Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold94
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: 2274668
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 33727 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1474917 original size:35 final size:35
Alignment explanation
Indices: 1474845--1474931 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
1474835 AGTTCCCTTC
* *
1474845 AAAATGACAACAAAAAGTCAAAAGCAAAAGCACAA
1 AAAATGAAAACAAAAAGTCAAAAGCAAAAGCAAAA
* *
1474880 AAAATGAAAAGAAAAAGTGCAAAAGCAAAA-TAAAA
1 AAAATGAAAACAAAAAGT-CAAAAGCAAAAGCAAAA
**
1474915 AAAGGGAACAACAAAAA
1 AAAATGAA-AACAAAAA
1474932 TAAAAAAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 25 0.58
36 18 0.42
ACGTcount: A:0.69, C:0.11, G:0.14, T:0.06
Consensus pattern (35 bp):
AAAATGAAAACAAAAAGTCAAAAGCAAAAGCAAAA
Found at i:1476304 original size:27 final size:27
Alignment explanation
Indices: 1476263--1477381 Score: 1860
Period size: 27 Copynumber: 41.0 Consensus size: 27
1476253 GTGGTATTTT
* *
1476263 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1476291 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476318 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1476346 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476373 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1476400 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476427 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476454 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1476482 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476509 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1476536 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1476564 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476591 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
1476619 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476646 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1476674 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476701 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1476728 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1476756 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476783 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1476811 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476838 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1476865 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1476892 CTTTTAAGTCCACAACTCCTTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1476919 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1476947 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1476974 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
1477002 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1477029 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1477056 CTATTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477083 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477110 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
1477137 CTTTTAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477164 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1477191 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477218 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477245 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1477273 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477300 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1477327 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1477354 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1477381 C
1 C
1477382 ATTTCAAAGC
Statistics
Matches: 1027, Mismatches: 54, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
27 767 0.75
28 260 0.25
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1476363 original size:82 final size:81
Alignment explanation
Indices: 1476263--1477381 Score: 1860
Period size: 82 Copynumber: 13.7 Consensus size: 81
1476253 GTGGTATTTT
* * *
1476263 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1476328 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* *
1476346 CTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1476411 ACAACTCTGTGGCACC
66 ACAACTCCGTGGCACC
*
1476427 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
1476492 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1476509 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
1476574 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
1476591 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1476656 CACAACTCCGTGGCATCC
65 CACAACTCCGTGGCA-CC
*
1476674 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
1476739 ATAACTCCGTGGCATCT
66 ACAACTCCGTGGCA-CC
*
1476756 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1476821 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
*
1476838 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1476903 ACAACTCCTTGGCACC
66 ACAACTCCGTGGCACC
* * *
1476919 CTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
1476984 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * *
1477002 CTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTATTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1477067 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
1477083 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
**
1477148 ACAACTCCGTGGCATT
66 ACAACTCCGTGGCACC
*
1477164 CTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1477229 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* *
1477245 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1477310 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* * *
1477327 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC
1477382 ATTTCAAAGC
Statistics
Matches: 979, Mismatches: 50, Indels: 16
0.94 0.05 0.02
Matches are distributed among these distances:
81 368 0.38
82 465 0.47
83 146 0.15
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1477419 original size:32 final size:32
Alignment explanation
Indices: 1477364--1477549 Score: 268
Period size: 32 Copynumber: 5.8 Consensus size: 32
1477354 CTTTTAAATC
* *
1477364 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1477395 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
* *
1477427 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
1477459 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
*
1477491 CACAAGTC-GATGGCAACCCATTTAAAAGCCCA
1 CACAAGTCAG-TGGCAACCCATTTCAAAGCCCA
** *
1477523 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCAGTGGCAACCCATTTCAAA
1477550 TCACCATTTT
Statistics
Matches: 142, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
31 13 0.09
32 128 0.90
33 1 0.01
ACGTcount: A:0.32, C:0.34, G:0.17, T:0.17
Consensus pattern (32 bp):
CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
Found at i:1478817 original size:17 final size:15
Alignment explanation
Indices: 1478797--1478845 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1478787 TTAAGTAAAA
1478797 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1478814 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
1478828 AA-AAAGAAA-AAA-
1 AAGAAAGAAAGAAAG
1478840 AAGAAA
1 AAGAAA
1478846 AAATATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.20
14 9 0.30
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1479212 original size:2 final size:2
Alignment explanation
Indices: 1479199--1479235 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1479189 TTATTTTATT
* *
1479199 TA TA TG TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1479236 TTTAAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1486909 original size:18 final size:18
Alignment explanation
Indices: 1486866--1486910 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1486856 ATCATAATGG
1486866 TATTAA-AATATTTTATA
1 TATTAATAATATTTTATA
1486883 T-TTATATAA-ATTTTAATA
1 TATTA-ATAATATTTT-ATA
1486901 TATTAATAAT
1 TATTAATAAT
1486911 TCGTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTAATAATATTTTATA
Found at i:1488553 original size:25 final size:26
Alignment explanation
Indices: 1488518--1488569 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
1488508 AAATCATGTA
1488518 TTTATATTATATCATATTT-TAATAAT
1 TTTATATTATATCATATTTGT-ATAAT
1488544 TTTATA-TATATCATATTTGTATAAT
1 TTTATATTATATCATATTTGTATAAT
1488569 T
1 T
1488570 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTATATTATATCATATTTGTATAAT
Found at i:1489444 original size:32 final size:31
Alignment explanation
Indices: 1489406--1489482 Score: 109
Period size: 31 Copynumber: 2.4 Consensus size: 31
1489396 TTATATTTTT
* *
1489406 ATAAATTTGAATATGTTAATAATTCGTATTAA
1 ATAAATTT-AATATATTAATAATTCATATTAA
*
1489438 ATAAATTTAAAATATTAATAATTCATATTAA
1 ATAAATTTAATATATTAATAATTCATATTAA
1489469 ATAAATTTTAATAT
1 ATAAA-TTTAATAT
1489483 TTTTTATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (31 bp):
ATAAATTTAATATATTAATAATTCATATTAA
Found at i:1489517 original size:38 final size:38
Alignment explanation
Indices: 1489462--1489549 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
1489452 TTAATAATTC
* *
1489462 ATATTAAATAAATTTTAATATTTTTTATAT-TTATATTA
1 ATATTATATAATTTTTAAT-TTTTTTATATGTTATATTA
* * *
1489500 ATTTTATATAATTTTTAATTTTTTTTTATGTTATATTT
1 ATATTATATAATTTTTAATTTTTTTATATGTTATATTA
1489538 ATATTATATAAT
1 ATATTATATAAT
1489550 CGTATTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 9 0.21
38 34 0.79
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (38 bp):
ATATTATATAATTTTTAATTTTTTTATATGTTATATTA
Found at i:1490199 original size:38 final size:38
Alignment explanation
Indices: 1490127--1490200 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
1490117 AATTATAACA
* * **
1490127 TATTTAAATTATAATTATAAATATATTTTTTATTATAT
1 TATTTAAATAATAATTATAAATATAATTACTATTATAT
*
1490165 TATTTATATAATAATTATAAATATAATTACTATTAT
1 TATTTAAATAATAATTATAAATATAATTACTATTAT
1490201 TATGATCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (38 bp):
TATTTAAATAATAATTATAAATATAATTACTATTATAT
Found at i:1492514 original size:25 final size:25
Alignment explanation
Indices: 1492481--1492534 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1492471 AAAAATAATA
* *
1492481 TTTATATATTTTT-ATTATATTTTAT
1 TTTAAATATTTTTAAGTAT-TTTTAT
1492506 TTTAAATATTTTTAAGTATTTTTAT
1 TTTAAATATTTTTAAGTATTTTTAT
1492531 TTTA
1 TTTA
1492535 TATTTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTAAATATTTTTAAGTATTTTTAT
Found at i:1492566 original size:17 final size:17
Alignment explanation
Indices: 1492525--1492594 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
1492515 TTTTAAGTAT
1492525 TTTTATTTTAT-ATTTCA
1 TTTTATTTTATAATTT-A
* * *
1492542 ATTCATTTTATATTTTA
1 TTTTATTTTATAATTTA
1492559 TTTTA-TTTATCAATTTA
1 TTTTATTTTAT-AATTTA
*
1492576 -TTTAATTTATAATTTA
1 TTTTATTTTATAATTTA
1492592 TTT
1 TTT
1492595 ACTTAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 15 0.35
17 25 0.58
18 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTTTATAATTTA
Found at i:1492571 original size:29 final size:27
Alignment explanation
Indices: 1492525--1492595 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 27
1492515 TTTTAAGTAT
1492525 TTTTATTTTATATT-TCAATTCATTTTATA
1 TTTTATTTTAT-TTATCAATTCA-TTTA-A
*
1492554 TTTTATTTTATTTATCAATTTATTTAA
1 TTTTATTTTATTTATCAATTCATTTAA
*
1492581 TTTATAATTTATTTA
1 TTT-TATTTTATTTA
1492596 CTTAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 4 0.11
28 16 0.42
29 18 0.47
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTATTTTATTTATCAATTCATTTAA
Found at i:1492579 original size:16 final size:15
Alignment explanation
Indices: 1492548--1492605 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
1492538 TTCAATTCAT
*
1492548 TTTATATTTTATTTTA
1 TTTATAATTTA-TTTA
1492564 TTTATCAATTTATTTAA
1 TTTAT-AATTTATTT-A
1492581 TTTATAATTTATTTA
1 TTTATAATTTATTTA
* *
1492596 CTTAAAATTT
1 TTTATAATTT
1492606 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.24
16 17 0.46
17 11 0.30
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATAATTTATTTA
Found at i:1495789 original size:16 final size:16
Alignment explanation
Indices: 1495768--1495800 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1495758 TAGCGAACTA
1495768 AATGTAGTATGAGTAG
1 AATGTAGTATGAGTAG
*
1495784 AATGTATTATGAGTAG
1 AATGTAGTATGAGTAG
1495800 A
1 A
1495801 GAATTCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.33
Consensus pattern (16 bp):
AATGTAGTATGAGTAG
Found at i:1496834 original size:22 final size:22
Alignment explanation
Indices: 1496788--1496835 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1496778 AAGTGAACGG
* *
1496788 TTAAGATATATCCGAATAAGTA
1 TTAAGATATATCCAAATAAGAA
1496810 TTAAGATATATCCAAATTAA-AA
1 TTAAGATATATCCAAA-TAAGAA
1496832 TTAA
1 TTAA
1496836 AGAGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (22 bp):
TTAAGATATATCCAAATAAGAA
Found at i:1504825 original size:30 final size:30
Alignment explanation
Indices: 1504791--1504875 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
1504781 AATTTTTATT
1504791 TTTTAATTTATATTTAAATAA-ATCTGTAAC
1 TTTTAATTTA-ATTTAAATAATATCTGTAAC
* * * *
1504821 TTTTAAATTAATTTAAAAAATATTTTTAAC
1 TTTTAATTTAATTTAAATAATATCTGTAAC
*
1504851 TTTCAATTTAAATTTAAATACATAT
1 TTTTAATTT-AATTTAAATA-ATAT
1504876 TTTAACATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 9 0.20
30 23 0.51
31 9 0.20
32 4 0.09
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (30 bp):
TTTTAATTTAATTTAAATAATATCTGTAAC
Found at i:1504966 original size:21 final size:21
Alignment explanation
Indices: 1504936--1504982 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1504926 TTTTATTTAA
1504936 ATTTA-AAATT-TAAAATTATT
1 ATTTATAAATTATAAAA-TATT
1504956 ATTTATAAATTAATAAAATATT
1 ATTTATAAATT-ATAAAATATT
1504978 -TTTAT
1 ATTTAT
1504983 TTATATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 4 0.17
23 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTATAAATTATAAAATATT
Found at i:1505012 original size:15 final size:15
Alignment explanation
Indices: 1504987--1505024 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1504977 TTTTATTTAT
1504987 ATATTTT-TTAAAAA
1 ATATTTTATTAAAAA
*
1505001 ATATTTTATTAAATA
1 ATATTTTATTAAAAA
*
1505016 ATAATTTAT
1 ATATTTTAT
1505025 ACTAATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTATTAAAAA
Found at i:1505432 original size:16 final size:16
Alignment explanation
Indices: 1505413--1505443 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1505403 AATAAATAAA
1505413 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
1505429 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
1505444 CGATTCAAAC
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:1505503 original size:16 final size:16
Alignment explanation
Indices: 1505484--1505526 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1505474 AATATTTTAA
1505484 AATATTAATTTAAAAT
1 AATATTAATTTAAAAT
* *
1505500 AATATGAATTTAAATT
1 AATATTAATTTAAAAT
1505516 AA-ATATAATTT
1 AATAT-TAATTT
1505527 TATAACTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATATTAATTTAAAAT
Found at i:1505747 original size:25 final size:26
Alignment explanation
Indices: 1505679--1505747 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
1505669 ATTTTTATTT
*
1505679 TAATAA-AATAATTAAATAGATCAATAA
1 TAATAATAATAATT-CA-AGATCAATAA
* * *
1505706 TAATTATATTAAATCAAGAT-AATAA
1 TAATAATAATAATTCAAGATCAATAA
1505731 TAATAATAATAATTCAA
1 TAATAATAATAATTCAA
1505748 TAAAAATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
25 19 0.56
26 4 0.12
27 6 0.18
28 5 0.15
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (26 bp):
TAATAATAATAATTCAAGATCAATAA
Found at i:1505830 original size:18 final size:20
Alignment explanation
Indices: 1505797--1505835 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1505787 ACAATTTAAT
1505797 TTTTAAATTAATATATGTTA
1 TTTTAAATTAATATATGTTA
*
1505817 TTTT-AATT-ATATATTTTA
1 TTTTAAATTAATATATGTTA
1505835 T
1 T
1505836 ATTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTAAATTAATATATGTTA
Found at i:1507906 original size:19 final size:19
Alignment explanation
Indices: 1507882--1507918 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1507872 GTTCATTGAT
**
1507882 ATATGTATTTATTATAATG
1 ATATGTATACATTATAATG
1507901 ATATGTATACATTATAAT
1 ATATGTATACATTATAAT
1507919 AACACTTATC
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:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
ATATGTATACATTATAATG
Found at i:1508696 original size:21 final size:22
Alignment explanation
Indices: 1508650--1508702 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
1508640 AATTAAATTT
*
1508650 AATTTGATTTTAAAAATTAATAA
1 AATTTGA-ATTAAAAATTAATAA
*
1508673 AA-TTGAATTAAAAA-TAATCCA
1 AATTTGAATTAAAAATTAAT-AA
1508694 AATTTGAAT
1 AATTTGAAT
1508703 AAATTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 10 0.38
23 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTGAATTAAAAATTAATAA
Found at i:1508700 original size:22 final size:21
Alignment explanation
Indices: 1508650--1508702 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1508640 AATTAAATTT
*
1508650 AATTTGATTTTAAAAATTAATA
1 AATTTGA-ATTAAAAATTAATA
*
1508672 AAATTGAATTAAAAA-TAATCCA
1 AATTTGAATTAAAAATTAAT--A
1508694 AATTTGAAT
1 AATTTGAAT
1508703 AAATTAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 15 0.58
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (21 bp):
AATTTGAATTAAAAATTAATA
Found at i:1513947 original size:22 final size:21
Alignment explanation
Indices: 1513904--1513947 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1513894 AAAATATCAG
*
1513904 TTTTTTCCTCTTAATTTTTCT
1 TTTTTTCCTCTTAATTTCTCT
1513925 TTTTATTCTCTCTT-ATTTCTCT
1 TTTT-TTC-CTCTTAATTTCTCT
1513947 T
1 T
1513948 CTTACTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTCCTCTTAATTTCTCT
Found at i:1515129 original size:78 final size:78
Alignment explanation
Indices: 1514998--1515152 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 78
1514988 AGCAGCTTAC
* * *
1514998 AGACAAGCTAAACTTCATGAGCTGTCAGTAGAGTTCGAGACAAGAAGATAAAAAGTAACCTTTAA
1 AGACAAGCTAAACTTCATAAGCTGTCAGTAGAGTTCGAGACAAGAAGACAAAAAGTAACCTCTAA
1515063 ACCAAGCCTAAAT
66 ACCAAGCCTAAAT
* * * *
1515076 AGACAAGTTAAGCTTCATAAGCTGTTAGTGGAGTTCGAGACAAGAAGACAAAAAGTAACCTCTAA
1 AGACAAGCTAAACTTCATAAGCTGTCAGTAGAGTTCGAGACAAGAAGACAAAAAGTAACCTCTAA
1515141 ACCAAGCCTAAA
66 ACCAAGCCTAAA
1515153 CACTACCCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (78 bp):
AGACAAGCTAAACTTCATAAGCTGTCAGTAGAGTTCGAGACAAGAAGACAAAAAGTAACCTCTAA
ACCAAGCCTAAAT
Found at i:1531290 original size:3 final size:3
Alignment explanation
Indices: 1531272--1531304 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1531262 ATTTTTAATT
*
1531272 TTA TTG TTA TTA -TA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1531305 GCATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1531384 original size:3 final size:3
Alignment explanation
Indices: 1531376--1531419 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1531366 AAATTTTTAG
1531376 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1531420 GTCTAGTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1532197 original size:19 final size:19
Alignment explanation
Indices: 1532153--1532199 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1532143 AAATAAGTGT
1532153 AAAAA-TAAATTTTTGACA
1 AAAAATTAAATTTTTGACA
* *
1532171 AAGGAATTAAATTTTTGATA
1 AA-AAATTAAATTTTTGACA
1532191 AAAAATTAA
1 AAAAATTAA
1532200 TATCATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 14 0.58
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (19 bp):
AAAAATTAAATTTTTGACA
Found at i:1532741 original size:19 final size:17
Alignment explanation
Indices: 1532719--1532779 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
1532709 GAATTTTATT
1532719 ATTTTATAATCATATATAA
1 ATTTTAT-AT-ATATATAA
* *
1532738 ATTTTATTTTAATATATTA
1 ATTTTA-TAT-ATATATAA
1532757 ATATTTATAT-TATATAA
1 AT-TTTATATATATATAA
1532774 ATTTTA
1 ATTTTA
1532780 AAATTATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 4 0.11
17 8 0.23
19 18 0.51
20 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATATATATAA
Found at i:1532760 original size:27 final size:27
Alignment explanation
Indices: 1532703--1532760 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1532693 TATCTATGTT
* * *
1532703 ATATATGAATTTTATTATTTTATAATC
1 ATATATAAATTTTATTATTATATAATA
*
1532730 ATATATAAATTTTATT-TTAATATATTA
1 ATATATAAATTTTATTATT-ATATAATA
1532757 ATAT
1 ATAT
1532761 TTATATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATATAAATTTTATTATTATATAATA
Found at i:1532828 original size:29 final size:28
Alignment explanation
Indices: 1532796--1532871 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
1532786 TTCATACATT
1532796 TATATTATATTAATATTACTTTT-ATATAA
1 TATATTATATTAATATT--TTTTAATATAA
* * *
1532825 TATAATATTTTAATTATTTTTTAATATTA
1 TATATTATATTAA-TATTTTTTAATATAA
1532854 TATAATTATATT-ATATTT
1 TAT-ATTATATTAATATTT
1532872 AATATTATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 9 0.23
29 20 0.51
30 10 0.26
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
TATATTATATTAATATTTTTTAATATAA
Found at i:1533520 original size:7 final size:6
Alignment explanation
Indices: 1533495--1533533 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1533485 TAAATTATAA
* *
1533495 AAAAAT CAAAAT TAAAAT AAATAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT AA
1533534 CATATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:1534425 original size:23 final size:21
Alignment explanation
Indices: 1534388--1534440 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1534378 AATATAGTAC
*
1534388 AAATTTAAATA-A-TA-ATTT
1 AAATTTAAATATATTATAATT
*
1534406 AATATTTATATATATTATAATT
1 AA-ATTTAAATATATTATAATT
1534428 AAATTTAAATATA
1 AAATTTAAATATA
1534441 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 8 0.29
20 1 0.04
21 12 0.43
22 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAAATATATTATAATT
Found at i:1534794 original size:2 final size:2
Alignment explanation
Indices: 1534787--1534816 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1534777 GACTCAAGAG
1534787 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
1534817 GCCATCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1539571 original size:27 final size:28
Alignment explanation
Indices: 1539532--1539588 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
1539522 ATGTTTGAAT
1539532 TAAATTAATTTATTAATAAAT-ATTAAA
1 TAAATTAATTTATTAATAAATAATTAAA
* *
1539559 TAAATATAA-TTATTGATATATAATTAAA
1 TAAAT-TAATTTATTAATAAATAATTAAA
1539587 TA
1 TA
1539589 TGTTTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAATTAATTTATTAATAAATAATTAAA
Found at i:1541197 original size:34 final size:32
Alignment explanation
Indices: 1541131--1541201 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
1541121 AAAATTTTAA
1541131 TTTTTTA--AAATATAATTTTAAATTAATATT
1 TTTTTTATTAAATATAATTTTAAATTAATATT
* *
1541161 TTTATTTATTAAATAATAA-TTTATATCTAATTTT
1 TTT-TTTATTAAAT-ATAATTTTAAAT-TAATATT
1541195 TTTTTTA
1 TTTTTTA
1541202 AAAAAAACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 3 0.09
31 4 0.12
33 14 0.41
34 13 0.38
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
TTTTTTATTAAATATAATTTTAAATTAATATT
Found at i:1542083 original size:36 final size:36
Alignment explanation
Indices: 1541990--1542089 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 36
1541980 TTTTATTTTT
* *
1541990 TTATTTTTAAACATAAATATAATTTCAATAATTTTAC
1 TTATTATT-AACATAAATATAATTTTAATAATTTTAC
* *
1542027 TTATTATTCAAAATACATATAATTTTAATCTATATTTTA-
1 TTATTATT-AACATAAATATAATTTTAA--TA-ATTTTAC
1542066 TTATT-TT-ACATAAATATAATTTTA
1 TTATTATTAACATAAATATAATTTTA
1542090 TTTTAATTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
36 15 0.28
37 23 0.43
38 2 0.04
39 7 0.13
40 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (36 bp):
TTATTATTAACATAAATATAATTTTAATAATTTTAC
Found at i:1542720 original size:16 final size:16
Alignment explanation
Indices: 1542701--1542735 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1542691 GAAAAAATTA
* *
1542701 ATAATAATTATAATAT
1 ATAAAAATTAAAATAT
1542717 ATAAAAATTAAAATAT
1 ATAAAAATTAAAATAT
1542733 ATA
1 ATA
1542736 TTATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAAATTAAAATAT
Found at i:1548618 original size:18 final size:18
Alignment explanation
Indices: 1548597--1548639 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1548587 TGCAGAAATT
*
1548597 GGAGGAGGTGGA-ACAAAA
1 GGAGGAGGAGGAGA-AAAA
1548615 GGAGGAGGAGGAGAAAAA
1 GGAGGAGGAGGAGAAAAA
1548633 GGAGGAG
1 GGAGGAG
1548640 ATCCTGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.51, T:0.02
Consensus pattern (18 bp):
GGAGGAGGAGGAGAAAAA
Found at i:1553330 original size:23 final size:26
Alignment explanation
Indices: 1553285--1553334 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1553275 AAATATTATC
1553285 ATTTAATAAAAAAAATTATAATAATA
1 ATTTAATAAAAAAAATTATAATAATA
*
1553311 ATTTAA-AAATAAAA-TA-AATAATA
1 ATTTAATAAAAAAAATTATAATAATA
1553334 A
1 A
1553335 AATTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 7 0.30
26 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
ATTTAATAAAAAAAATTATAATAATA
Found at i:1557756 original size:13 final size:13
Alignment explanation
Indices: 1557740--1557781 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1557730 TGTTATGTTT
1557740 TAAATATTTTTTA
1 TAAATATTTTTTA
1557753 TAAATATCATTTTTA
1 TAAATAT--TTTTTA
*
1557768 T-ATTATTTTTTA
1 TAAATATTTTTTA
1557780 TA
1 TA
1557782 TCATTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 7 0.28
13 7 0.28
14 4 0.16
15 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATATTTTTTA
Found at i:1558232 original size:19 final size:19
Alignment explanation
Indices: 1558204--1558244 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1558194 TCAGTTCGTG
*
1558204 AAGGGAGAG-AAAGAAGAA
1 AAGGGAGAGAAAAAAAGAA
1558222 AAGGAGAGAGAAAAAAAGAA
1 AAGG-GAGAGAAAAAAAGAA
1558242 AAG
1 AAG
1558245 AAAAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (19 bp):
AAGGGAGAGAAAAAAAGAA
Found at i:1558254 original size:10 final size:10
Alignment explanation
Indices: 1558234--1558277 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1558224 GGAGAGAGAA
1558234 AAAAAGAAAAG
1 AAAAAG-AAAG
1558245 AAAAAGAAAG
1 AAAAAGAAAG
*
1558255 AAAAAGATAG
1 AAAAAGAAAG
*
1558265 ATAAAGAAA-
1 AAAAAGAAAG
1558274 AAAA
1 AAAA
1558278 TTTTGTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 3 0.10
10 20 0.69
11 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1558593 original size:20 final size:19
Alignment explanation
Indices: 1558557--1558595 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1558547 CATGTTTATA
*
1558557 TTATTTTTCATGTTATGTT
1 TTATTTTTCATATTATGTT
*
1558576 TTATTTTTTATATATATGTT
1 TTATTTTTCATAT-TATGTT
1558596 AAGTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (19 bp):
TTATTTTTCATATTATGTT
Found at i:1559614 original size:11 final size:11
Alignment explanation
Indices: 1559600--1559648 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1559590 TAATTTATTT
*
1559600 TATTTTATGTA
1 TATTATATGTA
1559611 TATTATATGTA
1 TATTATATGTA
1559622 TA-TATAT-TCA
1 TATTATATGT-A
*
1559632 TATTATGTGTA
1 TATTATATGTA
1559643 TATTAT
1 TATTAT
1559649 TTTTATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
11 23 0.70
12 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (11 bp):
TATTATATGTA
Found at i:1559634 original size:21 final size:20
Alignment explanation
Indices: 1559610--1559649 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1559600 TATTTTATGT
1559610 ATATTATATGTATATATATTC
1 ATATTATATGTATAT-TATTC
*
1559631 ATATTATGTGTATATTATT
1 ATATTATATGTATATTATT
1559650 TTTATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (20 bp):
ATATTATATGTATATTATTC
Found at i:1559919 original size:16 final size:15
Alignment explanation
Indices: 1559898--1559940 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1559888 ATACAATTTT
1559898 TAATTAAATAAAATTA
1 TAATT-AATAAAATTA
1559914 TAATTAATAAAATT-
1 TAATTAATAAAATTA
*
1559928 TATTTAA-AAAATT
1 TAATTAATAAAATT
1559941 TAACAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
15 9 0.35
16 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTAATAAAATTA
Found at i:1559940 original size:13 final size:14
Alignment explanation
Indices: 1559896--1559956 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 14
1559886 TTATACAATT
1559896 TTTAATTAAATAAAA
1 TTTAATT-AATAAAA
1559911 TTATAATTAATAAAA
1 TT-TAATTAATAAAA
*
1559926 TTTATTTAA-AAAA
1 TTTAATTAATAAAA
**
1559939 TTTAACAAAT-AAA
1 TTTAATTAATAAAA
1559952 TTTAA
1 TTTAA
1559957 AGTGAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 18 0.45
14 6 0.15
15 11 0.28
16 5 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATTAATAAAA
Found at i:1560925 original size:22 final size:21
Alignment explanation
Indices: 1560874--1560932 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 21
1560864 GACATGATAC
*
1560874 AAATATTATATATTTGTATTT
1 AAATATTATATTTTTGTATTT
1560895 --ATA--AT-TTTTTGTATTT
1 AAATATTATATTTTTGTATTT
*
1560911 AAAATATTATATTTTTATATTT
1 -AAATATTATATTTTTGTATTT
1560933 TTTTACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
16 10 0.33
17 2 0.07
19 6 0.20
21 2 0.07
22 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
AAATATTATATTTTTGTATTT
Found at i:1562431 original size:17 final size:19
Alignment explanation
Indices: 1562409--1562456 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
1562399 TTATTTAAAA
1562409 TATATTAAATAT-TA-TTT
1 TATATTAAATATATATTTT
*
1562426 TATATTAATTTATATATTTT
1 TATATTAA-ATATATATTTT
1562446 TATAATTAAAT
1 TAT-ATTAAAT
1562457 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 2 0.08
20 7 0.28
21 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTAAATATATATTTT
Found at i:1563569 original size:17 final size:17
Alignment explanation
Indices: 1563536--1563584 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1563526 TGTTATTTAA
* *
1563536 TTAAA-ATAAAATATTT
1 TTAAATATAAATTTTTT
1563552 TTAAATATAAATTTTTT
1 TTAAATATAAATTTTTT
1563569 TTAAATATAAACTTTT
1 TTAAATATAAA-TTTT
1563585 ATCATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.17
17 20 0.69
18 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATATAAATTTTTT
Found at i:1563584 original size:16 final size:16
Alignment explanation
Indices: 1563536--1563604 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1563526 TGTTATTTAA
1563536 TTAAA-ATAAAATATTT
1 TTAAATATAAAAT-TTT
*
1563552 TTAAATATAAATTTTTT
1 TTAAATATAAA-ATTTT
*
1563569 TTAAATATAAACTTTT
1 TTAAATATAAAATTTT
* * * *
1563585 ATCATTAAAAAATTTT
1 TTAAATATAAAATTTT
1563601 TTAA
1 TTAA
1563605 GTAAAGACTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
16 22 0.52
17 19 0.45
18 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATATAAAATTTT
Found at i:1564398 original size:15 final size:15
Alignment explanation
Indices: 1564378--1564422 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1564368 TTTTCATTTT
1564378 TTCCTTTCCCTTCCC
1 TTCCTTTCCCTTCCC
* *
1564393 TTCCTTTCTCTTTCC
1 TTCCTTTCCCTTCCC
*
1564408 TTCCCTTCCCTTCCC
1 TTCCTTTCCCTTCCC
1564423 CTACCTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (15 bp):
TTCCTTTCCCTTCCC
Found at i:1564409 original size:20 final size:20
Alignment explanation
Indices: 1564377--1564421 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1564367 CTTTTCATTT
1564377 TTTCCTTTCCCTTCCCTTCC
1 TTTCCTTTCCCTTCCCTTCC
1564397 TTTCTCTTT-CCTTCCCTTCC
1 TTTC-CTTTCCCTTCCCTTCC
*
1564417 CTTCC
1 TTTCC
1564422 CCTACCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCCTTTCCCTTCCCTTCC
Found at i:1564421 original size:10 final size:10
Alignment explanation
Indices: 1564378--1564422 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1564368 TTTTCATTTT
*
1564378 TTCCTTTCCC
1 TTCCCTTCCC
*
1564388 TTCCCTTCCT
1 TTCCCTTCCC
* *
1564398 TTCTCTTTCC
1 TTCCCTTCCC
1564408 TTCCCTTCCC
1 TTCCCTTCCC
1564418 TTCCC
1 TTCCC
1564423 CTACCTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (10 bp):
TTCCCTTCCC
Found at i:1564429 original size:20 final size:20
Alignment explanation
Indices: 1564386--1564429 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1564376 TTTTCCTTTC
* * * *
1564386 CCTTCCCTTCCTTTCTCTTT
1 CCTTCCCTTCCCTTCCCCTA
1564406 CCTTCCCTTCCCTTCCCCTA
1 CCTTCCCTTCCCTTCCCCTA
1564426 CCTT
1 CCTT
1564430 TTCTTTCATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.45
Consensus pattern (20 bp):
CCTTCCCTTCCCTTCCCCTA
Found at i:1565481 original size:14 final size:14
Alignment explanation
Indices: 1565462--1565503 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1565452 TCGGTCAGTT
1565462 TTAAATATATTTTA
1 TTAAATATATTTTA
*
1565476 TTAAATGTATTTTA
1 TTAAATATATTTTA
1565490 TTAAATATATTTTA
1 TTAAATATATTTTA
1565504 AATATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:1565688 original size:29 final size:28
Alignment explanation
Indices: 1565632--1565688 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1565622 ATTAGCTAAA
*
1565632 TTAATTAAATCGAATTTAATCAATTTTT
1 TTAATTAAATCGAATTTAACCAATTTTT
* * *
1565660 TTAATTAAATTTGATTTTAACCGATTTTT
1 TTAATTAAA-TCGAATTTAACCAATTTTT
1565689 GAGATCTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
TTAATTAAATCGAATTTAACCAATTTTT
Found at i:1566854 original size:3 final size:3
Alignment explanation
Indices: 1566846--1566893 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1566836 TAGAAAGTTC
1566846 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1566894 GCGTAGGGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1570879 original size:21 final size:21
Alignment explanation
Indices: 1570846--1570885 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1570836 AACATTTGGG
1570846 TTAAATTAAGTTTCAGTCATT
1 TTAAATTAAGTTTCAGTCATT
* * *
1570867 TTAATTTAGGTTTGAGTCA
1 TTAAATTAAGTTTCAGTCA
1570886 ATCAGGTGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (21 bp):
TTAAATTAAGTTTCAGTCATT
Found at i:1571744 original size:21 final size:22
Alignment explanation
Indices: 1571720--1571760 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1571710 AACTAATTCA
*
1571720 AAGTTTTATATTA-TAACTTAT
1 AAGTATTATATTATTAACTTAT
*
1571741 AAGTATTATTTTATTAACTT
1 AAGTATTATATTATTAACTT
1571761 GATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (22 bp):
AAGTATTATATTATTAACTTAT
Found at i:1571881 original size:32 final size:32
Alignment explanation
Indices: 1571826--1571918 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
1571816 TATTTAGATT
* *
1571826 ATTTCGGG-TCGAGTAATTTTAGATTCGGATC
1 ATTTCGGGTTCGAGTAATTATAGATTCGAATC
*
1571857 ATTTCGGGTTCGAGTCATTATAGATTCGAATC
1 ATTTCGGGTTCGAGTAATTATAGATTCGAATC
* * * *
1571889 ATTTTGGATTCGAATTATT-TCAGATTCGAA
1 ATTTCGGGTTCGAGTAATTAT-AGATTCGAA
1571919 CTAGCTCAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 9 0.17
32 44 0.83
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.40
Consensus pattern (32 bp):
ATTTCGGGTTCGAGTAATTATAGATTCGAATC
Found at i:1571884 original size:16 final size:16
Alignment explanation
Indices: 1571865--1571918 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1571855 TCATTTCGGG
*
1571865 TTCGAGTCATTATAGA
1 TTCGAATCATTATAGA
* *
1571881 TTCGAATCATTTTGGA
1 TTCGAATCATTATAGA
*
1571897 TTCGAATTATT-TCAGA
1 TTCGAATCATTAT-AGA
1571913 TTCGAA
1 TTCGAA
1571919 CTAGCTCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (16 bp):
TTCGAATCATTATAGA
Found at i:1573190 original size:25 final size:25
Alignment explanation
Indices: 1573147--1573194 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1573137 AAGATTTTTT
1573147 TAATTATAAAATTTATATTTTATAA
1 TAATTATAAAATTTATATTTTATAA
*
1573172 TAATTACTATAATTT-TATTTTAT
1 TAATTA-TAAAATTTATATTTTAT
1573195 TAGTCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATTATAAAATTTATATTTTATAA
Found at i:1573288 original size:19 final size:19
Alignment explanation
Indices: 1573247--1573316 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1573237 TTATAAATTT
1573247 TTAAAAA-ATATTAATAAAAA
1 TTAAAAATATATT--TAAAAA
**
1573267 TTAAAAATATATTTAATTA
1 TTAAAAATATATTTAAAAA
*
1573286 TTAAAAATTAAATTTAAAAA
1 TTAAAAA-TATATTTAAAAA
*
1573306 TAAAAAATATA
1 TTAAAAATATA
1573317 ATATAAACGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.34
20 22 0.54
21 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAATATATTTAAAAA
Found at i:1573323 original size:20 final size:20
Alignment explanation
Indices: 1573248--1573323 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 20
1573238 TATAAATTTT
*
1573248 TAAAAAATATTA-ATAAAAA
1 TAAAAAATATAATATAAAAA
* * **
1573267 TTAAAAATAT-ATTTAATTA
1 TAAAAAATATAATATAAAAA
* *
1573286 TTAAAAAT-TAAATTTAAAAA
1 TAAAAAATAT-AATATAAAAA
1573306 TAAAAAATATAATATAAA
1 TAAAAAATATAATATAAA
1573324 CGTTCTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
18 2 0.04
19 21 0.47
20 21 0.47
21 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAATATAATATAAAAA
Found at i:1574689 original size:3 final size:3
Alignment explanation
Indices: 1574681--1574712 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1574671 TATAAGATTA
*
1574681 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1574713 AATGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1579131 original size:4 final size:4
Alignment explanation
Indices: 1579122--1579150 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1579112 TTTAGATGAT
1579122 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1579151 GTAATTGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1579538 original size:16 final size:16
Alignment explanation
Indices: 1579517--1579551 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1579507 ATTTCTTGTT
1579517 TTCTTATTTT-TTTATA
1 TTCTTATTTTATTTA-A
1579533 TTCTTATTTTATTTAA
1 TTCTTATTTTATTTAA
1579549 TTC
1 TTC
1579552 AGCAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTATTTTATTTAA
Found at i:1583364 original size:16 final size:16
Alignment explanation
Indices: 1583343--1583428 Score: 91
Period size: 16 Copynumber: 5.3 Consensus size: 16
1583333 TAAACTCGAT
* *
1583343 TGACCCGAATTTGAAA
1 TGACCCGAACTCGAAA
1583359 TGACCCGAACTCGAAA
1 TGACCCGAACTCGAAA
** *
1583375 TGATTCGAACACGAAA
1 TGACCCGAACTCGAAA
*
1583391 TGATCCGAACTCGAAA
1 TGACCCGAACTCGAAA
* *
1583407 TGATCCAAACTCGAAAA
1 TGACCCGAACTCG-AAA
1583424 TGACC
1 TGACC
1583429 AAAAATTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
16 53 0.88
17 7 0.12
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (16 bp):
TGACCCGAACTCGAAA
Found at i:1583393 original size:32 final size:32
Alignment explanation
Indices: 1583355--1583428 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
1583345 ACCCGAATTT
* *
1583355 GAAATGACCCGAACTCGAAATGATTCGAACAC
1 GAAATGACCCGAACTCGAAATGATCCAAACAC
* *
1583387 GAAATGATCCGAACTCGAAATGATCCAAACTC
1 GAAATGACCCGAACTCGAAATGATCCAAACAC
1583419 GAAAATGACC
1 G-AAATGACC
1583429 AAAAATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 29 0.81
33 7 0.19
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (32 bp):
GAAATGACCCGAACTCGAAATGATCCAAACAC
Found at i:1583458 original size:15 final size:15
Alignment explanation
Indices: 1583440--1583478 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1583430 AAAATTTTAA
1583440 AACCTGAAATGACCC
1 AACCTGAAATGACCC
* * *
1583455 AACCCGAAATGATCT
1 AACCTGAAATGACCC
1583470 AACCTGAAA
1 AACCTGAAA
1583479 CCAATCGACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (15 bp):
AACCTGAAATGACCC
Found at i:1583914 original size:34 final size:34
Alignment explanation
Indices: 1583868--1583936 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1583858 TGTGCTTAGC
*
1583868 TAGTTGTTTAAGTTAGTCTCTTAGATTTTTTTTT
1 TAGTAGTTTAAGTTAGTCTCTTAGATTTTTTTTT
1583902 TAGTAGTTTAAGTTAGTCTCTTAGATTTTTTTTT
1 TAGTAGTTTAAGTTAGTCTCTTAGATTTTTTTTT
1583936 T
1 T
1583937 TCTTTTTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (34 bp):
TAGTAGTTTAAGTTAGTCTCTTAGATTTTTTTTT
Found at i:1585356 original size:20 final size:21
Alignment explanation
Indices: 1585320--1585370 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1585310 TTCTATAATT
*
1585320 TATATTGATATAATAAGTAAA
1 TATATCGATATAATAAGTAAA
1585341 TATATCGATA-AATAAGTAAA
1 TATATCGATATAATAAGTAAA
1585361 -AGTATCGATA
1 TA-TATCGATA
1585371 CATATTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (21 bp):
TATATCGATATAATAAGTAAA
Found at i:1585491 original size:52 final size:52
Alignment explanation
Indices: 1585429--1585568 Score: 199
Period size: 52 Copynumber: 2.7 Consensus size: 52
1585419 TCTGAAAAGA
* * * *
1585429 AAATGTATCGATACTTTTTTCATTGTATCGATACATTTTAGATTTTTGACCC
1 AAATATATCGATACATTTTTCATTGTATTGATACATTCTAGATTTTTGACCC
* * *
1585481 AAATATATCGATACATTTTTCATTGTATTGATACATTCTGGGTTTTTGACCT
1 AAATATATCGATACATTTTTCATTGTATTGATACATTCTAGATTTTTGACCC
* *
1585533 AAATATATCAATACATTTTTCAATGTATTGATACAT
1 AAATATATCGATACATTTTTCATTGTATTGATACAT
1585569 GTAGGTAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (52 bp):
AAATATATCGATACATTTTTCATTGTATTGATACATTCTAGATTTTTGACCC
Found at i:1587277 original size:13 final size:13
Alignment explanation
Indices: 1587259--1587284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1587249 CTATTTATGA
1587259 TGTATCGATACAC
1 TGTATCGATACAC
1587272 TGTATCGATACAC
1 TGTATCGATACAC
1587285 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1587429 original size:22 final size:22
Alignment explanation
Indices: 1587374--1587429 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
1587364 ACAGTGACCT
1587374 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1587396 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
1587417 ATGAACAGTGATG
1 ATGAACAGTGATG
1587430 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:1587436 original size:10 final size:10
Alignment explanation
Indices: 1587417--1587447 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1587407 GTATCGATAC
1587417 ATGAACAGTG
1 ATGAACAGTG
*
1587427 ATGAATAGTG
1 ATGAACAGTG
1587437 ATGAACAGTG
1 ATGAACAGTG
1587447 A
1 A
1587448 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1587567 original size:20 final size:21
Alignment explanation
Indices: 1587542--1587595 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1587532 TACATATTTG
1587542 TGTGTATCGATACTA-TGAAA
1 TGTGTATCGATACTATTGAAA
* *
1587562 TTTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTATTGAAA
1587582 TGTGTATCGATACT
1 TGTGTATCGATACT
1587596 TTTCAGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (21 bp):
TGTGTATCGATACTATTGAAA
Found at i:1587660 original size:21 final size:21
Alignment explanation
Indices: 1587634--1587674 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1587624 GTCAACCTTG
1587634 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1587655 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1587675 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1591337 original size:21 final size:21
Alignment explanation
Indices: 1591311--1591353 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1591301 AATGTGTCCA
1591311 ATTATCCCATACTTACTGCAT
1 ATTATCCCATACTTACTGCAT
*
1591332 ATTATCCCATACTTATTGCAT
1 ATTATCCCATACTTACTGCAT
1591353 A
1 A
1591354 CCTTATGAAC
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:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTATCCCATACTTACTGCAT
Found at i:1598018 original size:12 final size:12
Alignment explanation
Indices: 1598001--1598050 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
1597991 CACTCTCTTC
1598001 TTTTTTTTGTG-
1 TTTTTTTTGTGT
1598012 TTTTTTTTG-GT
1 TTTTTTTTGTGT
1598023 TTTTGTTTT-TGT
1 TTTT-TTTTGTGT
*
1598035 TTTTTTGTGTGT
1 TTTTTTTTGTGT
1598047 TTTT
1 TTTT
1598051 ACTTTTGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 1 0.03
11 16 0.47
12 17 0.50
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:1598034 original size:24 final size:24
Alignment explanation
Indices: 1598001--1598050 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
1597991 CACTCTCTTC
*
1598001 TTTTT-TTTGTGTTTTTTT-TG-G
1 TTTTTGTTTTTGTTTTTTTGTGTG
1598022 TTTTTGTTTTTGTTTTTTTGTGTG
1 TTTTTGTTTTTGTTTTTTTGTGTG
1598046 TTTTT
1 TTTTT
1598051 ACTTTTGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 12 0.48
23 2 0.08
24 6 0.24
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (24 bp):
TTTTTGTTTTTGTTTTTTTGTGTG
Found at i:1598056 original size:24 final size:22
Alignment explanation
Indices: 1598010--1598057 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1598000 CTTTTTTTTG
**
1598010 TGTTTTTTTTGGTTTTTGTTTT
1 TGTTTTTTTTGGTTTTTACTTT
1598032 TGTTTTTTTGTGTGTTTTTACTTT
1 TGTTTTTTT-TG-GTTTTTACTTT
1598056 TG
1 TG
1598058 GCTTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.02, C:0.02, G:0.19, T:0.77
Consensus pattern (22 bp):
TGTTTTTTTTGGTTTTTACTTT
Found at i:1598064 original size:32 final size:32
Alignment explanation
Indices: 1598002--1598064 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1597992 ACTCTCTTCT
* ** *
1598002 TTTTTTTGTGTTTTTTTTGGTTTTTGTTTTTG
1 TTTTTTTGTGTTGTTTTTACTTTTGGTTTTTG
1598034 TTTTTTTGTG-TGTTTTTACTTTTGGCTTTTT
1 TTTTTTTGTGTTGTTTTTACTTTTGG-TTTTT
1598065 AATCATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.02, C:0.03, G:0.17, T:0.78
Consensus pattern (32 bp):
TTTTTTTGTGTTGTTTTTACTTTTGGTTTTTG
Found at i:1609547 original size:2 final size:2
Alignment explanation
Indices: 1609540--1609579 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1609530 TAGCAAGAGA
1609540 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
1609580 GAGAGAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1609820 original size:139 final size:139
Alignment explanation
Indices: 1609668--1609951 Score: 408
Period size: 139 Copynumber: 2.0 Consensus size: 139
1609658 TTGTTTAATT
* * *
1609668 TGATTATTGTATTTTATTGTTTATTTACGTAGATCATGTATATCGAGTTTCAAGTAAATAAAAAT
1 TGATTATTATATTTTATCGTTTATTTACGTAGATCATGCATATCGAGTTTCAAGTAAATAAAAAT
* * *
1609733 ATCTAAGTATTTACTTGATAAAAAAAATTCAACCCTT-AAATATTTATTGAAAGCACTACTATTC
66 ATCTAAGTATTTACTTGATAAAAAAAATTCAA-CCTTAAAAAATATATTGAAAACACTACTATTC
*
1609797 TTGATCAATA
130 CTGATCAATA
* * *
1609807 TGATTGTTATATTTTATCGTTTATTTATGTAGATTATGCATATCGAGTTTCAAGTAAATAAAAAT
1 TGATTATTATATTTTATCGTTTATTTACGTAGATCATGCATATCGAGTTTCAAGTAAATAAAAAT
* * * *
1609872 ATCTAAGTATTTATTTGATATAAAAAATTTAACTTTAAAAAATATATTGAAAACACTACTATTCC
66 ATCTAAGTATTTACTTGATAAAAAAAATTCAACCTTAAAAAATATATTGAAAACACTACTATTCC
**
1609937 TGATTGATA
131 TGATCAATA
1609946 TGATTA
1 TGATTA
1609952 AGATGTTAGA
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
138 3 0.02
139 124 0.98
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (139 bp):
TGATTATTATATTTTATCGTTTATTTACGTAGATCATGCATATCGAGTTTCAAGTAAATAAAAAT
ATCTAAGTATTTACTTGATAAAAAAAATTCAACCTTAAAAAATATATTGAAAACACTACTATTCC
TGATCAATA
Found at i:1610291 original size:2 final size:2
Alignment explanation
Indices: 1610284--1610316 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1610274 TTTAAGCTTC
1610284 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 A
1610317 ATAAATTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1611750 original size:43 final size:43
Alignment explanation
Indices: 1611697--1611784 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
1611687 TATGAATAAT
*
1611697 TATATGCAAATTATACTTCATTTTTAAATAAAAAATAAATTCA
1 TATATGCAAATTATACTTCACTTTTAAATAAAAAATAAATTCA
1611740 TATATGCAAATTATACTTCACTTTTAAATAAAAAATAAATTCA
1 TATATGCAAATTATACTTCACTTTTAAATAAAAAATAAATTCA
1611783 TA
1 TA
1611785 CTTTTTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (43 bp):
TATATGCAAATTATACTTCACTTTTAAATAAAAAATAAATTCA
Found at i:1616941 original size:2 final size:2
Alignment explanation
Indices: 1616934--1616963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1616924 CAATAATAGC
1616934 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
1616964 GTCTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1617101 original size:2 final size:2
Alignment explanation
Indices: 1617094--1617128 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1617084 CTCTTTAATG
1617094 TA 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 TA T
1617129 GCGCCTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1618773 original size:4 final size:4
Alignment explanation
Indices: 1618766--1618795 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1618756 ATAAATTAAT
1618766 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1618796 GATGTGTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1620431 original size:11 final size:11
Alignment explanation
Indices: 1620417--1620478 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
1620407 ATAAAAATAA
1620417 AATATTATTAT
1 AATATTATTAT
*
1620428 AATATTAATA-
1 AATATTATTAT
*
1620438 AATATT-TTAA
1 AATATTATTAT
1620448 AAT-TTA-TAT
1 AATATTATTAT
1620457 AATATATATTATT
1 AATAT-TATTA-T
1620470 AATA-TATTA
1 AATATTATTA
1620479 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 9 0.21
10 10 0.24
11 16 0.38
12 2 0.05
13 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATATTATTAT
Found at i:1620495 original size:33 final size:33
Alignment explanation
Indices: 1620402--1620495 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 33
1620392 TTTTTTTTTC
1620402 TATTAATAAA-A-A-TAAAATATTAT-T-ATA-A
1 TATTAATAAATATATTAAAAT-TTATATAATATA
*
1620430 TATTAATAAATATTTTAAAATTTATATAATATA
1 TATTAATAAATATATTAAAATTTATATAATATA
* * *
1620463 TATT-ATTAATATATTAAATTTTTTATAGATATA
1 TATTAATAAATATATTAAAATTTATATA-ATATA
1620496 AAATATTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
28 10 0.19
29 1 0.02
30 4 0.07
31 7 0.13
32 22 0.41
33 10 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
TATTAATAAATATATTAAAATTTATATAATATA
Found at i:1620837 original size:10 final size:10
Alignment explanation
Indices: 1620824--1620923 Score: 57
Period size: 10 Copynumber: 10.1 Consensus size: 10
1620814 ATTTATTATT
*
1620824 AAATTTTATA
1 AAATTATATA
*
1620834 AAATAATATA
1 AAATTATATA
*
1620844 TAATTATATA
1 AAATTATATA
1620854 AATATTATATAA
1 AA-ATTATAT-A
*
1620866 AAATTA-ATT
1 AAATTATATA
1620875 AAA--ATATA
1 AAATTATATA
* *
1620883 ACATAATATA
1 AAATTATATA
* *
1620893 TAATTTTATA
1 AAATTATATA
1620903 AATATT-T-TA
1 AA-ATTATATA
1620912 AAATTTATATA
1 AAA-TTATATA
1620923 A
1 A
1620924 TATGAATCAT
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
7 1 0.01
8 5 0.07
9 9 0.13
10 33 0.49
11 17 0.25
12 3 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATTATATA
Found at i:1620862 original size:19 final size:18
Alignment explanation
Indices: 1620829--1620865 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1620819 TTATTAAATT
1620829 TTATAAAATAATATATAA
1 TTATAAAATAATATATAA
*
1620847 TTATATAAATATTATATAA
1 TTATA-AAATAATATATAA
1620866 AAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATAAAATAATATATAA
Found at i:1622867 original size:29 final size:28
Alignment explanation
Indices: 1622827--1622905 Score: 65
Period size: 29 Copynumber: 2.8 Consensus size: 28
1622817 AATGACCTAA
*
1622827 AAATGCAT-AAATTACATAATAGTCC-TT
1 AAATACATGAAATTACATAATAG-CCTTT
* *
1622854 AAA-ACATGAAAAATAACTAAAATAGCCTTT
1 AAATACATG--AAATTAC-ATAATAGCCTTT
*
1622884 AAATGCATGAAATTACATAATA
1 AAATACATGAAATTACATAATA
1622906 ATTCCTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 5 0.12
29 14 0.35
30 11 0.28
31 4 0.10
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.28
Consensus pattern (28 bp):
AAATACATGAAATTACATAATAGCCTTT
Found at i:1622905 original size:58 final size:58
Alignment explanation
Indices: 1622806--1623062 Score: 235
Period size: 58 Copynumber: 4.4 Consensus size: 58
1622796 CAATGCATAG
*
1622806 AAAATGACTTAAAT-GACCTAAAAATGCAT-AAATTACATAATAGTCCTTAAA-ACATGA
1 AAAATGACTTAAATAG-CCTTAAAATGCATGAAATTACATAATAGTCC-TAAATACATGA
* * * * *
1622863 AAAATAACTAAAATAGCCTTTAAATGCATGAAATTACATAATAATTCCTAAATGCATGA
1 AAAATGACTTAAATAGCCTTAAAATGCATGAAATTACATAAT-AGTCCTAAATACATGA
* * * * *
1622922 AAAATGCCTTAAATAACC-TAAAAGTGAATGAATTTACATAACAGTCACTAAATACATGA
1 AAAATGACTTAAATAGCCTTAAAA-TGCATGAAATTACATAATAGTC-CTAAATACATGA
* * *
1622981 AAAATGACTTAAAT-G-ATCTAAAATGCATGAATTTGCATAATAGTCTCTAAA-AGCATGA
1 AAAATGACTTAAATAGCCT-TAAAATGCATGAAATTACATAATAGTC-CTAAATA-CATGA
*
1623039 AAAATG-CTTTAAATAACC-TAAAAT
1 AAAATGAC-TTAAATAGCCTTAAAAT
1623063 TGTAGCATGC
Statistics
Matches: 163, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
57 25 0.15
58 71 0.44
59 67 0.41
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.28
Consensus pattern (58 bp):
AAAATGACTTAAATAGCCTTAAAATGCATGAAATTACATAATAGTCCTAAATACATGA
Found at i:1623031 original size:117 final size:116
Alignment explanation
Indices: 1622797--1623061 Score: 306
Period size: 117 Copynumber: 2.3 Consensus size: 116
1622787 AATGATCCCC
* * * *
1622797 AATGCAT-AGAAAATGACTTAAATGACCTAAAAATGCATAAATTACATAATAGTCCTTAAAACAT
1 AATGCATGA-AAAATGCCTTAAATAACCTAAAAATGAATAAATTACATAACAGTCCTTAAAACAT
*
1622861 GAAAAATAACTAAAATAGCCTTTAAATGCATGAAATTACATAATAATTCCTA
65 GAAAAATAACTAAAATAGCCTTAAAATGCATGAAATTACATAATAATTCCTA
* *
1622913 AATGCATGAAAAATGCCTTAAATAACCTAAAAGTGAATGAATTTACATAACAGTCAC-TAAATAC
1 AATGCATGAAAAATGCCTTAAATAACCTAAAAATGAAT-AAATTACATAACAGTC-CTTAAA-AC
* * * * * *
1622977 ATGAAAAATGACTTAAAT-G-ATCTAAAATGCATGAATTTGCATAAT-AGTCTCTA
63 ATGAAAAATAACTAAAATAGCCT-TAAAATGCATGAAATTACATAATAATTC-CTA
* *
1623030 AAAGCATGAAAAATGCTTTAAATAACCTAAAA
1 AATGCATGAAAAATGCCTTAAATAACCTAAAA
1623062 TTGTAGCATG
Statistics
Matches: 128, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
116 36 0.28
117 73 0.57
118 19 0.15
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (116 bp):
AATGCATGAAAAATGCCTTAAATAACCTAAAAATGAATAAATTACATAACAGTCCTTAAAACATG
AAAAATAACTAAAATAGCCTTAAAATGCATGAAATTACATAATAATTCCTA
Found at i:1624466 original size:20 final size:20
Alignment explanation
Indices: 1624441--1624495 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
1624431 ATAAAAACAC
*
1624441 ATTGTATTAATAAAT-TTGCA
1 ATTGTATTGATAAATGTT-CA
*
1624461 ATTGTATCGATACAATGTTCA
1 ATTGTATTGATA-AATGTTCA
1624482 ATTGTATTGATAAA
1 ATTGTATTGATAAA
1624496 ATTGTATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
21 16 0.53
22 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTGTATTGATAAATGTTCA
Found at i:1625513 original size:30 final size:33
Alignment explanation
Indices: 1625477--1625609 Score: 119
Period size: 34 Copynumber: 4.0 Consensus size: 33
1625467 AACCTTACAA
*
1625477 CACTATCTTTTGA-AGGCTAAGATAAAAC-CTT
1 CACTATCTTTTCACAGGCTAAGATAAAACTCTT
* * *
1625508 C-CTATCTTTTCATAGCCTAAGATAGAACTTCTT
1 CACTATCTTTTCACAGGCTAAGATAAAAC-TCTT
* *
1625541 CACTATCTTTTCACAGGCTAAGATAGAACTTTT
1 CACTATCTTTTCACAGGCTAAGATAAAACTCTT
* * *
1625574 CTCCTTATCTTTTTCAAAAGCTAAGATAAAATCTCT
1 C-AC-TATC-TTTTCACAGGCTAAGATAAAA-CTCT
1625610 CAATTACTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
30 10 0.12
31 14 0.17
33 8 0.10
34 26 0.31
35 4 0.05
36 18 0.22
37 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (33 bp):
CACTATCTTTTCACAGGCTAAGATAAAACTCTT
Found at i:1625550 original size:34 final size:33
Alignment explanation
Indices: 1625477--1625571 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 33
1625467 AACCTTACAA
* *
1625477 CACTATCTTTTGAAGGCTAAGATAAAAC--CTT
1 CACTATCTTTTCAAGGCTAAGATAGAACTTCTT
*
1625508 C-CTATCTTTTCATAGCCTAAGATAGAACTTCTT
1 CACTATCTTTTCA-AGGCTAAGATAGAACTTCTT
1625541 CACTATCTTTTCACAGGCTAAGATAGAACTT
1 CACTATCTTTTCA-AGGCTAAGATAGAACTT
1625572 TTCTCCTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
30 10 0.18
31 14 0.25
33 4 0.07
34 27 0.49
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (33 bp):
CACTATCTTTTCAAGGCTAAGATAGAACTTCTT
Found at i:1627383 original size:23 final size:23
Alignment explanation
Indices: 1627357--1627404 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1627347 TCAAGATTCA
1627357 AATTCAAGCTCTGATCATTTTTG
1 AATTCAAGCTCTGATCATTTTTG
*
1627380 AATTCAAGCTCTGATCTTTTTTG
1 AATTCAAGCTCTGATCATTTTTG
1627403 AA
1 AA
1627405 GCCCAAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (23 bp):
AATTCAAGCTCTGATCATTTTTG
Found at i:1631233 original size:50 final size:50
Alignment explanation
Indices: 1631174--1631382 Score: 357
Period size: 50 Copynumber: 4.2 Consensus size: 50
1631164 TATACTTAGA
1631174 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
*
1631224 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* *
1631274 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
* *
1631324 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATT
1631374 GTCAACAAT
1 GTCAACAAT
1631383 GACAACAACT
Statistics
Matches: 153, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
50 152 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
Found at i:1635781 original size:50 final size:50
Alignment explanation
Indices: 1635721--1635880 Score: 252
Period size: 50 Copynumber: 3.2 Consensus size: 50
1635711 ATATACTTAG
1635721 AGTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
*
1635771 TGTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
1635821 CGTCAATAATTATGGCCACCT-CTCTCTATTGTCAAAGGTTGGTGAATG-AT
1 AGTCAACAATTATGGTCACCTCCT-TCTATTGTCAAAGGTTGGTGAA-GAAT
1635871 AGTCAACAAT
1 AGTCAACAAT
1635881 GACAACAACT
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
49 2 0.02
50 99 0.97
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (50 bp):
AGTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:1636807 original size:2 final size:2
Alignment explanation
Indices: 1636800--1636831 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1636790 AAAAGTGTAC
1636800 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
1636832 GCACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1638620 original size:43 final size:43
Alignment explanation
Indices: 1638571--1638659 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
1638561 AAGCTAAAAT
1638571 TTGGAGCTTCATCAAGCTGTTAGGCATGAAAATATTTATTCCC
1 TTGGAGCTTCATCAAGCTGTTAGGCATGAAAATATTTATTCCC
*
1638614 TTGGAGCTTCATCAAGCTGTTTGGCATGAAAATATTTATTCCC
1 TTGGAGCTTCATCAAGCTGTTAGGCATGAAAATATTTATTCCC
1638657 TTG
1 TTG
1638660 ACAATTTGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (43 bp):
TTGGAGCTTCATCAAGCTGTTAGGCATGAAAATATTTATTCCC
Found at i:1642406 original size:16 final size:15
Alignment explanation
Indices: 1642380--1642410 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1642370 GATAAAAAGA
1642380 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
1642395 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
1642411 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:1646974 original size:13 final size:13
Alignment explanation
Indices: 1646956--1646980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1646946 CAAAGATCAG
1646956 TGTATCGATACAA
1 TGTATCGATACAA
1646969 TGTATCGATACA
1 TGTATCGATACA
1646981 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1647060 original size:13 final size:13
Alignment explanation
Indices: 1647042--1647066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1647032 ACAAAACTTA
1647042 TGTATCGATACAT
1 TGTATCGATACAT
1647055 TGTATCGATACA
1 TGTATCGATACA
1647067 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1647062 original size:32 final size:33
Alignment explanation
Indices: 1647021--1647086 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1647011 AGTAGCTTAA
1647021 ATTGTATCGATACAA-AACTTATGTATCGATAC
1 ATTGTATCGATACAACAACTTATGTATCGATAC
** *
1647053 ATTGTATCGATACAACATTTTATGTATTGATAC
1 ATTGTATCGATACAACAACTTATGTATCGATAC
1647086 A
1 A
1647087 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACAACAACTTATGTATCGATAC
Found at i:1648668 original size:83 final size:83
Alignment explanation
Indices: 1648450--1649283 Score: 832
Period size: 83 Copynumber: 10.0 Consensus size: 83
1648440 CTTAGGGAAA
* * ** * * * *
1648450 GAAAAGTCTCCAGGGACAAAGCCAACAGATAGATTGAGGGAAGGAAAGTCTCCATGGTT-AACCA
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAACCG
* * *
1648514 ATAGGCAGACTGAGGGAA
66 ACAGGCAGACTAAGGGAT
* * * * ** *
1648532 GGAAAGTCTCCAGGGTTAAA-CCGACAGGCAGACTGAGAGCTGAAAAGTCTCCAGGGTTAAACCG
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAACCG
* *
1648596 ATAGGCAGACTAAGGGTT
66 ACAGGCAGACTAAGGGAT
** * * * **
1648614 GAAAAGTCTCCAAAGTCAAAGTCGACAAGTAGACTAAGGGATA-GAAAGTCTCCAGGGACAAAGC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA-AGGAAAGTCTCCAGGGTTAAA-C
* * *
1648678 CGACAAGCAGACTTAAGGAAA
64 CGACAGGCAGAC-TAAGGGAT
* * * ** * **
1648699 GAAAAATCTCCAAGGTCAAAGCCGACAGGTAGGTTGAGGGAAGGAAAGTCTCCAGGGACGAAACC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGG-TTAAACC
*
1648764 GACAGGAAGACTAAGGGAT
65 GACAGGCAGACTAAGGGAT
* * * * *
1648783 GAAAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAGAAAAGTCTCCAGGGTTAAACCG
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAACCG
1648848 ACAGGCAGACTAAGGGAT
66 ACAGGCAGACTAAGGGAT
* * *
1648866 GAAAAGTCTCCAGGGTCAAAACCGACAGGCAAACTAAGGGAAGGAAAGTCTCTAGGGTTAAACCG
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAACCG
* *
1648931 ACAGGCAGACTGAGGGTT
66 ACAGGCAGACTAAGGGAT
** * *
1648949 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAA-GCTAGGAAAGTTTCCAAGGTTAAACC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGGAAAGTCTCCAGGGTTAAACC
* *
1649013 GATAGGTAGACTAAGGGAT
65 GACAGGCAGACTAAGGGAT
* * *** *
1649032 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAGGGGAAAGAAAGTCTCCAAGGACGAAGCC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC-AGGGTTAAACC
* *
1649097 GACAGACAGACTGA-GGATT
65 GACAGGCAGACTAAGGGA-T
* *
1649116 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGGAAGGAAAGTCTCCAGGGTCAAGGC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGGAAAGTCTCCAGGGTTAA-AC
* * *
1649181 CGACAGACAGACTGAGGGAA
64 CGACAGGCAGACTAAGGGAT
* **** * * ** * *
1649201 AAAAAGTCTCCAAAAACGAAGCTGACAGGCAGACTAAGGGAAAAAAAGTCTCCAGGGTCAAAGTC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAA-CC
1649266 GACAGGCAGACTAAGGGA
65 GACAGGCAGACTAAGGGA
1649284 AAACAAAAAA
Statistics
Matches: 621, Mismatches: 116, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
81 29 0.05
82 53 0.09
83 244 0.39
84 164 0.26
85 125 0.20
86 6 0.01
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (83 bp):
GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAGGGTTAAACCG
ACAGGCAGACTAAGGGAT
Found at i:1649286 original size:42 final size:42
Alignment explanation
Indices: 1648443--1649284 Score: 781
Period size: 42 Copynumber: 20.1 Consensus size: 42
1648433 ACTGGCACTT
* * ** * *
1648443 AGGGAAAGAAAAGTCTCCAGGGACAAAGCCAACAGATAGATTG
1 AGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * * * * *
1648486 AGGGAAGGAAAGTCTCCATGGT-TAA-CCAATAGGCAGACTG
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * *
1648526 AGGGAAGGAAAGTCTCCAGGGTTAAA-CCGACAGGCAGACTG
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* ** * *
1648567 AGAGCTGAAAAGTCTCCAGGGTTAAA-CCGATAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
** ** * * *
1648608 AGGGTTGAAAAGTCTCCAAAGTCAAAGTCGACAAGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1648650 AGGGATAG-AAAGTCTCCAGGGACAAAGCCGACAAGCAGACTTA
1 AGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC-TA
* * * * ** *
1648693 AGGAAAGAAAAATCTCCAAGGTCAAAGCCGACAGGTAGGTTG
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * *
1648735 AGGGAAGGAAAGTCTCCAGGGACGAAA-CCGACAGGAAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTC-AAAGCCGACAGGCAGACTA
* * *
1648777 AGGGATGAAAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * *
1648819 AAGGTAGAAAAGTCTCCAGGGTTAAA-CCGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * *
1648860 AGGGATGAAAAGTCTCCAGGGTCAAAACCGACAGGCAAACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * * *
1648902 AGGGAAGGAAAGTCTCTAGGGTTAAA-CCGACAGGCAGACTG
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
**
1648943 AGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-A
** * * * * * *
1648986 A-GCTAGGAAAGTTTCCAAGGTTAAA-CCGATAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1649026 AGGGATGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * * * * *
1649068 GGGGAA-AGAAAGTCTCCAAGGACGAAGCCGACAGACAGACTG
1 AGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1649110 A-GGATTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGA
1 AGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-A
* * * *
1649153 AGGGAAGGAAAGTCTCCAGGGTCAAGGCCGACAGACAGACTG
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* **** * *
1649195 AGGGAAAAAAAGTCTCCAAAAACGAAGCTGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1649237 AGGGAAAAAAAGTCTCCAGGGTCAAAGTCGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
1649279 AGGGAA
1 AGGGAA
1649285 AACAAAAAAG
Statistics
Matches: 647, Mismatches: 135, Indels: 35
0.79 0.17 0.04
Matches are distributed among these distances:
40 34 0.05
41 179 0.28
42 357 0.55
43 74 0.11
44 3 0.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (42 bp):
AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
Found at i:1653800 original size:17 final size:17
Alignment explanation
Indices: 1653768--1653802 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1653758 CTCTGCAAAT
* *
1653768 AGAAAAAAATGGAAAAA
1 AGAAAAAAAAGAAAAAA
1653785 AGAAAAAAAAGAAAAAA
1 AGAAAAAAAAGAAAAAA
1653802 A
1 A
1653803 AGATATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAAGAAAAAA
Found at i:1653803 original size:10 final size:9
Alignment explanation
Indices: 1653780--1653805 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1653770 AAAAAAATGG
1653780 AAAAAAGAA
1 AAAAAAGAA
1653789 AAAAAAGAA
1 AAAAAAGAA
1653798 AAAAAAGA
1 AAAAAAGA
1653806 TATGATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:1661978 original size:16 final size:15
Alignment explanation
Indices: 1661952--1661992 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
1661942 ATAAAAAAGA
1661952 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
1661967 ATTTTGTTATTATTTTTT
1 ATTTT-TTATTA--TTTT
1661985 ATTTTTTA
1 ATTTTTTA
1661993 ATTTTACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 3 0.13
18 9 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Done.