Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 133 of 259
Found at i:43257841 original size:94 final size:92
Alignment explanation
Indices: 43257631--43257886 Score: 223
Period size: 94 Copynumber: 2.7 Consensus size: 92
43257621 TATGCCGGAT
** *
43257631 ATGGTCTTACATGGGGCCACGTATCAATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
1 ATGGTCTTACATGGGATCA--TATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGAT
* * * *
43257696 CACACTTATCGAAGCCGATAGCCCAGCTAC
64 CACAC-TAACGAAGCCAATAGCCCACCAAC
* * *
43257726 --GGTCTTACACGATGTGCTCATATCGATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
1 ATGGTCTT--AC-ATGGGATCATATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGA
*
43257789 TCACA-TAACGATGCCAAT-GCCGTGCACCAAAC
63 TCACACTAACGAAGCCAATAGCC---CACC-AAC
* * * * * *
43257821 ATGGTCTTACATGGGATCATAAACCAATGCCGATGCCATATCCCAGATATGGCCTTATACGGGAT
1 ATGGTCTTACATGGGATCAT--ATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGAT
43257886 C
64 C
43257887 TCATCAACAC
Statistics
Matches: 131, Mismatches: 19, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
91 3 0.02
92 10 0.08
93 6 0.05
94 57 0.44
95 6 0.05
96 43 0.33
97 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (92 bp):
ATGGTCTTACATGGGATCATATCAATGCCAATGCCATGTCCCAGACATGGTCTTATATGGGATCA
CACTAACGAAGCCAATAGCCCACCAAC
Found at i:43260485 original size:17 final size:18
Alignment explanation
Indices: 43260458--43260493 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
43260448 TCTGATTCAA
43260458 CACTCGACTCACATTGAG
1 CACTCGACTCACATTGAG
*
43260476 CACT-GACTCATATTGAG
1 CACTCGACTCACATTGAG
43260493 C
1 C
43260494 TCTCTTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (18 bp):
CACTCGACTCACATTGAG
Found at i:43261763 original size:81 final size:80
Alignment explanation
Indices: 43261673--43261944 Score: 346
Period size: 81 Copynumber: 3.4 Consensus size: 80
43261663 AGGGTAAATT
* * * * *
43261673 AGTCATTTTACCTTACAGGGGTATTACAGTCATTTTATCCTACAGGAGTATTACAGTCATATTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACAGG-GTATTTCGGTCATTTTAC
* *
43261738 CCTATAGGGGCATTTC
65 CCTATGGGGGTATTTC
* *
43261754 AGTCATTTTACCCTATAGGGGTATTTTAGTCATTTTATCCTACAGGGGTATTTCGGTCATTTTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACA-GGGTATTTCGGTCATTTTAC
*
43261819 CTTATGGGGGTATTTC
65 CCTATGGGGGTATTTC
* * * * * *
43261835 GGTCATTTTACCTTATGGGGGTATTTCAATCATTTTACCCTATGAGGGTATTTTGGTCATTTTAC
1 AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTA-CAGGGTATTTCGGTCATTTTAC
43261900 CCTATGGGGGTATTTC
65 CCTATGGGGGTATTTC
* * *
43261916 AGCCATTTTACCCTATGGGGGTATTTCAG
1 AGTCATTTTACCTTATAGGGGTATTTCAG
43261945 CCCAACATGG
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
81 163 0.98
82 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (80 bp):
AGTCATTTTACCTTATAGGGGTATTTCAGTCATTTTATCCTACAGGGTATTTCGGTCATTTTACC
CTATGGGGGTATTTC
Found at i:43261946 original size:27 final size:27
Alignment explanation
Indices: 43261673--43261944 Score: 312
Period size: 27 Copynumber: 10.1 Consensus size: 27
43261663 AGGGTAAATT
* * *
43261673 AGTCATTTTACCTTACAGGGGTATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * * *
43261700 AGTCATTTTATCCTACAGGAGTATTAC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43261727 AGTCATATTACCCTATAGGGGCATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
*
43261754 AGTCATTTTACCCTATAGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43261781 AGTCATTTTATCCTACAGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * *
43261808 GGTCATTTTACCTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* * *
43261835 GGTCATTTTACCTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43261862 AATCATTTTACCCTAT-GAGGGTATTTT
1 AGTCATTTTACCCTATAG-GGGTATTTC
* *
43261889 GGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
* *
43261916 AGCCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTC
43261943 AG
1 AG
43261945 CCCAACATGG
Statistics
Matches: 214, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
26 1 0.00
27 212 0.99
28 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
AGTCATTTTACCCTATAGGGGTATTTC
Found at i:43264918 original size:38 final size:38
Alignment explanation
Indices: 43264867--43264945 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
43264857 ATTATGCAAC
43264867 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
43264905 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
1 ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
43264943 ATG
1 ATG
43264946 GCCAAATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (38 bp):
ATGTACCATTGTAAAACCCCAAACCCGGCCTAGATGTT
Found at i:43265551 original size:34 final size:34
Alignment explanation
Indices: 43265479--43265551 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
43265469 AGTAACAGTC
* *
43265479 CAGTATCAGTTTGGGCCTTAGCCCATTACAGTAT
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
* * *
43265513 CAGTATCTGTGTGGGCCTTAGCCCATTTCATTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
43265547 CAGTA
1 CAGTA
43265552 ACAGAAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
Found at i:43267953 original size:44 final size:44
Alignment explanation
Indices: 43267902--43267986 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
43267892 TATGTAATCT
* * * *
43267902 GAACTCATTGAGTTGTGTTTGAGTTCATGATATATGTGACAGCA
1 GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACAGCA
*
43267946 GAACTCATTGAGTTATGGTCGAGTTCGTGATATATATGACA
1 GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACA
43267987 CATGTTTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (44 bp):
GAACTCATTGAGTTATGGTCGAGTTCATGATATATATGACAGCA
Found at i:43271580 original size:39 final size:40
Alignment explanation
Indices: 43271480--43271703 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
43271470 TTGAATGATG
* * * *
43271480 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
43271520 TCCGAACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43271560 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43271599 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
43271639 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43271680 -CCGGGCT-TGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43271704 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 50 0.31
40 101 0.63
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43271694 original size:119 final size:119
Alignment explanation
Indices: 43271480--43271701 Score: 272
Period size: 119 Copynumber: 1.9 Consensus size: 119
43271470 TTGAATGATG
*
43271480 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGAACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGAACTAAGATCCGAAGGCATTT
*
43271545 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
* * * * ***
43271599 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGAACTAAGAT-CCGAAGGCAT
* * *
43271662 TTGTGTGAGTTACT-ATAACCGGGCT-TGTCCCGAAGGCATT
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
43271702 TGAACGAGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 76 0.87
120 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGAACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
Found at i:43271722 original size:79 final size:79
Alignment explanation
Indices: 43271533--43271703 Score: 249
Period size: 79 Copynumber: 2.2 Consensus size: 79
43271523 GAACTAAGAT
*
43271533 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
43271597 AATCCGGGTTAAGTC
66 AATCCGGGTT-AGTC
* * * *
43271612 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
43271677 TAA-CCGGGCTT-GTC
66 -AATCCGGG-TTAGTC
43271691 CCGAAGGCATTTG
1 CCGAAGGCATTTG
43271704 AACGAGTAGC
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
79 51 0.61
80 29 0.35
81 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA
AATCCGGGTTAGTC
Found at i:43291197 original size:40 final size:40
Alignment explanation
Indices: 43291018--43291189 Score: 249
Period size: 40 Copynumber: 4.3 Consensus size: 40
43291008 AGACTAAGAT
* * **
43291018 CCGAAGGCATTTGTACGAGTTACTAAATCTGGACTAAGAT-
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TC
43291058 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
43291098 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
43291138 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
*
43291178 CCAAAGGCATTT
1 CCGAAGGCATTT
43291190 AAACGAGTAG
Statistics
Matches: 123, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.01
40 120 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:43291197 original size:80 final size:79
Alignment explanation
Indices: 43291021--43291223 Score: 241
Period size: 80 Copynumber: 2.5 Consensus size: 79
43291011 CTAAGATCCG
* **
43291021 AAGGCATTTGTACGAGTTACTAAATCTGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAAT
1 AAGGCATTTGTACGAGTTACTAAATCCGGGTTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
43291086 CCGGGTTAAGTCCCG
65 CCGGGCTAAGTCCCA
*
43291101 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 AAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
43291166 -CCGGGCTATGTCCCA
64 TCCGGGCTAAGTCCCA
** * *
43291181 AAGGCATTTAAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 AAGGCATTTGTACGAGTTA-CTAAATCCGGGTT-AAGTCCGAAGG
43291224 TACGTGATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
79 14 0.13
80 91 0.85
81 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (79 bp):
AAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATC
CGGGCTAAGTCCCA
Found at i:43299197 original size:120 final size:120
Alignment explanation
Indices: 43298965--43299223 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
43298955 TTGAATGATG
* * * *
43298965 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCTGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
43299030 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
66 GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
* * **
43299085 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
43299148 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
43299205 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43299224 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 90 0.76
121 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:43299204 original size:40 final size:40
Alignment explanation
Indices: 43298965--43299190 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
43298955 TTGAATGATG
* * * *
43298965 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* * *
43299005 TCTGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43299045 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43299085 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
43299125 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
43299166 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43299191 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:43310121 original size:3 final size:3
Alignment explanation
Indices: 43310113--43310145 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
43310103 AAACATACTA
*
43310113 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43310146 CAAAACATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43316951 original size:57 final size:57
Alignment explanation
Indices: 43316881--43317008 Score: 152
Period size: 57 Copynumber: 2.3 Consensus size: 57
43316871 GTCGATTTTG
* *
43316881 AAAATGGCACTTAGTGTGCGAGTTA-CTGAGGACAACACTTAGTGTGCGAAACATCCA
1 AAAATGGCACTTAGTGAGCGAATTATC-GAGGACAACACTTAGTGTGCGAAACATCCA
* *** *
43316938 AAAATGGCTCTTAGTGAGCGAATTATCGAGGATGGCACTTAGTGTGCGAGACATCC-
1 AAAATGGCACTTAGTGAGCGAATTATCGAGGACAACACTTAGTGTGCGAAACATCCA
**
43316994 AGGATGGCACTTAGT
1 AAAATGGCACTTAGT
43317009 TTGCAATACA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 12 0.20
57 47 0.78
58 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (57 bp):
AAAATGGCACTTAGTGAGCGAATTATCGAGGACAACACTTAGTGTGCGAAACATCCA
Found at i:43316981 original size:28 final size:28
Alignment explanation
Indices: 43316916--43317008 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 28
43316906 CTGAGGACAA
* * **
43316916 CACTTAGTGTGCGAAACATCCAAAAATGG
1 CACTTAGTGAGCGAGACATCC-AGGATGG
* * *
43316945 CTCTTAGTGAGCGA-ATTATCGAGGATGG
1 CACTTAGTGAGCGAGA-CATCCAGGATGG
*
43316973 CACTTAGTGTGCGAGACATCCAGGATGG
1 CACTTAGTGAGCGAGACATCCAGGATGG
43317001 CACTTAGT
1 CACTTAGT
43317009 TTGCAATACA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
28 36 0.69
29 16 0.31
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (28 bp):
CACTTAGTGAGCGAGACATCCAGGATGG
Found at i:43317019 original size:28 final size:28
Alignment explanation
Indices: 43316966--43317021 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
43316956 CGAATTATCG
*
43316966 AGGATGGCACTTAGTGTGCGAGACATCC
1 AGGATGGCACTTAGTGTGCAAGACATCC
* *
43316994 AGGATGGCACTTAGTTTGCAATACATCC
1 AGGATGGCACTTAGTGTGCAAGACATCC
43317022 GTGAAGGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (28 bp):
AGGATGGCACTTAGTGTGCAAGACATCC
Found at i:43322227 original size:46 final size:46
Alignment explanation
Indices: 43322174--43322310 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
43322164 TATATATACA
* * * *
43322174 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
43322220 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
43322266 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCAGATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
43322311 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:43322346 original size:47 final size:47
Alignment explanation
Indices: 43322284--43322475 Score: 249
Period size: 47 Copynumber: 4.1 Consensus size: 47
43322274 ACACATTTCG
* * * * **
43322284 CATTAGCCATTCGGCCTTACCAGATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * * * * *
43322331 CATCGGCCCTTCGGCCTTATCTCATATATGCATGTTTACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* *
43322378 CATTGGTCATTCGGCCTTATCGCACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
43322425 CATTGGCCATTCGGCCTTATCACACATACGCATATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
43322472 CATT
1 CATT
43322476 AAAATCCTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 127 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:43327705 original size:29 final size:27
Alignment explanation
Indices: 43327687--43327756 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
43327677 ATATTAAGTC
43327687 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
43327714 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
43327742 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
43327757 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:43327750 original size:28 final size:28
Alignment explanation
Indices: 43327687--43327784 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
43327677 ATATTAAGTC
*
43327687 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
43327714 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
43327742 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
43327771 CGCACACTTAGTGC
1 CGCACACTTAGTGC
43327785 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:43331292 original size:40 final size:41
Alignment explanation
Indices: 43331241--43331595 Score: 497
Period size: 40 Copynumber: 8.8 Consensus size: 41
43331231 ATTTGAATTT
* * * *
43331241 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
43331281 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
* *
43331321 TATTCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
*
43331361 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT-TA
*
43331403 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
*
43331443 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT-TA
* *
43331485 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
* *
43331525 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
** * *
43331565 TGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
43331596 TTGTGGTAAT
Statistics
Matches: 291, Mismatches: 18, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
40 211 0.73
41 3 0.01
42 77 0.26
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (41 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATTA
Found at i:43331442 original size:82 final size:82
Alignment explanation
Indices: 43331241--43331595 Score: 531
Period size: 82 Copynumber: 4.4 Consensus size: 82
43331231 ATTTGAATTT
* * *
43331241 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGCA
43331305 TTTGTGCGAGTTGATATA
65 TTTGTGCGAGTTGATATA
* * *
43331323 T-T-CGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
43331386 TTGTGCGAGTTGATATA
66 TTGTGCGAGTTGATATA
* * *
43331403 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
43331468 TTGTGCGAGTTGATATA
66 TTGTGCGAGTTGATATA
*
43331485 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
* *
43331550 TCGTGCGAGTTG--CTA
66 TTGTGCGAGTTGATATA
** *
43331565 TGCCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
43331596 TTGTGGTAAT
Statistics
Matches: 255, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
80 99 0.39
81 5 0.02
82 151 0.59
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (82 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCGAGTTGATATA
Found at i:43331456 original size:122 final size:123
Alignment explanation
Indices: 43331241--43331595 Score: 531
Period size: 122 Copynumber: 2.9 Consensus size: 123
43331231 ATTTGAATTT
* * *
43331241 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGAT-TTTATCCGGGCTAAGACCCGAAGGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGC
*
43331304 ATTTGTGCGAGTTGATATATTCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTG-ATA
66 ATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGAATA
* * * *
43331361 TATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGCAGGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGC
43331426 ATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATA
66 ATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGA-ATA
43331485 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG--ATATATCCGGGCTAAGACCCGAAGGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGC
* * ** * * *
43331548 ATTCGTGCGAGTTGCTATGCCCGGGTTAAGACCCGAAGGCAATTGTGC
66 ATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCATTTGTGC
43331596 TTGTGGTAAT
Statistics
Matches: 213, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
120 30 0.14
121 4 0.02
122 142 0.67
124 37 0.17
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (123 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGC
ATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGAATA
Found at i:43339726 original size:29 final size:27
Alignment explanation
Indices: 43339708--43339777 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
43339698 ATATTAAGTC
43339708 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
43339735 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
43339763 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
43339778 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:43339771 original size:28 final size:28
Alignment explanation
Indices: 43339708--43339805 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
43339698 ATATTAAGTC
*
43339708 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
43339735 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
43339763 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
43339792 CGCACACTTAGTGC
1 CGCACACTTAGTGC
43339806 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:43345829 original size:77 final size:77
Alignment explanation
Indices: 43345702--43345855 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
43345692 TCAGTTCTTG
43345702 CTCATATTAATATGCCTTGGTACATAATGTGGCAATGACATGTGCTAGTACATGACCTTTAGGTA
1 CTCATATTAATATGCCTTGGTACATAATGTGGCAATGACATGTGCTAGTACATGACCTTTAGGTA
43345767 TATATATATATA
66 TATATATATATA
43345779 CTCATATTAATATGCCTTGGTACATAATGTGGCAATGACATGTGCTAGTACATGACCTTTAGGTA
1 CTCATATTAATATGCCTTGGTACATAATGTGGCAATGACATGTGCTAGTACATGACCTTTAGGTA
43345844 TATATATATATA
66 TATATATATATA
43345856 TGTGTGTGTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (77 bp):
CTCATATTAATATGCCTTGGTACATAATGTGGCAATGACATGTGCTAGTACATGACCTTTAGGTA
TATATATATATA
Found at i:43348427 original size:65 final size:66
Alignment explanation
Indices: 43348323--43348469 Score: 208
Period size: 66 Copynumber: 2.2 Consensus size: 66
43348313 TATATTCACT
* *
43348323 ATTTATATATATATTACAAGTTTTTAATAAATAATAAATTA-TTTTTGAGTTTTTACACATTTAA
1 ATTTATATATATTTTACAAGTTTTTAATAAATAATAAATTATTTTTTGAGTTTTTAAACATTTAA
43348387 A
66 A
* * * *
43348388 ATTTATATATATTTTA-GATTTTATTAATAAATAATAAATTATTTTTTGATTTTTTAAACATTTG
1 ATTTATATATATTTTACAAGTTT-TTAATAAATAATAAATTATTTTTTGAGTTTTTAAACATTTA
43348452 AA
65 AA
*
43348454 ATCTATATATATTTTA
1 ATTTATATATATTTTA
43348470 AAAACTTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 4 0.05
65 33 0.45
66 36 0.49
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (66 bp):
ATTTATATATATTTTACAAGTTTTTAATAAATAATAAATTATTTTTTGAGTTTTTAAACATTTAA
A
Found at i:43348492 original size:9 final size:9
Alignment explanation
Indices: 43348464--43348499 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
43348454 ATCTATATAT
43348464 ATTTTAAAA
1 ATTTTAAAA
43348473 ACTTTTAAAAA
1 A-TTTT-AAAA
43348484 ATTTTAAAA
1 ATTTTAAAA
43348493 ATTTTAA
1 ATTTTAA
43348500 TTTTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.48
10 8 0.32
11 5 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:43349685 original size:40 final size:40
Alignment explanation
Indices: 43349630--43349709 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
43349620 GAAATGACAC
43349630 AATTTTCAAACATTCCCATTTGCAAATACTGTCCCCATTT
1 AATTTTCAAACATTCCCATTTGCAAATACTGTCCCCATTT
*
43349670 AATTTTTAAACATTCCCATTTGCAAATACTGTCCCCATTT
1 AATTTTCAAACATTCCCATTTGCAAATACTGTCCCCATTT
43349710 CTTCATATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (40 bp):
AATTTTCAAACATTCCCATTTGCAAATACTGTCCCCATTT
Found at i:43355856 original size:40 final size:40
Alignment explanation
Indices: 43355762--43355906 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
43355752 TACTCGAATG
*
43355762 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
43355803 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
43355843 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
43355883 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
43355907 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:43367242 original size:19 final size:19
Alignment explanation
Indices: 43367207--43367245 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43367197 TATGTATTTC
43367207 TTATTCATTTTTATTTTAT
1 TTATTCATTTTTATTTTAT
*
43367226 TTATT-ATTCTTTGTTTTAT
1 TTATTCATT-TTTATTTTAT
43367245 T
1 T
43367246 ATTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTCATTTTTATTTTAT
Found at i:43367247 original size:22 final size:21
Alignment explanation
Indices: 43367189--43367254 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
43367179 CCCTTCACTT
43367189 ATTTTCTTTATGTATTTCTTATTC
1 ATTTT-TTTAT-TATTT-TTATTC
43367213 ATTTTTATT-TTATTTATTATTC
1 ATTTTT-TTATTATTT-TTATTC
43367235 -TTTGTTTTATTATTTTTATT
1 ATTT-TTTTATTATTTTTATT
43367255 TCCCTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 10 0.26
22 19 0.50
23 2 0.05
24 7 0.18
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (21 bp):
ATTTTTTTATTATTTTTATTC
Found at i:43367450 original size:3 final size:3
Alignment explanation
Indices: 43367442--43367501 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
43367432 TTGTGTTTTC
*
43367442 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43367490 TAT TAT TAT TAT
1 TAT TAT TAT TAT
43367502 ATTTTTAATG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:43369694 original size:29 final size:28
Alignment explanation
Indices: 43369653--43369710 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
43369643 TTCCCTTTTC
43369653 ATTAAGAACAAAGCTAAACAGTGGATGA
1 ATTAAGAACAAAGCTAAACAGTGGATGA
* *
43369681 ATTAAGGAACAAAGCTAAATAGTGGTTGA
1 ATTAA-GAACAAAGCTAAACAGTGGATGA
43369710 A
1 A
43369711 CTCGTTACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.21
Consensus pattern (28 bp):
ATTAAGAACAAAGCTAAACAGTGGATGA
Found at i:43372360 original size:94 final size:94
Alignment explanation
Indices: 43372197--43372380 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 94
43372187 ACGACATGCC
* * *
43372197 CGTGTCTAACACCCGTGGCCAAACCTGTCAAATTAACACGGGCGTGGGGTTTTCATACACGGGCG
1 CGTGTCTAACACCCGTGGCCAAACCTGTCAAATTAACACGAGCGTGGAGTTTTCATACACAGGCG
*
43372262 TAGGAGAAGTGAACAACGCCAGCCACGGG
66 TAGGAGAAGCGAACAACGCCAGCCACGGG
* *
43372291 CGTGTTTAACACCCGTGGCCAAACCTGTCAAATTAACACGAGCGTGGAGTTTTCATACACAGGCT
1 CGTGTCTAACACCCGTGGCCAAACCTGTCAAATTAACACGAGCGTGGAGTTTTCATACACAGGCG
43372356 TAGGAGAAGCGAACAACGCCAGCCA
66 TAGGAGAAGCGAACAACGCCAGCCA
43372381 GGTCGTGCGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (94 bp):
CGTGTCTAACACCCGTGGCCAAACCTGTCAAATTAACACGAGCGTGGAGTTTTCATACACAGGCG
TAGGAGAAGCGAACAACGCCAGCCACGGG
Found at i:43378573 original size:39 final size:39
Alignment explanation
Indices: 43378530--43378738 Score: 292
Period size: 39 Copynumber: 5.3 Consensus size: 39
43378520 GGTCTTTAAC
** * *
43378530 CCGGATATTTTTCCAGCACGTAGCCTGCAGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
43378569 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
43378608 TCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * * *
43378647 CTGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
43378686 CCGGATATTTTTCCAGCATATAGCCTGTGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
43378725 CCGGATATATTTTC
1 CCGGATAT-TTTTC
43378739 AATCTCATAC
Statistics
Matches: 148, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 143 0.97
40 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:43378641 original size:78 final size:78
Alignment explanation
Indices: 43378530--43378736 Score: 351
Period size: 78 Copynumber: 2.7 Consensus size: 78
43378520 GGTCTTTAAC
** * *
43378530 CCGGATATTTTTCCAGCACGTAGCCTGCAGACCTCAAGTCCGGATATATTTCTAGCATATAGCCT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCTAGCATATAGCCT
43378595 GCGGATCTCATGT
66 GCGGATCTCATGT
* *
43378608 TCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCTGGATATATTTCTAGCATATAGCCT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCTAGCATATAGCCT
43378673 GCGGATCTCATGT
66 GCGGATCTCATGT
*
43378686 CCGGATATTTTTCCAGCATATAGCCTGTGGACCTCATGTCCGGATATATTT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTT
43378737 TCAATCTCAT
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 120 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (78 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCGGATATATTTCTAGCATATAGCCT
GCGGATCTCATGT
Found at i:43386630 original size:14 final size:14
Alignment explanation
Indices: 43386611--43386638 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43386601 AATGAGGTTA
43386611 GGAGATAAGTTTTT
1 GGAGATAAGTTTTT
43386625 GGAGATAAGTTTTT
1 GGAGATAAGTTTTT
43386639 CGAGTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
GGAGATAAGTTTTT
Found at i:43388166 original size:11 final size:11
Alignment explanation
Indices: 43388150--43388190 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
43388140 CTCTTTTAAC
43388150 CATTTAAAATT
1 CATTTAAAATT
43388161 CATTTAAAATT
1 CATTTAAAATT
43388172 CATTTAAAATT
1 CATTTAAAATT
*
43388183 CACTTAAA
1 CATTTAAA
43388191 TTAAATTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
CATTTAAAATT
Found at i:43389612 original size:14 final size:14
Alignment explanation
Indices: 43389613--43389651 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
43389603 ATAAAATTTA
*
43389613 AAAATTT-AAAACT
1 AAAATTTAAAAAAT
*
43389626 ATAATTTAAAAAAT
1 AAAATTTAAAAAAT
43389640 AAAATTTAAAAA
1 AAAATTTAAAAA
43389652 TTTAAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTTAAAAAAT
Found at i:43389617 original size:13 final size:13
Alignment explanation
Indices: 43389613--43389652 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
43389603 ATAAAATTTA
*
43389613 AAAATTTAAAACT
1 AAAATTTAAAAAT
*
43389626 ATAATTTAAAAAAT
1 AAAATTT-AAAAAT
43389640 AAAATTTAAAAAT
1 AAAATTTAAAAAT
43389653 TTAAAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATTTAAAAAT
Found at i:43389618 original size:8 final size:8
Alignment explanation
Indices: 43389567--43389687 Score: 67
Period size: 8 Copynumber: 15.5 Consensus size: 8
43389557 AGAAATAATT
43389567 ATTTAAAA
1 ATTTAAAA
*
43389575 TATTAAAAA
1 -ATTTAAAA
*
43389584 ATTAAAGATA
1 ATTTAA-A-A
43389594 ATTTAAAA
1 ATTTAAAA
*
43389602 A-AT-AAA
1 ATTTAAAA
43389608 ATTTAAAA
1 ATTTAAAA
43389616 ATTT-AAA
1 ATTTAAAA
* *
43389623 A-CT-ATA
1 ATTTAAAA
43389629 ATTTAAAA
1 ATTTAAAA
*
43389637 A-AT-AAA
1 ATTTAAAA
43389643 ATTTAAAA
1 ATTTAAAA
43389651 ATTTAAAA
1 ATTTAAAA
* * *
43389659 CTATATAA
1 ATTTAAAA
43389667 ATTTCAAAA
1 ATTT-AAAA
*
43389676 ATCTAAAA
1 ATTTAAAA
43389684 ATTT
1 ATTT
43389688 TGGAAAACAA
Statistics
Matches: 85, Mismatches: 18, Indels: 19
0.70 0.15 0.16
Matches are distributed among these distances:
6 12 0.14
7 9 0.11
8 43 0.51
9 15 0.18
10 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (8 bp):
ATTTAAAA
Found at i:43389637 original size:35 final size:35
Alignment explanation
Indices: 43389570--43389663 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
43389560 AATAATTATT
* *
43389570 TAAAATATTAAAAAATT-AAA-GATAATTTAAAAAA
1 TAAAAT-TTAAAAATTTAAAACTATAATTTAAAAAA
43389604 TAAAATTTAAAAATTTAAAACTATAATTTAAAAAA
1 TAAAATTTAAAAATTTAAAACTATAATTTAAAAAA
43389639 TAAAATTTAAAAATTTAAAACTATA
1 TAAAATTTAAAAATTTAAAACTATA
43389664 TAAATTTCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
33 9 0.16
34 9 0.16
35 38 0.68
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (35 bp):
TAAAATTTAAAAATTTAAAACTATAATTTAAAAAA
Found at i:43389639 original size:22 final size:22
Alignment explanation
Indices: 43389593--43389637 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
43389583 AATTAAAGAT
43389593 AATTTAAAAAATAAAATTTAAA
1 AATTTAAAAAATAAAATTTAAA
* *
43389615 AATTT-AAAACTATAATTTAAA
1 AATTTAAAAAATAAAATTTAAA
43389636 AA
1 AA
43389638 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTTAAAAAATAAAATTTAAA
Found at i:43393355 original size:22 final size:21
Alignment explanation
Indices: 43393298--43393339 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43393288 ATTTTTCGAA
43393298 GAAATTGGTTTAAAAAAAGAT
1 GAAATTGGTTTAAAAAAAGAT
43393319 GAAATTGGTTTAAAAAAAGAT
1 GAAATTGGTTTAAAAAAAGAT
43393340 ACATTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (21 bp):
GAAATTGGTTTAAAAAAAGAT
Found at i:43394174 original size:76 final size:76
Alignment explanation
Indices: 43394048--43394201 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
43394038 CCAAATAGAT
43394048 TAAAGATATCCTATGAGGGTAACACACTTATGACAAGGTTATTGGATGAACACTTATTAAGTAGC
1 TAAAGATATCCTATGAGGGTAACACACTTATGACAAGGTTATTGGATGAACACTTATTAAGTAGC
43394113 TTTCCTAATGG
66 TTTCCTAATGG
*
43394124 TAAAGATATCCTATGAGGGTAACATACTTATGACAAGGTTATTGGATGAACACTTATTAAGTAGC
1 TAAAGATATCCTATGAGGGTAACACACTTATGACAAGGTTATTGGATGAACACTTATTAAGTAGC
43394189 TTTCCTAATGG
66 TTTCCTAATGG
43394200 TA
1 TA
43394202 TGTAATAAGG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (76 bp):
TAAAGATATCCTATGAGGGTAACACACTTATGACAAGGTTATTGGATGAACACTTATTAAGTAGC
TTTCCTAATGG
Found at i:43407161 original size:29 final size:29
Alignment explanation
Indices: 43407098--43407165 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
43407088 TAATCAACCG
43407098 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
43407127 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
43407156 CGCACACTTA
1 CGCACACTTA
43407166 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:43407277 original size:174 final size:174
Alignment explanation
Indices: 43406987--43407314 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
43406977 AACTCAAGGT
* *
43406987 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
43407052 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
43407117 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
43407161 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
43407226 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
43407291 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
43407315 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:43407306 original size:29 final size:30
Alignment explanation
Indices: 43407267--43407345 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
43407257 CTTAATAATC
43407267 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
43407297 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
43407326 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
43407346 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:43413413 original size:58 final size:58
Alignment explanation
Indices: 43413319--43413434 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
43413309 CGGTGCCTCT
* *
43413319 GTTTGCACTTTGGTGCCTATGTTAGCATTTCGATGCTCTCTAGTGTAATTGGGCTAGC
1 GTTTGCACTTTGGTGCCTATGTTAGCATTTCAATGCTCTCTAGTATAATTGGGCTAGC
* * *
43413377 GTTTGCA-TTTCGGTGCCTATGTTAGCATTTTAATGCTCTCTAGTATGATTGGGTTAGC
1 GTTTGCACTTT-GGTGCCTATGTTAGCATTTCAATGCTCTCTAGTATAATTGGGCTAGC
43413435 TGAGTATCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.41
Consensus pattern (58 bp):
GTTTGCACTTTGGTGCCTATGTTAGCATTTCAATGCTCTCTAGTATAATTGGGCTAGC
Found at i:43415062 original size:19 final size:19
Alignment explanation
Indices: 43415034--43415077 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
43415024 GCACTTAAAG
*
43415034 TGCATACTAGCGCACGAAA
1 TGCATACTAGCACACGAAA
* *
43415053 TGCATCCTAGCACACGAAG
1 TGCATACTAGCACACGAAA
43415072 TGCATA
1 TGCATA
43415078 TTGACCCACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18
Consensus pattern (19 bp):
TGCATACTAGCACACGAAA
Found at i:43415126 original size:38 final size:38
Alignment explanation
Indices: 43415054--43415128 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
43415044 CGCACGAAAT
* *
43415054 GCATCCTAGCACACGAAGTGCATATTGACCCACAAAGC
1 GCATCCTAGCACACGAAGTGAATATTGACACACAAAGC
* *
43415092 GCATCCTGGCACACGAAGTGAATCTT-ATCACACAAAG
1 GCATCCTAGCACACGAAGTGAATATTGA-CACACAAAG
43415129 TGAATCTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (38 bp):
GCATCCTAGCACACGAAGTGAATATTGACACACAAAGC
Found at i:43415129 original size:19 final size:19
Alignment explanation
Indices: 43415101--43415137 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43415091 CGCATCCTGG
*
43415101 CACACGAAGTGAATCTTAT
1 CACACAAAGTGAATCTTAT
43415120 CACACAAAGTGAATCTTA
1 CACACAAAGTGAATCTTA
43415138 GCGCATAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (19 bp):
CACACAAAGTGAATCTTAT
Found at i:43421811 original size:30 final size:30
Alignment explanation
Indices: 43421777--43421838 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
43421767 ATGGCATGTC
43421777 ATGAAAACAGCAGCCGCAAAGAATGCAATG
1 ATGAAAACAGCAGCCGCAAAGAATGCAATG
*
43421807 ATGAAAACAGCAGCCGCAAAGAATGCGATG
1 ATGAAAACAGCAGCCGCAAAGAATGCAATG
43421837 AT
1 AT
43421839 CATTCAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (30 bp):
ATGAAAACAGCAGCCGCAAAGAATGCAATG
Found at i:43432247 original size:173 final size:172
Alignment explanation
Indices: 43431952--43432281 Score: 498
Period size: 173 Copynumber: 1.9 Consensus size: 172
43431942 TTTCTACATT
* * * *
43431952 ATTGATTATTCAGTGATTTTACCATATTGAGCTATGCTCATAATGTTTTGTAGTTTGGCAGATGG
1 ATTGATTATTCAGTGATTTTACCACATCGAGCTATGCTCATAATGTTTTGGAGTTTGGCAGACGG
* * * *
43432017 GTTATGGGGAACTCGTGGTGTGTAGTGAATGGTATAAGTAGGAAATTTTTAGCATTGCATCAAGT
66 GTTATAGAGAACGCGTGGTGTGTAGCGAATGGTATAAGTAGGAAATTTTTAGCATTGCATCAAGT
43432082 GCACGACATATTCGAATGTTATTGATTGATGCAATACACGAC
131 GCACGACATATTCGAATGTTATTGATTGATGCAATACACGAC
* *
43432124 ATTGTATTATTCAGTGGTTTTACGACATCGAGCTATGCTCATAATGTTTTGGAGTTTGGCAGACG
1 ATTG-ATTATTCAGTGATTTTACCACATCGAGCTATGCTCATAATGTTTTGGAGTTTGGCAGACG
* * * * **
43432189 GGTTATAGAGAACGCGTGGTGTGTAGCGGATGGTATAGGTAGGAACTTTTTTGCATTGCATCATT
65 GGTTATAGAGAACGCGTGGTGTGTAGCGAATGGTATAAGTAGGAAATTTTTAGCATTGCATCAAG
*
43432254 TGCATGACATATTCGAATGTTATTGATT
130 TGCACGACATATTCGAATGTTATTGATT
43432282 TATGTTACGC
Statistics
Matches: 140, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
172 4 0.03
173 136 0.97
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (172 bp):
ATTGATTATTCAGTGATTTTACCACATCGAGCTATGCTCATAATGTTTTGGAGTTTGGCAGACGG
GTTATAGAGAACGCGTGGTGTGTAGCGAATGGTATAAGTAGGAAATTTTTAGCATTGCATCAAGT
GCACGACATATTCGAATGTTATTGATTGATGCAATACACGAC
Found at i:43434599 original size:55 final size:53
Alignment explanation
Indices: 43434474--43434663 Score: 224
Period size: 55 Copynumber: 3.5 Consensus size: 53
43434464 AACTTACCAT
* * *
43434474 TGCCATGTCTTGACATGGTCTTACGTG-GTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGAG-A-CCTTGCCTTATAGAACTCATCAA
* *
43434527 TGCCATGCCTTGGCATGGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGAGACC-TTGCCTTATAG-AACTCATCAA
* **
43434582 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACAT-ATCAA
1 TGCCATGCCTTGACATGGTCTTACATGA-GACCTTGCCTTATAGAAC-TCATCAA
*
43434636 TGCCATGCCTTGGCATGGTCTTACATGA
1 TGCCATGCCTTGACATGGTCTTACATGA
43434664 TATCCTTATC
Statistics
Matches: 119, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
52 2 0.02
53 33 0.28
54 36 0.30
55 46 0.39
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGAGACCTTGCCTTATAGAACTCATCAA
Found at i:43434704 original size:47 final size:47
Alignment explanation
Indices: 43434649--43434770 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
43434639 CATGCCTTGG
* * *
43434649 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTTCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
43434696 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
43434743 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
43434771 GTGCCAATGC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:43444781 original size:48 final size:48
Alignment explanation
Indices: 43444705--43444931 Score: 211
Period size: 48 Copynumber: 4.8 Consensus size: 48
43444695 TAGGGTTATC
* *
43444705 TGTGATCCCATGTAAGACCATGTATGGGACATGGCATTGGCATTGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATTGATA
*
43444753 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCT-ATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCAT-TGATA
* * * * * *
43444801 TTTGATCCCATATAAGACTATATCTGGGATATGACATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATTGATA
* * * * *
43444849 TGAGA-CGTCGTGTAAGACCATAG-CTGGG-C-T---ATCGGC-TTCGATC
1 TGTGATC-CCATGTAAGACCAT-GTCTGGGACATGACATTGGCATT-GATA
* *
43444892 TGTGATCCCATGTAAGACCCTGTCTGGGATATGACATTGG
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGG
43444932 AATCTTACTA
Statistics
Matches: 142, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.01
43 28 0.20
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 107 0.75
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATTGATA
Found at i:43448608 original size:47 final size:46
Alignment explanation
Indices: 43448504--43448716 Score: 163
Period size: 47 Copynumber: 4.6 Consensus size: 46
43448494 TATACGTACT
* * *
43448504 GATGCATGTCCCAGACATGTCTTACACTAGCATGAA-A-C-T-TAGCC
1 GATGCATGTCCCAGACACGTCTTACACTGGC-T-AACATCATCGAGCC
43448548 GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCATCGATGCC
1 GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCATCGA-GCC
** * *
43448595 GATGCATGTCCCAGACATATCTTACACTGG-T-AC-TCACCTCTACGCT
1 GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCA--TCGA-GCC
* ** * * * *
43448641 GATGCCATGTCCCAAACGTGGTCTTACACGGGCTATCATGATACG-GCT
1 GATG-CATGTCCCAGAC-ACGTCTTACACTGGCTAACATCAT-CGAGCC
43448689 GATGCATGTCCCAGACACGTCTTACACT
1 GATGCATGTCCCAGACACGTCTTACACT
43448717 AGCCCTCGTC
Statistics
Matches: 136, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 33 0.24
45 3 0.02
46 20 0.15
47 53 0.39
48 17 0.12
49 2 0.01
50 2 0.01
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (46 bp):
GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCATCGAGCC
Found at i:43448703 original size:94 final size:93
Alignment explanation
Indices: 43448451--43448768 Score: 313
Period size: 94 Copynumber: 3.4 Consensus size: 93
43448441 GGGTTAAGTT
* * * * * * *
43448451 GCCGCTGCCATGTCCCAGACATGGTCTTACACTAGATCTCGTGTATACGTACTGATGCATGTCCC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTATCATG-ATACGTGCTGATGCATGTCCC
*
43448516 AGACATGTCTTACACTAGCA-TGAAACTTA
65 AGACATGTCTTACACTAGCACT-CAACTTA
* * * * *
43448545 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACATCAT-CGATGCCGATGCATGTCCC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTATCATGATACG-TGCTGATGCATGTCCC
* * * *
43448607 AGACATATCTTACACTGGTACTCACCTCTA
65 AGACATGTCTTACACTAGCACTCAACT-TA
* * *
43448637 CGCTGATGCCATGTCCCAAACGTGGTCTTACACGGGCTATCATGATACG-GCTGATGCATGTCCC
1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTATCATGATACGTGCTGATGCATGTCCC
* * **
43448701 AGACACGTCTTACACTAGCCCTCGTCTTAA
65 AGACATGTCTTACACTAGCACTCAACTT-A
*
43448731 TGCCGATGCCATGTCCCAAACATGGTCTTATACTGGCT
1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCT
43448769 TTCACATAAC
Statistics
Matches: 181, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
90 2 0.01
91 36 0.20
92 17 0.09
93 20 0.11
94 85 0.47
95 19 0.10
96 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (93 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTATCATGATACGTGCTGATGCATGTCCCA
GACATGTCTTACACTAGCACTCAACTTA
Found at i:43455226 original size:48 final size:48
Alignment explanation
Indices: 43455159--43455387 Score: 238
Period size: 48 Copynumber: 4.9 Consensus size: 48
43455149 AGGTTATGTA
*
43455159 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
*
43455207 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATT
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * * *
43455255 TGATCCCATATAAGACTATATCTGGGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * * * * * *
43455303 AGA-CGTCGTGTTAGACCATAG-CTGGG---T--TATCGGCTTCGATCTG
1 TGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATG
* *
43455346 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
43455388 TTACTATGTG
Statistics
Matches: 145, Mismatches: 27, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
43 30 0.21
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 111 0.77
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:43466739 original size:10 final size:10
Alignment explanation
Indices: 43466724--43466766 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
43466714 CTATCGAAAG
43466724 TAATAAAAAT
1 TAATAAAAAT
43466734 TAATAAAAAT
1 TAATAAAAAT
43466744 TAATTATAAAAT
1 TAA-TA-AAAAT
*
43466756 TAATTAAAAT
1 TAATAAAAAT
43466766 T
1 T
43466767 CATTATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 19 0.63
11 3 0.10
12 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:43466756 original size:12 final size:11
Alignment explanation
Indices: 43466727--43466764 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 11
43466717 TCGAAAGTAA
43466727 TAAAAATTAA-
1 TAAAAATTAAT
43466737 TAAAAATTAAT
1 TAAAAATTAAT
43466748 TATAAAATTAAT
1 TA-AAAATTAAT
43466760 TAAAA
1 TAAAA
43466765 TTCATTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.38
11 5 0.19
12 11 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATTAAT
Found at i:43466756 original size:22 final size:22
Alignment explanation
Indices: 43466729--43466772 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
43466719 GAAAGTAATA
43466729 AAAATTAATAAAAATTAATTAT
1 AAAATTAATAAAAATTAATTAT
* *
43466751 AAAATTAATTAAAATTCATTAT
1 AAAATTAATAAAAATTAATTAT
43466773 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTAATAAAAATTAATTAT
Found at i:43466771 original size:10 final size:10
Alignment explanation
Indices: 43466724--43466771 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
43466714 CTATCGAAAG
*
43466724 TAATAAAAAT
1 TAATTAAAAT
*
43466734 TAATAAAAAT
1 TAATTAAAAT
43466744 TAATTATAAAAT
1 TAA-T-TAAAAT
43466756 TAATTAAAAT
1 TAATTAAAAT
*
43466766 TCATTA
1 TAATTA
43466772 TGTTAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 24 0.71
11 2 0.06
12 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATTAAAAT
Found at i:43470286 original size:22 final size:22
Alignment explanation
Indices: 43470261--43470304 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
43470251 TAATTATAAT
* *
43470261 TAATATATATTATAATATATTA
1 TAATAGATATAATAATATATTA
* *
43470283 TAATGGATATAATTATATATTA
1 TAATAGATATAATAATATATTA
43470305 ATGATTATCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TAATAGATATAATAATATATTA
Found at i:43475546 original size:40 final size:40
Alignment explanation
Indices: 43475316--43475547 Score: 315
Period size: 40 Copynumber: 5.8 Consensus size: 40
43475306 TATTACCACA
* * * * * *
43475316 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* * * *
43475356 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* *
43475396 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
43475436 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
*
43475476 AGCACAAATGCCTTTGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
43475516 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
43475548 TCATTCAAAT
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
40 174 0.98
41 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
Found at i:43478507 original size:34 final size:34
Alignment explanation
Indices: 43478464--43478531 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
43478454 GAGTTCAACC
43478464 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
1 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
43478498 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
1 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
43478532 TAGCTTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (34 bp):
AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
Found at i:43480056 original size:40 final size:40
Alignment explanation
Indices: 43480003--43480234 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
43479993 TATTACCACA
* * * * * *
43480003 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* * * *
43480043 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
* *
43480083 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
43480123 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
43480163 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
43480203 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
43480235 TCATTCAAAT
Statistics
Matches: 180, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 176 0.98
41 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
Found at i:43483185 original size:34 final size:34
Alignment explanation
Indices: 43483147--43483214 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
43483137 GAGTTCAACC
*
43483147 AGGCTCAAGCTCTATCCCTTAATGAATATGGGAA
1 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
43483181 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
1 AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
43483215 CAGCTTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (34 bp):
AGGCTCAAGCTCTATCCCTTAACGAATATGGGAA
Found at i:43489376 original size:40 final size:40
Alignment explanation
Indices: 43489259--43489378 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
43489249 ACATTAGACT
* * * * *
43489259 GAAGCTATCTCGGTATCGCACACTTAGTGCCACATAAAGCT
1 GAAGCTATCTC-GAATCGCACACTAAGTGCCAAATATAGCC
* * * *
43489300 GAAACTAT-TCTAATTCGCACACTAACTGCTC-TATATAGCC
1 GAAGCTATCTCGAA-TCGCACACTAAGTGC-CAAATATAGCC
*
43489340 GAAGCTATCTCGAAACGCACACTAAGTGCCAAATATAGC
1 GAAGCTATCTCGAATCGCACACTAAGTGCCAAATATAGC
43489379 AGATTTGTCG
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
39 2 0.03
40 48 0.77
41 12 0.19
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
GAAGCTATCTCGAATCGCACACTAAGTGCCAAATATAGCC
Found at i:43495048 original size:16 final size:17
Alignment explanation
Indices: 43495018--43495049 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43495008 AGGCATGGAA
43495018 AGAATGAAGAAAATGAG
1 AGAATGAAGAAAATGAG
43495035 AGAATGAA-AAAATGA
1 AGAATGAAGAAAATGA
43495050 ATGGATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (17 bp):
AGAATGAAGAAAATGAG
Found at i:43499189 original size:33 final size:33
Alignment explanation
Indices: 43499147--43499213 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
43499137 AAAAAAATAA
43499147 TAAAAAAAACAATAACAACAACAAGCATTATAT
1 TAAAAAAAACAATAACAACAACAAGCATTATAT
*
43499180 TAAAAAAAACAATAACAACAACGAGCATTATAT
1 TAAAAAAAACAATAACAACAACAAGCATTATAT
43499213 T
1 T
43499214 TCTTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.61, C:0.15, G:0.04, T:0.19
Consensus pattern (33 bp):
TAAAAAAAACAATAACAACAACAAGCATTATAT
Found at i:43499770 original size:147 final size:143
Alignment explanation
Indices: 43499414--43499888 Score: 555
Period size: 147 Copynumber: 3.2 Consensus size: 143
43499404 TTTTGAATTA
* * *
43499414 AAAAAAAACAGTTTAGATTTTAAAAATAAAAAAATAT-TTTTTTAGTCATTTTAAAGGAAAGTTT
1 AAAAAGAA-AGTTTAGATTTTAAAAA-ATAAAAATATGTTTTTTAGTCATTTTAAAGGAAATTTT
* *
43499478 AAATTTTTAAAATAAAGTTTTCA-TTTTTTCAACTATTTCAAAATAAAAGCTTTATTCTTTAAGA
64 AAATTTTT-AAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTA-TCTTTAAGA
**
43499542 AAAGTAGTGATTTTTAAAAAAA
127 AAAGTAGTGATTTTT-----TT
* * *
43499564 AATAAAGAGAGTTTACATTTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGGAAATTTT
1 AA-AAAGAAAGTTTAGATTTTAAAAAATAAAAATATG-TTTTTTAGTCATTTTAAAGGAAATTTT
* * ** *
43499629 AAATTTTTATAACAAAATTTTGATTTTTTTCAACAATTTTGAAATAAAAACTTTTATCTTTAAGA
64 AAATTTTTA-AACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGC-TTTATCTTTAAGA
43499694 AAAGTAGTGATTTTTTT
127 AAAGTAGTGATTTTTTT
*
43499711 AAAAGAGAAAGTTTAGAATTTAAAAAATAAAAATATGTGTTTTTAGTCATTTTAAAGGAAAATTT
1 AAAA-AGAAAGTTTAGATTTTAAAAAATAAAAATATGT-TTTTTAGTCATTTTAAAGG-AAATTT
* * *
43499776 TAAATTTTTAAACTAAAGTTTTGATCTTTTTCAACTATTTCAAAAT-AAAGCATTGATTTTTAAG
63 TAAATTTTTAAAC-AAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGC-TTTATCTTTAAG
*
43499840 AAAAGTAATGATTTTTTT
126 AAAAGTAGTGATTTTTTT
* *
43499858 AAAAAAAAACTTT-GATTTTAAAAAA-AAAAAT
1 AAAAAGAAAGTTTAGATTTTAAAAAATAAAAAT
43499889 TCTGGCCACC
Statistics
Matches: 283, Mismatches: 32, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
144 6 0.02
145 11 0.04
146 10 0.04
147 87 0.31
148 43 0.15
149 9 0.03
150 18 0.06
151 48 0.17
152 47 0.17
153 4 0.01
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (143 bp):
AAAAAGAAAGTTTAGATTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAATTTTAA
ATTTTTAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTATCTTTAAGAAAAG
TAGTGATTTTTTT
Found at i:43500347 original size:31 final size:34
Alignment explanation
Indices: 43500299--43500361 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 34
43500289 ATTATTTACA
*
43500299 CTTATATATTCTCTTTC-ATT-TGCA-TTTATAC
1 CTTATATATTCTATTTCAATTATGCACTTTATAC
43500330 CTTATATATT-TAATTTCAATTATGCACTTTAT
1 CTTATATATTCT-ATTTCAATTATGCACTTTAT
43500362 TTTAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 1 0.04
31 14 0.52
32 3 0.11
33 4 0.15
34 5 0.19
ACGTcount: A:0.27, C:0.16, G:0.03, T:0.54
Consensus pattern (34 bp):
CTTATATATTCTATTTCAATTATGCACTTTATAC
Found at i:43508788 original size:25 final size:25
Alignment explanation
Indices: 43508760--43508853 Score: 81
Period size: 25 Copynumber: 3.8 Consensus size: 25
43508750 CTCGTATAAA
43508760 CTTATCGATTCTCAGCTCGTGAGAG
1 CTTATCGATTCTCAGCTCGTGAGAG
* *
43508785 CTTA-CTAATTCTCAGTTCGT-ATGAG
1 CTTATC-GATTCTCAGCTCGTGA-GAG
43508810 CTTAT-GATT-TACAGCTCGTGAGAG
1 CTTATCGATTCT-CAGCTCGTGAGAG
* *
43508834 CATACCGATTCAT-AGCTCGT
1 CTTATCGATTC-TCAGCTCGT
43508854 ATGAGCATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
23 1 0.02
24 18 0.33
25 35 0.64
27 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
CTTATCGATTCTCAGCTCGTGAGAG
Found at i:43508854 original size:49 final size:50
Alignment explanation
Indices: 43508747--43508859 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
43508737 GGACACACCA
* * * *
43508747 CAGCTCGTATAAACTTATCGATTCTCAGCTCGTGAGAGCTTACTAATTCT
1 CAGCTCGTATGAGCTTATCGATTCTCAGCTCGTGAGAGCATACCAATTCT
* *
43508797 CAGTTCGTATGAGCTTAT-GATT-TACAGCTCGTGAGAGCATACCGATTCAT
1 CAGCTCGTATGAGCTTATCGATTCT-CAGCTCGTGAGAGCATACCAATTC-T
43508847 -AGCTCGTATGAGC
1 CAGCTCGTATGAGC
43508860 ATACATGTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
48 1 0.02
49 37 0.69
50 16 0.30
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTATCGATTCTCAGCTCGTGAGAGCATACCAATTCT
Found at i:43511375 original size:17 final size:18
Alignment explanation
Indices: 43511353--43511386 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
43511343 AGTTGAATTG
43511353 AAATTGTG-AAATTAAAT
1 AAATTGTGAAAATTAAAT
43511370 AAATTGTGAAAATTAAA
1 AAATTGTGAAAATTAAA
43511387 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
AAATTGTGAAAATTAAAT
Found at i:43512139 original size:10 final size:10
Alignment explanation
Indices: 43512112--43512171 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
43512102 TTAAATTCTA
43512112 AAAGATAAAT
1 AAAGATAAAT
43512122 ACAA-ATAAAT
1 A-AAGATAAAT
* *
43512132 AAATATAATT
1 AAAGATAAAT
**
43512142 AAAGATACTT
1 AAAGATAAAT
43512152 AAAGATAAAT
1 AAAGATAAAT
*
43512162 AAAAATAAAT
1 AAAGATAAAT
43512172 CCTAAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
9 2 0.05
10 38 0.90
11 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:43516125 original size:15 final size:16
Alignment explanation
Indices: 43516094--43516127 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43516084 ATTTCAACAT
43516094 ATAAAAAAAGATAAAA
1 ATAAAAAAAGATAAAA
*
43516110 ATAAAAAAATA-AAAA
1 ATAAAAAAAGATAAAA
43516125 ATA
1 ATA
43516128 GGTGGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
ATAAAAAAAGATAAAA
Found at i:43527485 original size:33 final size:33
Alignment explanation
Indices: 43527445--43527512 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
43527435 AATTAAACTA
43527445 ATTTAATAAAAGAAAACATGAAATTAAAACACT
1 ATTTAATAAAAGAAAACATGAAATTAAAACACT
43527478 ATTTAATAAAAGAAAACATGAAATTAAAACACT
1 ATTTAATAAAAGAAAACATGAAATTAAAACACT
43527511 AT
1 AT
43527513 CTTCTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.25
Consensus pattern (33 bp):
ATTTAATAAAAGAAAACATGAAATTAAAACACT
Found at i:43528450 original size:25 final size:24
Alignment explanation
Indices: 43528372--43528451 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
43528362 TACACCACGG
*
43528372 CTCGTATGAGCTTACCGATTTGTAA
1 CTCGTATGAGCTTACTGATTT-TAA
* * *
43528397 CTTGTGA-GAGCTTA-TCGATTCTCAG
1 CTCGT-ATGAGCTTACT-GATT-TTAA
43528422 CTCGTATGAGCTTACTGATTTATAA
1 CTCGTATGAGCTTACTGATTT-TAA
43528447 CTCGT
1 CTCGT
43528452 TTATTTACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
24 2 0.05
25 37 0.88
26 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
CTCGTATGAGCTTACTGATTTTAA
Found at i:43531521 original size:154 final size:147
Alignment explanation
Indices: 43531214--43531681 Score: 478
Period size: 154 Copynumber: 3.0 Consensus size: 147
43531204 ATTTTAGGAT
* *
43531214 ATTTTTTTAAAAAAAAAAGAGAAAGTTTAGATGTTTAAAAATAAAAATCTATTTTTTTAGTCATT
1 ATTTTTTT-AAAAAAAAAGGGAAAGTTTAGAT-TTTTAAAATAAAAATCTA-TTTTTTAGTCATT
* *
43531279 TTAAAAGAAA-TTTAAATTTTTTAAAAAAA-ATTGA-TTTTTTCAACTATTTCAAAATAAAAGCT
63 TTAAAGGAAAGTTTAAA-TTTTTAAAAAAATTTTGATTTTTTTCAACTATTTCAAAATAAAAGCT
*
43531341 TTGATCTTTAAGAAAATTAGTT
127 TTGATCTTTAAGAAAATT-GTG
* ** *
43531363 ATTTTTTTAAAAAAAAAGGGCAAGTTTTTTATTTTTGAAAATAAAAATCTATTTTTTAGTGATTT
1 ATTTTTTTAAAAAAAAAGGGAAAG-TTTAGATTTTT-AAAATAAAAATCTATTTTTTAGTCATTT
* *
43531428 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAAAAA
64 TAAAGGAAAGTTTAAATTTTTAAAA-AAA-TTTTGA--TTTTTTTCAACTATTTCAAAATAAAAG
43531493 CTTTGATCTTTAAGAAAAGTTGTG
125 CTTTGATCTTTAAGAAAA-TTGTG
* * *
43531517 ATTTTTTAGAAGAAAAAAGAGAGAGAGAAAGTTTAGATTTTTAAAA-AAATATATATGTTTTTTT
1 ATTTTTT--TA-AAAAAA-A-AG-G-GAAAGTTTAGATTTTTAAAATAAA-A-ATCT-ATTTTTT
** **
43531581 AGTCATTTTAAAGGAAAAGTTTAAATTTTTAAAATAAAATTTTGATCCTTTTCAACTATTTCGGA
56 AGTCATTTTAAAGG-AAAGTTTAAATTTTT-AAA-AAAATTTTGATTTTTTTCAACTATTTCAAA
* * *
43531646 AT-ACAGCTTTGATTTTTAAGAAAAATAGTG
118 ATAAAAGCTTTGATCTTTAAG-AAAATTGTG
43531676 ATTTTT
1 ATTTTT
43531682 AAAAGAAAAC
Statistics
Matches: 268, Mismatches: 27, Indels: 38
0.80 0.08 0.11
Matches are distributed among these distances:
148 46 0.17
149 36 0.13
151 4 0.01
154 52 0.19
155 2 0.01
156 1 0.00
157 6 0.02
158 4 0.01
159 32 0.12
160 35 0.13
161 23 0.09
162 20 0.07
163 6 0.02
164 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (147 bp):
ATTTTTTTAAAAAAAAAGGGAAAGTTTAGATTTTTAAAATAAAAATCTATTTTTTAGTCATTTTA
AAGGAAAGTTTAAATTTTTAAAAAAATTTTGATTTTTTTCAACTATTTCAAAATAAAAGCTTTGA
TCTTTAAGAAAATTGTG
Found at i:43531697 original size:20 final size:20
Alignment explanation
Indices: 43531652--43531709 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
43531642 CGGAATACAG
43531652 CTTTGATTTTT--AAGAAAA
1 CTTTGATTTTTAAAAGAAAA
* *
43531670 ATAGTGATTTTTAAAAGAAAA
1 CT-TTGATTTTTAAAAGAAAA
*
43531691 CTTTGATTTTGAAAA-AAAA
1 CTTTGATTTTTAAAAGAAAA
43531710 ATTGTCCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 12 0.38
20 11 0.34
21 8 0.25
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
CTTTGATTTTTAAAAGAAAA
Found at i:43533251 original size:4 final size:4
Alignment explanation
Indices: 43533242--43533268 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
43533232 TGCCTAAGAT
43533242 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
43533269 AATGGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:43537228 original size:47 final size:47
Alignment explanation
Indices: 43537174--43537502 Score: 550
Period size: 47 Copynumber: 7.0 Consensus size: 47
43537164 GATTTTATGA
** * *
43537174 GATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* *
43537221 GATGAATGTGAACATGCATATATGTGCTAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
*
43537268 GATGAATCTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
43537315 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
*
43537362 GATGAATGTGAACATGCATATGTGTGCTAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
43537409 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* ** *
43537456 GATGAATGTGAACATGCATATGTGGGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
43537503 AATAAACGTG
Statistics
Matches: 268, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 268 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
Found at i:43537341 original size:141 final size:141
Alignment explanation
Indices: 43537174--43537551 Score: 571
Period size: 141 Copynumber: 2.7 Consensus size: 141
43537164 GATTTTATGA
** * *
43537174 GATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
43537239 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
66 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
43537304 ATGGCCAATGT
131 ATGGCCAATGT
43537315 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* *
43537380 TATGTGTGCTAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGA
66 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
43537445 ATGGCCAATGT
131 ATGGCCAATGT
* ** * * * * * *
43537456 GATGAATGTGAACATGCATATGTGGGATAAGGTAGAATGGCTAATGTAATAAACGTGGAA-GTGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATGC
* *
43537520 ATATATGTGGCGAA-GCCGAATGGCTAATGTGA
65 ATATATGT-GCTAAGGCCGAATGGCCAATGTGA
43537552 GATATGTATG
Statistics
Matches: 217, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
141 210 0.97
142 7 0.03
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (141 bp):
GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
ATGGCCAATGT
Found at i:43542707 original size:24 final size:23
Alignment explanation
Indices: 43542628--43542707 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
43542618 TATTTTTAAA
43542628 ATACATA-C-TTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
* *
43542649 AT-CTTACTTATCTATATACCCTTGTAT
1 ATACATACCT-T-TATATA--CTT-TAT
*
43542676 ATATATACCTTTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
43542699 AATACATAC
1 -ATACATAC
43542708 ATGCACATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
23 4 0.09
24 16 0.36
26 9 0.20
27 6 0.14
28 4 0.09
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.46
Consensus pattern (23 bp):
ATACATACCTTTATATACTTTAT
Found at i:43555028 original size:40 final size:40
Alignment explanation
Indices: 43554966--43555234 Score: 223
Period size: 40 Copynumber: 6.6 Consensus size: 40
43554956 AAAGAATTGC
*
43554966 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAT
*
43555006 AGTATCCTATCT-CCTGAGATTACAGTGGAGC-GATTAAA-
1 AG-ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAT
* * * ***
43555044 GGATCTTATCTCTCTGA-AGTTACAGTAGAG-AGATCGCAT
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAT
**
43555083 CAG-TCTTATCTCCCTGAGATTACAGTGGA-CAGACAAAGATTT
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAA-A--T
* *
43555125 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATGAAGA-
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAA-AT
* * *
43555166 ATATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAT
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAT
43555207 AAAGGATCTTATCTCCCTGA-AGTTACAG
1 --A-GATCTTATCTCCCTGAGA-TTACAG
43555235 CAGAGTAGAT
Statistics
Matches: 184, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
37 9 0.05
38 19 0.10
39 32 0.17
40 55 0.30
41 10 0.05
42 4 0.02
43 27 0.15
44 28 0.15
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (40 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAT
Found at i:43555135 original size:43 final size:42
Alignment explanation
Indices: 43554924--43555196 Score: 204
Period size: 40 Copynumber: 6.7 Consensus size: 42
43554914 ATTATACAGG
*
43554924 TCTTAT-TCCCTGAGATTACAGTGGAACAGACCAAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA-CAAAG-A-T-CAGA
* **
43554969 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAA-AT-AGTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACAAAGATCAG-A
* *
43555010 TCCTATCT-CCTGAGATTACAGTGGAGC-GATTAAAG----GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA-CAAAGATCAGA
* *
43555047 TCTTATCTCTCTGA-AGTTACAGTAGAG-AGATC---GCATCAG-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGA-CAAAG-ATCAGA
43555086 TCTTATCTCCCTGAGATTACAGTGGA-CAGACAAAGATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACAAAGA--TCAGA
* ** *
43555129 TCTTATCTCCCTGAGATTACAGCGGAGCAGATGAAGA--ATA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACAAAGATCAGA
*
43555169 TCCTATCTCCCTGAGATTACAGTGGAGC
1 TCTTATCTCCCTGAGATTACAGTGGAGC
43555197 GGATTAAAAT
Statistics
Matches: 188, Mismatches: 19, Indels: 47
0.74 0.07 0.19
Matches are distributed among these distances:
35 1 0.01
37 9 0.05
38 19 0.10
39 27 0.14
40 54 0.29
41 9 0.05
42 5 0.03
43 26 0.14
44 8 0.04
45 8 0.04
46 22 0.12
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACAAAGATCAGA
Found at i:43555188 original size:83 final size:82
Alignment explanation
Indices: 43554930--43555194 Score: 273
Period size: 83 Copynumber: 3.2 Consensus size: 82
43554920 CAGGTCTTAT
*
43554930 TCCCTGAGATTACAGTGGAACAGACCAAAGAATTGCAGATCTTATCTCCCTGAGATTACAGCGGA
1 TCCCTGAGATTACAGTGG-ACAGA-CAAAG-ATTACAGATCTTATCTCCCTGAGATTACAGCGGA
43554995 GCAGATTAA-ATAGTATCCTATC
63 GCAGA-TAAGA-A-TATCCTATC
* * **
43555017 T-CCTGAGATTACAGTGG--AG-C---GATTAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAG
1 TCCCTGAGATTACAGTGGACAGACAAAGATTACA-GATCTTATCTCCCTGAGA-TTACAGCGGAG
* * *
43555074 -AGAT-CGCATCAGTCTTATC
64 CAGATAAGAAT-A-TCCTATC
*
43555093 TCCCTGAGATTACAGTGGACAGACAAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCA
1 TCCCTGAGATTACAGTGGACAGACAAAGATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCA
43555158 GATGAAGAATATCCTATC
66 GAT-AAGAATATCCTATC
43555176 TCCCTGAGATTACAGTGGA
1 TCCCTGAGATTACAGTGGA
43555195 GCGGATTAAA
Statistics
Matches: 146, Mismatches: 16, Indels: 36
0.74 0.08 0.18
Matches are distributed among these distances:
74 1 0.01
75 2 0.01
76 8 0.05
77 24 0.16
78 25 0.17
79 2 0.01
80 1 0.01
81 1 0.01
82 24 0.16
83 37 0.25
84 1 0.01
85 3 0.02
86 16 0.11
87 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (82 bp):
TCCCTGAGATTACAGTGGACAGACAAAGATTACAGATCTTATCTCCCTGAGATTACAGCGGAGCA
GATAAGAATATCCTATC
Found at i:43555197 original size:160 final size:165
Alignment explanation
Indices: 43554923--43555284 Score: 517
Period size: 160 Copynumber: 2.2 Consensus size: 165
43554913 CATTATACAG
43554923 GTCTTATTCCCTGAGATTACAGTGGAACAGACCAAAGAATTGCAGATCTTATCTCCCTGAGATTA
1 GTCTTATTCCCTGAGATTACAGTGG-ACAGA-CAAAGAATTGCAGATCTTATCTCCCTGAGATTA
*
43554988 CAGCGGAGCAGATTAAATAGTATCCTATCTCCTGAGATTACAGTGGAGC-GA-T-TAAAGGATCT
64 CAGCGGAGCAGATGAAATAGTATCCTATCTCCTGAGATTACAGTGGAGCGGATTATAAAGGATCT
* *
43555050 TATCTCTCTGAAGTTACAGTAGAG-AGATCGCATC-A
129 TATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAA
*
43555085 GTCTTATCTCCCTGAGATTACAGTGGACAGACAAAG-ATTTCAGATCTTATCTCCCTGAGATTAC
1 GTCTTAT-TCCCTGAGATTACAGTGGACAGACAAAGAATTGCAGATCTTATCTCCCTGAGATTAC
43555149 AGCGGAGCAGATGAAGA-A-TATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGG
65 AGCGGAGCAGATGAA-ATAGTATCCTATCT-CCTGAGATTACAGTGGAGCGGATT---ATAAAGG
43555212 ATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAA
125 ATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAA
* *
43555253 GTCTTATTTCCCTGAAGA-TGCAGTGGAAAGAC
1 GTCTTA-TTCCCTG-AGATTACAGTGGACAGAC
43555285 GAAAACAACA
Statistics
Matches: 181, Mismatches: 6, Indels: 20
0.87 0.03 0.10
Matches are distributed among these distances:
159 10 0.06
160 61 0.34
161 8 0.04
162 13 0.07
163 18 0.10
166 32 0.18
167 10 0.06
168 25 0.14
169 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (165 bp):
GTCTTATTCCCTGAGATTACAGTGGACAGACAAAGAATTGCAGATCTTATCTCCCTGAGATTACA
GCGGAGCAGATGAAATAGTATCCTATCTCCTGAGATTACAGTGGAGCGGATTATAAAGGATCTTA
TCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAA
Found at i:43555235 original size:84 final size:81
Alignment explanation
Indices: 43554967--43555244 Score: 256
Period size: 83 Copynumber: 3.4 Consensus size: 81
43554957 AAGAATTGCA
*
43554967 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAA-ATAGTATCCTATCT-CCTGAGATTACA
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGA-TAAGA-A-TATCCTATCTCCCTGAGATTACA
43555030 GTGGAGCGAT----TAAAG
63 GTGGAGCGATAAAATAAAG
* * * * *
43555045 GATCTTATCTCTCTGA-AGTTACAGTAGAG-AGAT-CGCATCAGTCTTATCTCCCTGAGATTACA
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGATAAGAAT-A-TCCTATCTCCCTGAGATTACA
* **
43555107 GTGGA-CAGACAAAGATTTCA-
63 GTGGAGC-GATAAA-A-TAAAG
*
43555127 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATGAAGAATATCCTATCTCCCTGAGATTACAGT
1 GATCTTATCTCCCTGAGATTACAGCAGAGCAGAT-AAGAATATCCTATCTCCCTGAGATTACAGT
43555192 GGAGCGGATTAAAATAAAG
65 GGAGC-GA-TAAAATAAAG
*
43555211 GATCTTATCTCCCTGA-AGTTACAGCAGAGTAGAT
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGCAGAT
43555245 CGCATCAAGT
Statistics
Matches: 159, Mismatches: 21, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
74 1 0.01
75 2 0.01
76 9 0.06
77 23 0.14
78 24 0.15
82 24 0.15
83 35 0.22
84 35 0.22
85 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (81 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGCAGATAAGAATATCCTATCTCCCTGAGATTACAGTG
GAGCGATAAAATAAAG
Found at i:43556671 original size:22 final size:24
Alignment explanation
Indices: 43556643--43556702 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
43556633 AGTCCCTTTT
*
43556643 TTATTATTAATTGTTTT-TTATC-
1 TTATTATTAATTATTTTATTATCA
43556665 TTATTATTAATTATTTTATTATCA
1 TTATTATTAATTATTTTATTATCA
*
43556689 TTAGTATT-ATTATT
1 TTATTATTAATTATT
43556703 GCTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 16 0.47
23 11 0.32
24 7 0.21
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (24 bp):
TTATTATTAATTATTTTATTATCA
Found at i:43556810 original size:19 final size:18
Alignment explanation
Indices: 43556757--43556829 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 18
43556747 ATTATGTTAT
43556757 ATTATATTATTATATTATAC
1 ATTATATT-TTAT-TTATAC
* *
43556777 ATTATCCTTACTATTTATAC
1 ATTAT-ATT-TTATTTATAC
*
43556797 ATTTTATATTTATTTTTATAC
1 A--TTATATTT-TATTTATAC
43556818 ATTATATTTTAT
1 ATTATATTTTAT
43556830 ATATGTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
20 12 0.28
21 17 0.40
22 4 0.09
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATATTTTATTTATAC
Found at i:43556937 original size:20 final size:20
Alignment explanation
Indices: 43556754--43557071 Score: 113
Period size: 20 Copynumber: 15.3 Consensus size: 20
43556744 TTTATTATGT
43556754 TATATTATATTATTATA-TTA
1 TATATTATATT-TTATATTTA
* **
43556774 TACATTAT-CCTTACTATTTA
1 TATATTATATTTTA-TATTTA
* * *
43556794 TACATTTTATATTTATTTTTA
1 TATATTATAT-TTTATATTTA
*
43556815 TACATTATATTTTATATATGTTTA
1 TATATTATA-TTT-TATA--TTTA
*
43556839 CATATTA-ATTTT-TATTTA
1 TATATTATATTTTATATTTA
* *
43556857 TATATTGTATACTACTTATATATA
1 TATA-T-TATA-T-TTTATATTTA
* *
43556881 TACTTTTTATACTTTATATTTAA
1 TA--TATTATATTTTATATTT-A
* * *
43556904 TACATTAAATATTATATTT-
1 TATATTATATTTTATATTTA
*
43556923 TATATGTATATATTATTTATTT-
1 TATAT-TATAT-TT-TATATTTA
*
43556945 T-TATTATCATTTGTATATATTT
1 TATATTAT-ATTT-TATAT-TTA
*
43556967 TATAATTATATATTATATTTA
1 TAT-ATTATATTTTATATTTA
43556988 CT-TATTATATTTGTATATTTA
1 -TATATTATATTT-TATATTTA
* * *
43557009 T-TATTTTA-TATACA-TTA
1 TATATTATATTTTATATTTA
*
43557026 T-TATATATATTTTATTTTTA
1 TATAT-TATATTTTATATTTA
*
43557046 TATATACATATTTTAT-TTTA
1 TATAT-TATATTTTATATTTA
43557066 TATATT
1 TATATT
43557072 CATAATATAC
Statistics
Matches: 226, Mismatches: 41, Indels: 63
0.68 0.12 0.19
Matches are distributed among these distances:
17 7 0.03
18 16 0.07
19 11 0.05
20 62 0.27
21 61 0.27
22 32 0.14
23 10 0.04
24 25 0.11
25 1 0.00
26 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTATATTTTATATTTA
Found at i:43556938 original size:13 final size:12
Alignment explanation
Indices: 43556912--43557071 Score: 62
Period size: 11 Copynumber: 14.0 Consensus size: 12
43556902 AATACATTAA
*
43556912 ATATTATATTTT
1 ATATTATATATT
43556924 ATATGTATATATT
1 ATAT-TATATATT
43556937 AT-TTAT-T-TT
1 ATATTATATATT
43556946 -TATTATCAT-TT
1 ATATTAT-ATATT
* *
43556957 GTA-TATATTTT
1 ATATTATATATT
43556968 ATAATTATATATT
1 AT-ATTATATATT
43556981 ATATT-TACTTATT
1 ATATTATA--TATT
*
43556994 ATATTTGTATATT
1 ATA-TTATATATT
43557007 -TATTAT-T-TT
1 ATATTATATATT
*
43557016 ATA-TACATTATT
1 ATATTATA-TATT
*
43557028 ATA-TATATTTT
1 ATATTATATATT
*
43557039 AT-TTTTATA-T
1 ATATTATATATT
* *
43557049 ATA-CATATTTT
1 ATATTATATATT
*
43557060 ATTTTATATATT
1 ATATTATATATT
43557072 CATAATATAC
Statistics
Matches: 113, Mismatches: 15, Indels: 40
0.67 0.09 0.24
Matches are distributed among these distances:
8 1 0.01
9 10 0.09
10 12 0.11
11 30 0.27
12 27 0.24
13 29 0.26
14 2 0.02
15 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (12 bp):
ATATTATATATT
Found at i:43556964 original size:44 final size:42
Alignment explanation
Indices: 43556916--43557005 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 42
43556906 CATTAAATAT
43556916 TATATTTTAT-ATGTATATATTATTTATTT-TTATTATCATTTGTA
1 TATATTTTATAAT-TATATATTA--TATTTATTATTAT-ATTTGTA
43556960 TATATTTTATAATTATATATTATATTTACTTATTATATTTGTA
1 TATATTTTATAATTATATATTATATTTA-TTATTATATTTGTA
43557003 TAT
1 TAT
43557006 TTATTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
42 5 0.12
43 10 0.23
44 26 0.60
45 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (42 bp):
TATATTTTATAATTATATATTATATTTATTATTATATTTGTA
Found at i:43557004 original size:8 final size:7
Alignment explanation
Indices: 43556797--43557071 Score: 58
Period size: 7 Copynumber: 38.4 Consensus size: 7
43556787 CTATTTATAC
43556797 ATTTTAT
1 ATTTTAT
43556804 A-TTTAT
1 ATTTTAT
43556810 -TTTTAT
1 ATTTTAT
**
43556816 ACATTAT
1 ATTTTAT
43556823 ATTTTATAT
1 A-TTT-TAT
*
43556832 ATGTTTAC
1 AT-TTTAT
*
43556840 ATATTA-
1 ATTTTAT
43556846 ATTTT-T
1 ATTTTAT
43556852 ATTTATAT
1 ATTT-TAT
*
43556860 ATTGTAT
1 ATTTTAT
*
43556867 ACTACTTAT
1 A-T-TTTAT
*
43556876 A-TATAT
1 ATTTTAT
43556882 ACTTTTTAT
1 A--TTTTAT
*
43556891 ACTTTAT
1 ATTTTAT
*
43556898 ATTTAAT
1 ATTTTAT
** *
43556905 ACATTAA
1 ATTTTAT
*
43556912 ATATTAT
1 ATTTTAT
43556919 ATTTTAT
1 ATTTTAT
*
43556926 ATGTATAT
1 AT-TTTAT
43556934 ATTATT-T
1 ATT-TTAT
43556941 ATTTT-T
1 ATTTTAT
*
43556947 ATTATCAT
1 ATT-TTAT
43556955 -TTGTATAT
1 ATT-T-TAT
43556963 ATTTTAT
1 ATTTTAT
*
43556970 A-ATTAT
1 ATTTTAT
*
43556976 ATATTAT
1 ATTTTAT
43556983 A-TTTACT
1 ATTTTA-T
*
43556990 -TATTAT
1 ATTTTAT
43556996 ATTTGTAT
1 ATTT-TAT
43557004 A-TTTATT
1 ATTTTA-T
43557011 ATTTTAT
1 ATTTTAT
*
43557018 ATACATTAT
1 AT--TTTAT
*
43557027 -TATATAT
1 AT-TTTAT
43557034 ATTTTAT
1 ATTTTAT
43557041 -TTTTAT
1 ATTTTAT
**
43557047 ATATACAT
1 AT-TTTAT
43557055 ATTTTAT
1 ATTTTAT
43557062 -TTTATAT
1 ATTT-TAT
43557069 ATT
1 ATT
43557072 CATAATATAC
Statistics
Matches: 194, Mismatches: 41, Indels: 65
0.65 0.14 0.22
Matches are distributed among these distances:
6 48 0.25
7 86 0.44
8 39 0.20
9 21 0.11
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (7 bp):
ATTTTAT
Found at i:43557047 original size:51 final size:52
Alignment explanation
Indices: 43556971--43557069 Score: 123
Period size: 49 Copynumber: 1.9 Consensus size: 52
43556961 ATATTTTATA
* **
43556971 ATTATATATTATATTTACTTATTATATTTGTATATTTATTATTTTATATACATT
1 ATTATATATTATATTTACTTATTATATATACATA-TT-TTATTTTATATACATT
*
43557025 ATTATATA-TAT-TTTA-TTTTTATATATACATATTTTATTTTATATA
1 ATTATATATTATATTTACTTATTATATATACATATTTTATTTTATATA
43557070 TTCATAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 12 0.29
50 2 0.05
51 12 0.29
52 4 0.10
53 3 0.07
54 8 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (52 bp):
ATTATATATTATATTTACTTATTATATATACATATTTTATTTTATATACATT
Found at i:43580572 original size:40 final size:39
Alignment explanation
Indices: 43580522--43580624 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 39
43580512 GAAGAATTTA
* * *
43580522 GATCTTATCTCCTGAATTACAGT-GAGCAGATTGAAGATAG
1 GATCCTATCTCCTGAATTACAGTGGAGC-GATT-AAAAAAG
*
43580562 TATCCTATCTCCTGAGATTACAGTGGAGCGATTAAAAAAG
1 GATCCTATCTCCTGA-ATTACAGTGGAGCGATTAAAAAAG
*
43580602 GATCTTATCT-CTGAAGTTACAGT
1 GATCCTATCTCCTGAA-TTACAGT
43580625 AGAGTAGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.02
39 11 0.20
40 26 0.48
41 12 0.22
42 4 0.07
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (39 bp):
GATCCTATCTCCTGAATTACAGTGGAGCGATTAAAAAAG
Found at i:43580612 original size:80 final size:81
Alignment explanation
Indices: 43580521--43580932 Score: 264
Period size: 80 Copynumber: 5.0 Consensus size: 81
43580511 CGAAGAATTT
*
43580521 AGATCTTATCTCCTGAATTACAG-TGAGCAGATTGAAGATAGTATCCTATCT-CCTGAGATTACA
1 AGATCTTATCTCCTGAATTACAGCGGAGCAGATTGAAGATAGTATCCTATCTCCCTGAGATTACA
43580584 GTGGAGCGATTAAAAA
66 GTGGAGCGATTAAAAA
** * * * * *
43580600 AGGATCTTATCT-CTGAAGTTACAGTAGAGTAGAATCG--CATCAG-GTCTTATCTCCCTGAGAA
1 A-GATCTTATCTCCTGAA-TTACAGCGGAGCAG-ATTGAAGAT-AGTATCCTATCTCCCTGAG-A
** *
43580661 TTACAGTGGA-CAGACCGAAAGATTTC
61 TTACAGTGGAGC-GA-TTAAA-A---A
43580687 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTG-A-ATAGTAATCCTATCTCCCTGAGATT
1 AGATCTTATCT-CCTGA-ATTACAGCGGAGCAGATTGAAGATAGT-ATCCTATCTCCCTGAGATT
43580750 ACAGTGGAG-GATTAAAATAA
63 ACAGTGGAGCGATT-AAA-AA
* * * * * *
43580770 AGGATCTTATCTCCTGAAGTTACAGCAGAGTAGATCG--CATCAG-GTCTTATCT-CCTGAG-TT
1 A-GATCTTATCTCCTGAA-TTACAGCGGAGCAGATTGAAGAT-AGTATCCTATCTCCCTGAGATT
** ***
43580830 ACAGTGGCAGC-AGGAATTTC
63 ACAGTGG-AGCGATTAA-AAA
* *
43580850 AGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 AGATCTTATCT-CCTGA-ATTACAGCGGAGCAGATTGAAGATAGT-ATCCTATCTCCCTGAGATT
43580915 ACAGTGGA-CGGATTAAAA
63 ACAGTGGAGC-GATTAAAA
43580933 TAAAGGATTA
Statistics
Matches: 256, Mismatches: 39, Indels: 71
0.70 0.11 0.19
Matches are distributed among these distances:
79 16 0.06
80 58 0.23
81 26 0.10
82 25 0.10
83 34 0.13
84 20 0.08
85 12 0.05
86 18 0.07
87 17 0.07
88 29 0.11
89 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (81 bp):
AGATCTTATCTCCTGAATTACAGCGGAGCAGATTGAAGATAGTATCCTATCTCCCTGAGATTACA
GTGGAGCGATTAAAAA
Found at i:43580750 original size:42 final size:42
Alignment explanation
Indices: 43580689--43580918 Score: 162
Period size: 42 Copynumber: 5.5 Consensus size: 42
43580679 AAGATTTCAG
43580689 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATAGTA
* * * *
43580731 ATCCTATCTCCCTGAGATTACAGTGGAG--GATTAAAATAAAG-G
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAAT--AGTA
* * * *
43580773 ATCTTATCT-CCTGA-AGTTACAGCAGAGTAGATCGCATCAG--
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAT-AGTA
* * *
43580813 GTCTTATCT-CCTGAG-TTACAGTGGCAGCAG---GAAT-TTCA
1 ATCTTATCTCCCTGAGATTACAGCGG-AGCAGATTGAATAGT-A
*
43580851 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTA
1 -ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAA--TAGTA
*
43580896 ATCCTATCTCCCTGAGATTACAG
1 ATCTTATCTCCCTGAGATTACAG
43580919 TGGACGGATT
Statistics
Matches: 146, Mismatches: 22, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
37 3 0.02
39 15 0.10
40 32 0.22
41 27 0.18
42 36 0.25
43 8 0.05
44 22 0.15
45 2 0.01
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATAGTA
Found at i:43580967 original size:165 final size:167
Alignment explanation
Indices: 43580514--43580988 Score: 649
Period size: 165 Copynumber: 2.9 Consensus size: 167
43580504 AGTAGATCGA
*
43580514 AGAATTT-AGATCTTATCT-CCTGA-ATTACAG-TGAGCAGATTGAAGATAGT-ATCCTATCT-C
1 AGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-TAGTAATCCTATCTCC
*
43580573 CTGAGATTACAGTGGAGCGATT-AAA-AAAGGATCTTATCTCT-GAAGTTACAGTAGAGTAGAAT
65 CTGAGATTACAGTGGAG-GATTAAAATAAAGGA-CTTATCTCTCTAAGTTACAGTAGAGTAG-AT
*
43580635 CGCATCAGGTCTTATCTCCCTGAGAATTACAGTGGACAGACCG
127 CGCATCAGGTCTTATCT-CCTGAG-ATTACAGTGGACAGACAG
*
43580678 AAAGATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAA-TAGTAATCCTATCTCC
1 AGA-ATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGTAATCCTATCTCC
*
43580742 CTGAGATTACAGTGGAGGATTAAAATAAAGGATCTTATCTC-CTGAAGTTACAGCAGAGTAGATC
65 CTGAGATTACAGTGGAGGATTAAAATAAAGGA-CTTATCTCTCT-AAGTTACAGTAGAGTAGATC
43580806 GCATCAGGTCTTATCTCCTGAG-TTACAGTGG-CAG-CAG
128 GCATCAGGTCTTATCTCCTGAGATTACAGTGGACAGACAG
*
43580843 -GAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTCC
1 AGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-TAGTAATCCTATCTCC
43580907 CTGAGATTACAGTGGACGGATTAAAATAAAGGA-TTATCTCTCTAAGGTTACAGTAGAGTAGATC
65 CTGAGATTACAGTGGA-GGATTAAAATAAAGGACTTATCTCTCTAA-GTTACAGTAGAGTAGATC
** *
43580971 GTTTCAGATCTTATCTCC
128 GCATCAGGTCTTATCTCC
43580989 CAAAGTGGAG
Statistics
Matches: 284, Mismatches: 11, Indels: 31
0.87 0.03 0.10
Matches are distributed among these distances:
163 43 0.15
164 12 0.04
165 72 0.25
166 30 0.11
167 18 0.06
168 20 0.07
169 39 0.14
170 34 0.12
171 16 0.06
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (167 bp):
AGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTAGTAATCCTATCTCCC
TGAGATTACAGTGGAGGATTAAAATAAAGGACTTATCTCTCTAAGTTACAGTAGAGTAGATCGCA
TCAGGTCTTATCTCCTGAGATTACAGTGGACAGACAG
Found at i:43582627 original size:24 final size:23
Alignment explanation
Indices: 43582548--43582627 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
43582538 ATATTTTAAA
43582548 ATACATA-C-TTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
* *
43582569 AT-CTTACTTATCTATATACCCTTGTAT
1 ATACATACCT-T-TATATA--CTT-TAT
*
43582596 ATATATACCTTTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
43582619 AATACATAC
1 -ATACATAC
43582628 ATGCACATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
23 4 0.09
24 16 0.36
26 9 0.20
27 6 0.14
28 4 0.09
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.46
Consensus pattern (23 bp):
ATACATACCTTTATATACTTTAT
Found at i:43595335 original size:176 final size:176
Alignment explanation
Indices: 43594950--43595452 Score: 832
Period size: 176 Copynumber: 2.9 Consensus size: 176
43594940 AAGTAGATCG
*
43594950 AAGAATTTCAGATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
1 AAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
* *
43595015 CCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAATTTACAGTAGAGTAG
66 CCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAG
43595080 ATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGA
131 ATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGA
43595126 AAG-ATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
1 AAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
* * *
43595190 CCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATTCTCCCTGAAGTTACAGCAGAGTA
66 CCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA-TCTCTCTGAAGTTACAGTAGAGTA
*
43595255 GATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACC-A
130 GATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGA
* * *
43595301 AGGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCTATCTC
1 AAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
*
43595366 CCTGAGATTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCT-AAGGTTACAGTAGAGTA
66 CCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAA-GTTACAGTAGAGTA
** * *
43595430 GATCGTTTCAGATCTTACCTCCC
130 GATCGCATCAGGTCTTATCTCCC
43595453 AAAGTGGAGC
Statistics
Matches: 306, Mismatches: 18, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
174 2 0.01
175 139 0.45
176 165 0.54
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (176 bp):
AAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTC
CCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAG
ATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGA
Found at i:43595408 original size:44 final size:43
Alignment explanation
Indices: 43594960--43595432 Score: 293
Period size: 44 Copynumber: 10.8 Consensus size: 43
43594950 AAGAATTTCA
* * *
43594960 GATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGAT-AG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATCAG
* * ** *
43595003 TAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CAG
* * * ***
43595048 GATCTTATCTCTCTGA-ATTTACAGTAGAGTAGA-TCGCATCAG
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATCAG
**
43595090 G-TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAAGATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAAA-A--TCAG
* *
43595135 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATCAG
* * *
43595178 TAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CAG
** * ***
43595223 GATCTTATTCTCCCTGA-AGTTACAGCAGAGTAGA-TCGCATCAG
1 GATCTTA-TCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATCAG
* **
43595266 G-TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCAAGGAATTTCA-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAA--AA--TCAG
* * * *
43595311 GATCTTATCTCCCTGAGATTACAGCGGAGTAGATT-GAAGCTAG
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATC-AG
* * * * *
43595354 TAATCCTATCTCCCTGAGATTACAGTGGAACGGATTAAAATAAAG
1 -GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CAG
* * * * *
43595399 GATCTTATCTCTCTAAGGTTACAGTAGAGTAGAT
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGAT
43595433 CGTTTCAGAT
Statistics
Matches: 327, Mismatches: 73, Indels: 58
0.71 0.16 0.13
Matches are distributed among these distances:
41 48 0.15
42 11 0.03
43 18 0.06
44 152 0.46
45 32 0.10
46 66 0.20
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCAG
Found at i:43597309 original size:24 final size:23
Alignment explanation
Indices: 43597230--43597309 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
43597220 TATTTTTAAA
43597230 ATACATA-C-TTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
* *
43597251 AT-CTTACTTATCTATATACCCTTGTAT
1 ATACATACCT-T-TATATA--CTT-TAT
*
43597278 ATATATACCTTTATATACTTTAT
1 ATACATACCTTTATATACTTTAT
43597301 AATACATAC
1 -ATACATAC
43597310 ATGCACATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
23 4 0.09
24 16 0.36
26 9 0.20
27 6 0.14
28 4 0.09
ACGTcount: A:0.35, C:0.17, G:0.01, T:0.46
Consensus pattern (23 bp):
ATACATACCTTTATATACTTTAT
Found at i:43601449 original size:29 final size:28
Alignment explanation
Indices: 43601412--43601467 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
43601402 TTATTTTTAA
* *
43601412 AGGATTAAATTAAAATTTTATCATTATG
1 AGGATTAAAGTAAAATTTTACCATTATG
**
43601440 AGGAGTTAAAGTGCAATTTTACCATTAT
1 AGGA-TTAAAGTAAAATTTTACCATTAT
43601468 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AGGATTAAAGTAAAATTTTACCATTATG
Found at i:43601772 original size:15 final size:15
Alignment explanation
Indices: 43601754--43601782 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43601744 TAGGATTATT
43601754 TTATTTTATTTTTAA
1 TTATTTTATTTTTAA
43601769 TTATTTTATTTTTA
1 TTATTTTATTTTTA
43601783 TTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTATTTTTAA
Found at i:43601966 original size:10 final size:10
Alignment explanation
Indices: 43601938--43601970 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
43601928 CTGAAAAATT
43601938 AAAAAAATTA-
1 AAAAAAA-TAC
43601948 AAAAAAATAC
1 AAAAAAATAC
43601958 AAAAAAATAC
1 AAAAAAATAC
43601968 AAA
1 AAA
43601971 GCGGACGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 20 0.91
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:43603660 original size:13 final size:13
Alignment explanation
Indices: 43603621--43603681 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
43603611 CACTTAAATT
43603621 TTTTC-AAAGTAC
1 TTTTCAAAAGTAC
*
43603633 TTCTT-AAAAGCAC
1 TT-TTCAAAAGTAC
* *
43603646 TTTTCCACAGTAC
1 TTTTCAAAAGTAC
*
43603659 TTTTTAAAAGTAC
1 TTTTCAAAAGTAC
43603672 TTTTCAAAAG
1 TTTTCAAAAG
43603682 CAATGAAGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
12 4 0.11
13 34 0.89
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:43604929 original size:3 final size:3
Alignment explanation
Indices: 43604921--43604948 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43604911 TGTGTCCTTT
43604921 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
43604949 CCTATTCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:43609621 original size:35 final size:35
Alignment explanation
Indices: 43609582--43609649 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
43609572 AATAAATACT
43609582 TAGATTTTAGGGCGTTACAACTCTACCCCCTAAGA
1 TAGATTTTAGGGCGTTACAACTCTACCCCCTAAGA
43609617 TAGATTTTAGGGCGTTACAACTCTACCCCCTAA
1 TAGATTTTAGGGCGTTACAACTCTACCCCCTAA
43609650 AAGAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (35 bp):
TAGATTTTAGGGCGTTACAACTCTACCCCCTAAGA
Found at i:43629824 original size:15 final size:15
Alignment explanation
Indices: 43629800--43629834 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
43629790 TTTTTTTATT
43629800 TTTA-TTTTAATATA
1 TTTATTTTTAATATA
43629814 TTTATTTTTAATATA
1 TTTATTTTTAATATA
*
43629829 ATTATT
1 TTTATT
43629835 ATTGTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTTTTAATATA
Found at i:43629830 original size:20 final size:19
Alignment explanation
Indices: 43629794--43629834 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
43629784 TAGCTATTTT
* *
43629794 TTTATTTTTATTTTAATATA
1 TTTATTTTTAATATAAT-TA
43629814 TTTATTTTTAATATAATTA
1 TTTATTTTTAATATAATTA
43629833 TT
1 TT
43629835 ATTGTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTTTAATATAATTA
Found at i:43631231 original size:3 final size:3
Alignment explanation
Indices: 43631223--43631268 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
43631213 TTTTTTGCCC
43631223 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43631269 CATTTCATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43636545 original size:10 final size:10
Alignment explanation
Indices: 43636518--43636576 Score: 66
Period size: 10 Copynumber: 5.9 Consensus size: 10
43636508 TTAAATTCTA
43636518 AAAGATAAAT
1 AAAGATAAAT
*
43636528 ACAA-ATAATT
1 A-AAGATAAAT
* *
43636538 AATGATAATT
1 AAAGATAAAT
43636548 AAAGATAAAT
1 AAAGATAAAT
*
43636558 AAGGATAAAT
1 AAAGATAAAT
43636568 AAAGATAAA
1 AAAGATAAA
43636577 AGCTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 1 0.02
10 38 0.93
11 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Done.