Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold101
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: 827217
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.34
Warning! 25308 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:255529 original size:17 final size:19
Alignment explanation
Indices: 255491--255531 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
255481 TAATTCGAGT
*
255491 TTTTTAAATTTTTGAGTAA
1 TTTTTAAATTTATGAGTAA
255510 TTTTTAAATTTAT-A-TAA
1 TTTTTAAATTTATGAGTAA
255527 TTTTT
1 TTTTT
255532 GAGTTTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTAAATTTATGAGTAA
Found at i:255553 original size:16 final size:16
Alignment explanation
Indices: 255532--255562 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
255522 TATAATTTTT
*
255532 GAGTTTGAATTATTTC
1 GAGTTTAAATTATTTC
255548 GAGTTTAAATTATTT
1 GAGTTTAAATTATTT
255563 TTATTTCGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (16 bp):
GAGTTTAAATTATTTC
Found at i:255703 original size:32 final size:33
Alignment explanation
Indices: 255667--255743 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
255657 TATTTGAGTC
*
255667 ATTTTAGATTTAG-ATCGTTTCAGATTCAAATT
1 ATTTTAAATTTAGAATCGTTTCAGATTCAAATT
* **
255699 ATTTTAAATTT-GAATCGTTTTAGATTTGAATT
1 ATTTTAAATTTAGAATCGTTTCAGATTCAAATT
*
255731 ATTTCAAATTTAG
1 ATTTTAAATTTAG
255744 GTTAGTTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 1 0.03
32 36 0.95
33 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (33 bp):
ATTTTAAATTTAGAATCGTTTCAGATTCAAATT
Found at i:255725 original size:16 final size:16
Alignment explanation
Indices: 255658--255734 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
255648 TAAGTTAATT
*
255658 ATTTGAGTCATTTTAG
1 ATTTGAATCATTTTAG
* *
255674 ATTT-AGATCGTTTCAG
1 ATTTGA-ATCATTTTAG
** * *
255690 ATTCAAATTATTTTAA
1 ATTTGAATCATTTTAG
*
255706 ATTTGAATCGTTTTAG
1 ATTTGAATCATTTTAG
*
255722 ATTTGAATTATTT
1 ATTTGAATCATTT
255735 CAAATTTAGG
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
15 1 0.02
16 42 0.95
17 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (16 bp):
ATTTGAATCATTTTAG
Found at i:255741 original size:16 final size:16
Alignment explanation
Indices: 255695--255741 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
255685 TTCAGATTCA
255695 AATTATTTTAAATTTG
1 AATTATTTTAAATTTG
** *
255711 AATCGTTTTAGATTTG
1 AATTATTTTAAATTTG
*
255727 AATTATTTCAAATTT
1 AATTATTTTAAATTT
255742 AGGTTAGTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (16 bp):
AATTATTTTAAATTTG
Found at i:262011 original size:29 final size:30
Alignment explanation
Indices: 261958--262017 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
261948 GACATATTCG
* **
261958 TATATTCATTTCATATTTTTGTTATGTTTT
1 TATATTCATATCATATTTTAATTATGTTTT
*
261988 TATA-TCATATCATATTTTAATTATTTTTT
1 TATATTCATATCATATTTTAATTATGTTTT
262017 T
1 T
262018 TAATATTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (30 bp):
TATATTCATATCATATTTTAATTATGTTTT
Found at i:263299 original size:32 final size:32
Alignment explanation
Indices: 263263--263331 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
263253 TTTTAAATTA
* *
263263 GATGAATATTTGATATAATTACTTGTAAATAT
1 GATGAATATTAGATATAATTACTTATAAATAT
* *
263295 GATGAATATTAGATATAATTATTTATAAATTT
1 GATGAATATTAGATATAATTACTTATAAATAT
263327 GATGA
1 GATGA
263332 TCATTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.43
Consensus pattern (32 bp):
GATGAATATTAGATATAATTACTTATAAATAT
Found at i:264519 original size:17 final size:16
Alignment explanation
Indices: 264480--264522 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
264470 ATAATATAAT
* *
264480 TATTTAATTTATTAAA
1 TATTTATTTTATGAAA
264496 TATTTATTTTATGAAA
1 TATTTATTTTATGAAA
264512 TAATTTATTTT
1 T-ATTTATTTT
264523 GATTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTATTTTATGAAA
Found at i:265094 original size:25 final size:26
Alignment explanation
Indices: 265066--265119 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
265056 AATTTTAATA
*
265066 ATAAATTTAAATATCTTCGTAT-TTT
1 ATAAATTTAAATATATTCGTATATTT
*
265091 ATAAATTTTAATATATTCGTATATTT
1 ATAAATTTAAATATATTCGTATATTT
265117 ATA
1 ATA
265120 TTATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.52
Consensus pattern (26 bp):
ATAAATTTAAATATATTCGTATATTT
Found at i:265154 original size:12 final size:12
Alignment explanation
Indices: 265110--265206 Score: 87
Period size: 12 Copynumber: 8.2 Consensus size: 12
265100 AATATATTCG
265110 TATA-TTTATAT
1 TATATTTTATAT
265121 TATA-TTTATAT
1 TATATTTTATAT
* *
265132 TAATTTTTTATGT
1 T-ATATTTTATAT
*
265145 TATATTTTATGT
1 TATATTTTATAT
*
265157 TGTATTTTATAT
1 TATATTTTATAT
265169 TATATTTTA-AT
1 TATATTTTATAT
265180 TAT-TTTTAT-T
1 TATATTTTATAT
*
265190 AATCATATTTATAT
1 TAT-AT-TTTATAT
265204 TAT
1 TAT
265207 GGTGTTTAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.11
11 17 0.24
12 31 0.44
13 12 0.17
14 3 0.04
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:265456 original size:15 final size:15
Alignment explanation
Indices: 265310--265552 Score: 78
Period size: 16 Copynumber: 16.2 Consensus size: 15
265300 TGATAGCTTA
265310 AAAATAATTTAAATTT
1 AAAATAA-TTAAATTT
** *
265326 AAAATGTTTCAAATAT
1 AAAATAATT-AAATTT
**
265342 AAGAA-AATTAAAATAA
1 AA-AATAATT-AAATTT
*
265358 AAAATTAACTAAATTT
1 AAAA-TAATTAAATTT
*
265374 GAAATAAATTAAATTT
1 AAAAT-AATTAAATTT
*
265390 AAAATAATATGAATTT
1 AAAATAAT-TAAATTT
265406 --AA-AATT--A-TT
1 AAAATAATTAAATTT
* *
265415 GAAATAATTAACTTT
1 AAAATAATTAAATTT
* **
265430 AAATTACCTAAATTT
1 AAAATAATTAAATTT
265445 AAAATAATTAAATTT
1 AAAATAATTAAATTT
* * *
265460 TATA-AATTCAAGTGTT
1 AAAATAATT-AAAT-TT
* * * *
265476 AAATTTTATTAACTTG
1 AAA-ATAATTAAATTT
**
265492 AATTTAATT-AATTT
1 AAAATAATTAAATTT
265506 -AAAT-ATTAAATTT
1 AAAATAATTAAATTT
* *
265519 -AATTAATTTAAAATT
1 AAAATAA-TTAAATTT
265534 AAAATAATTTAAATTT
1 AAAATAA-TTAAATTT
265550 AAA
1 AAA
265553 TTTAAAAATA
Statistics
Matches: 165, Mismatches: 42, Indels: 40
0.67 0.17 0.16
Matches are distributed among these distances:
9 2 0.01
10 1 0.01
11 2 0.01
12 8 0.05
13 13 0.08
14 10 0.06
15 49 0.30
16 69 0.42
17 8 0.05
18 3 0.02
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATAATTAAATTT
Found at i:265520 original size:22 final size:22
Alignment explanation
Indices: 265492--265558 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
265482 TATTAACTTG
265492 AATTTAATTAATTTAAATATTA
1 AATTTAATTAATTTAAATATTA
265514 AATTTAATTAATTTAAA-ATTA
1 AATTTAATTAATTTAAATATTA
*
265535 AA-ATAATTTAAATTTAAAT-TTA
1 AATTTAA-TT-AATTTAAATATTA
265557 AA
1 AA
265559 AATAACGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
20 3 0.07
21 8 0.20
22 30 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTAATTAATTTAAATATTA
Found at i:265552 original size:37 final size:37
Alignment explanation
Indices: 265474--265557 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
265464 AATTCAAGTG
* * * *
265474 TTAAATTTTATTAACTTGAATTTAATTAATTTAAATA
1 TTAAATTTAATTAACTTAAATTAAAATAATTTAAATA
*
265511 TTAAATTTAATTAATTTAAAATTAAAATAATTTAAAT-
1 TTAAATTTAATTAACTT-AAATTAAAATAATTTAAATA
265548 TTAAATTTAA
1 TTAAATTTAA
265558 AAATAACGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 25 0.61
38 16 0.39
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
TTAAATTTAATTAACTTAAATTAAAATAATTTAAATA
Found at i:265623 original size:2 final size:2
Alignment explanation
Indices: 265616--265659 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
265606 CGTTCAATAG
265616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265658 AT
1 AT
265660 TATTGAGACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267629 original size:22 final size:21
Alignment explanation
Indices: 267604--267649 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
267594 AGGGGATGGG
*
267604 AATTCTATGTTGTTTATGTACC
1 AATTATATGTTGTTT-TGTACC
* *
267626 AATTATTTGTTGTTTTGTATC
1 AATTATATGTTGTTTTGTACC
267647 AAT
1 AAT
267650 CTGATATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (21 bp):
AATTATATGTTGTTTTGTACC
Found at i:270366 original size:12 final size:12
Alignment explanation
Indices: 270338--270373 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
270328 CAGATATATG
*
270338 ATATATGATAGAC
1 ATATAT-ATATAC
270351 ATATATATATAC
1 ATATATATATAC
270363 ATATATATATA
1 ATATATATATA
270374 GTGAAGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATATAC
Found at i:273783 original size:42 final size:42
Alignment explanation
Indices: 273722--273941 Score: 232
Period size: 42 Copynumber: 5.5 Consensus size: 42
273712 AGGTAGATTC
*
273722 TGCTTTGGTGGTTTAGGAGACGGCGGGTTTTTAGGCTGCTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
* *
273764 TGCTTTGGTGGTTTTGGAGACGGTGGGTTTTTAGGCTGCTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
* * * *
273806 TCCTCTGGTGGTTTCGGAGATGGCGGCTTTTT---CT-C-C-
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
* *
273842 TGCTTTGGTGGTTTCGGAGATGGC-GGCTTTT----T-CTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
* *
273878 TGCTTTGGTGGTTTCGGAGACGGTGGGTTTTTAGGCTGCTCC
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
*
273920 TCCTTTGGTGGGTTT-GGAGACG
1 TGCTTTGGT-GGTTTCGGAGACG
273942 ACGGAGGCGG
Statistics
Matches: 152, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
34 2 0.01
35 6 0.04
36 44 0.29
37 7 0.05
38 1 0.01
39 2 0.01
41 1 0.01
42 84 0.55
43 5 0.03
ACGTcount: A:0.07, C:0.16, G:0.36, T:0.40
Consensus pattern (42 bp):
TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTAGGCTGCTCT
Found at i:273909 original size:36 final size:37
Alignment explanation
Indices: 273722--273909 Score: 173
Period size: 36 Copynumber: 4.9 Consensus size: 37
273712 AGGTAGATTC
*
273722 TGCTTTGGTGGTTTAGGAGACGGCGGGTTTTTAGGCTGCTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGG-TTTT----TGCTCT
* *
273764 TGCTTTGGTGGTTTTGGAGACGGTGGGTTTTTAGGCTGCTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGG-TTTT----TGCTCT
* * * * *
273806 TCCTCTGGTGGTTTCGGAGATGGCGGCTTTTT-CTCC
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTGCTCT
* *
273842 TGCTTTGGTGGTTTCGGAGATGGCGGCTTTTT-CTCT
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTGCTCT
*
273878 TGCTTTGGTGGTTTCGGAGACGGTGGGTTTTT
1 TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTT
273910 AGGCTGCTCC
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
36 65 0.50
37 1 0.01
41 4 0.03
42 61 0.47
ACGTcount: A:0.07, C:0.15, G:0.36, T:0.41
Consensus pattern (37 bp):
TGCTTTGGTGGTTTCGGAGACGGCGGGTTTTTGCTCT
Found at i:274724 original size:17 final size:19
Alignment explanation
Indices: 274702--274756 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
274692 TTATATATTC
274702 ATATTTAA-AATTT-TGAT
1 ATATTTAATAATTTATGAT
*
274719 ATATTTAATAATTTATGTT
1 ATATTTAATAATTTATGAT
*
274738 ATATTT-AT-ATTTATAAT
1 ATATTTAATAATTTATGAT
274755 AT
1 AT
274757 TAACATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 17 0.52
18 7 0.21
19 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATATTTAATAATTTATGAT
Found at i:274742 original size:19 final size:17
Alignment explanation
Indices: 274702--274744 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
274692 TTATATATTC
274702 ATATTTAAAATTTTGAT
1 ATATTTAAAATTTTGAT
*
274719 ATATTTAATAATTTATGTT
1 ATATTTAA-AATTT-TGAT
274738 ATATTTA
1 ATATTTA
274745 TATTTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
ATATTTAAAATTTTGAT
Found at i:277746 original size:2 final size:2
Alignment explanation
Indices: 277733--277771 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
277723 GTTAAACAAA
*
277733 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
277772 GAGGTTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:279978 original size:2 final size:2
Alignment explanation
Indices: 279971--280004 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
279961 TACTTCTCAT
279971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
280005 TTAAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:282922 original size:14 final size:14
Alignment explanation
Indices: 282905--282936 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
282895 TAAGAGGCAA
282905 TTTGTAAGTTTAAG
1 TTTGTAAGTTTAAG
282919 TTTGTAAGTTTAAG
1 TTTGTAAGTTTAAG
282933 TTTG
1 TTTG
282937 CCTCTTGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (14 bp):
TTTGTAAGTTTAAG
Found at i:283216 original size:5 final size:5
Alignment explanation
Indices: 283206--283230 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
283196 ATAGTAGTAT
283206 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
283231 GATCGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:284187 original size:25 final size:26
Alignment explanation
Indices: 284153--284205 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
284143 ATAAATTATA
*
284153 AAAATTATATT-TATAAATAATA-ATT
1 AAAATTATATTAAATAAA-AATAGATT
284178 AAAATTATATTAAATAAAAATAGATT
1 AAAATTATATTAAATAAAAATAGATT
284204 AA
1 AA
284206 CAGATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATTATATTAAATAAAAATAGATT
Found at i:286582 original size:29 final size:30
Alignment explanation
Indices: 286508--286582 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
286498 TAAATATTAA
* *
286508 AATAAAAATAAATTTTTAATATTATTTTAAAT
1 AATAATAA-AAATTTTTAATA-TATTTCAAAT
*
286540 AATAATATAAATTTTTGAATA-ATTTCAAAT
1 AATAATAAAAATTTTT-AATATATTTCAAAT
*
286570 CA-AATAAAAATTT
1 AATAATAAAAATTT
286583 AAATTACAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 10 0.27
30 9 0.24
31 8 0.22
32 10 0.27
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
AATAATAAAAATTTTTAATATATTTCAAAT
Found at i:287947 original size:22 final size:22
Alignment explanation
Indices: 287903--287948 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
287893 CACATTTTTA
* *
287903 TTTATTAATTTTTTATATCTAT
1 TTTATTAACTTTTTATATATAT
287925 TTTATTAACTTTTTAT-TAATAT
1 TTTATTAACTTTTTATAT-ATAT
287947 TT
1 TT
287949 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATTAACTTTTTATATATAT
Found at i:290061 original size:16 final size:17
Alignment explanation
Indices: 290037--290074 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
290027 TAACTGAGAG
* *
290037 TTTTCTTTTGCTTTT-T
1 TTTTTTTTTCCTTTTCT
290053 TTTTTTTTTCCTTTTCT
1 TTTTTTTTTCCTTTTCT
290070 TTTTT
1 TTTTT
290075 CCTTCTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTTTTTCCTTTTCT
Found at i:291503 original size:73 final size:73
Alignment explanation
Indices: 291380--291525 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
291370 GGACATCGAG
*
291380 CCACCTTTTTGTGCAGGGATGTATTCAAGGATTTTACTAACGAGTTTTATAAGATATAATTTTTA
1 CCACCTTTTTGTGCAGGGATGTATTCAAGGATTTTACTAACGAGTATTATAAGATATAATTTTTA
291445 AGGTTATT
66 AGGTTATT
* * *
291453 CCACCTTTTTGTGCAGGGATGTATTCAAGGATTTTGCTAATGAGTATTATAAGATATACTTTTTA
1 CCACCTTTTTGTGCAGGGATGTATTCAAGGATTTTACTAACGAGTATTATAAGATATAATTTTTA
291518 AGGTTATT
66 AGGTTATT
291526 ATATATAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (73 bp):
CCACCTTTTTGTGCAGGGATGTATTCAAGGATTTTACTAACGAGTATTATAAGATATAATTTTTA
AGGTTATT
Found at i:292501 original size:14 final size:14
Alignment explanation
Indices: 292462--292493 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
292452 TTAAATTTTA
*
292462 AATTTGTTAAATAT
1 AATTTATTAAATAT
292476 AATTTATTAAATAT
1 AATTTATTAAATAT
292490 AATT
1 AATT
292494 ATATAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AATTTATTAAATAT
Found at i:292967 original size:10 final size:9
Alignment explanation
Indices: 292932--292963 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
292922 ATTTTTTTTT
292932 AATATTTAA
1 AATATTTAA
292941 AATATATTAA
1 AATAT-TTAA
292951 AATATTTAA
1 AATATTTAA
292960 AATA
1 AATA
292964 ATTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATTTAA
Found at i:292975 original size:12 final size:12
Alignment explanation
Indices: 292955--292996 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
292945 TATTAAAATA
*
292955 TTTAAAATAATT
1 TTTATAATAATT
*
292967 TTTATAATAATA
1 TTTATAATAATT
292979 TTTAT-ATAA-T
1 TTTATAATAATT
292989 TTTATAAT
1 TTTATAAT
292997 TAAACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 5 0.19
11 6 0.23
12 15 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATAATAATT
Found at i:293009 original size:22 final size:23
Alignment explanation
Indices: 292959--293009 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
292949 AAAATATTTA
*
292959 AAATAATTTTTATAATAATATTT
1 AAATAATTTTTATAATAATACTT
*
292982 ATATAA-TTTTATAATTAA-ACTT
1 AAATAATTTTTATAA-TAATACTT
293004 AAATAA
1 AAATAA
293010 AAATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATAATTTTTATAATAATACTT
Found at i:293440 original size:18 final size:17
Alignment explanation
Indices: 293412--293460 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
293402 TTATAATAGA
293412 ATAAA-TATATAAACTAC
1 ATAAATTATATAAA-TAC
293429 -TAATATTATATAAATAC
1 ATAA-ATTATATAAATAC
293446 ATAAATTAT-TAAATA
1 ATAAATTATATAAATA
293461 TAGTTATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.31
17 9 0.31
18 11 0.38
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATTATATAAATAC
Found at i:293774 original size:19 final size:18
Alignment explanation
Indices: 293752--293803 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
293742 AGTTGGTAAT
* *
293752 TTTTTTATAAAATGAATA
1 TTTTTTAAAAAATAAATA
*
293770 GTTTTCTAAAAAATTAAATA
1 -TTTTTTAAAAAA-TAAATA
293790 TTTTTTAAAAAATA
1 TTTTTTAAAAAATA
293804 TATTTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.07
19 21 0.75
20 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTTTTAAAAAATAAATA
Found at i:294042 original size:15 final size:15
Alignment explanation
Indices: 294017--294093 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 15
294007 AGAAAAAATT
294017 AAAATATTACATAATA
1 AAAATA-TACATAATA
*
294033 AAAATATACATAAAA
1 AAAATATACATAATA
294048 AATAATATGA-ATAAAATA
1 AA-AATAT-ACAT--AATA
* * *
294066 AAAATATAAATGATC
1 AAAATATACATAATA
294081 AAAATATACATAA
1 AAAATATACATAA
294094 CAAGAATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 23 0.46
16 14 0.28
17 8 0.16
18 5 0.10
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATATACATAATA
Found at i:294068 original size:21 final size:21
Alignment explanation
Indices: 294042--294086 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
294032 AAAAATATAC
294042 ATAAAAA-ATAATATGAAT-AAA
1 ATAAAAATATAA-ATG-ATCAAA
294063 ATAAAAATATAAATGATCAAA
1 ATAAAAATATAAATGATCAAA
294084 ATA
1 ATA
294087 TACATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
ATAAAAATATAAATGATCAAA
Found at i:294656 original size:21 final size:21
Alignment explanation
Indices: 294630--294673 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
294620 TGTTAATGAT
*
294630 TTCAATTTCAATTTAAATAAA
1 TTCAATTTCAATTTAAACAAA
294651 TTCAATTTCAATTTAAACAAA
1 TTCAATTTCAATTTAAACAAA
294672 TT
1 TT
294674 ATTATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TTCAATTTCAATTTAAACAAA
Found at i:294825 original size:31 final size:32
Alignment explanation
Indices: 294745--294835 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 32
294735 AAAATTGCAA
*
294745 TAAATATGATATATATCTATA-AAAATGATATACG
1 TAAATATGATATATATATATATAAAAT--T-TACG
*
294779 TAAA-AT--TTTATATATATATAAAATTTA-G
1 TAAATATGATATATATATATATAAAATTTACG
294807 TAAATATGATATATATATATATAAAATTT
1 TAAATATGATATATATATATATAAAATTT
294836 TAATAATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
28 5 0.10
29 4 0.08
30 1 0.02
31 29 0.58
32 5 0.10
33 2 0.04
34 4 0.08
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (32 bp):
TAAATATGATATATATATATATAAAATTTACG
Found at i:300495 original size:16 final size:17
Alignment explanation
Indices: 300463--300498 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
300453 TCTAAGTTGC
300463 TTCGACTTTTTATTTTT
1 TTCGACTTTTTATTTTT
300480 TTCGACTTTTTATTTTT
1 TTCGACTTTTTATTTTT
300497 TT
1 TT
300499 AGAAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (17 bp):
TTCGACTTTTTATTTTT
Found at i:301044 original size:14 final size:15
Alignment explanation
Indices: 301009--301043 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
300999 CATATTCGTA
301009 AAAAAATATTTTTTT
1 AAAAAATATTTTTTT
*
301024 AAAAAATATTTTTTC
1 AAAAAATATTTTTTT
301039 AAAAA
1 AAAAA
301044 TCTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAAATATTTTTTT
Found at i:302340 original size:21 final size:22
Alignment explanation
Indices: 302314--302354 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
302304 TATATAATTG
*
302314 TTAATATA-AAAATATATTTTA
1 TTAATAAATAAAATATATTTTA
*
302335 TTAATAAATAAAATCTATTT
1 TTAATAAATAAAATATATTT
302355 ATACTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATAAATAAAATATATTTTA
Found at i:304933 original size:2 final size:2
Alignment explanation
Indices: 304926--304971 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
304916 TTCCTTGACA
304926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
304968 AT AT
1 AT AT
304972 CATCTCATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307185 original size:18 final size:19
Alignment explanation
Indices: 307133--307182 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
307123 TTTATATTAG
307133 TATA-AATTAATTAATTTTA
1 TATATAATTAA-TAATTTTA
* *
307152 TATAT-TTTTATAATTTTA
1 TATATAATTAATAATTTTA
307170 TATATAATTAATA
1 TATATAATTAATA
307183 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATAATTAATAATTTTA
Found at i:307684 original size:51 final size:51
Alignment explanation
Indices: 307608--307711 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
307598 ATTTTAATAA
307608 TACCTTTAATATGAAATTATCGTTGTAAATAAAGATGTTTATGGATTGAGC
1 TACCTTTAATATGAAATTATCGTTGTAAATAAAGATGTTTATGGATTGAGC
307659 TACCTTTAATATGAAATTATCGTTGTAAATAAAGATGTTTATGGATTGAGC
1 TACCTTTAATATGAAATTATCGTTGTAAATAAAGATGTTTATGGATTGAGC
307710 TA
1 TA
307712 TCTATTCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (51 bp):
TACCTTTAATATGAAATTATCGTTGTAAATAAAGATGTTTATGGATTGAGC
Found at i:308780 original size:22 final size:22
Alignment explanation
Indices: 308744--308785 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
308734 AAATTAAAAA
308744 AATTAAAAAATTAAAATTTTTAT
1 AATTAAAAAATT-AAATTTTTAT
*
308767 AATTTAAAAA-TAAATTTTT
1 AATTAAAAAATTAAATTTTT
308786 GGATGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 1 0.06
23 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAAAAATTAAATTTTTAT
Found at i:309612 original size:2 final size:2
Alignment explanation
Indices: 309605--309637 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
309595 CAAGCTCGCC
309605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
309638 GCCTATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:310304 original size:32 final size:33
Alignment explanation
Indices: 310268--310338 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
310258 TATTATATAT
310268 TTATATAAATTTTAATAAATTAATA-ATTCATA
1 TTATATAAATTTTAATAAATTAATATATTCATA
* * * *
310300 TTATATAAATTTTGATATATTTATATATTCGTA
1 TTATATAAATTTTAATAAATTAATATATTCATA
310333 TTATAT
1 TTATAT
310339 TTATATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (33 bp):
TTATATAAATTTTAATAAATTAATATATTCATA
Found at i:317715 original size:50 final size:51
Alignment explanation
Indices: 317651--317748 Score: 162
Period size: 50 Copynumber: 1.9 Consensus size: 51
317641 TTGAGTTGAA
*
317651 TTAGCTTTTTATAATTTAAATTCAGCTCGATTCGAATGAGGTTTTTATGAT
1 TTAGCTTTTTATAATTTAAATTCAGCTCGATTCGAATGAGCTTTTTATGAT
* *
317702 TTAGC-TTTTATAATTTAAATTCAGCTTGATTTGAATGAGCTTTTTAT
1 TTAGCTTTTTATAATTTAAATTCAGCTCGATTCGAATGAGCTTTTTAT
317749 AGTTTGAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 39 0.89
51 5 0.11
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (51 bp):
TTAGCTTTTTATAATTTAAATTCAGCTCGATTCGAATGAGCTTTTTATGAT
Found at i:318020 original size:3 final size:3
Alignment explanation
Indices: 318012--318044 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
318002 ATGGGTTTTC
318012 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
318045 CTAGACGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:318418 original size:47 final size:45
Alignment explanation
Indices: 318367--318470 Score: 108
Period size: 47 Copynumber: 2.2 Consensus size: 45
318357 AAATATATGT
318367 ATTTTATCATATT-ATAA-TTATATT-TAAAATATTTTATATTTATATC
1 ATTTTATCATATTAATAATTTATATTATAAAA-A-TTTA-ATTTATA-C
*
318413 AATTTTAAT-ATATTAATAATTTATATTATATAAATTTAATTTATAC
1 -ATTTT-ATCATATTAATAATTTATATTATAAAAATTTAATTTATAC
318459 ATTTATATCATA
1 ATTT-TATCATA
318471 ACTTGTCATA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
45 6 0.12
46 5 0.10
47 17 0.34
48 10 0.20
49 8 0.16
50 4 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (45 bp):
ATTTTATCATATTAATAATTTATATTATAAAAATTTAATTTATAC
Found at i:318448 original size:15 final size:15
Alignment explanation
Indices: 318421--318466 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
318411 TCAATTTTAA
318421 TATATTA-AT-AATT
1 TATATTATATAAATT
318434 TATATTATATAAATT
1 TATATTATATAAATT
*
318449 TA-ATT-TATACATT
1 TATATTATATAAATT
318462 TATAT
1 TATAT
318467 CATAACTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 16 0.55
14 7 0.24
15 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:333847 original size:2 final size:2
Alignment explanation
Indices: 333840--333866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
333830 TATTTTCATA
333840 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
333867 ATTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:334570 original size:2 final size:2
Alignment explanation
Indices: 334563--334603 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
334553 AAACAGCGAA
334563 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
334604 AATTAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:335785 original size:19 final size:20
Alignment explanation
Indices: 335746--335789 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
335736 AAAATAATTT
335746 ATATTAATATTATTAAATAA
1 ATATTAATATTATTAAATAA
**
335766 ATATTAATA-TATTATTTAA
1 ATATTAATATTATTAAATAA
335785 ATATT
1 ATATT
335790 CAATGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTAATATTATTAAATAA
Found at i:335913 original size:13 final size:14
Alignment explanation
Indices: 335880--335917 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
335870 TATCATATCA
* *
335880 ATATTTATTTAACG
1 ATATTTATATAAAG
335894 ATATTTATATAAAG
1 ATATTTATATAAAG
335908 -TATTTATATA
1 ATATTTATATA
335918 TTTGATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATTTATATAAAG
Found at i:338780 original size:11 final size:11
Alignment explanation
Indices: 338764--338799 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
338754 TCTTCCTTTC
338764 TCTTTTTTTTT
1 TCTTTTTTTTT
338775 TCTTTTTTTTT
1 TCTTTTTTTTT
338786 TCCTTTTTTTTT
1 T-CTTTTTTTTT
338798 TC
1 TC
338800 AAAAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:338782 original size:13 final size:13
Alignment explanation
Indices: 338760--338798 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
338750 TCTCTCTTCC
*
338760 TTTCTCTTTTTTT
1 TTTCTTTTTTTTT
338773 TTTC-TTTTTTTT
1 TTTCTTTTTTTTT
*
338785 TTCCTTTTTTTTT
1 TTTCTTTTTTTTT
338798 T
1 T
338799 CAAAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:338799 original size:12 final size:12
Alignment explanation
Indices: 338760--338799 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
338750 TCTCTCTTCC
338760 TTTCTCTTTTTTT
1 TTTC-CTTTTTTT
338773 TTT-CTTTTTTT
1 TTTCCTTTTTTT
338784 TTTCCTTTTTTT
1 TTTCCTTTTTTT
338796 TTTC
1 TTTC
338800 AAAAATAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.42
12 12 0.46
13 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCCTTTTTTT
Found at i:339341 original size:37 final size:38
Alignment explanation
Indices: 339272--339345 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
339262 TTTTATTATT
*
339272 AAAATATTATTTTATATTTATATATATAAATTTAAATA
1 AAAATATTATTTTATATTTAAATATATAAATTTAAATA
339310 AAAATATTATATTTAT-TATTAAATA-AT-AATTTAAAT
1 AAAATATTAT-TTTATAT-TTAAATATATAAATTTAAAT
339346 TAAATTAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 9 0.27
38 13 0.39
39 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
AAAATATTATTTTATATTTAAATATATAAATTTAAATA
Found at i:339453 original size:27 final size:27
Alignment explanation
Indices: 339408--339459 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
339398 AAAACCCACC
*
339408 TTTGAGATGTGTTAATTAATGGGGATA
1 TTTGAGATGTGTTAATTAACGGGGATA
* *
339435 TTTGAGATGTTTTATTTAACGGGGA
1 TTTGAGATGTGTTAATTAACGGGGA
339460 CATAAGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (27 bp):
TTTGAGATGTGTTAATTAACGGGGATA
Found at i:339468 original size:27 final size:27
Alignment explanation
Indices: 339411--339468 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
339401 ACCCACCTTT
* * **
339411 GAGATGTGTTAATTAATGGGGATATTT
1 GAGATGTGTTAATTAACGGGGACATAA
* *
339438 GAGATGTTTTATTTAACGGGGACATAA
1 GAGATGTGTTAATTAACGGGGACATAA
339465 GAGA
1 GAGA
339469 AACACACCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (27 bp):
GAGATGTGTTAATTAACGGGGACATAA
Found at i:346478 original size:21 final size:22
Alignment explanation
Indices: 346454--346500 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
346444 ATATATTACA
* *
346454 AATTAATAATAATTTA-TAAGT
1 AATTAATAATAACTTATTAAGC
346475 AATTAATAATAACTTATTAAGC
1 AATTAATAATAACTTATTAAGC
346497 AATT
1 AATT
346501 TGCTTATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTAATAATAACTTATTAAGC
Found at i:346607 original size:21 final size:22
Alignment explanation
Indices: 346578--346623 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
346568 CTAGTATTTT
346578 ATTTAT-TTTT-AAAT-AATAA
1 ATTTATATTTTAAAATAAATAA
346597 ATTTATATTTTAAAATAAATAA
1 ATTTATATTTTAAAATAAATAA
346619 ATTTA
1 ATTTA
346624 GTAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 4 0.17
22 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATATTTTAAAATAAATAA
Found at i:346876 original size:16 final size:16
Alignment explanation
Indices: 346855--346887 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
346845 TTTTTTTATT
346855 AAAAAT-CTTATTAATA
1 AAAAATACTTA-TAATA
346871 AAAAATACTTATAATA
1 AAAAATACTTATAATA
346887 A
1 A
346888 TAGTTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATACTTATAATA
Found at i:346972 original size:14 final size:14
Alignment explanation
Indices: 346953--347012 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
346943 TTGAGTTTTA
346953 TATATATTTTATAT
1 TATATATTTTATAT
* *
346967 TATATATTTAAAAT
1 TATATATTTTATAT
*
346981 TA-A-ATTTGATAAT
1 TATATATTTTAT-AT
346994 T-TATATATTTATAT
1 TATATAT-TTTATAT
347008 TATAT
1 TATAT
347013 TTAATGAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 19 0.53
15 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATATATTTTATAT
Found at i:347434 original size:32 final size:32
Alignment explanation
Indices: 347374--347435 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
347364 ACTGAACCTG
**
347374 AAATAACTTAAAACTAAAATGATTCAAACTTA
1 AAATAACTTAAAACTAAAATGACCCAAACTTA
*
347406 AAATAA-TTTAAACTTAAAATGACCCAAACT
1 AAATAACTTAAAAC-TAAAATGACCCAAACT
347436 CTAATGACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (32 bp):
AAATAACTTAAAACTAAAATGACCCAAACTTA
Found at i:347435 original size:16 final size:16
Alignment explanation
Indices: 347384--347427 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
347374 AAATAACTTA
347384 AAAC-TAAAATGATTC
1 AAACTTAAAATGATTC
* *
347399 AAACTTAAAATAATTT
1 AAACTTAAAATGATTC
347415 AAACTTAAAATGA
1 AAACTTAAAATGA
347428 CCCAAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (16 bp):
AAACTTAAAATGATTC
Found at i:348761 original size:77 final size:77
Alignment explanation
Indices: 348676--348830 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
348666 TTTAAGCTGA
348676 GTTTCAAATCGAATTTGAAATTCTTATTACTTAAACTCGATTCAAATTGTTTACTTTGTCGAAAT
1 GTTTCAAATCGAATTTGAAATTCTTATTACTTAAACTCGATTCAAATTGTTTACTTTGTCGAAAT
348741 GAATCCTTTCCG
66 GAATCCTTTCCG
348753 GTTTCAAATCGAATTTGAAATTCTTATTACTTAAACTCGATTCAAATTGTTTACTTTGTCGAAAT
1 GTTTCAAATCGAATTTGAAATTCTTATTACTTAAACTCGATTCAAATTGTTTACTTTGTCGAAAT
348818 GAATCCTTTCCG
66 GAATCCTTTCCG
348830 G
1 G
348831 GTAGAAATAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (77 bp):
GTTTCAAATCGAATTTGAAATTCTTATTACTTAAACTCGATTCAAATTGTTTACTTTGTCGAAAT
GAATCCTTTCCG
Found at i:348950 original size:15 final size:14
Alignment explanation
Indices: 348920--349002 Score: 62
Period size: 15 Copynumber: 5.9 Consensus size: 14
348910 GAAGTTATTC
*
348920 ATTTAATTTGATAA
1 ATTTAATTTAATAA
348934 ATTTAATTTAAATAA
1 ATTTAATTT-AATAA
* *
348949 ATTAAATCATAA-AA
1 ATTTAAT-TTAATAA
* * *
348963 ATTAAATTT-TTAT
1 ATTTAATTTAATAA
*
348976 ATTTAATTTAATTTA
1 ATTTAATTTAA-TAA
348991 ATTTAATTTAAT
1 ATTTAATTTAAT
349003 TTATTATTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
13 10 0.19
14 19 0.35
15 24 0.44
16 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTAATTTAATAA
Found at i:348984 original size:5 final size:5
Alignment explanation
Indices: 348971--349015 Score: 63
Period size: 5 Copynumber: 8.4 Consensus size: 5
348961 AAATTAAATT
348971 TTTATA TTTAA TTTAA TTTAA TTTAA TTTAA TTTATTA TTTAA TT
1 TTTA-A TTTAA TTTAA TTTAA TTTAA TTTAA TTTA--A TTTAA TT
349016 AATAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 28 0.76
6 4 0.11
7 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:349003 original size:15 final size:16
Alignment explanation
Indices: 348971--349015 Score: 74
Period size: 15 Copynumber: 2.8 Consensus size: 16
348961 AAATTAAATT
348971 TTTATATTTAATTTAA
1 TTTATATTTAATTTAA
348987 TTTA-ATTTAATTTAA
1 TTTATATTTAATTTAA
349002 TTTATTATTTAATT
1 TTTA-TATTTAATT
349016 AATAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.56
16 4 0.15
17 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTATATTTAATTTAA
Found at i:349057 original size:36 final size:38
Alignment explanation
Indices: 348992--349074 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 38
348982 TTTAATTTAA
* *
348992 TTTAATTTAATTTATTATTTAATTAAT-AAAAAT-ATT
1 TTTAATTTAATTTATTATTAAAATAATAAAAAATAATT
349028 TTTAATTTAAATTTAATTA-TAAAAT-ATAAAAAATAATT
1 TTTAATTT-AATTT-ATTATTAAAATAATAAAAAATAATT
349066 TTTATATTT
1 TTTA-ATTT
349075 TAATAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 10 0.25
37 15 0.38
38 11 0.28
39 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAATTTAATTTATTATTAAAATAATAAAAAATAATT
Found at i:351048 original size:13 final size:14
Alignment explanation
Indices: 351011--351056 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
351001 ATTATTAATT
351011 ATATAATAAATATTTA
1 ATAT-ATAAATA-TTA
351027 AT-TATAAATATTA
1 ATATATAAATATTA
*
351040 ATATA-AAATTTTA
1 ATATATAAATATTA
351053 ATAT
1 ATAT
351057 TATTTTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 16 0.57
14 9 0.32
15 1 0.04
16 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATAAATATTA
Found at i:354760 original size:21 final size:21
Alignment explanation
Indices: 354734--354775 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
354724 GAGAAGGAGC
354734 ATTCAAGGTTGATTTGATCGT
1 ATTCAAGGTTGATTTGATCGT
354755 ATTCAAGGTTGATTTGATCGT
1 ATTCAAGGTTGATTTGATCGT
354776 TTGGAGTCGA
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:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (21 bp):
ATTCAAGGTTGATTTGATCGT
Found at i:354989 original size:19 final size:19
Alignment explanation
Indices: 354956--354992 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
354946 TAATTTTAGT
**
354956 TTTTTTTATTTTATTTATC
1 TTTTTTTATAATATTTATC
354975 TTTTTTTATAATATTTAT
1 TTTTTTTATAATATTTAT
354993 GATAGTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTATAATATTTATC
Found at i:356324 original size:16 final size:16
Alignment explanation
Indices: 356261--356320 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
356251 TTTAATTATC
356261 CGGGTTATTTTGAGTT
1 CGGGTTATTTTGAGTT
* *
356277 CAGATTATTTTGAGTT
1 CGGGTTATTTTGAGTT
* * *
356293 CGGGTCATTTCGGGTT
1 CGGGTTATTTTGAGTT
356309 CGGGTTATTTTG
1 CGGGTTATTTTG
356321 GGTTTGAGTC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.13, C:0.10, G:0.30, T:0.47
Consensus pattern (16 bp):
CGGGTTATTTTGAGTT
Found at i:356334 original size:16 final size:16
Alignment explanation
Indices: 356283--356335 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
356273 AGTTCAGATT
* *
356283 ATTTTGAGTTCGGGTC
1 ATTTTGGGTTCGAGTC
* * *
356299 ATTTCGGGTTCGGGTT
1 ATTTTGGGTTCGAGTC
*
356315 ATTTTGGGTTTGAGTC
1 ATTTTGGGTTCGAGTC
356331 ATTTT
1 ATTTT
356336 CAAATTTGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.11, C:0.09, G:0.30, T:0.49
Consensus pattern (16 bp):
ATTTTGGGTTCGAGTC
Found at i:357567 original size:23 final size:21
Alignment explanation
Indices: 357522--357568 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
357512 GATGAGATTC
357522 ATAAAAAAAAAAGTAAAAAAA
1 ATAAAAAAAAAAGTAAAAAAA
* *
357543 ATAAAAATATAAAGGTAAAATAA
1 ATAAAAA-A-AAAAGTAAAAAAA
357566 ATA
1 ATA
357569 TGGGCTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (21 bp):
ATAAAAAAAAAAGTAAAAAAA
Found at i:363680 original size:23 final size:24
Alignment explanation
Indices: 363643--363688 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
363633 TAAAAAATTT
*
363643 AAATTATTATCTAATTTATAAATA
1 AAATTATTATCTAATTAATAAATA
363667 AAATTATTAT-TAATTAATAAAT
1 AAATTATTATCTAATTAATAAAT
363689 TAATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTATTATCTAATTAATAAATA
Found at i:365042 original size:20 final size:18
Alignment explanation
Indices: 365005--365041 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
364995 TCAATTTGAT
365005 TTATTTTTTAATTATATA
1 TTATTTTTTAATTATATA
365023 TTATTTTTTATATT-TATA
1 TTATTTTTTA-ATTATATA
365041 T
1 T
365042 AATATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTTTAATTATATA
Found at i:365046 original size:25 final size:25
Alignment explanation
Indices: 365025--365094 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
365015 ATTATATATT
*
365025 ATTTTTTAT-ATTTATATAATATAA
1 ATTTTATATAATTTATATAATATAA
*
365049 ATTTTATATAATTTATATCATATAA
1 ATTTTATATAATTTATATAATATAA
*
365074 A---TATATAATAT-TATAATATAA
1 ATTTTATATAATTTATATAATATAA
365095 TCATTAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.22
22 9 0.22
24 8 0.20
25 15 0.37
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTATATAATTTATATAATATAA
Found at i:365534 original size:22 final size:22
Alignment explanation
Indices: 365509--365550 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
365499 AATAAAAAAT
365509 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
365531 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
365551 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:366025 original size:2 final size:2
Alignment explanation
Indices: 366018--366051 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
366008 CGACAAGGCC
366018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
366052 TATCAGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366486 original size:14 final size:15
Alignment explanation
Indices: 366467--366498 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
366457 GATGATGAGA
366467 AAGCTTT-ATAAAAG
1 AAGCTTTAATAAAAG
366481 AAGCTTTAATAAAAG
1 AAGCTTTAATAAAAG
366496 AAG
1 AAG
366499 TAAAGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AAGCTTTAATAAAAG
Found at i:368097 original size:11 final size:11
Alignment explanation
Indices: 368067--368104 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
368057 AATTTTATTT
368067 TATTATGTAAAA
1 TATTAT-TAAAA
368079 TA-TATTAAAA
1 TATTATTAAAA
*
368089 TATTATTAATA
1 TATTATTAAAA
368100 TATTA
1 TATTA
368105 ATATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 7 0.29
11 15 0.62
12 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:370257 original size:23 final size:22
Alignment explanation
Indices: 370212--370257 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
370202 GTAAAAGAAA
* **
370212 AAAAAATAATAGACAAAGTTAC
1 AAAAAATAAAAGACAAAAATAC
370234 AAAAAATAAAAGCACAAAAATAC
1 AAAAAATAAAAG-ACAAAAATAC
370257 A
1 A
370258 TAAAGATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.13
Consensus pattern (22 bp):
AAAAAATAAAAGACAAAAATAC
Found at i:370549 original size:79 final size:79
Alignment explanation
Indices: 370479--371023 Score: 554
Period size: 78 Copynumber: 6.9 Consensus size: 79
370469 AAATTTAATA
* * * * *
370479 TTTTGGAGATAAAAATAGGGTTAGAGTAT-CCCTCAGAAATGACAGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
*
370543 GTGAAAAATTGATG
66 GTGAAAAATCGATG
* * * ** *
370557 TTTTGAAAAT-AAAATCAGGGTTGGAGTATTCCCTCAAAAATAA-TAGGTTGGAGTAACCCCGAT
1 TTTTGGAAATAAAAAT-AGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
370620 TGTGAAAAATCGATG
65 TGTGAAAAATCGATG
* ** * * *
370635 TTTTAGAAAT-AAAACCGGAGTTGGAGTATCCCCTC-GAAAATAATGGGGTTGGAGTATTCTCGA
1 TTTTGGAAATAAAAATAGG-GTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGA
370698 TTGTGAAAAATC-AGTG
64 TTGTGAAAAATCGA-TG
** * *
370714 TTTTTGGAAATAAAACCAAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1 -TTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
* *
370779 GGTGAAAAATCGGTG
65 TGTGAAAAATCGATG
* * * * * *
370794 CTGTGGAAAT-AAAATCGAGATTAGAATATCCCCTCA-AAATTAACGGGGTTGGAGTAT-CCCGA
1 TTTTGGAAATAAAAATAG-GGTTGGAGTATCCCCTCAGAAA-TAACGGGGTTGGAGTATCCCCGA
370856 TTGTGAAAAATCGATG
64 TTGTGAAAAATCGATG
** * * * *
370872 TTTTAAAAATAAAATTATGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
* *
370937 GTGAAAAATTGGTG
66 GTGAAAAATCGATG
* * * * *
370951 TTTTAGAAATAAAACTGGGGTTAGAGTATCCCCTC-GAAAATAA-TGGGTTGGAGTATCCCCGAT
1 TTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGAT
371014 TGTGAAAAAT
65 TGTGAAAAAT
371024 TGGTATTTTA
Statistics
Matches: 389, Mismatches: 62, Indels: 32
0.81 0.13 0.07
Matches are distributed among these distances:
77 7 0.02
78 175 0.45
79 140 0.36
80 61 0.16
81 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
TTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
GTGAAAAATCGATG
Found at i:370716 original size:157 final size:157
Alignment explanation
Indices: 370498--371042 Score: 663
Period size: 157 Copynumber: 3.5 Consensus size: 157
370488 TAAAAATAGG
* ** * *
370498 GTTAGAGTAT-CCCTC-AGAAATGACAGGGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTTT
1 GTTAGAGTATCCCCTCGA-AAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTT
* * * ** * *
370561 GAAAATAAAATCAGGGTTGGAGTATTCCCTCAAAAATAATAGGTTGGAGTAACCCCGATTGTGAA
65 AAAAATAAAATCAAGGTTGGAGTATCCCCTCGGAAATAATGGGTTGGAGTATCCCCGATTGTGAA
*
370626 AAATCGATGTTTTAGAAATAAAACCGGA
130 AAATCGGTGTTTTAGAAATAAAACCGGA
* * *
370654 GTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATTCTCGATTGTGAAAAATC-AGTGTTTT
1 GTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGA-TG-TTT
** * * *
370718 TGGAAATAAAACCAAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGGTG
64 TAAAAATAAAATCAAGGTTGGAGTATCCCCTCGGAAATAA-TGGGTTGGAGTATCCCCGATTGTG
* * * *
370783 AAAAATCGGTGCTGTGGAAATAAAATC-GA
128 AAAAATCGGTGTTTTAGAAATAAAACCGGA
* *
370812 GATTAGAATATCCCCTC-AAAATTAACGGGGTTGGAGTAT-CCCGATTGTGAAAAATCGATGTTT
1 G-TTAGAGTATCCCCTCGAAAA-TAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTT
* *
370875 TAAAAATAAAATTATGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTGTG
64 TAAAAATAAAATCAAGGTTGGAGTATCCCCTCGGAAATAAT-GGGTTGGAGTATCCCCGATTGTG
* * *
370940 AAAAATTGGTGTTTTAGAAATAAAACTGGG
128 AAAAATCGGTGTTTTAGAAATAAAACCGGA
* * *
370970 GTTAGAGTATCCCCTCGAAAATAAT-GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTA
1 GTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTA
371034 AAAATAAAA
66 AAAATAAAA
371043 ATATGAATGA
Statistics
Matches: 331, Mismatches: 46, Indels: 23
0.83 0.12 0.06
Matches are distributed among these distances:
156 22 0.07
157 168 0.51
158 69 0.21
159 72 0.22
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (157 bp):
GTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTA
AAAATAAAATCAAGGTTGGAGTATCCCCTCGGAAATAATGGGTTGGAGTATCCCCGATTGTGAAA
AATCGGTGTTTTAGAAATAAAACCGGA
Found at i:370861 original size:237 final size:236
Alignment explanation
Indices: 370479--371023 Score: 704
Period size: 237 Copynumber: 2.3 Consensus size: 236
370469 AAATTTAATA
* * * *
370479 TTTTGGAGATAAAAATAGGGTTAGAGTAT-CCCTCAGAAATGACAGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATG
* * * * * * * *
370543 GTGAAAAATTGATGTTTTGAAAATAAAATCAGGGTTGGAGTATTCCCTCAAAAATAATAGGTTGG
66 GTGAAAAATCGATGCTGTGAAAATAAAATCAGGATTAGAATATCCCCTCAAAAATAAGAGGTTGG
* *
370608 AGTAACCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAA-CCGGAGTTGGAGTATCCCCTCGA
131 AGTAACCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATCAGG-GTTGGAGTATCCCCTCGA
* *
370672 AAATAATGGGGTTGGAGTATTCTCGATTGTGAAAAATCAGTG
195 AAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
* * * *
370714 TTTTTGGAAATAAAACCAAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1 -TTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGAT
* * * *
370779 GGTGAAAAATCGGTGCTGTGGAAATAAAATC-GAGATTAGAATATCCCCTCAAAATTAACGGGGT
65 GGTGAAAAATCGATGCTGTGAAAATAAAATCAG-GATTAGAATATCCCCTCAAAAATAA-GAGGT
* * *
370843 TGGAGT-ATCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATTATGGTTGGAGTATCCCCTC
128 TGGAGTAACCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATCAGGGTTGGAGTATCCCCTC
* **
370907 GGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG
193 GAAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
* * * * *
370951 TTTTAGAAATAAAACTGGGGTTAGAGTATCCCCTCGAAAATAA-TGGGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATG
371015 GTGAAAAAT
66 GTGAAAAAT
371024 TGGTATTTTA
Statistics
Matches: 267, Mismatches: 38, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
235 28 0.10
236 62 0.23
237 167 0.63
238 10 0.04
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (236 bp):
TTTTGGAAATAAAACTAGGGTTAGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATG
GTGAAAAATCGATGCTGTGAAAATAAAATCAGGATTAGAATATCCCCTCAAAAATAAGAGGTTGG
AGTAACCCCGATTGTGAAAAATCGATGTTTTAAAAATAAAATCAGGGTTGGAGTATCCCCTCGAA
AATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
Found at i:372055 original size:183 final size:183
Alignment explanation
Indices: 371747--372104 Score: 572
Period size: 183 Copynumber: 2.0 Consensus size: 183
371737 AAAAAAATTG
* * * *
371747 TTTCATATTTTTTACATAATTTTCAATCTCATATTATAGTGCTGTCAAACCAAAACAAAGGAGGT
1 TTTCATATTTTTTACATAATTTTCAAACTCATACTACAGTGCTGCCAAACCAAAACAAAGGAGGT
* *
371812 ATTTAGCATTTTTGGTTTTTCCATTGGGTTGAACTCGTGCCATAGACATTCGAATGTCCATAATC
66 ATTTAGCATTTTTGGTTTTTCCATTGGGTTGAACTCATGCCACAGACATTCGAATGTCCATAATC
** *
371877 GAGATGGGAAAGTGACATGGGCATCATGTGTTCGTTCCACAATCCTGGAGTAA
131 GAGATGGGAAAGTGACATGGGCATCACATGTTCATTCCACAATCCTGGAGTAA
* * *
371930 TTTCATATTTTTTACATAATTTTCAAACTCATACTACAGTGTTGCCAGACCAAAACAAATGAGGT
1 TTTCATATTTTTTACATAATTTTCAAACTCATACTACAGTGCTGCCAAACCAAAACAAAGGAGGT
* *
371995 ATTTAGCGTTTTTGGTTTTTCCATTGGGTTGAACTCATGCCACGGACATTCGAATGTCCATAATC
66 ATTTAGCATTTTTGGTTTTTCCATTGGGTTGAACTCATGCCACAGACATTCGAATGTCCATAATC
* *
372060 GAGATGGGGAAGTGACATGGTCATCACATGTTCATTCCACAATCC
131 GAGATGGGAAAGTGACATGGGCATCACATGTTCATTCCACAATCC
372105 CGAAGTAGTT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
183 159 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (183 bp):
TTTCATATTTTTTACATAATTTTCAAACTCATACTACAGTGCTGCCAAACCAAAACAAAGGAGGT
ATTTAGCATTTTTGGTTTTTCCATTGGGTTGAACTCATGCCACAGACATTCGAATGTCCATAATC
GAGATGGGAAAGTGACATGGGCATCACATGTTCATTCCACAATCCTGGAGTAA
Found at i:374535 original size:2 final size:2
Alignment explanation
Indices: 374528--374570 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
374518 GATTTTCAAA
*
374528 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
374568 AT A
1 AT A
374571 AATAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:374559 original size:24 final size:23
Alignment explanation
Indices: 374527--374575 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
374517 AGATTTTCAA
*
374527 AATATATATATATATATATAATAT
1 AATATATATATATACATATAA-AT
374551 AATATATATATATACATATAAAT
1 AATATATATATATACATATAAAT
374574 AA
1 AA
374576 ACAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATATATATACATATAAAT
Found at i:374972 original size:19 final size:21
Alignment explanation
Indices: 374945--375000 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
374935 CCATTTCATA
374945 TTTTT-TTTCTTTTT-TT-TC
1 TTTTTCTTTCTTTTTCTTATC
374963 TTTTTCTTTCTTTCTTCTTATC
1 TTTTTCTTTCTTT-TTCTTATC
374985 TTCTTTCTTTCTTTTT
1 TT-TTTCTTTCTTTTT
375001 ACCTAACCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 2 0.06
21 2 0.06
22 6 0.18
23 11 0.33
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTCTTTTTCTTATC
Found at i:376284 original size:32 final size:32
Alignment explanation
Indices: 376228--376665 Score: 605
Period size: 32 Copynumber: 13.8 Consensus size: 32
376218 AAAATGGTGA
* ** **
376228 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
376260 TTTTAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
376292 TTTGAAAAGGGTCGCCACCCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCA-CCGACTTGTGTGGGC
* *
376325 TTTGAAATGAGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
376357 TTTGGAATGGGTTGCCACCTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACC-GACTTGTGTGGGC
376390 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
376422 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
376454 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376486 TTTGAAATGAGTTGCCATCGACTT-AGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
376517 -TTG-GATAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
376547 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
376579 TTTGAAATGGGTTGCCACAGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376611 TTTGAAAAGGGTCGCCATCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
376643 TTTG-AATGAGTTGCCACCGACTT
1 TTTGAAATGGGTTGCCACCGACTT
376666 ATGCCACCGA
Statistics
Matches: 357, Mismatches: 44, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
29 15 0.04
30 9 0.03
31 24 0.07
32 251 0.70
33 58 0.16
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:376333 original size:65 final size:64
Alignment explanation
Indices: 376228--376856 Score: 789
Period size: 64 Copynumber: 9.8 Consensus size: 64
376218 AAAATGGTGA
** ** * *
376228 TTTGAAAAGGGTTGCCACTAACTTGCATGGGCTTTTAAATGGGTTGCCATCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376292 TTTGAAAAGGGTCGCCACCCGACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTATGTGGGC
1 TTTGAAAAGGGTTGCCA-CCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
376357 TTTGGAATGGGTTGCCACCTGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACC-GACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376422 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * * *
376486 TTTGAAATGAGTTGCCATCGACTT-AGTGGGC-TTG-GATAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376547 TTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACAGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
376611 TTTGAAAAGGGTCGCCATCGACTTGTGTGGGCTTTG-AATGAGTTGCCACCGACTTATGCCACCG
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGAC-T-T------G
376675 ACTTGTGTGGC
58 ---TGTG-GGC
376686 -TTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTG-GGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
376748 TTTGAAAA-GGTTGCCA-CGACTTGTGTGGGCTTTGAAAAT-GG-TGCCACCGACTTGTGTGGGC
1 TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
376809 TTTGAAATA--G-TGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCAC
1 TTTGAAA-AGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCAC
376857 GAAGTTGTGG
Statistics
Matches: 502, Mismatches: 38, Indels: 52
0.85 0.06 0.09
Matches are distributed among these distances:
60 24 0.05
61 98 0.20
62 31 0.06
63 32 0.06
64 142 0.28
65 115 0.23
67 1 0.00
71 1 0.00
73 1 0.00
74 38 0.08
75 19 0.04
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.30
Consensus pattern (64 bp):
TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:376672 original size:13 final size:13
Alignment explanation
Indices: 376654--376678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
376644 TTGAATGAGT
376654 TGCCACCGACTTA
1 TGCCACCGACTTA
376667 TGCCACCGACTT
1 TGCCACCGACTT
376679 GTGTGGCTTG
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:0.20, C:0.40, G:0.16, T:0.24
Consensus pattern (13 bp):
TGCCACCGACTTA
Found at i:376701 original size:43 final size:44
Alignment explanation
Indices: 376624--376708 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 44
376614 GAAAAGGGTC
* *
376624 GCCATCGACTTGTGTGGGCTTTGAATGAGTTGCCACCGACTTAT
1 GCCACCGACTTGTGTGGGCTTTGAAAGAGTTGCCACCGACTTAT
*
376668 GCCACCGACTTGTGT-GGC-TTGAAAAGGGTTGCCACCGACTT
1 GCCACCGACTTGTGTGGGCTTTG-AAAGAGTTGCCACCGACTT
376709 GTGTGGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 3 0.08
43 20 0.54
44 14 0.38
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (44 bp):
GCCACCGACTTGTGTGGGCTTTGAAAGAGTTGCCACCGACTTAT
Found at i:376714 original size:74 final size:77
Alignment explanation
Indices: 376591--376740 Score: 243
Period size: 74 Copynumber: 2.0 Consensus size: 77
376581 TGAAATGGGT
*
376591 TGCCACAGACTTGTGTGGGCTTTGAAAAGGGTCGCCATCGACTTGTGTGGGCTTTG-AATGAGTT
1 TGCCACAGACTTGTGTGGGCTTTGAAAAGGGTCGCCACCGACTTGTGTGGGCTTTGAAATGAGTT
376655 GCCACCGACTTA
66 GCCACCGACTTA
* * *
376667 TGCCACCGACTTGTGT-GGC-TTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTT
1 TGCCACAGACTTGTGTGGGCTTTGAAAAGGGTCGCCACCGACTTGTGTGGGCTTTGAAATGAGTT
376730 GCCACCGACTT
66 GCCACCGACTT
376741 GTGGGGCTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 33 0.48
75 21 0.30
76 15 0.22
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.29
Consensus pattern (77 bp):
TGCCACAGACTTGTGTGGGCTTTGAAAAGGGTCGCCACCGACTTGTGTGGGCTTTGAAATGAGTT
GCCACCGACTTA
Found at i:376841 original size:30 final size:31
Alignment explanation
Indices: 376667--376856 Score: 243
Period size: 30 Copynumber: 6.2 Consensus size: 31
376657 CACCGACTTA
376667 TGCCACCGACTTGTGT-GGC-TTGAAA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAATA--GT
*
376697 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAT-AGT
376729 TGCCACCGACTTGTG-GGGCTTTGAAA-AGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAATA-GT
*
376759 TGCCA-CGACTTGTGTGGGCTTTGAAA-ATGG
1 TGCCACCGACTTGTGTGGGCTTTGAAATA-GT
376789 TGCCACCGACTTGTGTGGGCTTTGAAATAG-
1 TGCCACCGACTTGTGTGGGCTTTGAAATAGT
*
376819 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAT-AGT
376851 TGCCAC
1 TGCCAC
376857 GAAGTTGTGG
Statistics
Matches: 145, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.06
30 69 0.48
31 37 0.26
32 30 0.21
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTGAAATAGT
Found at i:376841 original size:61 final size:64
Alignment explanation
Indices: 376667--376856 Score: 292
Period size: 61 Copynumber: 3.1 Consensus size: 64
376657 CACCGACTTA
376667 TGCCACCGACTTGTGT-GGC-TTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTG-AAATGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAA-GGTTGCCACCGACTTGTGTGGGCTTTGAAAATGGGT
376729 TGCCACCGACTTGTG-GGGCTTTGAAAAGGTTGCCA-CGACTTGTGTGGGCTTTGAAAAT-GG-
1 TGCCACCGACTTGTGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAATGGGT
376789 TGCCACCGACTTGTGTGGGCTTTGAAATA-G-TGCCACCGACTTGTGTGGGCTTTG-AAATGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAA-AGGTTGCCACCGACTTGTGTGGGCTTTGAAAATGGGT
376851 TGCCAC
1 TGCCAC
376857 GAAGTTGTGG
Statistics
Matches: 120, Mismatches: 0, Indels: 16
0.88 0.00 0.12
Matches are distributed among these distances:
60 24 0.20
61 52 0.43
62 37 0.31
63 7 0.06
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (64 bp):
TGCCACCGACTTGTGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAATGGGT
Found at i:376920 original size:27 final size:27
Alignment explanation
Indices: 376851--377314 Score: 633
Period size: 27 Copynumber: 16.7 Consensus size: 27
376841 TGAAATGGGT
*
376851 TGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
376878 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
** *
376906 TATCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
*
376934 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
376961 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
376988 TGCCACGGAGTTGTGGACTTAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
377015 TGCCACGGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
377042 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
377070 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
377097 TGCCACGGAGTTGTGGACTTGAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
377124 TGCCACGAAGTTGTGGATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
377151 TGCCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
377179 TGCCACGGAGTTGTGGACTTTAAAA-GG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
** * **
377206 TGCCATAGAGTTATGGACTTAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
377233 TGCCACGGAGTTGTGGACTTATTACTTAAAAGGA
1 TGCCACGGAGTTGTGG-------ACTTAAAAGGG
* *
377267 TACCACGAAGTTGTGGACTCTAAAAGGG
1 TGCCACGGAGTTGTGGACT-TAAAAGGG
377295 TGCCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
377315 TAGAGAGGTC
Statistics
Matches: 390, Mismatches: 33, Indels: 27
0.87 0.07 0.06
Matches are distributed among these distances:
26 6 0.02
27 228 0.58
28 132 0.34
34 24 0.06
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:376995 original size:82 final size:81
Alignment explanation
Indices: 376851--377314 Score: 633
Period size: 82 Copynumber: 5.6 Consensus size: 81
376841 TGAAATGGGT
* **
376851 TGCCACGAAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTATCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
376916 TTGTGGACTTAAAAGGAA
65 TTGTGGACTTAAAAGG-G
*
376934 TGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
376999 TGTGGACTTAAAAGAG
66 TGTGGACTTAAAAGGG
*
377015 TGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAG
377080 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* * *
377097 TGCCACGGAGTTGTGGACTTGAAAGGGTGCCACGAAGTTGTGGATTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
377162 TGTGGATTTTAAAAGGG
66 TGTGGA-CTTAAAAGGG
** * **
377179 TGCCACGGAGTTGTGGACTTTAAAA-GGTGCCATAGAGTTATGGACTTAAAAGAATGCCACGGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
377243 TTGTGGACTTATTACTTAAAAGGA
65 TTGTGG-------ACTTAAAAGGG
* *
377267 TACCACGAAGTTGTGGACTCTAAAAGGGTGCCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACT-TAAAAGGGTGCCACGGAGTTGTGGACTT
377315 TAGAGAGGTC
Statistics
Matches: 340, Mismatches: 29, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
81 69 0.20
82 191 0.56
83 30 0.09
87 1 0.00
88 29 0.09
89 20 0.06
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGG
Found at i:377022 original size:109 final size:108
Alignment explanation
Indices: 376851--377314 Score: 635
Period size: 109 Copynumber: 4.2 Consensus size: 108
376841 TGAAATGGGT
* * **
376851 TGCCACGAAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTATCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAG
*
376916 TTGTGGACTTAAAAGGAATGCCATGGAGTTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGG-ATGCCACGGAGTTGTGGACTTAAAAGGG
376961 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGT
377026 TGTGGACTTAAAAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGG
66 TGTGGACTT-AAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
377070 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTGAAAGGGTGCCACGAAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGT
* * *
377135 TGTGGATTTAAAAGGGTGCCACGGAGTTGTGGATTTTAAAAGGG
66 TGTGGACTTAAAAGGATGCCACGGAGTTGTGGA-CTTAAAAGGG
** * *
377179 TGCCACGGAGTTGTGGACTTTAAAA-GGTGCCATAGAGTTATGGACTTAAAAGAATGCCACGGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAG
* *
377243 TTGTGGACTTATTACTTAAAAGGATACCACGAAGTTGTGGACTCTAAAAGGG
65 TTGTGG-------ACTTAAAAGGATGCCACGGAGTTGTGGACT-TAAAAGGG
377295 TGCCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
377315 TAGAGAGGTC
Statistics
Matches: 319, Mismatches: 22, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
108 23 0.07
109 205 0.64
110 38 0.12
115 3 0.01
116 50 0.16
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (108 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGT
TGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:378350 original size:13 final size:12
Alignment explanation
Indices: 378332--378364 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
378322 AGGGTGAAAA
378332 GTTTTTTTTTTT
1 GTTTTTTTTTTT
*
378344 GGTTTTTTTTTT
1 GTTTTTTTTTTT
378356 GTTTTTTTT
1 GTTTTTTTT
378365 AGGATTAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:378351 original size:11 final size:11
Alignment explanation
Indices: 378335--378364 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
378325 GTGAAAAGTT
378335 TTTTTTTTTGG
1 TTTTTTTTTGG
*
378346 TTTTTTTTTTG
1 TTTTTTTTTGG
378357 TTTTTTTT
1 TTTTTTTT
378365 AGGATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGG
Found at i:387128 original size:20 final size:20
Alignment explanation
Indices: 387103--387177 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
387093 AAAATGCCTG
387103 AATGTATCGATACATTGAGA
1 AATGTATCGATACATTGAGA
* *
387123 AATGTATCGATATATTAAGA
1 AATGTATCGATACATTGAGA
387143 AATGTATCGATACATTGAGA
1 AATGTATCGATACATTGAGA
*
387163 AATGTATCAATACAT
1 AATGTATCGATACAT
387178 CTGGGTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAGA
Found at i:387219 original size:20 final size:20
Alignment explanation
Indices: 387194--387248 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
387184 TAAAACCCAG
387194 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAA
387214 AATGTATCGATACAATGAAA
1 AATGTATCGATACAATGAAA
* *
387234 AATATACCGATACAA
1 AATGTATCGATACAA
387249 ATGGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAATGAAA
Found at i:388896 original size:31 final size:31
Alignment explanation
Indices: 388858--388919 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
388848 TGTCAGACGC
388858 CGCCTTTGTCGTGACACTCGTAGGTTTAGGT
1 CGCCTTTGTCGTGACACTCGTAGGTTTAGGT
* *
388889 CGCCTTTGTCGTGGCGCTCGTAGGTTTAGGT
1 CGCCTTTGTCGTGACACTCGTAGGTTTAGGT
388920 ACCTGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.10, C:0.23, G:0.32, T:0.35
Consensus pattern (31 bp):
CGCCTTTGTCGTGACACTCGTAGGTTTAGGT
Found at i:389013 original size:43 final size:43
Alignment explanation
Indices: 388952--389077 Score: 243
Period size: 43 Copynumber: 2.9 Consensus size: 43
388942 ATATTGAAGT
388952 TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTCAGC
1 TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTCAGC
*
388995 TGTTCTGTCCTCTAGTTCTTTCATCCTTATCCAATTGGTCAGC
1 TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTCAGC
389038 TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTC
1 TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTC
389078 TGTCTTAGGG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.12, C:0.29, G:0.13, T:0.45
Consensus pattern (43 bp):
TGTTCTGTCCTCTCGTTCTTTCATCCTTATCCAATTGGTCAGC
Found at i:389271 original size:12 final size:12
Alignment explanation
Indices: 389254--389292 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
389244 AATAAAAATA
389254 AATTTAATTTTT
1 AATTTAATTTTT
*
389266 AATTTAAATTTTA
1 AATTT-AATTTTT
389279 AATTTAATTATTT
1 AATTTAATT-TTT
389292 A
1 A
389293 TATTCGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AATTTAATTTTT
Found at i:389277 original size:13 final size:13
Alignment explanation
Indices: 389252--389285 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
389242 TTAATAAAAA
389252 TAAATTT-AATTT
1 TAAATTTAAATTT
*
389264 TTAATTTAAATTT
1 TAAATTTAAATTT
389277 TAAATTTAA
1 TAAATTTAA
389286 TTATTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTAAATTT
Found at i:391253 original size:34 final size:34
Alignment explanation
Indices: 391166--391378 Score: 233
Period size: 34 Copynumber: 6.5 Consensus size: 34
391156 AAGTAGGAGA
*
391166 ATTG-TGATTAAATGGG-GATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
391198 ATTGTTGA-TAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
391231 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
391265 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
391299 ATT-ATGATTAAATAGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
391332 ATTGTTGACT-AA-GGTAGATTTGGTAGATTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
391364 ATTGTTGA-TAAATGG
1 ATTGTTGATTAAATGG
391379 TGGTTTTTAC
Statistics
Matches: 152, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.01
32 36 0.24
33 56 0.37
34 59 0.39
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:391258 original size:67 final size:67
Alignment explanation
Indices: 391166--391378 Score: 233
Period size: 67 Copynumber: 3.2 Consensus size: 67
391156 AAGTAGGAGA
* * *
391166 ATTG-TGATTAAATGGGGATTTGGTAGTTTACCATTGTTGA-TAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGGGATTTGGTAGCTTACCATTGTTGACTAAATGGGTGATTTGGTAGATTG
391229 CC
66 CC
* * * ** *
391231 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTT
1 ATTGTTGATTAAATGGG-GATTTGGTAGCTTACCATTGTTGACTAAATGGGTGATTTGGTAGATT
*
391296 ACC
65 GCC
* * *
391299 ATT-ATGATTAAATAGGTGATTTGGTGGCTTACCATTGTTGACT-AA--GGTAGATTTGGTAGAT
1 ATTGTTGATTAAAT-GGGGATTTGGTAGCTTACCATTGTTGACTAAATGGGT-GATTTGGTAGAT
391360 TGCC
64 TGCC
391364 ATTGTTGA-TAAATGG
1 ATTGTTGATTAAATGG
391379 TGGTTTTTAC
Statistics
Matches: 123, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
64 3 0.02
65 25 0.20
66 16 0.13
67 55 0.45
68 24 0.20
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (67 bp):
ATTGTTGATTAAATGGGGATTTGGTAGCTTACCATTGTTGACTAAATGGGTGATTTGGTAGATTG
CC
Found at i:418576 original size:26 final size:26
Alignment explanation
Indices: 418562--418610 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
418552 ATAATAAATT
*
418562 AAATATAATTATAATATATAATATAA
1 AAATATAAATATAATATATAATATAA
418588 AAATATAAATATAATATA-AATAT
1 AAATATAAATATAATATATAATAT
418611 TTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATATAAATATAATATATAATATAA
Found at i:418582 original size:13 final size:12
Alignment explanation
Indices: 418564--418610 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
418554 AATAAATTAA
418564 ATATAATTATAAT
1 ATATAA-TATAAT
*
418577 ATATAATATAAAA
1 ATATAATAT-AAT
418590 ATATAAATATAAT
1 ATAT-AATATAAT
418603 ATA-AATAT
1 ATATAATAT
418611 TTAATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.17
12 3 0.10
13 17 0.57
14 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:418598 original size:32 final size:31
Alignment explanation
Indices: 418547--418610 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 31
418537 TTACTTTTAT
418547 TAATAATAATAAATTAAATATAATTATAATATA
1 TAATAATAATAAATTAAATATAA-TATAA-ATA
418580 TAAT-ATAA-AAATATAAATATAATATAAATA
1 TAATAATAATAAAT-TAAATATAATATAAATA
418610 T
1 T
418611 TTAATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 4 0.13
31 9 0.30
32 13 0.43
33 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
TAATAATAATAAATTAAATATAATATAAATA
Found at i:418599 original size:6 final size:6
Alignment explanation
Indices: 418555--418610 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
418545 ATTAATAATA
* *
418555 ATAAAT -TAAAT ATAATT ATAATAT ATAATAT AAAAAT ATAAAT AT-AAT
1 ATAAAT ATAAAT ATAAAT ATAA-AT ATAA-AT ATAAAT ATAAAT ATAAAT
418603 ATAAAT AT
1 ATAAAT AT
418611 TTAATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
5 10 0.23
6 22 0.51
7 11 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAAAT
Found at i:421476 original size:2 final size:2
Alignment explanation
Indices: 421469--421506 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
421459 CATGTAGTTC
421469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
421507 TCTAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:422642 original size:16 final size:17
Alignment explanation
Indices: 422617--422658 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
422607 TGTATTCGTG
* *
422617 TTATAATTATAT-TATT
1 TTATATTTATATAAATT
422633 TTATATTTATATAAATT
1 TTATATTTATATAAATT
422650 TTAATATTT
1 TT-ATATTT
422659 CTCTGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 11 0.50
17 5 0.23
18 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTATATAAATT
Done.