Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 29 of 276
Found at i:9181217 original size:37 final size:37
Alignment explanation
Indices: 9181175--9181248 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
9181165 TACTTGAAGT
*
9181175 AAGGATTAAATTCTGGACCACTAATTAATATAAGAGA
1 AAGGATTAAATTCTCGACCACTAATTAATATAAGAGA
* *
9181212 AAGGATTAAATTCTCGACCACTGATTAATGTAAGAGA
1 AAGGATTAAATTCTCGACCACTAATTAATATAAGAGA
9181249 GAGCCTTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (37 bp):
AAGGATTAAATTCTCGACCACTAATTAATATAAGAGA
Found at i:9183633 original size:27 final size:27
Alignment explanation
Indices: 9183603--9183764 Score: 227
Period size: 27 Copynumber: 6.0 Consensus size: 27
9183593 AAGTATCCTT
* * * * *
9183603 GATTTATAGAATTACCGTTTCACCATC
1 GATTTACAAAATTACCATTTTACCCTC
9183630 GATTTACAAAATTACCATTTTACCCTC
1 GATTTACAAAATTACCATTTTACCCTC
* *
9183657 GATTTATAGAATTACCATTTTACCCTC
1 GATTTACAAAATTACCATTTTACCCTC
* *
9183684 GATTTACAAAATTACTATTTTACCCTT
1 GATTTACAAAATTACCATTTTACCCTC
9183711 GATTTACAAAATTACCATTTTACCCTC
1 GATTTACAAAATTACCATTTTACCCTC
9183738 -AGTTTACAAAATTACCATTTTACCCTC
1 GA-TTTACAAAATTACCATTTTACCCTC
9183765 TATTATGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.01
27 120 0.99
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (27 bp):
GATTTACAAAATTACCATTTTACCCTC
Found at i:9183646 original size:54 final size:54
Alignment explanation
Indices: 9183599--9183763 Score: 251
Period size: 54 Copynumber: 3.1 Consensus size: 54
9183589 ACCAAAGTAT
* * *
9183599 CCTTGATTTATAGAATTACCGTTTCACCATCGATTTACAAAATTACCATTTTAC
1 CCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCATTTTAC
* *
9183653 CCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACTATTTTAC
1 CCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCATTTTAC
* *
9183707 CCTTGATTTACAAAATTACCATTTTACCCTC-AGTTTACAAAATTACCATTTTAC
1 CCTTGATTTATAGAATTACCATTTTACCCTCGA-TTTACAAAATTACCATTTTAC
9183761 CCT
1 CCT
9183764 CTATTATGAA
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 100 0.99
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (54 bp):
CCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCATTTTAC
Found at i:9183826 original size:27 final size:26
Alignment explanation
Indices: 9183572--9183976 Score: 204
Period size: 27 Copynumber: 15.1 Consensus size: 26
9183562 ACTAAAATGT
* * *
9183572 CCTCAATTTGTAAAATTACCAAAGTAT
1 CCTCGATTTATAAAATTACCAAA-TAC
* * ***
9183599 CCTTGATTTATAGAATTACCGTTTCAC
1 CCTCGATTTATAAAATTACCAAAT-AC
* * **
9183626 CATCGATTTACAAAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCA-AATAC
* **
9183653 CCTCGATTTATAGAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCA-AATAC
* * **
9183680 CCTCGATTTACAAAATTACTATTTTAC
1 CCTCGATTTATAAAATTACCA-AATAC
* * **
9183707 CCTTGATTTACAAAATTACCATTTTAC
1 CCTCGATTTATAAAATTACCA-AATAC
* **
9183734 CCTC-AGTTTACAAAATTACCATTTTAC
1 CCTCGA-TTTATAAAATTACCA-AATAC
* * *
9183761 CCTCTA-TTATGAAATTACTGAAATAC
1 CCTCGATTTATAAAATTAC-CAAATAC
* * *
9183787 CC-CCAGTTGTAAAATTACCAAAGTAC
1 CCTCGATTTATAAAATTACCAAA-TAC
* * *
9183813 CCCCGGTTTATAAAATTACCCAAATAT
1 CCTCGATTTATAAAATTA-CCAAATAC
* *
9183840 CCTCGATTTGTAAAATTACTGAAATAC
1 CCTCGATTTATAAAATTAC-CAAATAC
* * *
9183867 CCTCAATTTGTAAAATTACTGAAATAC
1 CCTCGATTTATAAAATTAC-CAAATAC
**
9183894 CCTCGATCAATAAAATTACCAAAATAC
1 CCTCGATTTATAAAATTACC-AAATAC
* * * *
9183921 CCTTGGTTTGTAAAATTACCAAAATGC
1 CCTCGATTTATAAAATTACC-AAATAC
* * *
9183948 CCTTGGTTTACAAAATTACCGAAATAC
1 CCTCGATTTATAAAATTACC-AAATAC
9183975 CC
1 CC
9183977 CTGTAGGGTA
Statistics
Matches: 310, Mismatches: 57, Indels: 22
0.80 0.15 0.06
Matches are distributed among these distances:
25 5 0.02
26 33 0.11
27 263 0.85
28 9 0.03
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (26 bp):
CCTCGATTTATAAAATTACCAAATAC
Found at i:9183991 original size:27 final size:27
Alignment explanation
Indices: 9183961--9184497 Score: 655
Period size: 27 Copynumber: 20.3 Consensus size: 27
9183951 TGGTTTACAA
9183961 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
9183988 AATTACCGGAATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
9184015 AATTACCGGAATACCCTTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184042 AATTACCGGAATACCCCTGTAGGTTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184069 AATTATCGAATTACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184096 AATAACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184123 AATTACCGAAATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
9184150 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
9184177 AATTATCGTAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
9184204 AATTACCGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
9184230 AA-T-------TACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184249 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
9184276 AATTACCGAGATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
9184303 AATTACCGAGATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
9184330 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
9184357 AATTATCGCAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
9184384 AATTACCGAAATACCCCTGTAGGTTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
9184411 AATTACTAAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
9184438 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
9184465 AATTACC-AAGATA-CCTTGTGGGGTAA
1 AATTACCGAA-ATACCCCTGTAGGGTAG
9184491 AATTACC
1 AATTACC
9184498 ATTTTGCCCT
Statistics
Matches: 448, Mismatches: 52, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
18 2 0.00
19 15 0.03
20 1 0.00
25 1 0.00
26 32 0.07
27 397 0.89
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:9184241 original size:19 final size:19
Alignment explanation
Indices: 9184217--9184253 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
9184207 TACCGAAATA
9184217 CCCTGTAGGGTAGAATTAC
1 CCCTGTAGGGTAGAATTAC
9184236 CCCTGTAGGGTAGAATTA
1 CCCTGTAGGGTAGAATTA
9184254 TCGCAATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (19 bp):
CCCTGTAGGGTAGAATTAC
Found at i:9184975 original size:22 final size:22
Alignment explanation
Indices: 9184923--9184987 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
9184913 TTAAAGCCTT
* *
9184923 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
9184945 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
9184967 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
9184988 ACGTATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:9185175 original size:27 final size:27
Alignment explanation
Indices: 9185145--9185246 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
9185135 ATTCTGTTAA
*
9185145 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTTTGCCACAATATCTGTTTCTG
*
9185172 GTGGCTATGCCACAAATATCTGTTT-TG
1 GTGGCTTTGCCAC-AATATCTGTTTCTG
* *
9185199 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTTTGCCACAATATCTGTTTCTG
* *
9185226 GTGACTTTGTCACAATATCTG
1 GTGGCTTTGCCACAATATCTG
9185247 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.15
27 46 0.70
28 10 0.15
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
GTGGCTTTGCCACAATATCTGTTTCTG
Found at i:9185442 original size:30 final size:30
Alignment explanation
Indices: 9185378--9185535 Score: 175
Period size: 30 Copynumber: 5.4 Consensus size: 30
9185368 TTGCATTCAC
* *
9185378 ATTCTGGTTCTGATTCTGTCACGTAATTCTG
1 ATTCTGATTCTGATTCTGTCAC-TAATACTG
* * *
9185409 ATTCTAATTCTGATTTTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTCACTAATACTG
9185439 ATTCTGATTCTGATTCTG----T--TACTG
1 ATTCTGATTCTGATTCTGTCACTAATACTG
*
9185463 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTCA-CTAATACTG
* * *
9185494 ATTCTGATTCTGATTCTATTACTAATATTG
1 ATTCTGATTCTGATTCTGTCACTAATACTG
9185524 ATTCTGATTCTG
1 ATTCTGATTCTG
9185536 TTACTGATTC
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
24 23 0.21
26 1 0.01
29 1 0.01
30 42 0.39
31 41 0.38
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTCACTAATACTG
Found at i:9185526 original size:79 final size:79
Alignment explanation
Indices: 9185378--9186269 Score: 1660
Period size: 79 Copynumber: 11.2 Consensus size: 79
9185368 TTGCATTCAC
* * * * *
9185378 ATTCTGGTTCTGATTCTGTCACGTAATTCTGATTCTAATTCTGATTTTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACT-A-A-T-A-T-
9185443 TGATTCTGATTCTGTTACTG
60 TGATTCTGATTCTGTTACTG
9185463 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185528 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185542 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185607 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185621 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185686 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185700 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185765 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185779 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185844 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185858 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9185923 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9185937 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9186002 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9186016 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9186081 TGATTCTGTTACTG
66 TGATTCTGTTACTG
*
9186095 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTGAT-TCTGATT
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATAT-TGATT
9186159 CTGATTCTGTTACTG
65 CTGATTCTGTTACTG
9186174 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
9186239 TGATTCTGTTACTG
66 TGATTCTGTTACTG
9186253 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
9186270 CATTTTGGTT
Statistics
Matches: 798, Mismatches: 7, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
78 1 0.00
79 742 0.93
80 2 0.00
81 1 0.00
82 1 0.00
83 1 0.00
84 1 0.00
85 49 0.06
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (79 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTATTACTAATATTGATTC
TGATTCTGTTACTG
Found at i:9191462 original size:48 final size:48
Alignment explanation
Indices: 9191391--9191658 Score: 410
Period size: 48 Copynumber: 5.6 Consensus size: 48
9191381 TGTTACAACA
*
9191391 TTCACATTAGTCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
*
9191439 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
* * * * *
9191487 TTCACATTCGCCATTCGGCTTTACCATATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
9191535 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
* * * * * *
9191583 TTCACATTCGCCATTCGGCTTTACCACATACACATGTCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
*
9191631 TTCACATTAGCCATTCGGCTTCACCACA
1 TTCACATTAGCCATTCGGCTTTACCACA
9191659 CAGATATATA
Statistics
Matches: 201, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 201 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
Found at i:9191578 original size:144 final size:144
Alignment explanation
Indices: 9191391--9191656 Score: 460
Period size: 144 Copynumber: 1.8 Consensus size: 144
9191381 TGTTACAACA
*
9191391 TTCACATTAGTCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
* * * * *
9191456 GCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCGGCTTTACCATATATACA
66 GCTTTACCACATACACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCATATATACA
9191521 TATCACACATATAT
131 TATCACACATATAT
9191535 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
* *
9191600 GCTTTACCACATACACATGTCACACATATATTTCACATTAGCCATTCGGCTTCACCA
66 GCTTTACCACATACACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCA
9191657 CACAGATATA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 114 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.35
Consensus pattern (144 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
GCTTTACCACATACACATATCACACACATATTTCACATTAGCCATTCGGCTTCACCATATATACA
TATCACACATATAT
Found at i:9202194 original size:22 final size:22
Alignment explanation
Indices: 9202114--9202188 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
9202104 TAATAACTGT
* *
9202114 AAGCTCAATTAAGCTAGAAACGGG
1 AAGCTCTATTGAGC-AG-AACGGG
9202138 AAGCTCTATTGAGCAGAACGGG
1 AAGCTCTATTGAGCAGAACGGG
* *
9202160 AAGCTCTATTGAGCTGAACGAG
1 AAGCTCTATTGAGCAGAACGGG
9202182 AAGCTCT
1 AAGCTCT
9202189 TATGAGGTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 33 0.70
23 2 0.04
24 12 0.26
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.20
Consensus pattern (22 bp):
AAGCTCTATTGAGCAGAACGGG
Found at i:9207606 original size:28 final size:28
Alignment explanation
Indices: 9207559--9207630 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
9207549 TGATGTCTCA
*
9207559 CACACTAAGTGCCATACTCAATATCTTG
1 CACACTAAGTGTCATACTCAATATCTTG
* * *
9207587 CACACCAAGTGTCATTCTCAATATTTTG
1 CACACTAAGTGTCATACTCAATATCTTG
9207615 CACACTAAGTGTCATA
1 CACACTAAGTGTCATA
9207631 TATATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (28 bp):
CACACTAAGTGTCATACTCAATATCTTG
Found at i:9213029 original size:22 final size:22
Alignment explanation
Indices: 9212999--9213050 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
9212989 AGCTAGAAAC
9212999 GGGAAGCTCTATTGAGCTGAA-
1 GGGAAGCTCTATTGAGCTGAAT
9213020 GGAGAAGCTCTATTGAGCTGAAT
1 GG-GAAGCTCTATTGAGCTGAAT
9213043 GGGAAGCT
1 GGGAAGCT
9213051 TTTATGAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.23
Consensus pattern (22 bp):
GGGAAGCTCTATTGAGCTGAAT
Found at i:9215239 original size:19 final size:20
Alignment explanation
Indices: 9215185--9215240 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
9215175 TAGGATACAC
9215185 TTCATGTGCTAGTATGCGAT
1 TTCATGTGCTAGTATGCGAT
* * *
9215205 TT-GTGCGCCAAG-ATGCG-T
1 TTCATGTG-CTAGTATGCGAT
9215223 TTCATGTGCTAGTATGCG
1 TTCATGTGCTAGTATGCG
9215241 CCTTACATGC
Statistics
Matches: 27, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.36
Consensus pattern (20 bp):
TTCATGTGCTAGTATGCGAT
Found at i:9218202 original size:70 final size:66
Alignment explanation
Indices: 9218097--9218228 Score: 174
Period size: 70 Copynumber: 1.9 Consensus size: 66
9218087 ATAAACAATA
** ** *
9218097 TAATGGTTTTGCTTTTAACTTAATGGGTAAACATTTATCAAAGTGACGTAGTTTTGCCTTTTAAC
1 TAATGGTTTTGCTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTGCCTTTTAAC
9218162 T
66 T
*
9218163 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGACATAGTTTTTCCTTT
1 TAATGGTTTTG-CTTTTAAC-TT--AAAAGGTAAACATTTATCAAAACGACATAGTTTTGCCTTT
9218228 T
62 T
9218229 CTTATTCAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 11 0.20
67 8 0.14
68 2 0.04
70 35 0.62
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (66 bp):
TAATGGTTTTGCTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTGCCTTTTAAC
T
Found at i:9225329 original size:26 final size:27
Alignment explanation
Indices: 9225300--9225351 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
9225290 ATATTTTTTT
*
9225300 TATTTCCCA-AAATAAAATTCTCAATA
1 TATTTCCAATAAATAAAATTCTCAATA
*
9225326 TATTTCCAATTAAATAATATTCTCAA
1 TATTTCCAA-TAAATAAAATTCTCAA
9225352 CCCAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.38
Consensus pattern (27 bp):
TATTTCCAATAAATAAAATTCTCAATA
Found at i:9225598 original size:57 final size:57
Alignment explanation
Indices: 9225512--9225639 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 57
9225502 TTTTTCAGGT
* * * *
9225512 CATTTTAATTTTTTATTTTGGAGAAAACCACATTCATTTCTAAATGATTT-CATTTCTC
1 CATTTTCA-TTTTCATTTTGGAGAAAACCACAATCATTTCCAAATG-TTTCCATTTCTC
*
9225570 CATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTCTC
1 CATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCCATTTCTC
*
9225627 TATTTTCATTTTC
1 CATTTTCATTTTC
9225640 GAATGATTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
56 3 0.05
57 53 0.84
58 7 0.11
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (57 bp):
CATTTTCATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGTTTCCATTTCTC
Found at i:9225656 original size:32 final size:30
Alignment explanation
Indices: 9225602--9225666 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 30
9225592 AAAACCATAA
*
9225602 TCATTTCCAAATGTTTCCATTTCTCTATTT
1 TCATTTCCAAATGTTTCCATTTCTCCATTT
* *
9225632 TCATTTTCGAATGATTTCTCATTTCTCCATTT
1 TCATTTCCAAATG-TTTC-CATTTCTCCATTT
9225664 TCA
1 TCA
9225667 CCATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 11 0.37
31 4 0.13
32 15 0.50
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (30 bp):
TCATTTCCAAATGTTTCCATTTCTCCATTT
Found at i:9227103 original size:34 final size:34
Alignment explanation
Indices: 9227036--9227103 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
9227026 AGCCTATAAG
** *
9227036 AGTGTAAGACCATAGCTGGATTATGGCATCATAT
1 AGTGTAAGACCATAGCTGGATTATGAAAACATAT
* *
9227070 AGTGTAAGACCATAGTTGGGTTATGAAAACATAT
1 AGTGTAAGACCATAGCTGGATTATGAAAACATAT
9227104 GAAGTCCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (34 bp):
AGTGTAAGACCATAGCTGGATTATGAAAACATAT
Found at i:9230577 original size:19 final size:21
Alignment explanation
Indices: 9230536--9230577 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
9230526 TAGTGTGTTT
*
9230536 AATTAGGCTCTAATTAAGTGA
1 AATTAGGCTCTAATTAAGAGA
*
9230557 AATTA-GCTC-AATTTAGAGA
1 AATTAGGCTCTAATTAAGAGA
9230576 AA
1 AA
9230578 ATAGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (21 bp):
AATTAGGCTCTAATTAAGAGA
Found at i:9230911 original size:29 final size:28
Alignment explanation
Indices: 9230873--9230929 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
9230863 ATGTATTTAC
* *
9230873 TTTTATTAAAGTAAATAGATATTTATTA
1 TTTTATTAAAGTAAAAAGATAGTTATTA
*
9230901 TTTTGATTAAATTAAAAAGATAGTTATTA
1 TTTT-ATTAAAGTAAAAAGATAGTTATTA
9230930 GTTAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTTATTAAAGTAAAAAGATAGTTATTA
Found at i:9231624 original size:17 final size:18
Alignment explanation
Indices: 9231602--9231637 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9231592 TAAATGAGTT
9231602 AATTA-GGAATAAATTGG
1 AATTAGGGAATAAATTGG
*
9231619 AATTAGGGTATAAATTGG
1 AATTAGGGAATAAATTGG
9231637 A
1 A
9231638 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (18 bp):
AATTAGGGAATAAATTGG
Found at i:9232848 original size:21 final size:21
Alignment explanation
Indices: 9232824--9232866 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9232814 CAGAGTCTCG
*
9232824 GTTCAGCGTCCAAGCGATCCC
1 GTTCAGCATCCAAGCGATCCC
*
9232845 GTTCAGCATCCAGGCGATCCC
1 GTTCAGCATCCAAGCGATCCC
9232866 G
1 G
9232867 ACTCCAGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.19
Consensus pattern (21 bp):
GTTCAGCATCCAAGCGATCCC
Found at i:9234285 original size:282 final size:282
Alignment explanation
Indices: 9233781--9234344 Score: 1128
Period size: 282 Copynumber: 2.0 Consensus size: 282
9233771 ATTAAGATAA
9233781 TTACTTTAATATTAAATTAAAAAATATTATTAAGATAAGTATTAAATTTAATTTACTATTAAACT
1 TTACTTTAATATTAAATTAAAAAATATTATTAAGATAAGTATTAAATTTAATTTACTATTAAACT
9233846 ATTAAAATAATATTATTTTTGGAATAGTTAATCTGAAATCAAATTCTCTGGTAGAGTTCTAATAG
66 ATTAAAATAATATTATTTTTGGAATAGTTAATCTGAAATCAAATTCTCTGGTAGAGTTCTAATAG
9233911 GAGTGTAACTCTTCCACTACTCAACCACTGACAACCAATTACCATTGGCCACCGAGGCACTGTCG
131 GAGTGTAACTCTTCCACTACTCAACCACTGACAACCAATTACCATTGGCCACCGAGGCACTGTCG
9233976 TCCCAGCCACTGGCACCGTCGTGTTCGGTGATACAGGTGCGACATCCTTAAAGCACCCTGAGCTG
196 TCCCAGCCACTGGCACCGTCGTGTTCGGTGATACAGGTGCGACATCCTTAAAGCACCCTGAGCTG
9234041 GTTTGGCTACTGTCGGTTCTGT
261 GTTTGGCTACTGTCGGTTCTGT
9234063 TTACTTTAATATTAAATTAAAAAATATTATTAAGATAAGTATTAAATTTAATTTACTATTAAACT
1 TTACTTTAATATTAAATTAAAAAATATTATTAAGATAAGTATTAAATTTAATTTACTATTAAACT
9234128 ATTAAAATAATATTATTTTTGGAATAGTTAATCTGAAATCAAATTCTCTGGTAGAGTTCTAATAG
66 ATTAAAATAATATTATTTTTGGAATAGTTAATCTGAAATCAAATTCTCTGGTAGAGTTCTAATAG
9234193 GAGTGTAACTCTTCCACTACTCAACCACTGACAACCAATTACCATTGGCCACCGAGGCACTGTCG
131 GAGTGTAACTCTTCCACTACTCAACCACTGACAACCAATTACCATTGGCCACCGAGGCACTGTCG
9234258 TCCCAGCCACTGGCACCGTCGTGTTCGGTGATACAGGTGCGACATCCTTAAAGCACCCTGAGCTG
196 TCCCAGCCACTGGCACCGTCGTGTTCGGTGATACAGGTGCGACATCCTTAAAGCACCCTGAGCTG
9234323 GTTTGGCTACTGTCGGTTCTGT
261 GTTTGGCTACTGTCGGTTCTGT
9234345 CCATGTCAAT
Statistics
Matches: 282, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
282 282 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (282 bp):
TTACTTTAATATTAAATTAAAAAATATTATTAAGATAAGTATTAAATTTAATTTACTATTAAACT
ATTAAAATAATATTATTTTTGGAATAGTTAATCTGAAATCAAATTCTCTGGTAGAGTTCTAATAG
GAGTGTAACTCTTCCACTACTCAACCACTGACAACCAATTACCATTGGCCACCGAGGCACTGTCG
TCCCAGCCACTGGCACCGTCGTGTTCGGTGATACAGGTGCGACATCCTTAAAGCACCCTGAGCTG
GTTTGGCTACTGTCGGTTCTGT
Found at i:9235987 original size:42 final size:41
Alignment explanation
Indices: 9235824--9235990 Score: 131
Period size: 42 Copynumber: 4.0 Consensus size: 41
9235814 AATCGTACCA
* ** *
9235824 ATGCCATATCCCAAATATGGTCTTATATGGGAC-CTTACATCG
1 ATGCCATATCCCAAATATGGTCTTACATGAAACTCATA-A-CG
* * ** * *
9235866 ATGCCAATAGCCCAACTATGGTCTTAC-TCGATTCTCATATCT
1 ATGCC-ATATCCCAAATATGGTCTTACAT-GAAACTCATAACG
* * **
9235908 ATGCCATGTCCCAAACATGGTCTTACACAAAATCTCATAACG
1 ATGCCATATCCCAAATATGGTCTTACATGAAA-CTCATAACG
*
9235950 ATGCCATATCCCAGATATGGTCTTACATGTAAACTCATAAC
1 ATGCCATATCCCAAATATGGTCTTACATG-AAACTCATAAC
9235991 CCTAATGTCA
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
41 18 0.19
42 51 0.54
43 23 0.24
44 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAAATATGGTCTTACATGAAACTCATAACG
Found at i:9250928 original size:65 final size:63
Alignment explanation
Indices: 9250817--9250938 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 63
9250807 GAGAATCATT
* * *
9250817 AGAAAAGTTGGTGTTATTTTAGCATTTTATGTTGTTTTTAAGTATGTTTCGTTTTCTTGCATAA
1 AGAAAAGTTGGTGTTATTTTAGCATTTTATGTTGATTTTAAATATGTTT-ATTTTCTTGCATAA
9250881 AGAATAAGTTGGTGTTATTTT-GACATATTTATGTT-ATTTTAAATATGTTTATTTTCTT
1 AGAA-AAGTTGGTGTTATTTTAG-CAT-TTTATGTTGATTTTAAATATGTTTATTTTCTT
9250939 AATTCAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
64 12 0.23
65 32 0.62
66 8 0.15
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.53
Consensus pattern (63 bp):
AGAAAAGTTGGTGTTATTTTAGCATTTTATGTTGATTTTAAATATGTTTATTTTCTTGCATAA
Found at i:9256543 original size:3 final size:3
Alignment explanation
Indices: 9256535--9256589 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
9256525 GACGTTGCCT
9256535 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
9256583 CTA CTA C
1 CTA CTA C
9256590 ATCAATGGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:9257350 original size:22 final size:23
Alignment explanation
Indices: 9257313--9257355 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9257303 CATAAAAAAT
*
9257313 AATTTTTAAATATATTTTTAATA
1 AATTTTTAAATATATTATTAATA
*
9257336 AATTTTTAAA-GTATTATTAA
1 AATTTTTAAATATATTATTAA
9257356 ATTTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTTTTAAATATATTATTAATA
Found at i:9257398 original size:18 final size:18
Alignment explanation
Indices: 9257375--9257413 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
9257365 AATATTAAGT
9257375 AAAATTCAAAATTAA-AAA
1 AAAATT-AAAATTAATAAA
9257393 AAAATTAAAATTAATAAA
1 AAAATTAAAATTAATAAA
9257411 AAA
1 AAA
9257414 CCATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAAAATTAATAAA
Found at i:9257412 original size:17 final size:18
Alignment explanation
Indices: 9257375--9257413 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
9257365 AATATTAAGT
9257375 AAAATTCAAAATTAAAAA
1 AAAATTCAAAATTAAAAA
*
9257393 AAAATT-AAAATTAATAA
1 AAAATTCAAAATTAAAAA
9257410 AAAA
1 AAAA
9257414 CCATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTCAAAATTAAAAA
Found at i:9257683 original size:11 final size:11
Alignment explanation
Indices: 9257647--9257692 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
9257637 CATTATTATA
*
9257647 TTTTATTAATAT
1 TTTTAATAA-AT
*
9257659 TTTTTATAAA-
1 TTTTAATAAAT
9257669 TTTTAATAAAT
1 TTTTAATAAAT
9257680 TTTTAA-AAAT
1 TTTTAATAAAT
9257690 TTT
1 TTT
9257693 ATAGTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 16 0.53
11 7 0.23
12 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAATAAAT
Found at i:9257844 original size:10 final size:10
Alignment explanation
Indices: 9257812--9257868 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
9257802 TAACTTTTTG
9257812 AATTTTAATTA
1 AATTTTAA-TA
*
9257823 ATATTTTTATA
1 A-ATTTTAATA
9257834 AATTTTAATA
1 AATTTTAATA
* *
9257844 AAGTTTCA-A
1 AATTTTAATA
*
9257853 AATTTTATTA
1 AATTTTAATA
9257863 AATTTT
1 AATTTT
9257869 TTATCATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.16
10 21 0.57
11 4 0.11
12 6 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (10 bp):
AATTTTAATA
Found at i:9260053 original size:21 final size:22
Alignment explanation
Indices: 9260020--9260062 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
9260010 GAATAATAGC
* *
9260020 AGAATATATAAGAG-AAGAAAG
1 AGAAGATAGAAGAGAAAGAAAG
9260041 AGAAGATAGAAGAGAAAGAAAG
1 AGAAGATAGAAGAGAAAGAAAG
9260063 GGGAAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (22 bp):
AGAAGATAGAAGAGAAAGAAAG
Found at i:9260120 original size:33 final size:32
Alignment explanation
Indices: 9260083--9260157 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
9260073 TAAGAACTGA
* *
9260083 AAGAAAAAGATTTTATTAAGGATTTGGGGTTTG
1 AAGAAAAAGATTTT-TTAAGAATTTAGGGTTTG
* * *
9260116 AAGAAAATGATTTTTTTAGAATTTAGTGTTTG
1 AAGAAAAAGATTTTTTAAGAATTTAGGGTTTG
*
9260148 AATAAAAAGA
1 AAGAAAAAGA
9260158 GGGATTAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.37
Consensus pattern (32 bp):
AAGAAAAAGATTTTTTAAGAATTTAGGGTTTG
Found at i:9263078 original size:14 final size:14
Alignment explanation
Indices: 9263055--9263085 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9263045 TTATCAACTT
*
9263055 ATATACATGCAAAA
1 ATATAAATGCAAAA
9263069 ATATAAATGCAAAA
1 ATATAAATGCAAAA
9263083 ATA
1 ATA
9263086 ACAAAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.23
Consensus pattern (14 bp):
ATATAAATGCAAAA
Found at i:9263154 original size:45 final size:45
Alignment explanation
Indices: 9263085--9263188 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
9263075 ATGCAAAAAT
* *
9263085 AACAAAATTTG-AAATTTAAATGAGATGTATTGGAACAAACTTAG
1 AACAAACTTTGTAATTTTAAATGAGATGTATTGGAACAAACTTAG
* *
9263129 AACAAACTTTGTAATTTTAAATGAGATGTGTTGGAACAAACTTGG
1 AACAAACTTTGTAATTTTAAATGAGATGTATTGGAACAAACTTAG
*
9263174 AACAAACTATGTAAT
1 AACAAACTTTGTAAT
9263189 ATATATATCC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 10 0.19
45 44 0.81
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (45 bp):
AACAAACTTTGTAATTTTAAATGAGATGTATTGGAACAAACTTAG
Found at i:9268296 original size:16 final size:15
Alignment explanation
Indices: 9268277--9268311 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9268267 TGAACTTTTG
9268277 AAAAATAATAATTGAT
1 AAAAATAATAATT-AT
*
9268293 AAAAATAATACTTAT
1 AAAAATAATAATTAT
9268308 AAAA
1 AAAA
9268312 TATTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAATAATAATTAT
Found at i:9268815 original size:31 final size:31
Alignment explanation
Indices: 9268775--9268833 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
9268765 ACAAGTAGTT
9268775 ACATATTTTAATTTCCTTCAAAACTCAAGAA
1 ACATATTTTAATTTCCTTCAAAACTCAAGAA
* *
9268806 ACATGTTTTAATTTCCTTCAGAACTCAA
1 ACATATTTTAATTTCCTTCAAAACTCAA
9268834 CAAGCATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (31 bp):
ACATATTTTAATTTCCTTCAAAACTCAAGAA
Found at i:9279496 original size:17 final size:17
Alignment explanation
Indices: 9279474--9279507 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9279464 AAACTCAACG
9279474 GGATTAACATGGGATAT
1 GGATTAACATGGGATAT
9279491 GGATTAACATGGGATAT
1 GGATTAACATGGGATAT
9279508 ACATATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
GGATTAACATGGGATAT
Found at i:9281136 original size:92 final size:88
Alignment explanation
Indices: 9280977--9281185 Score: 269
Period size: 90 Copynumber: 2.3 Consensus size: 88
9280967 CAGACAATCC
*
9280977 AGTTTGTGGATGAACCACAAGTG-TTGCAAGTTAATACGCTGCCAGTAGTTGTGAATACACAACA
1 AGTTTGTGGAT-AACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAGTTGTGAATACACAACA
9281041 GGTTTGCAAATAAAAGATGCCAGTAGA
65 GGTTTGCAAATAAAAGATG-CA--AGA
* * *
9281068 AG-TTGTGGATATACCACCAGTGTTTGTAGGTTAATACGCTGCCAGTAGATTGTGAATGCACAAC
1 AGTTTGTGGATA-ACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAG-TTGTGAATACACAAC
* * *
9281132 AGGTTTGCAGATAAAAGTTGCAATA
64 AGGTTTGCAAATAAAAGATGCAAGA
*
9281157 AGTTTGTGGATAAACCACCAATGTTTGCA
1 AGTTTGTGGAT-AACCACCAGTGTTTGCA
9281186 GATAATCTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
89 5 0.05
90 39 0.38
91 28 0.27
92 32 0.31
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (88 bp):
AGTTTGTGGATAACCACCAGTGTTTGCAAGTTAATACGCTGCCAGTAGTTGTGAATACACAACAG
GTTTGCAAATAAAAGATGCAAGA
Found at i:9284213 original size:30 final size:29
Alignment explanation
Indices: 9284156--9284214 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
9284146 TTACAAGGGC
*
9284156 GATCACATAGCCTGCCACACGCTCGTGTG
1 GATCACACAGCCTGCCACACGCTCGTGTG
*
9284185 GATCACACAGCCTAGTCACACG-TCCGTGTG
1 GATCACACAGCCT-GCCACACGCT-CGTGTG
9284215 CGTAGCCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (29 bp):
GATCACACAGCCTGCCACACGCTCGTGTG
Found at i:9284906 original size:13 final size:14
Alignment explanation
Indices: 9284864--9284908 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
9284854 TAAAAATGAT
9284864 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
9284879 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
9284892 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
9284905 TAAA
1 TAAA
9284909 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:9285466 original size:35 final size:35
Alignment explanation
Indices: 9285420--9285490 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
9285410 TACATGAGTA
9285420 TGTTATTAAATAATATATATTGATAATTTTAAATG
1 TGTTATTAAATAATATATATTGATAATTTTAAATG
9285455 TGTTATTAAATAATATATATTGATAATTTTAAATG
1 TGTTATTAAATAATATATATTGATAATTTTAAATG
9285490 T
1 T
9285491 TAAATTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (35 bp):
TGTTATTAAATAATATATATTGATAATTTTAAATG
Found at i:9292541 original size:21 final size:23
Alignment explanation
Indices: 9292488--9292541 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 23
9292478 TAAAACTGTG
9292488 AACCAGAAAGAAT-TTGATATAT
1 AACCAGAAAGAATATTGATATAT
*
9292510 AA-CA-AAA-AATATTTA-AT-T
1 AACCAGAAAGAATATTGATATAT
9292528 AACCAGAAAGAATA
1 AACCAGAAAGAATA
9292542 CAGATAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
18 3 0.11
19 7 0.26
20 9 0.33
21 6 0.22
22 2 0.07
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (23 bp):
AACCAGAAAGAATATTGATATAT
Found at i:9298387 original size:21 final size:20
Alignment explanation
Indices: 9298363--9298401 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9298353 GAACTTGTAT
*
9298363 ATCTATCAACAAACATTCATA
1 ATCTATCAAAAAAC-TTCATA
9298384 ATCTATCAAAAAACTTCA
1 ATCTATCAAAAAACTTCA
9298402 AAATACACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
ATCTATCAAAAAACTTCATA
Found at i:9308107 original size:49 final size:50
Alignment explanation
Indices: 9307985--9308163 Score: 167
Period size: 49 Copynumber: 3.7 Consensus size: 50
9307975 GTATAGAGGT
* **
9307985 GTCAGTGGAAGACCATGTCTGGGACATGGCATCAGCACGGATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCAATATGTGAGA
* * * *
9308035 G-CTAGTGTAAGACCATGTCTGGGACATGGTATCGGC-CTCAAT-TTTGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCAC-CAATATGTGAGA
*
9308084 GTCAGTGTAAGACCATGTCTGGGACATGGCATCA--A-C-TTGATG-GATGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCAAT-ATGTGA-GA
* * *
9308131 GCCAGTATAAGACCATGTCTAGGACATGGCATC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
9308164 GGCATTATAC
Statistics
Matches: 107, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
45 1 0.01
46 3 0.03
47 32 0.30
49 37 0.35
50 34 0.32
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCAATATGTGAGA
Found at i:9308112 original size:99 final size:96
Alignment explanation
Indices: 9307985--9308166 Score: 251
Period size: 96 Copynumber: 1.9 Consensus size: 96
9307975 GTATAGAGGT
* *
9307985 GTCAGTGGAAGACCATGTCTGGGACATGGCATCAGCACGGAT-ATGTGA-GAGCTAGTGTAAGAC
1 GTCAGTGGAAGACCATGTCTGGGACATGGCATCA--AC--ATGATG-GATGAGCCAGTATAAGAC
* *
9308048 CATGTCTGGGACATGGTATCGGCCTCAATTTTGATA
61 CATGTCTAGGACATGGCATCGGCCTCAATTTTGATA
* *
9308084 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATGGATGAGCCAGTATAAGACCATGT
1 GTCAGTGGAAGACCATGTCTGGGACATGGCATCAACATGATGGATGAGCCAGTATAAGACCATGT
9308149 CTAGGACATGGCATCGGC
66 CTAGGACATGGCATCGGC
9308167 ATTATACCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
95 3 0.04
96 37 0.49
97 2 0.03
99 33 0.44
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (96 bp):
GTCAGTGGAAGACCATGTCTGGGACATGGCATCAACATGATGGATGAGCCAGTATAAGACCATGT
CTAGGACATGGCATCGGCCTCAATTTTGATA
Found at i:9332562 original size:3 final size:3
Alignment explanation
Indices: 9332554--9332579 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9332544 TTCAGAAGCT
9332554 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
9332580 TTAGCCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9336177 original size:30 final size:30
Alignment explanation
Indices: 9336143--9336231 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
9336133 TCGTACTTCC
* *
9336143 TTTTTCATTTTTTAATAAATGATTCAATTT
1 TTTTTCATTTTTTAATAAATGACTCAATAT
9336173 TTTTTCATTTTTTAATAAATGACTCAATAT
1 TTTTTCATTTTTTAATAAATGACTCAATAT
* **
9336203 TTTTAC-TTTTTGCATAAATGACTCAATAT
1 TTTTTCATTTTTTAATAAATGACTCAATAT
9336232 GTTTATGCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 21 0.39
30 33 0.61
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (30 bp):
TTTTTCATTTTTTAATAAATGACTCAATAT
Found at i:9336205 original size:29 final size:29
Alignment explanation
Indices: 9336143--9336231 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 29
9336133 TCGTACTTCC
* *
9336143 TTTTTCATTTTTTAATAAATGATTCAATTT
1 TTTTTCATTTTTTAATAAATGACTCAA-TA
9336173 TTTTTCATTTTTTAATAAATGACTCAATA
1 TTTTTCATTTTTTAATAAATGACTCAATA
**
9336202 TTTTT-ACTTTTTGCATAAATGACTCAATA
1 TTTTTCA-TTTTTTAATAAATGACTCAATA
9336231 T
1 T
9336232 GTTTATGCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
28 1 0.02
29 27 0.50
30 26 0.48
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTTCATTTTTTAATAAATGACTCAATA
Found at i:9337949 original size:3 final size:3
Alignment explanation
Indices: 9337941--9338039 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
9337931 CTAGAAGTTT
9337941 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9337989 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9338037 TAA
1 TAA
9338040 ATAAGCAATA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9338609 original size:92 final size:92
Alignment explanation
Indices: 9338452--9338623 Score: 301
Period size: 92 Copynumber: 1.9 Consensus size: 92
9338442 GACCTACTAA
9338452 TCTAATCCAATTCCAACAACCTTCATTCTTTGACAACCTATAAAAATAAGTGGTTGAAATTGTGT
1 TCTAATCCAATTCCAACAACCTTCATTCTTTGACAACCTATAAAAATAAGTGGTTGAAATTGTGT
9338517 GTAAAAGGCTTGGAAGTGATGTAGCAC
66 GTAAAAGGCTTGGAAGTGATGTAGCAC
* *
9338544 TCTAATCCAATTCCATCAACCTTCATTCTTTGACAACCTATAAAAATAATTGGTT-AAAGTTGTG
1 TCTAATCCAATTCCAACAACCTTCATTCTTTGACAACCTATAAAAATAAGTGGTTGAAA-TTGTG
*
9338608 TGTAAAATGCTTGGAA
65 TGTAAAAGGCTTGGAA
9338624 CTGACATAGC
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 3 0.04
92 73 0.96
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (92 bp):
TCTAATCCAATTCCAACAACCTTCATTCTTTGACAACCTATAAAAATAAGTGGTTGAAATTGTGT
GTAAAAGGCTTGGAAGTGATGTAGCAC
Found at i:9346915 original size:26 final size:26
Alignment explanation
Indices: 9346879--9346929 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
9346869 CAGCCCAAAA
9346879 TTGACCCTAGTCGGGAAGTGGTTTCG
1 TTGACCCTAGTCGGGAAGTGGTTTCG
*
9346905 TTGACTCTAGTCGGGAAGTGGTTTC
1 TTGACCCTAGTCGGGAAGTGGTTTC
9346930 AGGACCGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (26 bp):
TTGACCCTAGTCGGGAAGTGGTTTCG
Found at i:9354245 original size:43 final size:43
Alignment explanation
Indices: 9354198--9354287 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
9354188 ACTTATCCGA
*
9354198 CACCTAACTAAATGACATTCAGATTCACCAAAAACAATATATT
1 CACCTAACTAAATGACATTCAGATTCACCAAAAAAAATATATT
* * *
9354241 CACCTAACTAAATGATATTTAGATTCATCAAAAAAAATATATT
1 CACCTAACTAAATGACATTCAGATTCACCAAAAAAAATATATT
9354284 CACC
1 CACC
9354288 ACAATATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (43 bp):
CACCTAACTAAATGACATTCAGATTCACCAAAAAAAATATATT
Found at i:9354899 original size:16 final size:16
Alignment explanation
Indices: 9354864--9354919 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
9354854 GCACTTCAGT
*
9354864 AACCTTTTCAA-TCAA
1 AACCTTTTCAATTGAA
9354879 TAACCTTTTCAATTGAA
1 -AACCTTTTCAATTGAA
*
9354896 AACCTTTCCAATTGAA
1 AACCTTTTCAATTGAA
9354912 AACCTTTT
1 AACCTTTT
9354920 TATCATTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 33 0.92
17 3 0.08
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (16 bp):
AACCTTTTCAATTGAA
Found at i:9359542 original size:19 final size:19
Alignment explanation
Indices: 9359516--9359560 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
9359506 ACTAAATTAG
9359516 ACTT-AAAATACTAAAAAA
1 ACTTAAAAATACTAAAAAA
* *
9359534 ACTTAAAAATTCTAAAAGA
1 ACTTAAAAATACTAAAAAA
*
9359553 ATTTAAAA
1 ACTTAAAA
9359561 CCTAAGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (19 bp):
ACTTAAAAATACTAAAAAA
Found at i:9359754 original size:5 final size:5
Alignment explanation
Indices: 9359746--9359772 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9359736 TTAAATGATA
9359746 AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
9359773 ATTACTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:9361673 original size:30 final size:30
Alignment explanation
Indices: 9361639--9361698 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
9361629 AAAAAAAAGG
9361639 ATTGAACAAGATAAAGAAGACAACATATTA
1 ATTGAACAAGATAAAGAAGACAACATATTA
*
9361669 ATTGAACAAGGTAAAGAAGACAACATATTA
1 ATTGAACAAGATAAAGAAGACAACATATTA
9361699 GAGTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (30 bp):
ATTGAACAAGATAAAGAAGACAACATATTA
Found at i:9367281 original size:94 final size:93
Alignment explanation
Indices: 9367087--9367357 Score: 271
Period size: 94 Copynumber: 2.8 Consensus size: 93
9367077 TCACTTGTGT
* *
9367087 GAGCTAGTGTAAGACATGTCTGGGACATACATCGGCAACATTATGGGAGCCAGTGTAAGACCATG
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAACAGTATGGGAGCCA-TGTAAGACCATG
* **
9367152 TCTGGGACATGGCATCGGCATTGAGATGA
65 TCTGGGACATGGCATCGACACAGAGATGA
* * *** *
9367181 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTAA-ACGT-TGTGTTTC-TGTAATACCAT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-AACA-GTATGGGAGCCATGTAAGACCAT
* *
9367243 GTCTGGGATATGGCATCGACACAGATATGCAA
64 GTCTGGGACATGGCATCGACACAGAGATG--A
* ** *
9367275 GAGCTAGTATAAGACCATGTCTGGGACATGACATCGGCCTCGACG-ATGGTAGCCAGTGTAAGAC
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCAAC-A-GTATGGGAGCCA-TGTAAGAC
9367339 CATGTCTGGGACATGGCAT
61 CATGTCTGGGACATGGCAT
9367358 TAGCATCTCA
Statistics
Matches: 142, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
92 34 0.24
94 52 0.37
95 18 0.13
96 7 0.05
97 6 0.04
99 25 0.18
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (93 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAACAGTATGGGAGCCATGTAAGACCATGT
CTGGGACATGGCATCGACACAGAGATGA
Found at i:9380748 original size:16 final size:16
Alignment explanation
Indices: 9380717--9380746 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9380707 AGTCCATTTA
9380717 TTTTATTTTATTTTTG
1 TTTTATTTTATTTTTG
9380733 TTTTA-TTTATTTTT
1 TTTTATTTTATTTTT
9380747 TGAAGACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTATTTTATTTTTG
Found at i:9382943 original size:19 final size:20
Alignment explanation
Indices: 9382919--9382956 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
9382909 GGTACCACCA
9382919 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
9382938 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
9382957 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:9383326 original size:46 final size:43
Alignment explanation
Indices: 9383183--9383318 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 43
9383173 CCCGCCCCTA
*
9383183 AGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCA-TT
* * * *
9383230 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATA
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATT
9383276 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
9383319 CCTAGTGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 29 0.39
47 29 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:9383759 original size:30 final size:30
Alignment explanation
Indices: 9383725--9383784 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9383715 ATTTAATACG
9383725 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
9383755 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
9383785 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:9386570 original size:13 final size:13
Alignment explanation
Indices: 9386552--9386577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9386542 TAACTTTTTC
9386552 ACATTTCACATAT
1 ACATTTCACATAT
9386565 ACATTTCACATAT
1 ACATTTCACATAT
9386578 TCCCAATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTCACATAT
Found at i:9386589 original size:20 final size:21
Alignment explanation
Indices: 9386548--9386598 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
9386538 TTAATAACTT
9386548 TTTCACAT-TTCACATATACA
1 TTTCACATATTCACATATACA
* *
9386568 TTTCACATATTCCCA-ATTCA
1 TTTCACATATTCACATATACA
9386588 TTTACACATAT
1 TTT-CACATAT
9386599 AGCATATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTCACATATTCACATATACA
Found at i:9386858 original size:43 final size:42
Alignment explanation
Indices: 9386811--9386923 Score: 113
Period size: 42 Copynumber: 2.6 Consensus size: 42
9386801 CAAACGTGGT
*
9386811 CTTACATGTAATCAAATATCGATGCCACTATCCTAGACAGGGG
1 CTTACACGTAATCAAATATCGATGCCAC-ATCCTAGACAGGGG
* ** * *
9386854 CTTACACGAAATCAAATA-CGACACCAACATCCTAGACATGGT
1 CTTACACGTAATCAAATATCGATGCC-ACATCCTAGACAGGGG
*
9386896 CTTACACGTAAATACCAA-ATCGATGCCA
1 CTTACACGT-AAT-CAAATATCGATGCCA
9386924 ACGTCCTAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
42 25 0.45
43 23 0.41
44 8 0.14
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (42 bp):
CTTACACGTAATCAAATATCGATGCCACATCCTAGACAGGGG
Found at i:9386900 original size:42 final size:42
Alignment explanation
Indices: 9386789--9386945 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
9386779 AGCTCGTACA
* * * * * *
9386789 ATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCTAGACATGGTCTTACACGAAATCAAATA-CG
* *
9386832 ATGCC-ACTATCCTAGACAGGGGCTTACACGAAATCAAATACG
1 ATGCCAAC-ATCCTAGACATGGTCTTACACGAAATCAAATACG
**
9386874 ACACCAACATCCTAGACATGGTCTTACACGTAAATACCAAAT-CG
1 ATGCCAACATCCTAGACATGGTCTTACACG-AAAT--CAAATACG
* * *
9386918 ATGCCAACGTCCTAAACGTGGTCTTACA
1 ATGCCAACATCCTAGACATGGTCTTACA
9386946 TGATTTCACA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 27 0.29
43 35 0.38
44 25 0.27
45 5 0.05
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (42 bp):
ATGCCAACATCCTAGACATGGTCTTACACGAAATCAAATACG
Found at i:9388719 original size:10 final size:11
Alignment explanation
Indices: 9388684--9388722 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
9388674 CTTAATAGAA
9388684 ATTTAAACTACT
1 ATTTAAACTA-T
9388696 ATTGTAAACTAT
1 ATT-TAAACTAT
9388708 ATTTAAAC-AT
1 ATTTAAACTAT
9388718 ATTTA
1 ATTTA
9388723 TTATTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.27
11 5 0.19
12 7 0.27
13 7 0.27
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (11 bp):
ATTTAAACTAT
Found at i:9391892 original size:47 final size:46
Alignment explanation
Indices: 9391789--9391958 Score: 161
Period size: 47 Copynumber: 3.6 Consensus size: 46
9391779 GTAAGGTGCT
* *
9391789 GATGCCATGTCCCAGACATAGTCTTACACTGACTATCATCTC-GTAGCC
1 GATG-CATGTCCCAGACATAGTCTTACACTGA-TCTC-TCTCAATAGCC
9391837 GATGCATGTCCCAGACAT-GTCTTACACTAGATCTCGTCTCAAT-GCC
1 GATGCATGTCCCAGACATAGTCTTACACT-GATCTC-TCTCAATAGCC
* * * ** *
9391883 AATGCCATGTCCCAGACATGGTCTTACACTG-GCTCTCAAAATTTGGCC
1 GATG-CATGTCCCAGACATAGTCTTACACTGATCTCTCTCAA--TAGCC
9391931 GATGCATGTCCCAGACAT-GTCTTACACT
1 GATGCATGTCCCAGACATAGTCTTACACT
9391959 AGCTCACAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
45 4 0.04
46 36 0.34
47 47 0.44
48 20 0.19
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATAGTCTTACACTGATCTCTCTCAATAGCC
Found at i:9391951 original size:94 final size:94
Alignment explanation
Indices: 9391790--9391960 Score: 263
Period size: 94 Copynumber: 1.8 Consensus size: 94
9391780 TAAGGTGCTG
**
9391790 ATGCCATGTCCCAGACATAGTCTTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACAT
1 ATGCCATGTCCCAGACATAGTCTTACACTGACTATCAAATCGTAGCCGATGCATGTCCCAGACAT
9391855 GTCTTACACTAGATCTCGTCTCAATGCCA
66 GTCTTACACTAGATCTCGTCTCAATGCCA
* * * * *
9391884 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAAAAT-TTGGCCGATGCATGTCCCAGACA
1 ATGCCATGTCCCAGACATAGTCTTACACTGACTATC-AAATCGTAGCCGATGCATGTCCCAGACA
9391948 TGTCTTACACTAG
65 TGTCTTACACTAG
9391961 CTCACAAACA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
94 67 0.97
95 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (94 bp):
ATGCCATGTCCCAGACATAGTCTTACACTGACTATCAAATCGTAGCCGATGCATGTCCCAGACAT
GTCTTACACTAGATCTCGTCTCAATGCCA
Found at i:9393584 original size:42 final size:42
Alignment explanation
Indices: 9393431--9393594 Score: 163
Period size: 42 Copynumber: 3.9 Consensus size: 42
9393421 TACTGTACCA
* * * *
9393431 ATGTCATATCCCAGATATGGTCTTACATGTAAT-TCGTATCA
1 ATGTCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
* * *** *
9393472 ATGCCAATAGCCCA-ACTATGGTCTTACATAAAATCTCATATCG
1 ATGTC-ATATCCCAGA-TATGGTCTTACACGTAGTCTCATATCG
* * *
9393515 AT-TCCATATCCCGGATATGGTCTTACACGTAGTTTCATATTG
1 ATGT-CATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
9393557 ATGTCATATCCCAGATATGGTCTTACACGTAGTCTCAT
1 ATGTCATATCCCAGATATGGTCTTACACGTAGTCTCAT
9393595 TAACCCTAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 5 0.05
42 84 0.84
43 11 0.11
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (42 bp):
ATGTCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG
Found at i:9401558 original size:46 final size:46
Alignment explanation
Indices: 9401491--9401583 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
9401481 GAGTCTATTT
*
9401491 TCAAGATAAAAAAATGAGAACAACATCCGTTTTCCATACGAGGAGA
1 TCAAGATAAAAAAATGAGAACAACATCCGTATTCCATACGAGGAGA
* * *
9401537 TCAAGATAAACAAATGAGAACATCATCCGTATTCCGTACGAGGAGA
1 TCAAGATAAAAAAATGAGAACAACATCCGTATTCCATACGAGGAGA
9401583 T
1 T
9401584 AATTAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (46 bp):
TCAAGATAAAAAAATGAGAACAACATCCGTATTCCATACGAGGAGA
Found at i:9402301 original size:20 final size:20
Alignment explanation
Indices: 9402259--9402303 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9402249 TGCTTTCTGT
* *
9402259 TTAACTCTTACGAGCTTCCG
1 TTAACTCATACGAGCTTCAG
* *
9402279 TTAACTCATATGAGTTTCAG
1 TTAACTCATACGAGCTTCAG
9402299 TTAAC
1 TTAAC
9402304 CCTTTTGGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (20 bp):
TTAACTCATACGAGCTTCAG
Found at i:9402438 original size:39 final size:39
Alignment explanation
Indices: 9402334--9402476 Score: 205
Period size: 39 Copynumber: 3.6 Consensus size: 39
9402324 GCTCTGATGA
**
9402334 GCTTCAGTTAGCCTTCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
9402373 ACTTCAATTAGTAGCCTTCGGGCTTCCATTTAGCACTTATGT
1 GCTTC-AGT--TAGCCTTCGGGCTTCCATTTAGCACTTATGT
9402415 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
9402454 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
9402477 ACATCACGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
39 56 0.60
40 2 0.02
41 2 0.02
42 33 0.35
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
Found at i:9407278 original size:49 final size:49
Alignment explanation
Indices: 9407211--9408018 Score: 1523
Period size: 49 Copynumber: 16.5 Consensus size: 49
9407201 ACGAGAGATA
9407211 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407260 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407309 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407358 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407407 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407456 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407505 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407554 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407603 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407652 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407701 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407750 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407799 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407848 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
9407897 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
* * * * * *
9407946 GTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA--TGGATGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGAT-AGTCG
*
9407993 GTGTAAGACCATTTCTGGGACATGGC
1 GTGTAAGACCATGTCTGGGACATGGC
9408019 ATCGGCATTA
Statistics
Matches: 751, Mismatches: 7, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
46 4 0.01
47 28 0.04
48 5 0.01
49 714 0.95
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (49 bp):
GTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGATTTTGATAGTCG
Found at i:9412942 original size:20 final size:20
Alignment explanation
Indices: 9412917--9412959 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
9412907 ATAGTATCTC
9412917 ACTCACTTATATTCAACCTA
1 ACTCACTTATATTCAACCTA
9412937 ACTCACTTATATTCAACCTA
1 ACTCACTTATATTCAACCTA
9412957 ACT
1 ACT
9412960 GTACATCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (20 bp):
ACTCACTTATATTCAACCTA
Found at i:9418801 original size:35 final size:33
Alignment explanation
Indices: 9418742--9418806 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
9418732 GAAAATATAT
*
9418742 TATATAAATTTATATTTAAAAAATAATAATTCA
1 TATATAAATTTACATTTAAAAAATAATAATTCA
*
9418775 TATATAAAATTTACATTTTAAGAAATAATAAT
1 TATAT-AAATTTACA-TTTAAAAAATAATAAT
9418807 ATTTAGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.18
34 8 0.29
35 15 0.54
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (33 bp):
TATATAAATTTACATTTAAAAAATAATAATTCA
Found at i:9420445 original size:297 final size:297
Alignment explanation
Indices: 9419942--9420506 Score: 1130
Period size: 297 Copynumber: 1.9 Consensus size: 297
9419932 GACCAAAGAT
9419942 AAAAATTATGACATATAACCGTTGTATTATTTAATATAGATTTATTAATAATAAATATAATGTAT
1 AAAAATTATGACATATAACCGTTGTATTATTTAATATAGATTTATTAATAATAAATATAATGTAT
9420007 TGCTGAAAACCATTCAAATTATTCAGATTCCAATATCACGACATTATATTAAGTAGGAATGGATT
66 TGCTGAAAACCATTCAAATTATTCAGATTCCAATATCACGACATTATATTAAGTAGGAATGGATT
9420072 TTCAGATTTTTTGAATTTTATATATAAGTTATAATGTATTTTTAGATTTGCTATCTACATTGTAT
131 TTCAGATTTTTTGAATTTTATATATAAGTTATAATGTATTTTTAGATTTGCTATCTACATTGTAT
9420137 AACATTCGACCTTTTTGGCCTCATATAATTCATTTTCTTAAACTATAATGTTATATTTTATATTA
196 AACATTCGACCTTTTTGGCCTCATATAATTCATTTTCTTAAACTATAATGTTATATTTTATATTA
9420202 ACAAAGTAACTTTATAAATTCTGGATAAATTATGGAC
261 ACAAAGTAACTTTATAAATTCTGGATAAATTATGGAC
9420239 AAAAATTATGACATATAACCGTTGTATTATTTAATATAGATTTATTAATAATAAATATAATGTAT
1 AAAAATTATGACATATAACCGTTGTATTATTTAATATAGATTTATTAATAATAAATATAATGTAT
9420304 TGCTGAAAACCATTCAAATTATTCAGATTCCAATATCACGACATTATATTAAGTAGGAATGGATT
66 TGCTGAAAACCATTCAAATTATTCAGATTCCAATATCACGACATTATATTAAGTAGGAATGGATT
9420369 TTCAGATTTTTTGAATTTTATATATAAGTTATAATGTATTTTTAGATTTGCTATCTACATTGTAT
131 TTCAGATTTTTTGAATTTTATATATAAGTTATAATGTATTTTTAGATTTGCTATCTACATTGTAT
9420434 AACATTCGACCTTTTTGGCCTCATATAATTCATTTTCTTAAACTATAATGTTATATTTTATATTA
196 AACATTCGACCTTTTTGGCCTCATATAATTCATTTTCTTAAACTATAATGTTATATTTTATATTA
9420499 ACAAAGTA
261 ACAAAGTA
9420507 TTTTTCAGTT
Statistics
Matches: 268, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 268 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (297 bp):
AAAAATTATGACATATAACCGTTGTATTATTTAATATAGATTTATTAATAATAAATATAATGTAT
TGCTGAAAACCATTCAAATTATTCAGATTCCAATATCACGACATTATATTAAGTAGGAATGGATT
TTCAGATTTTTTGAATTTTATATATAAGTTATAATGTATTTTTAGATTTGCTATCTACATTGTAT
AACATTCGACCTTTTTGGCCTCATATAATTCATTTTCTTAAACTATAATGTTATATTTTATATTA
ACAAAGTAACTTTATAAATTCTGGATAAATTATGGAC
Found at i:9422674 original size:28 final size:28
Alignment explanation
Indices: 9422634--9422689 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
9422624 CACAAACCTT
9422634 TCAATATATAAGAGTTCAATACTTGTTA
1 TCAATATATAAGAGTTCAATACTTGTTA
9422662 TCAATATATAAGAGTTCAATACTTGTTA
1 TCAATATATAAGAGTTCAATACTTGTTA
9422690 AACTAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (28 bp):
TCAATATATAAGAGTTCAATACTTGTTA
Found at i:9423163 original size:18 final size:18
Alignment explanation
Indices: 9423140--9423191 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
9423130 ACTTAATCAG
*
9423140 AGAAAGAATAAGTACCAA
1 AGAAAGAATAAATACCAA
9423158 AGAAAGAATAAATACC--
1 AGAAAGAATAAATACCAA
*
9423174 AGCAGAGAATAAATACCA
1 AG-AAAGAATAAATACCA
9423192 GCATAAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 2 0.07
17 13 0.43
18 15 0.50
ACGTcount: A:0.60, C:0.13, G:0.15, T:0.12
Consensus pattern (18 bp):
AGAAAGAATAAATACCAA
Found at i:9423184 original size:17 final size:17
Alignment explanation
Indices: 9423162--9423194 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9423152 TACCAAAGAA
9423162 AGAATAAATACCAGCAG
1 AGAATAAATACCAGCAG
9423179 AGAATAAATACCAGCA
1 AGAATAAATACCAGCA
9423195 TAAGGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (17 bp):
AGAATAAATACCAGCAG
Found at i:9423206 original size:20 final size:17
Alignment explanation
Indices: 9423142--9423194 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
9423132 TTAATCAGAG
*
9423142 AAAGAATAAGTACCAAAG-
1 AAAGAATAAATACC--AGC
9423160 AAAGAATAAATACCAGC
1 AAAGAATAAATACCAGC
*
9423177 AGAGAATAAATACCAGC
1 AAAGAATAAATACCAGC
9423194 A
1 A
9423195 TAAGGTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 2 0.06
17 17 0.53
18 13 0.41
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.11
Consensus pattern (17 bp):
AAAGAATAAATACCAGC
Found at i:9424830 original size:13 final size:13
Alignment explanation
Indices: 9424812--9424838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9424802 CATATGTAAA
9424812 TCTTAAAAATAAC
1 TCTTAAAAATAAC
9424825 TCTTAAAAATAAC
1 TCTTAAAAATAAC
9424838 T
1 T
9424839 TGCATATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TCTTAAAAATAAC
Found at i:9432501 original size:14 final size:14
Alignment explanation
Indices: 9432484--9432543 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
9432474 AGCTAATTCT
*
9432484 TAAACCCTAAATCA
1 TAAACCCTAAACCA
* *
9432498 TAAACACTAAACCT
1 TAAACCCTAAACCA
*
9432512 TAAACCCTAAACCC
1 TAAACCCTAAACCA
***
9432526 TAAATAATAAACCA
1 TAAACCCTAAACCA
9432540 TAAA
1 TAAA
9432544 ACCATAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:9432508 original size:7 final size:7
Alignment explanation
Indices: 9432484--9432529 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
9432474 AGCTAATTCT
9432484 TAAACCC
1 TAAACCC
* *
9432491 TAAATCA
1 TAAACCC
*
9432498 TAAACAC
1 TAAACCC
*
9432505 TAAACCT
1 TAAACCC
9432512 TAAACCC
1 TAAACCC
9432519 TAAACCC
1 TAAACCC
9432526 TAAA
1 TAAA
9432530 TAATAAACCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:9432510 original size:21 final size:21
Alignment explanation
Indices: 9432484--9432543 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
9432474 AGCTAATTCT
*
9432484 TAAACCCTAAATCATAAACAC
1 TAAACCCTAAACCATAAACAC
* * *
9432505 TAAACCTTAAACCCTAAACCC
1 TAAACCCTAAACCATAAACAC
***
9432526 TAAATAATAAACCATAAA
1 TAAACCCTAAACCATAAA
9432544 ACCATAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACAC
Found at i:9433002 original size:141 final size:139
Alignment explanation
Indices: 9432780--9433038 Score: 322
Period size: 141 Copynumber: 1.8 Consensus size: 139
9432770 AACACTTAGG
* **
9432780 AAAATATTGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGCATTGCCTTAGATATGTATACC
1 AAAATATTGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGCATTGCCTTAGACATACATACC
* * * *
9432845 TCAACCTTTATACAAAGAGTTGGCTAGAGCGTATGTTGACAAGTCTATCCCAACACTTAGAAAAG
66 TCAACCTTTACACAAAGAGTTGGCCAAAGCGTATGTTGACAACTCTATCCCAACACTTAGAAAAG
9432910 TGTCACCCC
131 TGTCACCCC
* * * ** *
9432919 AAAATTTTCGTCTTAGGAGTAGACAAAAGCCAACTCTTATTTAAGCGTTGTTTTAGGCATACATA
1 AAAATATT-GTCTTAGGACTAGAC-AAAGCCAACTCTTATTTAAGCATTGCCTTAGACATACATA
* * * * *
9432984 TCTCAAACC-TTACGCAAAGAGTTGTCCAAAGTGTATGTTGGCAACTCTATCCCAA
64 CCTC-AACCTTTACACAAAGAGTTGGCCAAAGCGTATGTTGACAACTCTATCCCAA
9433039 TGTGTCGTCT
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
139 7 0.07
140 14 0.14
141 74 0.75
142 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (139 bp):
AAAATATTGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGCATTGCCTTAGACATACATACC
TCAACCTTTACACAAAGAGTTGGCCAAAGCGTATGTTGACAACTCTATCCCAACACTTAGAAAAG
TGTCACCCC
Found at i:9433137 original size:117 final size:117
Alignment explanation
Indices: 9432926--9433155 Score: 327
Period size: 117 Copynumber: 2.0 Consensus size: 117
9432916 CCCAAAATTT
* * ** ** *
9432926 TCGTCTTAGGAGTAGACAAAAGCCAACTCTTATTTAAGCGTTGTTTTAGGCATACATATCTCAAA
1 TCGTCTTAGGACTACACAAAAGCCAACTCTTATACAAGCGTTGCCTTAGGAATACATATCTCAAA
* * * *
9432991 CCTTACGCAAAGAGTTGTCCAAAGTGTATGTTGGCAACTCTATCCCAATGTG
66 CCTTACACAAAGAGTTGGCCAAAGCGTATGTTCGCAACTCTATCCCAATGTG
*
9433043 TCGTCTTAGGACTACACAAAAGCCAACTCTTATACAAGCGTTGCCTTAGGAATACATATC-CCAA
1 TCGTCTTAGGACTACACAAAAGCCAACTCTTATACAAGCGTTGCCTTAGGAATACATATCTCAAA
*
9433107 CTCTTATACAAAGAGTTGGCCAAAGCGTATGTTCGCAACTCTATCCCAA
66 C-CTTACACAAAGAGTTGGCCAAAGCGTATGTTCGCAACTCTATCCCAA
9433156 CACTTAGGAA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 4 0.04
117 95 0.96
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (117 bp):
TCGTCTTAGGACTACACAAAAGCCAACTCTTATACAAGCGTTGCCTTAGGAATACATATCTCAAA
CCTTACACAAAGAGTTGGCCAAAGCGTATGTTCGCAACTCTATCCCAATGTG
Found at i:9433293 original size:140 final size:140
Alignment explanation
Indices: 9433040--9433472 Score: 695
Period size: 140 Copynumber: 3.1 Consensus size: 140
9433030 CTATCCCAAT
* ** * ** *
9433040 GTGTCGTCTTAGGACTACACAAAAGCCAACTCTTATACAAGCGTTGCCTTAGGAATACATATCCC
1 GTGTCGTCTTAGGACTAGAC-AAAGCCAACTCTTATTTAAGTGTTGCCTTAGTCATGCATATCCC
* * * *
9433105 AACTCTTATACAAAGAGTTGGCCAAAGCGTATGTTCGCAACTCTATCCCAACACTTAGGAAAGTG
65 AACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGGAAAGTG
* *
9433170 TCGCCCTAAAA
130 TCGCCCCATAA
* * *
9433181 GTGTCGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGTATTTCCTTAGTCATGCATATCCCT
1 GTGTCGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGTCATGCATATCCCA
*
9433246 ACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGAAAAGTGT
66 ACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGGAAAGTGT
9433311 CGCCCCATAA
131 CGCCCCATAA
9433321 GTGTCGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGTCATGCATATCCCA
1 GTGTCGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGTCATGCATATCCCA
*
9433386 ACCTTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGGAAAGTGT
66 ACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGGAAAGTGT
9433451 CGCCCCATAA
131 CGCCCCATAA
9433461 GTGTCGTCTTAG
1 GTGTCGTCTTAG
9433473 CACTGTTTTG
Statistics
Matches: 270, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
140 251 0.93
141 19 0.07
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (140 bp):
GTGTCGTCTTAGGACTAGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGTCATGCATATCCCA
ACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTGGCCAGTCTATCCCAACACTTAGGAAAGTGT
CGCCCCATAA
Found at i:9438551 original size:48 final size:48
Alignment explanation
Indices: 9438420--9438560 Score: 192
Period size: 48 Copynumber: 2.9 Consensus size: 48
9438410 TACTTCGAAG
* ** * *
9438420 TCTCACACCCTAAGTGCTAATATCATGGCCCGAAGAAAACTCAGTGAA
1 TCTCACACCCTAAGTGCCAATATCATGGCCCGAAGCCAACTCAATAAA
* *
9438468 TCTCACACCCGAAGTGCCAATATCATGGCCCGAAGCCAACCCAATAAA
1 TCTCACACCCTAAGTGCCAATATCATGGCCCGAAGCCAACTCAATAAA
** *
9438516 TCTTGCATCCTAAGTGCCAATATCATGGCCCGAAGCCAACTCAAT
1 TCTCACACCCTAAGTGCCAATATCATGGCCCGAAGCCAACTCAAT
9438561 GTAACCCCTA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (48 bp):
TCTCACACCCTAAGTGCCAATATCATGGCCCGAAGCCAACTCAATAAA
Found at i:9441741 original size:30 final size:30
Alignment explanation
Indices: 9441698--9441758 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
9441688 CTTCAACAAA
9441698 TGTGCTTCCTAAAATATTACCATATAATTC
1 TGTGCTTCCTAAAATATTACCATATAATTC
* * *
9441728 TGTGTTTCTTAAAATATTACTATATAATTC
1 TGTGCTTCCTAAAATATTACCATATAATTC
9441758 T
1 T
9441759 AGTTGTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (30 bp):
TGTGCTTCCTAAAATATTACCATATAATTC
Found at i:9444895 original size:21 final size:21
Alignment explanation
Indices: 9444871--9444913 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9444861 CAATCAAAAA
*
9444871 GTATAAAACAAGGGTTTAAAG
1 GTATAAAACAAAGGTTTAAAG
9444892 GTATAAAACAAAGGTTTAAAG
1 GTATAAAACAAAGGTTTAAAG
9444913 G
1 G
9444914 CAAAAAGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (21 bp):
GTATAAAACAAAGGTTTAAAG
Found at i:9457719 original size:108 final size:106
Alignment explanation
Indices: 9457429--9457737 Score: 329
Period size: 104 Copynumber: 2.9 Consensus size: 106
9457419 GTCCACTCAC
* ** * * *
9457429 ATTGCAGACTACATGGCCGATACATTCTGAAAGAAAGACTAAAAGTTGTGAATAAGTGA-TGGGT
1 ATTGCAGACTCCATGGTTGATATATTCTGAAAGAAAGACTAAAAGTTGTAAATAAGTGATTGGTT
* * * * * *
9457493 TTGCTTGGTTTATTTAAAATTTCGTGAACTATAATATTGTA
66 TTGTTTGGTTTATTTAAAATTTCATAAACTCTAACATTGCA
* * * * * * * * *
9457534 TTTGCTGATTCCATGGTTGATACTA--CTGGATGGAAGACT-AATGTAGTAAATAAGTGGTTGGT
1 ATTGCAGACTCCATGGTTGATA-TATTCTGAAAGAAAGACTAAAAGTTGTAAATAAGTGATTGGT
* * *
9457596 TTTGTTGGGTTTATTTAAAATTTCATCAACTCTGACATTGCA
65 TTTGTTTGGTTTATTTAAAATTTCATAAACTCTAACATTGCA
* *
9457638 ATTGCAGACTCCATGGTTTGATATATTCTGAAAGCAAGACTAAAAAGTTGTAAATGAGTGATTGG
1 ATTGCAGACTCCATGG-TTGATATATTCTGAAAGAAAGACT-AAAAGTTGTAAATAAGTGATTGG
9457703 TTTTGTTTGGTTTATTTAAAATTTCATAAACTCTA
64 TTTTGTTTGGTTTATTTAAAATTTCATAAACTCTA
9457738 TTGTTTGAAT
Statistics
Matches: 161, Mismatches: 36, Indels: 11
0.77 0.17 0.05
Matches are distributed among these distances:
103 14 0.09
104 63 0.39
105 22 0.14
106 12 0.07
108 50 0.31
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (106 bp):
ATTGCAGACTCCATGGTTGATATATTCTGAAAGAAAGACTAAAAGTTGTAAATAAGTGATTGGTT
TTGTTTGGTTTATTTAAAATTTCATAAACTCTAACATTGCA
Found at i:9462021 original size:19 final size:21
Alignment explanation
Indices: 9461983--9462025 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
9461973 TTAAAAATCA
*
9461983 AAAAATAATTTTCCGAAAAAT
1 AAAAATAATTTTCAGAAAAAT
9462004 AAAAAT-ATTTT-AGAAAAAT
1 AAAAATAATTTTCAGAAAAAT
9462023 AAA
1 AAA
9462026 TAATCTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 5 0.24
21 6 0.29
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAATAATTTTCAGAAAAAT
Found at i:9465595 original size:34 final size:35
Alignment explanation
Indices: 9465548--9465616 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
9465538 GGAATTTTTG
*
9465548 TAGGGAAAAGGGTATATGTATGAGAGCATGTTCAA
1 TAGGGAAAAGGGTATATGTATGAGAGCAGGTTCAA
*
9465583 TAGGG-AAAGGGTATATGTATGAGAGTAGGTTCAA
1 TAGGGAAAAGGGTATATGTATGAGAGCAGGTTCAA
9465617 ACTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.36, C:0.04, G:0.33, T:0.26
Consensus pattern (35 bp):
TAGGGAAAAGGGTATATGTATGAGAGCAGGTTCAA
Found at i:9470999 original size:20 final size:21
Alignment explanation
Indices: 9470974--9471014 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
9470964 AAAGAAAAAG
9470974 TTAAAAGTAAATTTAT-TTTA
1 TTAAAAGTAAATTTATATTTA
* *
9470994 TTAAAATTTAATTTATATTTA
1 TTAAAAGTAAATTTATATTTA
9471015 AATGATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAAAAGTAAATTTATATTTA
Found at i:9471880 original size:39 final size:36
Alignment explanation
Indices: 9471837--9471928 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 36
9471827 TTAAATTAAA
9471837 TATTAAGATAATCACTTTAATATTAATTTAATA-AAATAC
1 TATTAAGATAAT-A-TTT-ATATTAATTTAATATAAAT-C
*
9471876 TATTAAGATAAGTATTTATTTTAATTTAATATTAAATC
1 TATTAAGATAA-TATTTATATTAATTTAATA-TAAATC
*
9471914 TATTAAAATAATATT
1 TATTAAGATAATATT
9471929 ATTTTTGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
37 17 0.35
38 14 0.29
39 16 0.33
40 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (36 bp):
TATTAAGATAATATTTATATTAATTTAATATAAATC
Found at i:9472275 original size:37 final size:37
Alignment explanation
Indices: 9472225--9472297 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
9472215 ATTTACACTA
*
9472225 AAAATTATAATATTTAAATTTAAATAGAGGTTAATCC
1 AAAATTATAATATTTAAATTTAAATAGAGATTAATCC
*
9472262 AAAATTATAATATTTATATTTAAATAGAGATTAATC
1 AAAATTATAATATTTAAATTTAAATAGAGATTAATC
9472298 AGACTGTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (37 bp):
AAAATTATAATATTTAAATTTAAATAGAGATTAATCC
Found at i:9473181 original size:19 final size:19
Alignment explanation
Indices: 9473136--9473200 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
9473126 TAAATATTAA
* ** *
9473136 AATAAAAATAAAAATTTAG
1 AATAAAAATTAAAATAAAT
*
9473155 AATCAAAATTAAAATAAAT
1 AATAAAAATTAAAATAAAT
* * *
9473174 AATAAAAACTAGATTAAAT
1 AATAAAAATTAAAATAAAT
9473193 -ATAAAAAT
1 AATAAAAAT
9473201 ATCAATAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
18 7 0.19
19 29 0.81
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AATAAAAATTAAAATAAAT
Found at i:9473200 original size:31 final size:32
Alignment explanation
Indices: 9473125--9473210 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 32
9473115 AATAGTTATC
*
9473125 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATATTAAAATAAAAATAAAAATCTAGAA
*
9473157 TCAAA-ATTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATATTAAAATAAA-AATAAAAATCTAGAA
* **
9473187 TTAAATATAAAAATATCAATAAAA
1 TTAAATATTAAAATAAAAATAAAA
9473211 TAAGATATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 12 0.26
31 22 0.48
32 12 0.26
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.28
Consensus pattern (32 bp):
TTAAATATTAAAATAAAAATAAAAATCTAGAA
Found at i:9476845 original size:8 final size:8
Alignment explanation
Indices: 9476832--9476859 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
9476822 TGGCTTTGGC
9476832 AAAAAAAG
1 AAAAAAAG
9476840 AAAAAAAG
1 AAAAAAAG
9476848 AAAAAAAG
1 AAAAAAAG
9476856 AAAA
1 AAAA
9476860 TGCAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9480565 original size:14 final size:15
Alignment explanation
Indices: 9480548--9480576 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9480538 AACCCCTAAA
9480548 CCCTAAA-TCATAAT
1 CCCTAAACTCATAAT
9480562 CCCTAAACTCATAAT
1 CCCTAAACTCATAAT
9480577 TCATCATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (15 bp):
CCCTAAACTCATAAT
Found at i:9480650 original size:46 final size:46
Alignment explanation
Indices: 9480598--9480691 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
9480588 CTTCAAATAC
*
9480598 TAGTTAACTCCTAAACCTGAAACCCTAAA-TCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTGAAACCCTAAACT-ATATATCTTAAACCA
*
9480644 TAGTTAACTCATAAACCTTAAACCCTAAACTATATATCTTAAACCA
1 TAGTTAACTCATAAACCTGAAACCCTAAACTATATATCTTAAACCA
9480690 TA
1 TA
9480692 AACCTTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTGAAACCCTAAACTATATATCTTAAACCA
Found at i:9480663 original size:25 final size:25
Alignment explanation
Indices: 9480580--9480667 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
9480570 TCATAATTCA
*
9480580 TCATAAACCTTCAAA-TACTAGTTAAC
1 TCATAAACCTT-AAACCA-TAGTTAAC
* * *
9480606 TCCTAAACCTGAAACCCTA---AA-
1 TCATAAACCTTAAACCATAGTTAAC
* *
9480627 TCATATATCTTAAACCATAGTTAAC
1 TCATAAACCTTAAACCATAGTTAAC
9480652 TCATAAACCTTAAACC
1 TCATAAACCTTAAACC
9480668 CTAAACTATA
Statistics
Matches: 46, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
24 2 0.04
25 19 0.41
26 9 0.20
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.28
Consensus pattern (25 bp):
TCATAAACCTTAAACCATAGTTAAC
Found at i:9480684 original size:21 final size:22
Alignment explanation
Indices: 9480617--9480694 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
9480607 CCTAAACCTG
*
9480617 AAACCCTAAA-TCATATATCTT
1 AAACCATAAACTCATATATCTT
* *
9480638 AAACCATAGTTAACTCATAAACCTT
1 AAACCATA---AACTCATATATCTT
*
9480663 AAACCCTAAACT-ATATATCTT
1 AAACCATAAACTCATATATCTT
9480684 AAACCATAAAC
1 AAACCATAAAC
9480695 CTTAAACTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
21 24 0.52
22 4 0.09
24 2 0.04
25 16 0.35
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.28
Consensus pattern (22 bp):
AAACCATAAACTCATATATCTT
Found at i:9480686 original size:14 final size:14
Alignment explanation
Indices: 9480662--9480706 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
9480652 TCATAAACCT
*
9480662 TAAACCCTAAACTA
1 TAAACCTTAAACTA
* * *
9480676 TATATCTTAAACCA
1 TAAACCTTAAACTA
9480690 TAAACCTTAAACTA
1 TAAACCTTAAACTA
9480704 TAA
1 TAA
9480707 TGATAATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACCTTAAACTA
Found at i:9480946 original size:17 final size:18
Alignment explanation
Indices: 9480902--9480947 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
9480892 TCATCACTTT
*
9480902 AATATTAAAT-TTAATCT
1 AATATTAAATCTTAATCA
*
9480919 AATATT-TATCTTAAT-A
1 AATATTAAATCTTAATCA
9480935 AATATTAAATCTT
1 AATATTAAATCTT
9480948 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTAAATCTTAATCA
Found at i:9481033 original size:39 final size:36
Alignment explanation
Indices: 9480988--9481079 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 36
9480978 TAAACATAAA
9480988 TATTAAGATAATCACTTTAATATTAATTTAATA-AAATAC
1 TATTAAGATAAT-A-TTTAAT-TTAATTTAATATAAAT-C
9481027 TATTAAGATAAGTATTTAATTTAATTTAATATTAAATC
1 TATTAAGATAA-TATTTAATTTAATTTAATA-TAAATC
*
9481065 TATTAAAATAATATT
1 TATTAAGATAATATT
9481080 ATTTTTGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
37 15 0.31
38 17 0.35
39 16 0.33
40 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
TATTAAGATAATATTTAATTTAATTTAATATAAATC
Found at i:9481427 original size:37 final size:37
Alignment explanation
Indices: 9481377--9481449 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
9481367 ATTTACACTA
*
9481377 AAAATTATAATATTTAAATTTAAATAGAGGTTAATCC
1 AAAATTATAATATTTAAATTTAAATAGAGATTAATCC
*
9481414 AAAATTATAATATTTATATTTAAATAGAGATTAATC
1 AAAATTATAATATTTAAATTTAAATAGAGATTAATC
9481450 AGACTGTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (37 bp):
AAAATTATAATATTTAAATTTAAATAGAGATTAATCC
Found at i:9483295 original size:13 final size:13
Alignment explanation
Indices: 9483260--9483299 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 13
9483250 AGATTGTTAG
9483260 AAAAAT-AAATAA
1 AAAAATAAAATAA
9483272 AAAACATTAAAATAA
1 AAAA-A-TAAAATAA
9483287 AAAAATAAAATAA
1 AAAAATAAAATAA
9483300 GGTTAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.16
13 9 0.36
14 2 0.08
15 10 0.40
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:9487506 original size:38 final size:38
Alignment explanation
Indices: 9487464--9487539 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
9487454 ATTTCATATA
9487464 TAACAATAATAACATGAATAATATGCTTATTAAATCAC
1 TAACAATAATAACATGAATAATATGCTTATTAAATCAC
9487502 TAACAATAATAACATGAATAATATGCTTATTAAATCAC
1 TAACAATAATAACATGAATAATATGCTTATTAAATCAC
9487540 GCGAACTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (38 bp):
TAACAATAATAACATGAATAATATGCTTATTAAATCAC
Found at i:9487745 original size:30 final size:30
Alignment explanation
Indices: 9487695--9487751 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
9487685 AAATTCATTT
* *
9487695 TTTGGCAAAATTACATTTTTGCCCTTAATC
1 TTTGGCAAAATCACACTTTTGCCCTTAATC
*
9487725 TTTGTCAAAATCACACTTTTGCCCTTA
1 TTTGGCAAAATCACACTTTTGCCCTTA
9487752 GGCTTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTGGCAAAATCACACTTTTGCCCTTAATC
Found at i:9498724 original size:16 final size:16
Alignment explanation
Indices: 9498705--9498735 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9498695 TGTTGATTGA
9498705 CTGCATGTGTAGGGAC
1 CTGCATGTGTAGGGAC
9498721 CTGCATGTGTAGGGA
1 CTGCATGTGTAGGGA
9498736 AATTATTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (16 bp):
CTGCATGTGTAGGGAC
Found at i:9501454 original size:13 final size:13
Alignment explanation
Indices: 9501436--9501460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9501426 TTTGTAAACT
9501436 TGTTCATTTCCCA
1 TGTTCATTTCCCA
9501449 TGTTCATTTCCC
1 TGTTCATTTCCC
9501461 TTCTCTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (13 bp):
TGTTCATTTCCCA
Found at i:9503080 original size:46 final size:46
Alignment explanation
Indices: 9503013--9503374 Score: 275
Period size: 46 Copynumber: 7.8 Consensus size: 46
9503003 TATTTGGGCA
*
9503013 TCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
9503059 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACCAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-C--G
* *
9503104 CATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
9503152 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACCAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-C--G
* *
9503197 CATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
9503245 TCCGAACTCGTTTAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* **
9503290 CATCCGAGCTCGTTGAGTTGAGTCTAAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
9503338 CCCGAGCTCATTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9503375 GCGGGTTACA
Statistics
Matches: 251, Mismatches: 34, Indels: 62
0.72 0.10 0.18
Matches are distributed among these distances:
42 15 0.06
43 14 0.06
45 7 0.03
46 105 0.42
47 74 0.29
48 7 0.03
50 14 0.06
51 15 0.06
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:9503128 original size:47 final size:47
Alignment explanation
Indices: 9503059--9503313 Score: 219
Period size: 47 Copynumber: 5.5 Consensus size: 47
9503049 GATGCGAACG
9503059 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
* * * *
9503106 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-C--G--
1 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACCAGGCA
9503152 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
* * * *
9503199 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-C--G--
1 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACCAGGCA
* * * *
9503245 TCCGAACTCGTTTAGTTGAGTCTGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
*
9503292 TCCGAGCTCGTTGAGTTGAGTC
1 TCCGAACTCGTTGAGTTGAGTC
9503314 TAAGTTCACT
Statistics
Matches: 164, Mismatches: 22, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
42 11 0.07
43 9 0.05
45 4 0.02
46 46 0.28
47 68 0.41
48 4 0.02
50 10 0.06
51 12 0.07
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACCAGGCA
Found at i:9503168 original size:93 final size:93
Alignment explanation
Indices: 9503009--9503365 Score: 597
Period size: 93 Copynumber: 3.8 Consensus size: 93
9502999 CAGATATTTG
* *
9503009 GGCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
9503074 TTGAGTCCGAGTTTGTGAGATGTAACCA
66 TTGAGTCCGAGTTTGTGAGATGTAACCA
9503102 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
9503167 TTGAGTCCGAGTTTGTGAGATGTAACCA
66 TTGAGTCCGAGTTTGTGAGATGTAACCA
*
9503195 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTTAG
1 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
* * *
9503260 TTGAGTCTGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTTGTGAGATGTAACCA
* ** * * *
9503288 GGCATCCGAGCTCGTTGAGTTGAGTCTAAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
9503353 TTGAGTTCGAGTT
66 TTGAGTCCGAGTT
9503366 CGCTTATGGG
Statistics
Matches: 249, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 249 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTTGTGAGATGTAACCA
Found at i:9506100 original size:15 final size:15
Alignment explanation
Indices: 9506063--9506101 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9506053 TATCGTATCT
9506063 TGGGTTTCTTTATTC
1 TGGGTTTCTTTATTC
* * *
9506078 TAGATTTCTTTATTG
1 TGGGTTTCTTTATTC
9506093 TGGGTTTCT
1 TGGGTTTCT
9506102 CTATCTTAGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (15 bp):
TGGGTTTCTTTATTC
Done.