCATGAGACGCGAATGAGTCAATTTGGGTTCCTTGACCCAATTAC
*
40081374 CCACATGTTC
66 CCACAAGTTC
* *
40081384 TCTTGGTCATTAGCTACCATTCATGAGACGTGAATGAGTCAATTTGGGTTCCTTGACCCAATTAT
1 TCTTGGTCATTAGCTACCATTCATGAGACGCGAATGAGTCAATTTGGGTTCCTTGACCCAATTAC
40081449 CCACAAGTTC
66 CCACAAGTTC
40081459 TC
1 TC
40081461 ATTCCCCTAG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (75 bp):
TCTTGGTCATTAGCTACCATTCATGAGACGCGAATGAGTCAATTTGGGTTCCTTGACCCAATTAC
CCACAAGTTC
Found at i:40086789 original size:91 final size:91
Alignment explanation
Indices: 40086628--40086842 Score: 295
Period size: 91 Copynumber: 2.4 Consensus size: 91
40086618 TGTAATTTAG
* * *
40086628 AAATTGACTGCAAAATGCTGTTCAATTGTGGTTAATATACTGCCCAAAACTTTCTATATAATGCT
1 AAATTGACTGCAAAATGCTGTTCAATTGTGGTTAATATACTACCCAAAAATTACTATATAATGCT
40086693 ACACAATCGTGGTTAGATTGTTGTCC
66 ACACAATCGTGGTTAGATTGTTGTCC
* * * * *
40086719 AAATTGATTGCATAATGTTGTTCAATTGTGGTTAATATACTATCCAAAAATTACTATATAATGTT
1 AAATTGACTGCAAAATGCTGTTCAATTGTGGTTAATATACTACCCAAAAATTACTATATAATGCT
* * **
40086784 GCACAATCGTGGTTAGATTGCTACCC
66 ACACAATCGTGGTTAGATTGTTGTCC
* * *
40086810 AAATTGACTGTAAAATGCTGCTCAAATGTGGTT
1 AAATTGACTGCAAAATGCTGTTCAATTGTGGTT
40086843 TTTATATGTC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
91 106 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (91 bp):
AAATTGACTGCAAAATGCTGTTCAATTGTGGTTAATATACTACCCAAAAATTACTATATAATGCT
ACACAATCGTGGTTAGATTGTTGTCC
Found at i:40086796 original size:46 final size:46
Alignment explanation
Indices: 40086650--40086798 Score: 124
Period size: 46 Copynumber: 3.3 Consensus size: 46
40086640 AAATGCTGTT
* * * * * *
40086650 CAATTGTGGTTAATATACTGCCCAAAACTTTCTATATAATGCTACA
1 CAATCGTGGTTAATATACTGTCCAAAAATTACTATATAATGTTGCA
** * ** **
40086696 CAATCGTGGTTAGAT-TGTTGTCC--AAATTGATTGCATAATGTTGTT
1 CAATCGTGGTTA-ATATACTGTCCAAAAATT-ACTATATAATGTTGCA
* *
40086741 CAATTGTGGTTAATATACTATCCAAAAATTACTATATAATGTTGCA
1 CAATCGTGGTTAATATACTGTCCAAAAATTACTATATAATGTTGCA
40086787 CAATCGTGGTTA
1 CAATCGTGGTTA
40086799 GATTGCTACC
Statistics
Matches: 75, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
44 6 0.08
45 24 0.32
46 38 0.51
47 7 0.09
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (46 bp):
CAATCGTGGTTAATATACTGTCCAAAAATTACTATATAATGTTGCA
Found at i:40090801 original size:22 final size:21
Alignment explanation
Indices: 40090758--40090803 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
40090748 TTAAAAACAA
*
40090758 ATTAAATACTTAGCTAAATTT
1 ATTAAATACTTAACTAAATTT
*
40090779 ATTAAATACTTAAACTAATTTT
1 ATTAAATACTT-AACTAAATTT
40090801 ATT
1 ATT
40090804 CCAGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTAAATACTTAACTAAATTT
Found at i:40090869 original size:20 final size:20
Alignment explanation
Indices: 40090844--40090884 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40090834 ATTTAAACTG
40090844 AGCTCAAACGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
***
40090864 AGCTCATGTGAGCTGAAATA
1 AGCTCAAACGAGCTGAAATA
40090884 A
1 A
40090885 AATTAGGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAAATA
Found at i:40092420 original size:21 final size:22
Alignment explanation
Indices: 40092384--40092429 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
40092374 TATTTGCTGG
40092384 AATAAAATTAGTTTAAGTATTT
1 AATAAAATTAGTTTAAGTATTT
* *
40092406 AATAAATTTAG-TTAAGTGTTT
1 AATAAAATTAGTTTAAGTATTT
40092427 AAT
1 AAT
40092430 TTGTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
AATAAAATTAGTTTAAGTATTT
Found at i:40101770 original size:38 final size:38
Alignment explanation
Indices: 40101719--40101794 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
40101709 AGAATTCTTC
40101719 CTCTATTTCTTATCATGTTTCTTCGCGAGCTTAATTGA
1 CTCTATTTCTTATCATGTTTCTTCGCGAGCTTAATTGA
* * * *
40101757 CTCTATTTCTTATCTTGTTTCTTTGTGAGCTTATTTGA
1 CTCTATTTCTTATCATGTTTCTTCGCGAGCTTAATTGA
40101795 TAAAGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (38 bp):
CTCTATTTCTTATCATGTTTCTTCGCGAGCTTAATTGA
Found at i:40106752 original size:27 final size:27
Alignment explanation
Indices: 40106721--40107078 Score: 331
Period size: 27 Copynumber: 13.3 Consensus size: 27
40106711 CCCTAAAATA
* *
40106721 GGTAAAATGACTAAAATACCCCTACAG
1 GGTAAAATGACTGAAATACCCCTATAG
* ** *
40106748 GGTAAAATAACCAAAATA-CCGTCATAG
1 GGTAAAATGACTGAAATACCCCT-ATAG
* * *
40106775 GGTAGAATGACCGAAATA-CTCTCATAG
1 GGTAAAATGACTGAAATACCCCT-ATAG
* *
40106802 GGTAAAATGACCGAAATACCCTTATAG
1 GGTAAAATGACTGAAATACCCCTATAG
* *
40106829 GGTAGAATGACTGAAATATCCCTATAG
1 GGTAAAATGACTGAAATACCCCTATAG
40106856 GGTAAAATGACTGAAATACTCCCTA-A-
1 GGTAAAATGACTGAAATAC-CCCTATAG
* * *
40106882 GGTAGAATGATTGAAATA-ACCTCATAG
1 GGTAAAATGACTGAAATACCCCT-ATAG
40106909 GGTAAAATGA-TAGAAATACTCCC-ATAG
1 GGTAAAATGACT-GAAATAC-CCCTATAG
* *
40106936 GGTAAAATGACTAAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCTATAG
* *
40106963 GGTAGAATGA-TCGAAATACCCCAATAG
1 GGTAAAATGACT-GAAATACCCCTATAG
* *
40106990 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCTATAG
*
40107017 GGTAAAATGACTGAAATACCCTCT-TAA
1 GGTAAAATGACTGAAATACCC-CTATAG
* **
40107044 AGTAGTATGACTGAAATA-CCCTCATAG
1 GGTAAAATGACTGAAATACCCCT-ATAG
40107071 GGTAAAAT
1 GGTAAAAT
40107079 AAAAGTTATA
Statistics
Matches: 275, Mismatches: 40, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
24 3 0.01
25 3 0.01
26 27 0.10
27 231 0.84
28 9 0.03
29 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCTATAG
Found at i:40107092 original size:81 final size:81
Alignment explanation
Indices: 40106720--40107078 Score: 379
Period size: 81 Copynumber: 4.4 Consensus size: 81
40106710 ACCCTAAAAT
* * * * ** *
40106720 AGGTAAAATGACTAAAATACCC-CTACAGGGTAAAATAACCA-AAATACCGTCATAGGGTAGAAT
1 AGGTAGAATGACTGAAATACCCTC-ATAGGGTAAAATGA-CAGAAATACCCCCATAGGGTAAAAT
* *
40106783 GACCGAAATACTCTCATA
64 GACTGAAATACCCTCATA
* * * * * * * *
40106801 GGGTAAAATGACCGAAATACCCTTATAGGGTAGAATGACTGAAATATCCCTATAGGGTAAAATGA
1 AGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCCATAGGGTAAAATGA
40106866 CTGAAATACTCC-C-TA
66 CTGAAATAC-CCTCATA
* * * *
40106881 AGGTAGAATGATTGAAATAACCTCATAGGGTAAAATGATAGAAATACTCCCATAGGGTAAAATGA
1 AGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCCATAGGGTAAAATGA
* *
40106946 CTAAAATACCCCCATA
66 CTGAAATACCCTCATA
* *
40106962 GGGTAGAATGA-TCGAAATACCC-CAATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAAT
1 AGGTAGAATGACT-GAAATACCCTC-ATAGGGTAAAATGACAGAAATACCCCCATAGGGTAAAAT
*
40107025 GACTGAAATACCCTCTTA
64 GACTGAAATACCCTCATA
* *
40107043 AAGTAGTATGACTGAAATACCCTCATAGGGTAAAAT
1 AGGTAGAATGACTGAAATACCCTCATAGGGTAAAAT
40107079 AAAAGTTATA
Statistics
Matches: 230, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
79 2 0.01
80 67 0.29
81 158 0.69
82 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (81 bp):
AGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACAGAAATACCCCCATAGGGTAAAATGA
CTGAAATACCCTCATA
Found at i:40107614 original size:33 final size:32
Alignment explanation
Indices: 40107550--40107619 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
40107540 ATGACAGATT
** *
40107550 TATATTACTGTTATGGGCCAACGCCCCACTGA
1 TATATTACTGAAATGGGCAAACGCCCCACTGA
* *
40107582 TATATTACTGAAATTGGGCAAAGGCCCTACTGA
1 TATATTACTGAAA-TGGGCAAACGCCCCACTGA
40107615 T-TATT
1 TATATT
40107620 TGCATCGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (32 bp):
TATATTACTGAAATGGGCAAACGCCCCACTGA
Found at i:40129136 original size:14 final size:15
Alignment explanation
Indices: 40129117--40129145 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40129107 TCATGCTAAG
40129117 TCATATCAAA-CATA
1 TCATATCAAATCATA
40129131 TCATATCAAATCATA
1 TCATATCAAATCATA
40129146 ACATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TCATATCAAATCATA
Found at i:40133167 original size:22 final size:23
Alignment explanation
Indices: 40133142--40133185 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40133132 GAACTGGCGT
*
40133142 AGTCAAAACAAGGA-ATAGGAAA
1 AGTCAAAACAAGAACATAGGAAA
*
40133164 AGTCAATACAAGAACATAGGAA
1 AGTCAAAACAAGAACATAGGAA
40133186 TAGATTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.11, G:0.20, T:0.11
Consensus pattern (23 bp):
AGTCAAAACAAGAACATAGGAAA
Found at i:40135743 original size:13 final size:13
Alignment explanation
Indices: 40135725--40135749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40135715 GAGGAGAGAA
40135725 AAAATGAAAAGTG
1 AAAATGAAAAGTG
40135738 AAAATGAAAAGT
1 AAAATGAAAAGT
40135750 CTAGGTGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (13 bp):
AAAATGAAAAGTG
Found at i:40148083 original size:25 final size:25
Alignment explanation
Indices: 40148055--40148108 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40148045 AAGTATTATA
*
40148055 CAGAGAACATAAATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
** **
40148080 CAGAGTGCACCGATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
40148105 CAGA
1 CAGA
40148109 CAGCACGCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
CAGAGAACACAAATGTGCTAATAAT
Found at i:40148114 original size:25 final size:25
Alignment explanation
Indices: 40148067--40148114 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40148057 GAGAACATAA
**
40148067 ATGTGCTAATAATCAGAGTGCACCG
1 ATGTGCTAATAATCAGACAGCACCG
40148092 ATGTGCTAATAATCAGACAGCAC
1 ATGTGCTAATAATCAGACAGCAC
40148115 GCTAAACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (25 bp):
ATGTGCTAATAATCAGACAGCACCG
Found at i:40149166 original size:50 final size:50
Alignment explanation
Indices: 40149087--40149293 Score: 272
Period size: 50 Copynumber: 4.1 Consensus size: 50
40149077 TCCTAGATAA
** * * * *
40149087 GGTCTTACATGGGATTTCTCATATCGGTGCCCATGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACAT
* * *
40149137 GGTCTTAC-GGAGGACCTCTCATCTTGGTGCCAATGCCATGTCCCAAACAT
1 GGTCTTACATG-GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACAT
* * **
40149187 GGTCTTACATGGGATCTCTCATCTCGGTGCCAACGACATGTCCCAGTCAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACAT
*
40149237 GGTCTTACATGGGACCTCTCATCTCGGCGCCAACGCCATGTCCCAAACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACAT
40149287 GGTCTTA
1 GGTCTTA
40149294 TCGAGATCGC
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 134 0.99
51 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
GGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACAT
Found at i:40149197 original size:100 final size:100
Alignment explanation
Indices: 40149087--40149293 Score: 308
Period size: 100 Copynumber: 2.1 Consensus size: 100
40149077 TCCTAGATAA
* * * *
40149087 GGTCTTACATGGGATTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGA
1 GGTCTTACATGGGATCTCTCATATCGGTGCCAACGACATGTCCCAGACATGGTCTTACAGG-GGA
* * *
40149151 CCTCTCATCTTGGTGCCAATGCCATGTCCCAAACAT
65 CCTCTCATCTCGGCGCCAACGCCATGTCCCAAACAT
* * *
40149187 GGTCTTACATGGGATCTCTCATCTCGGTGCCAACGACATGTCCCAGTCATGGTCTTACATGGGAC
1 GGTCTTACATGGGATCTCTCATATCGGTGCCAACGACATGTCCCAGACATGGTCTTACAGGGGAC
40149252 CTCTCATCTCGGCGCCAACGCCATGTCCCAAACAT
66 CTCTCATCTCGGCGCCAACGCCATGTCCCAAACAT
40149287 GGTCTTA
1 GGTCTTA
40149294 TCGAGATCGC
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 95 0.99
101 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (100 bp):
GGTCTTACATGGGATCTCTCATATCGGTGCCAACGACATGTCCCAGACATGGTCTTACAGGGGAC
CTCTCATCTCGGCGCCAACGCCATGTCCCAAACAT
Found at i:40157054 original size:91 final size:91
Alignment explanation
Indices: 40156898--40157079 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
40156888 GTGACTTGTA
* * *
40156898 GGTTCGTGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTGGTCATTGTCTTGTCCACACGGCCTA
1 GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
40156963 ACACATGGGCATTTATCTCAGCCGTG
66 ACACATGGGCATTTATCTCAGCCGTG
* * * * *
40156989 GGTTCGCGTTTTAAATGGTGAGGAAAATGGCTTGATTTTCGTCATTTTCTTGTCTACATGACCTA
1 GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
* * *
40157054 AGACATGGGCGTTTGTCTCAGCCGTG
66 ACACATGGGCATTTATCTCAGCCGTG
40157080 TGTAACACGC
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (91 bp):
GGTTCGCGTTTTAAAGGGCGAGGAAAATGGCTTGATTTTCGTCATTGTCTTGTCCACACGACCTA
ACACATGGGCATTTATCTCAGCCGTG
Found at i:40161813 original size:30 final size:30
Alignment explanation
Indices: 40161778--40161838 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40161768 CAATTTGTTG
* * * *
40161778 TGAGCTGAACTAAGCTCCATTTCAGCTCAA
1 TGAGCTCAAATAAGCTCAAATTCAGCTCAA
*
40161808 TGAGCTCAAATCAGCTCAAATTCAGCTCAA
1 TGAGCTCAAATAAGCTCAAATTCAGCTCAA
40161838 T
1 T
40161839 TTCATTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (30 bp):
TGAGCTCAAATAAGCTCAAATTCAGCTCAA
Found at i:40161825 original size:10 final size:10
Alignment explanation
Indices: 40161799--40161837 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
40161789 AAGCTCCATT
40161799 TCAGCTC-AA
1 TCAGCTCAAA
*
40161808 TGAGCTCAAA
1 TCAGCTCAAA
40161818 TCAGCTCAAA
1 TCAGCTCAAA
40161828 TTCAGCTCAA
1 -TCAGCTCAA
40161838 TTTCATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 6 0.23
10 11 0.42
11 9 0.35
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (10 bp):
TCAGCTCAAA
Done.