Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 27 of 82
Found at i:9378019 original size:3 final size:3
Alignment explanation
Indices: 9378005--9378039 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9377995 ACATTTCCAT
*
9378005 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
9378040 GTGCACTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:9378196 original size:45 final size:45
Alignment explanation
Indices: 9378132--9378226 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
9378122 CGGTCCTCAA
* *
9378132 CTCATGTGCAGTCCCTACA-TCTGTACATAGCTAGGTCATCATCAG
1 CTCATGTGCACTCCCTACATTC-GCACATAGCTAGGTCATCATCAG
* *
9378177 CTCATGTGCACTCCCTACATTCGCACATAGCTGGGTCATCATTAG
1 CTCATGTGCACTCCCTACATTCGCACATAGCTAGGTCATCATCAG
9378222 CTCAT
1 CTCAT
9378227 CATTATTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (45 bp):
CTCATGTGCACTCCCTACATTCGCACATAGCTAGGTCATCATCAG
Found at i:9385361 original size:37 final size:37
Alignment explanation
Indices: 9385320--9385397 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
9385310 GTTGTGTGAG
* * * *
9385320 GATGTTGAAGTGTGCGAGTAGGGGGTTCACACATGAT
1 GATGTTGAAGTGTACGAGTAGAGAGTGCACACATGAT
9385357 GATGTTGAAGTGTACGAGTAGAGAGTGCACACATGAT
1 GATGTTGAAGTGTACGAGTAGAGAGTGCACACATGAT
9385394 GATG
1 GATG
9385398 AATGCATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.10, G:0.36, T:0.26
Consensus pattern (37 bp):
GATGTTGAAGTGTACGAGTAGAGAGTGCACACATGAT
Found at i:9391118 original size:16 final size:16
Alignment explanation
Indices: 9391094--9391124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9391084 AATTAAGTTT
9391094 TAGACATAATTATAAA
1 TAGACATAATTATAAA
*
9391110 TAGATATAATTATAA
1 TAGACATAATTATAA
9391125 GGCCTTGATT
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:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TAGACATAATTATAAA
Found at i:9392316 original size:19 final size:17
Alignment explanation
Indices: 9392269--9392319 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
9392259 CCGGTAAGTG
*
9392269 AAAGAAAAGAGAGAAGAAA
1 AAAGAAAA-AGA-AAAAAA
9392288 AAAGAAAAAGAAAAAAA
1 AAAGAAAAAGAAAAAAA
9392305 AAAGAGAGAAAGAAA
1 AAAGA-A-AAAGAAA
9392320 GAACTAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 15 0.52
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAA
Found at i:9392419 original size:7 final size:7
Alignment explanation
Indices: 9392395--9392435 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
9392385 GGCGTCGAAG
9392395 AGAAG-A
1 AGAAGAA
*
9392401 AGAAGAG
1 AGAAGAA
*
9392408 GGAAGAA
1 AGAAGAA
9392415 AGAAGAA
1 AGAAGAA
9392422 AGAA-AA
1 AGAAGAA
9392428 AGAAGAA
1 AGAAGAA
9392435 A
1 A
9392436 AAAGGGAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:9392494 original size:69 final size:70
Alignment explanation
Indices: 9392339--9392494 Score: 160
Period size: 69 Copynumber: 2.2 Consensus size: 70
9392329 GCTTGAGAAA
* ** * *
9392339 AAGAAAGAGAGAGAAGAAAAAGAAGAAGGAAGGGAGAAGGAGCAATGGCGTCGAAGAGAAGAAGA
1 AAGAAAGA-AAAGAAGAAAAAGAAGAAAAAAGGGAGAAGGAGCAACGACGTCGAAGAGAAGAAGA
9392404 AGAGGG
65 AGAGGG
* * * *
9392410 AAGAAAGAAGA-AAGAAAAAGAAGAAAAAAGGGAGAGGGAGCAACGACGGT-GCTAGAGGAG-A-
1 AAGAAAGAAAAGAAGAAAAAGAAGAAAAAAGGGAGAAGGAGCAACGAC-GTCG-AAGAGAAGAAG
9392471 AAGA-GG
64 AAGAGGG
9392477 AAGAAGAGAAAAGAAGAA
1 AAGAA-AGAAAAGAAGAA
9392495 GGAAAAAGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
67 7 0.10
68 9 0.12
69 38 0.52
70 11 0.15
71 8 0.11
ACGTcount: A:0.55, C:0.04, G:0.38, T:0.03
Consensus pattern (70 bp):
AAGAAAGAAAAGAAGAAAAAGAAGAAAAAAGGGAGAAGGAGCAACGACGTCGAAGAGAAGAAGAA
GAGGG
Found at i:9392497 original size:20 final size:19
Alignment explanation
Indices: 9392474--9392523 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
9392464 GAGGAGAAAG
*
9392474 AGGAAGAAGAGAAAAGAAGA
1 AGGAAAAAGAG-AAAGAAGA
9392494 AGGAAAAAGAGAAAGAAGA
1 AGGAAAAAGAGAAAGAAGA
9392513 AGAGAAAAAGA
1 AG-GAAAAAGA
9392524 AGGGCCGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AGGAAAAAGAGAAAGAAGA
Found at i:9392581 original size:9 final size:10
Alignment explanation
Indices: 9392555--9392595 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
9392545 CTGTAGCAAG
9392555 GAAAAAAAACA
1 GAAAAAAAA-A
*
9392566 GGAAAAAGAAA
1 -GAAAAAAAAA
9392577 GAAAAAAAAA
1 GAAAAAAAAA
9392587 GAAAAAAAA
1 GAAAAAAAA
9392596 GGGGAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 1 0.04
12 8 0.30
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:9393484 original size:60 final size:59
Alignment explanation
Indices: 9393388--9393565 Score: 259
Period size: 60 Copynumber: 3.0 Consensus size: 59
9393378 TTGATTGTAA
* * *
9393388 AAAGGGGGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTTCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTTATAAT-GGTGGCATGGGTAGTTCCCACGAGTAGGT
*
9393448 AAAGGGGGACCTGAAGCCCTGATTTATAATGAGTGGCATGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTTATAATG-GTGGCATGGGTAGTTCCCACGAGTAGGT
** * *
9393508 AAAAAGGGACTTGAAGCCCCGATTCAT-ATGGTGGCATGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTTATAATGGTGGCATGGGTAGTTCCCACGAGTAGGT
9393566 GATGATGTTT
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
58 28 0.26
59 4 0.04
60 76 0.70
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (59 bp):
AAAGGGGGACCTGAAGCCCCGATTTATAATGGTGGCATGGGTAGTTCCCACGAGTAGGT
Found at i:9414358 original size:20 final size:21
Alignment explanation
Indices: 9414333--9414372 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
9414323 ACGGTGCAAG
9414333 AGGAAGAAGAGAAAG-GAAGA
1 AGGAAGAAGAGAAAGAGAAGA
9414353 AGGAAGAAGAGAAAGAGAAG
1 AGGAAGAAGAGAAAGAGAAG
9414373 CGCCGACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (21 bp):
AGGAAGAAGAGAAAGAGAAGA
Found at i:9414451 original size:14 final size:14
Alignment explanation
Indices: 9414398--9414454 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
9414388 AGATCGGTAG
*
9414398 CAAGGAAAAAAAAA
1 CAAGAAAAAAAAAA
* * *
9414412 CAAGAAAGACAAAG
1 CAAGAAAAAAAAAA
9414426 CAAGAAATAAAAAAA
1 CAAGAAA-AAAAAAA
*
9414441 AAAGAAAAAAAAAA
1 CAAGAAAAAAAAAA
9414455 GGGGAGGGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (14 bp):
CAAGAAAAAAAAAA
Found at i:9426426 original size:39 final size:39
Alignment explanation
Indices: 9426339--9426446 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 39
9426329 GGTGTCGGTA
* * **
9426339 GTGTGCGGTATGGGAGAGCACACGCCGATGATATATGCC
1 GTGTGCGGTGTGGGAGAGCACATGATGATGATATATGCC
*
9426378 ATGTGCGGTGTGGGAGAGCACATGATGATGATATATGCC
1 GTGTGCGGTGTGGGAGAGCACATGATGATGATATATGCC
* *
9426417 GTGTGCGGTGT-GGA-CGCACATGATGGTGAT
1 GTGTGCGGTGTGGGAGAGCACATGATGATGAT
9426447 GGTAAGGCGC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 14 0.23
38 3 0.05
39 44 0.72
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (39 bp):
GTGTGCGGTGTGGGAGAGCACATGATGATGATATATGCC
Found at i:9451785 original size:17 final size:17
Alignment explanation
Indices: 9451763--9451797 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9451753 ATAAAACTAT
9451763 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
*
9451780 GCACACACTTAGGGGGA
1 GCACACACTAAGGGGGA
9451797 G
1 G
9451798 GAAAACCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.37, T:0.09
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:9460057 original size:46 final size:46
Alignment explanation
Indices: 9460007--9460100 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
9459997 AATATTTCGA
9460007 AAGTTCAACACCATTCATATATAGGCAGGGCAAACTTAATTAACAC
1 AAGTTCAACACCATTCATATATAGGCAGGGCAAACTTAATTAACAC
*
9460053 AAGTTCAACACCATTCATATATGGGCAGGGCAAACTTAATTAACAC
1 AAGTTCAACACCATTCATATATAGGCAGGGCAAACTTAATTAACAC
9460099 AA
1 AA
9460101 TACACTTACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.23
Consensus pattern (46 bp):
AAGTTCAACACCATTCATATATAGGCAGGGCAAACTTAATTAACAC
Found at i:9465641 original size:32 final size:32
Alignment explanation
Indices: 9465605--9465710 Score: 117
Period size: 32 Copynumber: 3.2 Consensus size: 32
9465595 TTTACTGAGA
9465605 TCAACCAACACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAACACCCAAAGTGGTTTTTCAAAGGC
* **
9465637 TCAACC-ACAACCTTTCACAA-TGGGTTTTCATGGGC
1 TCAACCAAC-ACC---CA-AAGTGGTTTTTCAAAGGC
*
9465672 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAACACCCAAAGTGGTTTTTCAAAGGC
9465704 TCAACCA
1 TCAACCA
9465711 CAACCTACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
31 4 0.07
32 30 0.50
35 23 0.38
36 3 0.05
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (32 bp):
TCAACCAACACCCAAAGTGGTTTTTCAAAGGC
Found at i:9465652 original size:67 final size:67
Alignment explanation
Indices: 9465578--9465751 Score: 246
Period size: 67 Copynumber: 2.6 Consensus size: 67
9465568 GCTTAGCCAA
*
9465578 AACCTTTCACAATGGTTTTTACTGAGATCAACCAACACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTACTGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
9465643 AC
66 AC
* * *
9465645 AACCTTTCACAATGGGTTTT-CATGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTAC-TGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
9465709 CAC
65 CAC
* *
9465712 AACC-TACAACAATGGTTTTTCAC-GAGATCAATCAAAACCC
1 AACCTTTC-ACAATGGTTTTT-ACTGAGATCAACCAAAACCC
9465752 GACAACTAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
66 3 0.03
67 90 0.96
69 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTACTGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:9465673 original size:35 final size:33
Alignment explanation
Indices: 9465622--9465733 Score: 129
Period size: 35 Copynumber: 3.3 Consensus size: 33
9465612 ACACCCAAAG
9465622 TGGTTTTTCAAAGGCTCAACCACAACCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCACAACC--TCACAA
* ** *
9465657 TGGGTTTTCATGGGCTCAACCAAAACC-CA-AA
1 TGGTTTTTCAAAGGCTCAACCACAACCTCACAA
9465688 GTGGTTTTTCAAAGGCTCAACCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCACAACCT-C-ACAA
9465724 TGGTTTTTCA
1 TGGTTTTTCA
9465734 CGAGATCAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.03
32 25 0.39
34 1 0.02
35 34 0.53
36 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (33 bp):
TGGTTTTTCAAAGGCTCAACCACAACCTCACAA
Found at i:9467145 original size:19 final size:20
Alignment explanation
Indices: 9467117--9467155 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9467107 ACATTTTTTT
9467117 TTAATTTTCC-CTT-TCCCC
1 TTAATTTTCCACTTCTCCCC
9467135 TTAACTTTTCCACTTCTCCCC
1 TTAA-TTTTCCACTTCTCCCC
9467156 CTTTTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 3 0.17
21 5 0.28
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATTTTCCACTTCTCCCC
Found at i:9474770 original size:43 final size:43
Alignment explanation
Indices: 9474707--9474825 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
9474697 GTAATTATAT
* * *
9474707 TGACTCGGCTATGTGTGAGTAGGGAGTGCGCATAAATCGAG-GA
1 TGACTCAGCTATGTGAGAGTAGGGAGTGCGCATAAACCG-GTGA
* *
9474750 TGACTCAGTTATGTGAGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACTCAGCTATGTGAGAGTAGGGAGTGCGCATAAACCGGTGA
* * *
9474793 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACTCAGCTATGTGAGAGTAGGGAGTGCGCAT
9474826 GAGTTGGTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (43 bp):
TGACTCAGCTATGTGAGAGTAGGGAGTGCGCATAAACCGGTGA
Found at i:9474862 original size:23 final size:23
Alignment explanation
Indices: 9474835--9474894 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
9474825 TGAGTTGGTG
*
9474835 ATGATAATGATGGGATGGTGTGC
1 ATGATGATGATGGGATGGTGTGC
*
9474858 ATGATGATGATGGGATTGTGTGC
1 ATGATGATGATGGGATGGTGTGC
*
9474881 ATGATGGTGATGGG
1 ATGATGATGATGGG
9474895 TATATGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.42, T:0.32
Consensus pattern (23 bp):
ATGATGATGATGGGATGGTGTGC
Found at i:9475285 original size:21 final size:21
Alignment explanation
Indices: 9475246--9475287 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9475236 TTCATCAGTT
** *
9475246 GAATTTCGCTGTGGTGAGAAA
1 GAATTTCGCTGCAGCGAGAAA
9475267 GAATTTCGCTGCAGCGAGAAA
1 GAATTTCGCTGCAGCGAGAAA
9475288 CCTTCTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (21 bp):
GAATTTCGCTGCAGCGAGAAA
Found at i:9480541 original size:32 final size:32
Alignment explanation
Indices: 9480505--9480653 Score: 140
Period size: 35 Copynumber: 4.5 Consensus size: 32
9480495 TTTACCGGGA
*
9480505 TCAACCAAAACCCAAAGTGATTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* *
9480537 TCAACCACAACCTTTCACAA-TGGTTTTTCATAGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
*
9480572 TCAACCAAAACCCAAAGTGGTTTTACAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * *
9480604 TCAGCCACAACCTACAATAATGGTTTTTCACAA-GA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA-AAGGC
9480639 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
9480654 CAACTAACTT
Statistics
Matches: 95, Mismatches: 13, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
31 2 0.02
32 36 0.38
33 3 0.03
34 3 0.03
35 47 0.49
36 4 0.04
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:9480559 original size:67 final size:67
Alignment explanation
Indices: 9480479--9480653 Score: 237
Period size: 67 Copynumber: 2.6 Consensus size: 67
9480469 CTTAGCCAAG
* *
9480479 ACCTTTCATAATGGTTTTT-ACCGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
1 ACCTTTCATAATGGTTTTTCA-CAGGATCAACCAAAACCCAAAGTGATTTTACAAAGGCTCAACC
9480543 ACA
65 ACA
* * * * *
9480546 ACCTTTCACAATGGTTTTTCATAGGCTCAACCAAAACCCAAAGTGGTTTTACAAAGGCTCAGCCA
1 ACCTTTCATAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTACAAAGGCTCAACCA
9480611 CA
66 CA
* *
9480613 ACC-TACAATAATGGTTTTTCACAAGATCAACCAAAACCCAA
1 ACCTTTC-ATAATGGTTTTTCACAGGATCAACCAAAACCCAA
9480654 CAACTAACTT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
66 2 0.02
67 91 0.97
68 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (67 bp):
ACCTTTCATAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTACAAAGGCTCAACCA
CA
Found at i:9483964 original size:17 final size:17
Alignment explanation
Indices: 9483942--9483974 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9483932 ACGCAGTTGC
*
9483942 ATAAAAAAATTAAAATA
1 ATAAAAAAATAAAAATA
9483959 ATAAAAAAATAAAAAT
1 ATAAAAAAATAAAAAT
9483975 CACGCCTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAAAAAATAAAAATA
Found at i:9484659 original size:20 final size:18
Alignment explanation
Indices: 9484605--9484659 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
9484595 TTATAATATT
9484605 ATTAATTAATTAATTTAA
1 ATTAATTAATTAATTTAA
*
9484623 ATGAATTATATTTAATTTCAA
1 ATTAATTA-A-TTAATTT-AA
*
9484644 ATTAACTAATTCAATT
1 ATTAATTAATT-AATT
9484660 CCATAGACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 12 0.40
21 8 0.27
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTAATTAATTAATTTAA
Found at i:9492952 original size:16 final size:15
Alignment explanation
Indices: 9492907--9492952 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9492897 TGCCTCAAAA
9492907 TCTAAAAACA-TGAAG
1 TCTAAAAACAGTG-AG
*
9492922 TTTAAAAAC-GTGAG
1 TCTAAAAACAGTGAG
9492936 TCTAAAACACAGTGAG
1 TCTAAAA-ACAGTGAG
9492952 T
1 T
9492953 GAACATAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (15 bp):
TCTAAAAACAGTGAG
Found at i:9493773 original size:37 final size:37
Alignment explanation
Indices: 9493726--9493844 Score: 170
Period size: 37 Copynumber: 3.2 Consensus size: 37
9493716 AATGCAATAT
9493726 CATCATCATGTGTGCACTCCCTACTCTCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCTCACACTTCAA
* * *
9493763 CATCATCATGTGTGCACTCCTTACTCGCATAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCTCACACTTC-AA
*
9493800 CATCATCGTGTGTGCACTCCCTACTCGT-ACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTC-TCACACTTCAA
9493837 CATCATCA
1 CATCATCA
9493845 CACAACATTA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 2 0.03
37 67 0.94
38 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.10, T:0.30
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCTCACACTTCAA
Found at i:9498269 original size:21 final size:20
Alignment explanation
Indices: 9498245--9498284 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9498235 AAAAACTCAT
*
9498245 AAATAATAAACAAATTAAAAG
1 AAATAACAAA-AAATTAAAAG
*
9498266 AAATAACATAAAATTAAAA
1 AAATAACAAAAAATTAAAA
9498285 TAACTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAACAAAAAATTAAAAG
Found at i:9498281 original size:20 final size:20
Alignment explanation
Indices: 9498256--9498303 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9498246 AATAATAAAC
9498256 AAATTAAAAGAAATAACATA
1 AAATTAAAAGAAATAACATA
* * *
9498276 AAATTAAAATAACTAACTTA
1 AAATTAAAAGAAATAACATA
*
9498296 AAAATAAA
1 AAATTAAA
9498304 CTAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATTAAAAGAAATAACATA
Found at i:9498329 original size:27 final size:30
Alignment explanation
Indices: 9498266--9498340 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
9498256 AAATTAAAAG
9498266 AAATAACATAAAATTA-AAATAACTAACTTAA
1 AAATAA-AT-AAATTATAAATAACTAACTTAA
9498297 AAATAAACT-AATTATAAA-AAC-AAC-TAA
1 AAATAAA-TAAATTATAAATAACTAACTTAA
9498324 AAATAAATAAATTATAA
1 AAATAAATAAATTATAA
9498341 TTAAAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
26 1 0.02
27 18 0.44
28 3 0.07
29 8 0.20
30 4 0.10
31 7 0.17
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (30 bp):
AAATAAATAAATTATAAATAACTAACTTAA
Found at i:9503125 original size:28 final size:27
Alignment explanation
Indices: 9503089--9503141 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
9503079 ATATCCTGGT
*
9503089 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
9503116 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
9503142 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:9503209 original size:20 final size:20
Alignment explanation
Indices: 9503186--9503231 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
9503176 CTTCTAAACC
9503186 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
9503206 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
9503226 TCAAAT
1 TCAAAT
9503232 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:9503697 original size:29 final size:28
Alignment explanation
Indices: 9503656--9503819 Score: 157
Period size: 29 Copynumber: 5.5 Consensus size: 28
9503646 CAGCTTTAAC
*
9503656 ATGTTTGTCTTAATTTAGACAAGGAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAT
*
9503684 ATGTTTGGTCTTAATTTAGATAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAT
*
9503713 ATGTTTGTCTGAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT
* * * *
9503743 ATTTTTTGTCTTAATCTAGACAAGAATAC
1 A-TGTTTGTCTTAATTTAGACAAGAAAAT
* *
9503772 ATATTTGTCTCAAATTTAGACAAGATCAAAT
1 ATGTTTGTCT-TAATTTAGACAAGA--AAAT
*
9503803 ATTTTTTTGTCTTAATT
1 A--TGTTTGTCTTAATT
9503820 ACGAACAAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
28 23 0.21
29 48 0.43
30 13 0.12
31 15 0.14
32 4 0.04
33 8 0.07
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAT
Found at i:9503768 original size:59 final size:58
Alignment explanation
Indices: 9503653--9503818 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 58
9503643 TGGCAGCTTT
* * * * * *
9503653 AACATGTTTGTCTTAATTTAGACAAG-GAAATATGTTTGGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTAAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
* *
9503710 AATATGTTTGTCTGAATTTAAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTAAATTT-AGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
* * *
9503769 TACATATTTGTCTCAAATTTAGACAAGATCAAATATTTTTTTGTCTTAAT
1 AACATGTTTGTCT-AAATTTAGACAAGA-AAAATA-TTTTTTGTCTTAAT
9503819 TACGAACAAG
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 17 0.18
58 7 0.08
59 44 0.48
60 10 0.11
61 14 0.15
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (58 bp):
AACATGTTTGTCTAAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
Found at i:9503992 original size:17 final size:17
Alignment explanation
Indices: 9503970--9504002 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9503960 ATAATAATAA
9503970 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
9503987 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
9504003 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:9507980 original size:2 final size:2
Alignment explanation
Indices: 9507975--9508022 Score: 53
Period size: 2 Copynumber: 23.5 Consensus size: 2
9507965 ATATCATGTT
* *
9507975 TA TA TA TA TA TA TA TA TA TA TA TA TG TA AA TA TA TGA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
9508017 TGA TA T
1 T-A TA T
9508023 GTATTGATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 1 0.03
2 34 0.87
3 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9513194 original size:14 final size:15
Alignment explanation
Indices: 9513170--9513198 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9513160 TTTTAGAGGA
9513170 ATATACAAGGAAATG
1 ATATACAAGGAAATG
9513185 ATAT-CAAGGAAATG
1 ATATACAAGGAAATG
9513199 TAATATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (15 bp):
ATATACAAGGAAATG
Found at i:9532795 original size:39 final size:39
Alignment explanation
Indices: 9532741--9532828 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
9532731 ATTGAATTTT
* * *
9532741 GCTACAGCGAAATTATGACCTAGAAACA-AAATGTTTCTC
1 GCTACAGCAAAATTATAACCCAGAAACAGAAA-GTTTCTC
9532780 GCTACAGCAAAATTATAACCCAGAAACAGAAAGTTTCTC
1 GCTACAGCAAAATTATAACCCAGAAACAGAAAGTTTCTC
*
9532819 GCTGCAGCAA
1 GCTACAGCAA
9532829 GAATGAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 41 0.93
40 3 0.07
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (39 bp):
GCTACAGCAAAATTATAACCCAGAAACAGAAAGTTTCTC
Found at i:9533233 original size:42 final size:42
Alignment explanation
Indices: 9533186--9533309 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
9533176 ATCTCATATA
*
9533186 CAATGGCTTATGCGCACTCCCACTCGCACATAGTCGGGTCAG
1 CAATGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCAG
*
9533228 CAATGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAG
1 CAATGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCAG
* **
9533270 CAACGGCTTATGTGCACTCTTACTCGCACATAGTCGGGTC
1 CAATGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTC
9533310 CACATCAACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.23
Consensus pattern (42 bp):
CAATGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCAG
Found at i:9534679 original size:18 final size:18
Alignment explanation
Indices: 9534642--9534680 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9534632 AAATTAGCAT
**
9534642 AAAATAAAATAATTTTAA
1 AAAATAAAATAATTAGAA
*
9534660 AAAATAAACTAATTAGAA
1 AAAATAAAATAATTAGAA
9534678 AAA
1 AAA
9534681 TAACTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAATAAAATAATTAGAA
Found at i:9539173 original size:54 final size:53
Alignment explanation
Indices: 9539043--9539194 Score: 245
Period size: 54 Copynumber: 2.9 Consensus size: 53
9539033 ATTCGTATAC
9539043 CACCCCATCTAACCCAGCTCATGTGCAT-CCCCCACATCGTGCACATAGCGGA
1 CACCCCATCTAACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCGGA
*
9539095 CACCCCATCTTAA-CCAGCTTATGTGCATCCCCCCACATCGTGCACATAGCCGGA
1 CACCCCATC-TAACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAG-CGGA
* *
9539149 CACCCCTTCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACA
1 CACCCCATCTAACCCAGCTCATGTGCATCCCCCCACATCGTGCACA
9539195 GTTAATGCCA
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
52 23 0.25
53 25 0.27
54 44 0.48
ACGTcount: A:0.23, C:0.44, G:0.14, T:0.19
Consensus pattern (53 bp):
CACCCCATCTAACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCGGA
Found at i:9539351 original size:2 final size:2
Alignment explanation
Indices: 9539344--9539375 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9539334 TATGACATAG
9539344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9539376 ACAACTATTA
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):
TA
Found at i:9543323 original size:43 final size:43
Alignment explanation
Indices: 9543259--9543373 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
9543249 GTAATTATAT
* *
9543259 TGACTCGGCTATGTGCAAGTAGGGAGTGCACATAAGCCGAGGA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGAGGA
* * *
9543302 TGACTCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGATGA
1 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGAGGA
* * * *
9543345 TGACCCAGCCACGTGCGAGTAGGGAGTGC
1 TGACTCGGCTATGTGCGAGTAGGGAGTGC
9543374 GCATGAGCTA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.19
Consensus pattern (43 bp):
TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAACCCGAGGA
Found at i:9543667 original size:21 final size:21
Alignment explanation
Indices: 9543612--9543667 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
9543602 TTTAGTGCCC
* *
9543612 TGTATTTCGCTGTAGCGAGAA
1 TGTATTTCGCTGCAACGAGAA
* **
9543633 T-CATTCTCATTGCAACGAGAA
1 TGTATT-TCGCTGCAACGAGAA
9543654 TGTATTTCGCTGCA
1 TGTATTTCGCTGCA
9543668 GTGAGATAGT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (21 bp):
TGTATTTCGCTGCAACGAGAA
Found at i:9545571 original size:66 final size:66
Alignment explanation
Indices: 9545484--9545632 Score: 244
Period size: 66 Copynumber: 2.3 Consensus size: 66
9545474 CTTTTATCAA
* * * *
9545484 GCTCAGCCACAACCTTTTACACTAGTTTTTCACGGGCTCAACTAAAATCCAAAGTGGTTTTCCAA
1 GCTCAACCATAACCTTTTACACTAGTTTTTCACGAGCTCAACTAAAACCCAAAGTGGTTTTCCAA
9545549 G
66 G
* *
9545550 GCTCAACCATAACCTTTTACACTAGTTTTTCACTAGCTCAACTAAAACCCGAAGTGGTTTTCCAA
1 GCTCAACCATAACCTTTTACACTAGTTTTTCACGAGCTCAACTAAAACCCAAAGTGGTTTTCCAA
9545615 G
66 G
9545616 GCTCAACCATAACCTTT
1 GCTCAACCATAACCTTT
9545633 AACTATCAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (66 bp):
GCTCAACCATAACCTTTTACACTAGTTTTTCACGAGCTCAACTAAAACCCAAAGTGGTTTTCCAA
G
Found at i:9545620 original size:31 final size:31
Alignment explanation
Indices: 9545518--9545622 Score: 77
Period size: 31 Copynumber: 3.3 Consensus size: 31
9545508 GTTTTTCACG
*
9545518 GGCTCAACTAAAATCCAAAGTGGTTTTCCAA
1 GGCTCAACTAAAACCCAAAGTGGTTTTCCAA
* * * * * * *
9545549 GGCTCAACCATAACCTTTTACACTAGTTTTTCACTA
1 GGCTCAACTAAAACC---CAAAGT-GGTTTTC-CAA
*
9545585 -GCTCAACTAAAACCCGAAGTGGTTTTCCAA
1 GGCTCAACTAAAACCCAAAGTGGTTTTCCAA
9545615 GGCTCAAC
1 GGCTCAAC
9545623 CATAACCTTT
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
30 2 0.04
31 25 0.48
32 2 0.04
34 3 0.06
35 18 0.35
36 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (31 bp):
GGCTCAACTAAAACCCAAAGTGGTTTTCCAA
Found at i:9547480 original size:42 final size:42
Alignment explanation
Indices: 9547414--9547530 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 42
9547404 GTTGATGTGG
* * * *
9547414 ACCCAGTTATGTGTGAGTAGGAGTGCACATAAGCCATTGCTA
1 ACCCAGCTATGTGCGAATCGGAGTGCACATAAGCCATTGCTA
* * * *
9547456 ACCCGGCTATGTGCGAATCGGAGTGCACATAAGCCGTTGTTG
1 ACCCAGCTATGTGCGAATCGGAGTGCACATAAGCCATTGCTA
* * *
9547498 ACCCAGCTATGTGCGAGTGGGAGTGCGCATAAG
1 ACCCAGCTATGTGCGAATCGGAGTGCACATAAG
9547531 TTGTTGCATA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (42 bp):
ACCCAGCTATGTGCGAATCGGAGTGCACATAAGCCATTGCTA
Found at i:9553667 original size:39 final size:39
Alignment explanation
Indices: 9553624--9553713 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
9553614 AGACCAAAAT
* **
9553624 AAAAAGTTTTTCGCTGTAGCGAAATTGTAACCCAGAAAC
1 AAAAAGTTTCTCGCTACAGCGAAATTGTAACCCAGAAAC
* * * *
9553663 AAAAAATTTCTCGCTACAGTGAAATTTTAACCTAGAAAC
1 AAAAAGTTTCTCGCTACAGCGAAATTGTAACCCAGAAAC
*
9553702 AGAAAGTTTCTC
1 AAAAAGTTTCTC
9553714 CCTGCAGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (39 bp):
AAAAAGTTTCTCGCTACAGCGAAATTGTAACCCAGAAAC
Found at i:9576584 original size:19 final size:19
Alignment explanation
Indices: 9576536--9576584 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
9576526 TGAGAGGGAA
9576536 GAAGAAGAAGAAGCTGTTG
1 GAAGAAGAAGAAGCTGTTG
*
9576555 G-AGAATGAAGAAGTTGTTG
1 GAAGAA-GAAGAAGCTGTTG
*
9576574 GAAGAAAAAGA
1 GAAGAAGAAGA
9576585 TATTTATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.35, T:0.16
Consensus pattern (19 bp):
GAAGAAGAAGAAGCTGTTG
Found at i:9578037 original size:2 final size:2
Alignment explanation
Indices: 9578030--9578084 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
9578020 CTTTATGCAA
9578030 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
9578072 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
9578085 TATATACACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9580225 original size:2 final size:2
Alignment explanation
Indices: 9580218--9580257 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
9580208 TAGACATTGT
*
9580218 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9580258 TTTATCCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9583782 original size:74 final size:75
Alignment explanation
Indices: 9583678--9583821 Score: 211
Period size: 74 Copynumber: 1.9 Consensus size: 75
9583668 TGAAATGGGG
* * *
9583678 TGAATAAAGCTGGAATTTGCATTGGAATTTGGTTTTTGAGCTTGTTAGT-TTTTTCTTTTTGTTG
1 TGAATAAAGCTGGAATTTGCATTGGAATTTGGTTGTTGAGCTTGCTAGTCTTTCT-TTTTTGTTG
9583742 ATATTTAGTGC
65 ATATTTAGTGC
* * *
9583753 TGAATAAAGTTGGACTTTG-ATTGGGATTTGGTTGTTGAGCTTGCTAGTCTTTCTTTTTTGTTGA
1 TGAATAAAGCTGGAATTTGCATTGGAATTTGGTTGTTGAGCTTGCTAGTCTTTCTTTTTTGTTGA
9583817 TATTT
66 TATTT
9583822 GTTGTTGGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
74 41 0.66
75 21 0.34
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.51
Consensus pattern (75 bp):
TGAATAAAGCTGGAATTTGCATTGGAATTTGGTTGTTGAGCTTGCTAGTCTTTCTTTTTTGTTGA
TATTTAGTGC
Found at i:9592765 original size:3 final size:3
Alignment explanation
Indices: 9592757--9592797 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9592747 ACCAAAGATA
9592757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9592798 AGAAGCATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9593623 original size:17 final size:16
Alignment explanation
Indices: 9593579--9593629 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
9593569 CTTAAAATTA
9593579 ATTTAAATTATTAAAAT
1 ATTTAAATTA-TAAAAT
*
9593596 -TTT-AATGATAATAAT
1 ATTTAAATTATAA-AAT
9593611 ATTTAAATTATAAAAT
1 ATTTAAATTATAAAAT
9593627 ATT
1 ATT
9593630 AATATTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 12 0.41
17 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTTAAATTATAAAAT
Found at i:9593682 original size:27 final size:26
Alignment explanation
Indices: 9593652--9593704 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
9593642 TGTTAATAAT
* *
9593652 TAAATTATCACTTACTAATATCTTAAA
1 TAAATTATAAATTACTAATAT-TTAAA
*
9593679 TAAATTATAAATTATTAATATTTAAA
1 TAAATTATAAATTACTAATATTTAAA
9593705 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATTATAAATTACTAATATTTAAA
Found at i:9593866 original size:26 final size:26
Alignment explanation
Indices: 9593837--9593886 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
9593827 TATCATAAAT
*
9593837 ATTAAATTATAAATAAAATATTAATG
1 ATTAAATTAAAAATAAAATATTAATG
9593863 ATTAAATTAAAAATAAAATATTAA
1 ATTAAATTAAAAATAAAATATTAA
9593887 AACTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
ATTAAATTAAAAATAAAATATTAATG
Found at i:9593868 original size:19 final size:20
Alignment explanation
Indices: 9593833--9593874 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
9593823 TAATTATCAT
*
9593833 AAATATTAAATTATAAA-TA
1 AAATATTAAATGATAAATTA
9593852 AAATATT-AATGATTAAATTA
1 AAATATTAAATGA-TAAATTA
9593872 AAA
1 AAA
9593875 ATAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATATTAAATGATAAATTA
Found at i:9593966 original size:12 final size:12
Alignment explanation
Indices: 9593949--9593975 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9593939 ATAGCAGATA
9593949 AATGGAGAAAGG
1 AATGGAGAAAGG
9593961 AATGGAGAAAGG
1 AATGGAGAAAGG
9593973 AAT
1 AAT
9593976 ACAGGAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.37, T:0.11
Consensus pattern (12 bp):
AATGGAGAAAGG
Found at i:9597717 original size:841 final size:839
Alignment explanation
Indices: 9596094--9597754 Score: 2052
Period size: 840 Copynumber: 2.0 Consensus size: 839
9596084 TCATTCCTTC
** *
9596094 ATCATATATCTCAGAGATGATAAGAGCTTGGTGTAGTGCGTACTTTTATTGAACTCCATATTTGT
1 ATCATATATCTCAGAGACCATAAGAGCTTGGTGTAGTGCGTACTCTTATTGAACTCCATATTTGT
* * * * * *
9596159 TCCTGCAGTTATATCATTAGCTTTATTGAGACTTATGAAACTCATTTCATATTTCCTAATCACTT
66 TCCTGCAGTTAGATCATTAGCTTTATAGAGACTTATAAAACTCATTTCAAATCTCCTAATCACCT
* * * * *
9596224 TGGCCATGGACTTGATTATGCTAATGCCAACCAAGAACTAATGAGATATTTACCCTTGAATCACT
131 TGGCCAAGGACTTGATTAAGCTAATACCAACCAAGAACAAATAAGATATTTACCCTTGAATCACT
* * * * *
9596289 AGGGGAGATTATTATTATCTTGACCACCCATTTGCCTTTATATGCTTCATACTGTACATAAAAAC
196 AGGGGAGATGATTACTATCTTGACCACCCATTTGCCTTCATATGCTTCATACTATACACAAAAAC
* * * * ** *
9596354 ATCATGTTTTGGCATCCTTGGTTAGGCATCCGTAGGGATGAAATCAAAGCGTAGTTCTCCATATA
261 ATCATATTTTGGCATCCTTGGTTAAGCATCCATAGGGATGAAATCAAAGCATAGCACTCCACATA
* * * * *
9596419 TAAGACAACTTGGAGTCTCAAGTCTAGGAAGTAGTTACACAACTGACACATGAGAAGTATTACAT
326 TAAAACAACATGGAGTCTCAAGTCAAGGAAGTAGTTACACAACTGACACATGAAAAGCATTACAT
* ** * *
9596484 AGACACTTGAGTGGTACCAAATGCAATTCTCATGGCGGGTCATGTTCAGTGAACTCGCTCTCCCA
391 AGACACTAGAGTGACACCAAACGCAATTCTCATGGCGGGTCATGTTCAATGAACTCGCTCTCCCA
* *
9596549 TAGTAAGCACCCACATGCTAGTTCCAAGTATCTTTATACTGCAACCTATGATAGCAGTTGCTTAC
456 TAGCAAGCACCCACATGCTAGTTCCAAGTATCTTTATACTGCAACCTATGAGAGCAGTTGCTTAC
* * * * **
9596614 TTCACAAGTAAGGAACATAACTTGTGCCAATTTTTTGAACATTATTGATGCTTTGTCTCAATAAT
521 TTCACAAGTAAAGAACATAACATGTGCCAA-TTCTTCAACATTATTGATGCCCTGTCTCAATAAT
* * * * * * *
9596679 ACAATGATTAGGAACTCTTAGGAACAATGTTTTGATGCATAAGGATCTCATAATTGTATCTCAAT
585 ACAATGATAAGGAACTCTTAGAAACAATGCTATAATGCATAAGAATCTCATAATTGTATCCCAAT
* * * *
9596744 ACAATTCCTTTGTAAAGCATATATAGTTTCATGGGCTTTATCCATATAAGTACAAAAAGTAATTA
650 ACAATTCCTTTGCAAAGCATATATAGTTCCATGGGCTTTATCCACATAAGGACAAAAAGTAATTA
* * * *
9596809 AATTACAAACTTATGGATAAAGAACTACCTCATAATTATTATAAATTAATAAAATGTCATACATG
715 AATCACAAACTTATGAATAAAGAACTACCTCATAATTATTACAAATTAACAAAATGTCATACATG
* * *
9596874 AATACCT-TAAAATGTAATTCCCATACGACTAGAGATTGGTTTGCAAGCTCATACTAAAA
780 AATACCTCAAAAATGCAATTCCCATACAACTAGAGATTGGTTTGCAAGCTCATACTAAAA
* *
9596933 ATCATATATCTC-GAAGACCATAAGTGCTTGGTGTAGTGTC-TACTCTTATTGACCTCCATATTT
1 ATCATATATCTCAG-AGACCATAAGAGCTTGGTGTAGTG-CGTACTCTTATTGAACTCCATATTT
*
9596996 GTTCCTGCAGTTAGATTATTAGCTTTATAGAGACTTATAAAACTCATTTCAAAATCTCCTAATCA
64 GTTCCTGCAGTTAGATCATTAGCTTTATAGAGACTTATAAAACTCATTTC-AAATCTCCTAATCA
* * * * *
9597061 CCTTGGTCAAGGATTTGATTAAGCTAATATCAACCATGAACAAATAAGATATTTCCCCTTGAATC
128 CCTTGGCCAAGGACTTGATTAAGCTAATACCAACCAAGAACAAATAAGATATTTACCCTTGAATC
* * * * * *
9597126 ACTTA-GGGTGATGATTCCTATCTTGAGCACTCATTTGCCTTCATATGCTTCATATTATACGCAA
193 AC-TAGGGGAGATGATTACTATCTTGACCACCCATTTGCCTTCATATGCTTCATACTATACACAA
* * * **
9597190 AATCATCCTATTTTGGCATCTTTGGTTAAGCATCCATAGGGATGAAATCAAAGCATAGCACTGTA
257 AAACATCATATTTTGGCATCCTTGGTTAAGCATCCATAGGGATGAAATCAAAGCATAGCACTCCA
* * * *
9597255 CATATAAAACAACATGGTGTCTTAAGTCCAAGG-AGTAGTTACACAATTGACATATGAAAAGCAT
322 CATATAAAACAACATGGAGTCTCAAGT-CAAGGAAGTAGTTACACAACTGACACATGAAAAGCAT
* * * *
9597319 TGCATAGACACTAGAGTGAAACACCAAACGCACTTTTCATGTCGGGTCATGTTCAATGAACTTC-
386 TACATAGACACTAGAGTG--ACACCAAACGCAATTCTCATGGCGGGTCATGTTCAATGAAC-TCG
* * * * * *
9597383 CTCAT-CCATGGCAAGCGCCCACATGTTATTTCCAAGTATCTTTATACTTCAACCTATGAGAGCG
448 CTC-TCCCATAGCAAGCACCCACATGCTAGTTCCAAGTATCTTTATACTGCAACCTATGAGAGCA
* * * *
9597447 GTTGCTTATTTCACAAGTAAAGAACATAGCATGTGTCGA-TCTTCAAGCATTATTGATGCCCTGT
512 GTTGCTTACTTCACAAGTAAAGAACATAACATGTGCCAATTCTTCAA-CATTATTGATGCCCTGT
*
9597511 CTCAATAATACAATGATCAAGG-ACTTTTCA-AAACAATGCTATAATGCATAAGAATCTCATAAT
576 CTCAATAATACAATGAT-AAGGAACTCTT-AGAAACAATGCTATAATGCATAAGAATCTCATAAT
* * * *
9597574 TGTATCCCAATAGAATTCCTTTGCAAGGCATATATAGTTCCATGGGCTTTATCTACATAAGGATA
639 TGTATCCCAATACAATTCCTTTGCAAAGCATATATAGTTCCATGGGCTTTATCCACATAAGGACA
* * * * *
9597639 AATAA-TACTTAAATCACGAACTTATGAATAAAGAACTATCTCA-ATGTTATTACGAA-TAACCA
704 AA-AAGTAATTAAATCACAAACTTATGAATAAAGAACTACCTCATA-ATTATTACAAATTAA-CA
* * * * * *
9597701 AAATGTGATGCATGAATATCTCAAAAATGCAATTCTCATGCAACTATAGATTGG
766 AAATGTCATACATGAATACCTCAAAAATGCAATTCCCATACAACTAGAGATTGG
9597755 CTTGTAGGGT
Statistics
Matches: 691, Mismatches: 115, Indels: 29
0.83 0.14 0.03
Matches are distributed among these distances:
838 1 0.00
839 100 0.14
840 245 0.35
841 189 0.27
842 153 0.22
843 3 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (839 bp):
ATCATATATCTCAGAGACCATAAGAGCTTGGTGTAGTGCGTACTCTTATTGAACTCCATATTTGT
TCCTGCAGTTAGATCATTAGCTTTATAGAGACTTATAAAACTCATTTCAAATCTCCTAATCACCT
TGGCCAAGGACTTGATTAAGCTAATACCAACCAAGAACAAATAAGATATTTACCCTTGAATCACT
AGGGGAGATGATTACTATCTTGACCACCCATTTGCCTTCATATGCTTCATACTATACACAAAAAC
ATCATATTTTGGCATCCTTGGTTAAGCATCCATAGGGATGAAATCAAAGCATAGCACTCCACATA
TAAAACAACATGGAGTCTCAAGTCAAGGAAGTAGTTACACAACTGACACATGAAAAGCATTACAT
AGACACTAGAGTGACACCAAACGCAATTCTCATGGCGGGTCATGTTCAATGAACTCGCTCTCCCA
TAGCAAGCACCCACATGCTAGTTCCAAGTATCTTTATACTGCAACCTATGAGAGCAGTTGCTTAC
TTCACAAGTAAAGAACATAACATGTGCCAATTCTTCAACATTATTGATGCCCTGTCTCAATAATA
CAATGATAAGGAACTCTTAGAAACAATGCTATAATGCATAAGAATCTCATAATTGTATCCCAATA
CAATTCCTTTGCAAAGCATATATAGTTCCATGGGCTTTATCCACATAAGGACAAAAAGTAATTAA
ATCACAAACTTATGAATAAAGAACTACCTCATAATTATTACAAATTAACAAAATGTCATACATGA
ATACCTCAAAAATGCAATTCCCATACAACTAGAGATTGGTTTGCAAGCTCATACTAAAA
Found at i:9605280 original size:5 final size:5
Alignment explanation
Indices: 9605266--9605298 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
9605256 GCAACAGTCC
9605266 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AA
9605299 TTCTATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:9612067 original size:2 final size:2
Alignment explanation
Indices: 9612060--9612098 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9612050 CCAGCATAAA
9612060 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 A
9612099 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9612355 original size:8 final size:8
Alignment explanation
Indices: 9612342--9612370 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9612332 AATTAGCTCT
9612342 TTTTATTA
1 TTTTATTA
9612350 TTTTATTA
1 TTTTATTA
9612358 TTTTATT-
1 TTTTATTA
9612365 TTTTAT
1 TTTTAT
9612371 GTGAGGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTA
Found at i:9616274 original size:23 final size:23
Alignment explanation
Indices: 9616245--9616293 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
9616235 ATATATATCA
* *
9616245 ATCATCATGTACACCATCCCGTC
1 ATCATCATGCACACCATCCCATC
*
9616268 ATCATCATGCACATCATCCCATC
1 ATCATCATGCACACCATCCCATC
9616291 ATC
1 ATC
9616294 CCTCAACTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.39, G:0.06, T:0.27
Consensus pattern (23 bp):
ATCATCATGCACACCATCCCATC
Found at i:9616378 original size:43 final size:43
Alignment explanation
Indices: 9616303--9616405 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
9616293 CCCTCAACTC
** **
9616303 ATGCGCACTCCCTACTCGCACATGGCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGACTT
* * *
9616346 ATGCGCACTCTCTACTCGCACATAAAC-GGGTCATCATCGACTT
1 ATGCGCACTCCCTACTCGCACAT-AACTAGGTCATCACCGACTT
9616389 ATGCGCACTCCCTACTC
1 ATGCGCACTCCCTACTC
9616406 ACATATAGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGACTT
Found at i:9619254 original size:18 final size:18
Alignment explanation
Indices: 9619227--9619262 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9619217 ATATAGTTAC
* *
9619227 TACTATTATTATTGCTAG
1 TACTACTATTATTACTAG
9619245 TACTACTATTATTACTAG
1 TACTACTATTATTACTAG
9619263 AGATAAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (18 bp):
TACTACTATTATTACTAG
Found at i:9625852 original size:25 final size:25
Alignment explanation
Indices: 9625807--9625866 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
9625797 GTGGTCACAA
***
9625807 CCACATATATCAACTTGTGGCC-TAG
1 CCACATATATCAACCCATGGCCAT-G
9625832 CCACATATATCAACCCATGGCCATG
1 CCACATATATCAACCCATGGCCATG
*
9625857 CCACGTATAT
1 CCACATATAT
9625867 ATCACAGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 29 0.97
26 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.13, T:0.25
Consensus pattern (25 bp):
CCACATATATCAACCCATGGCCATG
Found at i:9628323 original size:19 final size:19
Alignment explanation
Indices: 9628299--9628337 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9628289 ATTATTTTAA
9628299 TATTATTTTATCTA-AAAAT
1 TATTATTTTAT-TACAAAAT
9628318 TATTATTTTATTACAAAAT
1 TATTATTTTATTACAAAAT
9628337 T
1 T
9628338 TTTCTCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATTTTATTACAAAAT
Found at i:9628882 original size:75 final size:74
Alignment explanation
Indices: 9628710--9628905 Score: 259
Period size: 75 Copynumber: 2.6 Consensus size: 74
9628700 TAAATTTTTA
* *
9628710 GACAGCGTGCTCTTAGTTGACTAACCATGCTTCTTAGTCGGTTAAGTTTTCTCTATCTTGAAATT
1 GACAGTGTGCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTTTCTCTATCTTGAAATT
9628775 GAATTCTCT
66 GAATTCTCT
* * * * * *
9628784 GGCAGTGAGCTCTTAGTTGACTAACCATGTTTTTTAGTTGATTAAGTTTCTCTCTATCTTGTAAT
1 GACAGTGTGCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTT-TCTCTATCTTGAAAT
9628849 TGAGATT-TCT
65 TGA-ATTCTCT
* * * *
9628859 GATAGTGTGCTCTTAGTTGACTAATCATGCTTCTTGGTCGACTAAGT
1 GACAGTGTGCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGT
9628906 CCTCTCTGTC
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
74 42 0.41
75 58 0.56
76 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (74 bp):
GACAGTGTGCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTTTCTCTATCTTGAAATT
GAATTCTCT
Found at i:9630034 original size:21 final size:21
Alignment explanation
Indices: 9630005--9630093 Score: 110
Period size: 21 Copynumber: 4.2 Consensus size: 21
9629995 CTAATTTTGA
*
9630005 ATGATGGCATCAGT-TCTTGTC
1 ATGAAGGCATCAGTCT-TTGTC
*
9630026 ATGAAGGCATCCA-ACTTTGTC
1 ATGAAGGCAT-CAGTCTTTGTC
* *
9630047 ATGCAGGCATTAGTCTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
9630068 ATGAAGGCATCAGTCTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
9630089 ATGAA
1 ATGAA
9630094 TTGCATGAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 54 0.93
22 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
ATGAAGGCATCAGTCTTTGTC
Found at i:9632090 original size:22 final size:23
Alignment explanation
Indices: 9632065--9632111 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
9632055 ATTTCTATGC
9632065 ATTACTA-CAAGAATTAAG-CCAA
1 ATTACTATCAA-AATTAAGCCCAA
*
9632087 ATTATTATCAAAATTAAGCCCAA
1 ATTACTATCAAAATTAAGCCCAA
9632110 AT
1 AT
9632112 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAATTAAGCCCAA
Found at i:9634202 original size:35 final size:36
Alignment explanation
Indices: 9634124--9634250 Score: 161
Period size: 36 Copynumber: 3.5 Consensus size: 36
9634114 TCTCACCAAC
9634124 TCATGTGCACTCCCACACCGCACATA-GCTAGA-ATCA
1 TCATGTGCACTCCCACACCGCACA-AGGCTA-ATATCA
9634160 TCATGTGCACTCCCACACCGCACAAGGC-AATATCA
1 TCATGTGCACTCCCACACCGCACAAGGCTAATATCA
* *
9634195 TCATGTGCACTCCCACACCGCACATGGCTTATATCA
1 TCATGTGCACTCCCACACCGCACAAGGCTAATATCA
*
9634231 TTAGTGTGTACACTCCCACA
1 TCA-TGTG--CACTCCCACA
9634251 GCACACCACT
Statistics
Matches: 82, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
34 1 0.01
35 33 0.40
36 34 0.41
37 4 0.05
39 10 0.12
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.22
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACAAGGCTAATATCA
Found at i:9636388 original size:48 final size:48
Alignment explanation
Indices: 9636317--9636412 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
9636307 TTGGGTAGTG
*
9636317 AATTAAGCTAGCTTTTTACTTTATCCCTTAGAGAAAATGGAAACAATC
1 AATTAAGCTAGCTCTTTACTTTATCCCTTAGAGAAAATGGAAACAATC
*
9636365 AATTAAGCTAGCTCTTTGCTTTATCCCTTAGAGAAAATGGAAACAATC
1 AATTAAGCTAGCTCTTTACTTTATCCCTTAGAGAAAATGGAAACAATC
9636413 TCAATTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (48 bp):
AATTAAGCTAGCTCTTTACTTTATCCCTTAGAGAAAATGGAAACAATC
Found at i:9640978 original size:2 final size:2
Alignment explanation
Indices: 9640971--9640995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9640961 ATTATGTTGG
9640971 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 T
9640996 GAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9641072 original size:37 final size:38
Alignment explanation
Indices: 9641030--9641112 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
9641020 TAATGTTGTG
*
9641030 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACAC-A
1 TGATGATGTTGAAGTGTGCGAGTACGGAGTGCACACAA
* *
9641067 TGATGATATTGAAGTGTGCGAGTACGGAGTGCGCACAA
1 TGATGATGTTGAAGTGTGCGAGTACGGAGTGCACACAA
9641105 TGATGATG
1 TGATGATG
9641113 ATATTGCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 33 0.80
38 8 0.20
ACGTcount: A:0.28, C:0.11, G:0.36, T:0.25
Consensus pattern (38 bp):
TGATGATGTTGAAGTGTGCGAGTACGGAGTGCACACAA
Found at i:9650133 original size:43 final size:43
Alignment explanation
Indices: 9650045--9650154 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
9650035 TCACCAGCTC
** * * **
9650045 ATGCGCACTCCCTACTCGCACATGGCTGGGTTATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCACCGACTT
*
9650088 ATGCACACTCCCTACTCGCACATAACCGGGTCATC-CTCGACTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCAC-CGACTT
* *
9650131 ATGCGTATTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
9650155 GCCAAGTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCACCGACTT
Found at i:9659988 original size:73 final size:72
Alignment explanation
Indices: 9659884--9660046 Score: 163
Period size: 73 Copynumber: 2.2 Consensus size: 72
9659874 ACCAAAAACT
*
9659884 AAGTTAGTCGACTAAGAGCCTACTACTAGAAATCT-GGACTTC-AAGACAGAAACAACTTAATCG
1 AAGTTAGTCGACTAAGAGCCTACTACAAGAAA-CTGGGA--TCAAAGACAGAAACAACTTAATCG
9659947 ACTAAGAAG-G
63 ACTAAG-AGCG
* * * ** *
9659957 AAGTTAGTCGACTAAGTG-TTCACTGCAAGAAACTGGGATCAAAAGACAGAAATGACTTAGTCGA
1 AAGTTAGTCGACTAAGAGCCT-ACTACAAGAAACTGGGATC-AAAGACAGAAACAACTTAATCGA
9660021 CTAAGAGCG
64 CTAAGAGCG
* *
9660030 CAGTTAGTCAACTAAGA
1 AAGTTAGTCGACTAAGA
9660047 TCATTCTACC
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
71 2 0.03
72 5 0.07
73 68 0.91
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (72 bp):
AAGTTAGTCGACTAAGAGCCTACTACAAGAAACTGGGATCAAAGACAGAAACAACTTAATCGACT
AAGAGCG
Found at i:9664136 original size:2 final size:2
Alignment explanation
Indices: 9664129--9664154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9664119 GTGTATGTAC
9664129 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
9664155 GGAGATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9665882 original size:17 final size:19
Alignment explanation
Indices: 9665841--9665882 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
9665831 ATATATATAT
9665841 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
9665862 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
9665879 ATGA
1 ATGA
9665883 TGTTGGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:9670707 original size:52 final size:52
Alignment explanation
Indices: 9670651--9670768 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
9670641 GTAGGAATTT
9670651 TATCGATACATTTGGAAATTTGATGAACATATATAGATACATTACCCCAATA
1 TATCGATACATTTGGAAATTTGATGAACATATATAGATACATTACCCCAATA
9670703 TATCGATACATTTGGAAATTTGATGAACATATATAGATACATTACCCCAATA
1 TATCGATACATTTGGAAATTTGATGAACATATATAGATACATTACCCCAATA
9670755 TATCGATACATTTG
1 TATCGATACATTTG
9670769 AAGCAAAAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (52 bp):
TATCGATACATTTGGAAATTTGATGAACATATATAGATACATTACCCCAATA
Found at i:9676480 original size:15 final size:16
Alignment explanation
Indices: 9676460--9676494 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
9676450 TGTTTATTAG
9676460 TTTAGTTTAA-GTTAT
1 TTTAGTTTAATGTTAT
*
9676475 TTTAGTTTAATTTTAT
1 TTTAGTTTAATGTTAT
9676491 TTTA
1 TTTA
9676495 TTTGACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (16 bp):
TTTAGTTTAATGTTAT
Found at i:9678320 original size:43 final size:43
Alignment explanation
Indices: 9678272--9678437 Score: 190
Period size: 43 Copynumber: 3.9 Consensus size: 43
9678262 TTGTGTGATA
** * *
9678272 ATGATGACCTAGCTATGTGCGATGT-GGGAGTGCACATGAGCTG
1 ATGATGACCCGGCTATGTGCGA-GTAGGGAGTGCACATAAGCCG
* * *
9678315 ATGATGACCCGGCTATGTACGAGTAGGAAGTGCGCATAAGCCG
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCG
* * * * *
9678358 ATGATGACTCGGCTATCTGCAAGTAAGGAGTGCGCATAAGCCG
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCG
* *
9678401 ATGATGACCCGGTTATGTGCGGGTAGGGAGTGCACAT
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACAT
9678438 GACGGTGAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 2 0.02
43 100 0.98
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (43 bp):
ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCG
Found at i:9705323 original size:43 final size:43
Alignment explanation
Indices: 9705275--9705438 Score: 235
Period size: 43 Copynumber: 3.9 Consensus size: 43
9705265 ACCATCCCAC
9705275 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGT
9705318 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGT
** * *
9705361 CATCATCAGCTCATGTGCACTCTCTGA--CGCACATAGCTAGGT
1 CATCATCAGCTCATGTGCACT-TCCCACTCGCACATAGTTGGGT
* * *
9705403 CATTATCAACTCATGTGCAC-TCCCACACGCACATAG
1 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAG
9705439 CCGAGTCATC
Statistics
Matches: 110, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
40 3 0.03
42 40 0.36
43 64 0.58
44 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (43 bp):
CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGT
Found at i:9705416 original size:85 final size:84
Alignment explanation
Indices: 9705275--9705438 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 84
9705265 ACCATCCCAC
* * *
9705275 CATCATCAGCTCATGTGCACTTCCCACTCGCACATAGTTGGGTCATCATCAGCTCATGTGCACTT
1 CATCATCAGCTCATGTGCACTTCCCAC-CGCACATAGCTAGGTCATCATCAACTCATGTGCAC-T
*
9705340 CCCACTCGCACATAGTTGGGT
64 CCCACACGCACATAGTTGGGT
** *
9705361 CATCATCAGCTCATGTGCACTCTCTGA-CGCACATAGCTAGGTCATTATCAACTCATGTGCACTC
1 CATCATCAGCTCATGTGCACT-TCCCACCGCACATAGCTAGGTCATCATCAACTCATGTGCACTC
9705425 CCACACGCACATAG
65 CCACACGCACATAG
9705439 CCGAGTCATC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 15 0.21
85 31 0.44
86 21 0.30
87 3 0.04
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (84 bp):
CATCATCAGCTCATGTGCACTTCCCACCGCACATAGCTAGGTCATCATCAACTCATGTGCACTCC
CACACGCACATAGTTGGGT
Found at i:9707945 original size:61 final size:61
Alignment explanation
Indices: 9707661--9707946 Score: 383
Period size: 61 Copynumber: 4.7 Consensus size: 61
9707651 CAGCTCATGT
* * * *
9707661 GCATCATTACCGGCATGTGCACTGCCCACTTCGCACATTCACGATTGTAAATATCACAATA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGATTGTAAATATCACGACA
* ** * * * * *
9707722 GCATCATTATCGATATGTGCACTACCCACTCTGCACATGCACGGTTGTGAATATCACGATA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGATTGTAAATATCACGACA
* *
9707783 GCATCATTACCGGCATGTGCACTGCACACTCTGCACATGCACGATTGTAAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGATTGTAAATATCACGACA
** * * *
9707844 GCATCATTACTAGCATGTGCACTGCCCATTCCGCACATGCATGGTTGTAAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGATTGTAAATATCACGACA
* *
9707905 GCATCATTACCGGCATGTGCACTGCCCACTCCGTAGATGCAC
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCAC
9707947 AGTTACATCA
Statistics
Matches: 194, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 194 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (61 bp):
GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGATTGTAAATATCACGACA
Found at i:9714989 original size:61 final size:61
Alignment explanation
Indices: 9714893--9715115 Score: 338
Period size: 61 Copynumber: 3.7 Consensus size: 61
9714883 CAGCTCATGT
*
9714893 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTTGTAAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCATGGTTGTAAATATCACGACA
* * * * * *
9714954 ACATCATTATCGGCATGTGCACTGCCCACTCCGCACATCCATGGTTGTGAATATCATGATA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCATGGTTGTAAATATCACGACA
*
9715015 GCATCATTACCGGCATGTGCACTGCACACTCCGCACATGCATGGTTGTAAATATCACGACA
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCATGGTTGTAAATATCACGACA
* * * *
9715076 GCATCATTACCGGCATGCGCACGGTCCACTCCGCAGATGC
1 GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGC
9715116 CATTCTATAT
Statistics
Matches: 143, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 143 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (61 bp):
GCATCATTACCGGCATGTGCACTGCCCACTCCGCACATGCATGGTTGTAAATATCACGACA
Found at i:9718785 original size:42 final size:42
Alignment explanation
Indices: 9718699--9718830 Score: 203
Period size: 42 Copynumber: 3.1 Consensus size: 42
9718689 CCATCCCACA
* *
9718699 ATCATCAGCTCATGCGCACTTCCCACTCGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCAC-TCCCACACGCACATAGCTGGGTC
*
9718742 ATCATCAGCTCATGTGCACT-CCACACCGCACACAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACA-CGCACATAGCTGGGTC
*
9718784 ATCATCAACTCATGTGCACTCCCACACGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGTC
9718826 ATCAT
1 ATCAT
9718831 TATCTCATAA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
41 4 0.05
42 55 0.67
43 23 0.28
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
ATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGTC
Found at i:9720509 original size:20 final size:20
Alignment explanation
Indices: 9720471--9720509 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9720461 AAATCTGATT
* * *
9720471 TTTTCTCATTTTTCTCCCAA
1 TTTTCTCATTCTCCACCCAA
9720491 TTTTCTCATTCTCCACCCA
1 TTTTCTCATTCTCCACCCA
9720510 TTTGCTCTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.36, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTCTCATTCTCCACCCAA
Found at i:9720886 original size:49 final size:49
Alignment explanation
Indices: 9720813--9720912 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
9720803 TTTTTGAATT
*
9720813 GACTGGATATTTATGGTAAGCAATAGCACAACCTAACTTGTAAGATATG
1 GACTGGATATTTATGGTAAACAATAGCACAACCTAACTTGTAAGATATG
9720862 GACTGGATATTTATGGTAAACAATAGCACAACCTAACTTGTAAGATATG
1 GACTGGATATTTATGGTAAACAATAGCACAACCTAACTTGTAAGATATG
9720911 GA
1 GA
9720913 TTAGCCCATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (49 bp):
GACTGGATATTTATGGTAAACAATAGCACAACCTAACTTGTAAGATATG
Found at i:9725350 original size:56 final size:55
Alignment explanation
Indices: 9725211--9725378 Score: 187
Period size: 55 Copynumber: 3.0 Consensus size: 55
9725201 TAGTACTAAC
* * * * *
9725211 GGTGGTGATTCCAGCTATGTGTGATGTGGGGGGACACATAAGCTGATGACCGGTG
1 GGTGATGATTCCAACTATGTGCGATGTGGGGGGACACATAGGCTGAGGACCGGTG
* * *
9725266 GGTGATGATTCCAAC-AGTGTGCGATGTGGGAGGACACATGGGCTGAGGACTGGT-
1 GGTGATGATTCCAACTA-TGTGCGATGTGGGGGGACACATAGGCTGAGGACCGGTG
* * * *
9725320 GGTGGTCTATATCCAACTATGTGCGATGTGGGGGGACACATAGGTTGAGGACCGTTG
1 GGTGAT-GAT-TCCAACTATGTGCGATGTGGGGGGACACATAGGCTGAGGACCGGTG
9725377 GG
1 GG
9725379 CTTATACATG
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
54 6 0.06
55 46 0.49
56 38 0.41
57 3 0.03
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.24
Consensus pattern (55 bp):
GGTGATGATTCCAACTATGTGCGATGTGGGGGGACACATAGGCTGAGGACCGGTG
Found at i:9731738 original size:68 final size:69
Alignment explanation
Indices: 9731621--9731805 Score: 198
Period size: 68 Copynumber: 2.7 Consensus size: 69
9731611 ATATTGAATA
* * * * * * *
9731621 GCCATGATGCTAGGTGTATGATGCAAATTCCATATACCATATGAGATGATTCAGCA-TGCATGAT
1 GCCATGATGCTATGTATATGATGTAGATTCCATATACCACATGAGATGATTCAACAGTACATGAT
9731685 AAAT
66 AAAT
* * *
9731689 GCCATGATGTTATGTATATGATGTAGATTCCATATACCACAT-AGAATGA-TGAATAGTACATGA
1 GCCATGATGCTATGTATATGATGTAGATTCCATATACCACATGAG-ATGATTCAACAGTACATGA
9731752 TAAAT
65 TAAAT
** * * *
9731757 GGTATGATGCTAT-TATGTGAGGTAGATTCCATATAACACATGAGATGAT
1 GCCATGATGCTATGTATATGATGTAGATTCCATATACCACATGAGATGAT
9731806 AAAGAGTACT
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
67 34 0.35
68 63 0.65
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (69 bp):
GCCATGATGCTATGTATATGATGTAGATTCCATATACCACATGAGATGATTCAACAGTACATGAT
AAAT
Found at i:9731835 original size:67 final size:68
Alignment explanation
Indices: 9731679--9731814 Score: 177
Period size: 67 Copynumber: 2.0 Consensus size: 68
9731669 ATTCAGCATG
** * * * * *
9731679 CATGATAAATGCCATGATGTTATGTATATGATGTAGATTCCATATACCACATAGAATGATGAATA
1 CATGATAAATGGTATGATGCTATGTATATGAGGTAGATTCCATATAACACATAGAATGATAAAGA
9731744 GTA
66 GTA
*
9731747 CATGATAAATGGTATGATGCTAT-TATGTGAGGTAGATTCCATATAACACAT-GAGATGATAAAG
1 CATGATAAATGGTATGATGCTATGTATATGAGGTAGATTCCATATAACACATAGA-ATGATAAAG
9731810 AGTA
65 AGTA
9731814 C
1 C
9731815 TTATTGAAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
66 2 0.03
67 37 0.63
68 20 0.34
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (68 bp):
CATGATAAATGGTATGATGCTATGTATATGAGGTAGATTCCATATAACACATAGAATGATAAAGA
GTA
Found at i:9733557 original size:43 final size:43
Alignment explanation
Indices: 9733457--9733575 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 43
9733447 GTAATGACAT
* * * *
9733457 TGACTAGACTATGTACGAGTAGGGAGTGTGCATAAGCCGAGGA
1 TGACCAGACCATGTGCGAGTAGGGAGTGTGCATAACCCGAGGA
***
9733500 TGACCAGGTTATGTGCGAGTAGGGAGTGTGCATAACCCG-GTGA
1 TGACCAGACCATGTGCGAGTAGGGAGTGTGCATAACCCGAG-GA
* * *
9733543 TGACTCA-ACCATGTGTGAGTATGGAGTGCGCAT
1 TGAC-CAGACCATGTGCGAGTAGGGAGTGTGCAT
9733576 GAGCTGGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 60 0.95
44 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (43 bp):
TGACCAGACCATGTGCGAGTAGGGAGTGTGCATAACCCGAGGA
Found at i:9741285 original size:68 final size:68
Alignment explanation
Indices: 9741198--9741361 Score: 186
Period size: 75 Copynumber: 2.3 Consensus size: 68
9741188 ATCCCTTTTA
*
9741198 AAGTAGGAAACAATTTCCTATGAATAAC-CCAAATTAAAATGCAAACCATAATTTTAAGAATTCA
1 AAGTAGGAAACAATTTCCTATGAATAACTCAAAATT-AAATGCAAACCATAATTTTAAGAATTCA
9741262 CTTT
65 CTTT
* * * *
9741266 AAGTAGGAAACAATTTCCTATTCTTTATGAATCACTTAAAATTAAATGCTAACCATAATTTTAGG
1 AAGTAGGAAACAATTT-C----C--TATGAATAACTCAAAATTAAATGCAAACCATAATTTTAAG
9741331 AATTCACTTT
59 AATTCACTTT
* *
9741341 AAGCAGGAACCAATTTCCTAT
1 AAGTAGGAAACAATTTCCTAT
9741362 TCTTTATGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
68 19 0.23
69 1 0.01
70 1 0.01
73 1 0.01
74 1 0.01
75 53 0.65
76 5 0.06
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.32
Consensus pattern (68 bp):
AAGTAGGAAACAATTTCCTATGAATAACTCAAAATTAAATGCAAACCATAATTTTAAGAATTCAC
TTT
Found at i:9741313 original size:75 final size:74
Alignment explanation
Indices: 9741224--9741385 Score: 245
Period size: 75 Copynumber: 2.2 Consensus size: 74
9741214 CCTATGAATA
*
9741224 ACCC-AAATTAAAATGCAAACCATAATTTTAAGAATTCACTTTAAGTAGGAAACAATTTCCTATT
1 ACCCAAAATT-AAATGCAAACCATAATTTTAAGAATTCACTTTAAGCAGGAAACAATTTCCTATT
9741288 CTTTATGAATC
65 CTTTATG-ATC
** * * *
9741299 ACTTAAAATTAAATGCTAACCATAATTTTAGGAATTCACTTTAAGCAGGAACCAATTTCCTATTC
1 ACCCAAAATTAAATGCAAACCATAATTTTAAGAATTCACTTTAAGCAGGAAACAATTTCCTATTC
9741364 TTTATGATC
66 TTTATGATC
9741373 ACCCAAAATTAAA
1 ACCCAAAATTAAA
9741386 ATAGATGGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
74 14 0.18
75 59 0.76
76 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (74 bp):
ACCCAAAATTAAATGCAAACCATAATTTTAAGAATTCACTTTAAGCAGGAAACAATTTCCTATTC
TTTATGATC
Found at i:9747740 original size:39 final size:39
Alignment explanation
Indices: 9747649--9747825 Score: 189
Period size: 39 Copynumber: 4.6 Consensus size: 39
9747639 TCAACTCAGC
* ** * *
9747649 TCATGTGCACTCCCACAAAGCACATAGC-TA-AT-ATCC
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
9747685 TCATGTGCACTTCCACACCGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
9747724 TCATGTGCTCTCCCACACTGCACATGGCACATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * *
9747763 GCATGTGCTCTCCCACATCGCACATGGCATATATCATCG
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * * *
9747802 GCGTGTGTTCTCCCATACCGCACA
1 TCATGTGCTCTCCCACACCGCACA
9747826 CTACCGGCAC
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
36 24 0.20
37 2 0.02
38 2 0.02
39 92 0.77
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
Found at i:9748993 original size:20 final size:20
Alignment explanation
Indices: 9748962--9749010 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
9748952 CTTCCAAGCT
9748962 TTTCTCTTCCTTT-TTCCTTTC
1 TTTCT-TTCCTTTCTT-CTTTC
9748983 TTTCTTTCCTTTCTTCTTTC
1 TTTCTTTCCTTTCTTCTTTC
*
9749003 TTCCTTTC
1 TTTCTTTC
9749011 TCTTCGTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTTTCCTTTCTTCTTTC
Found at i:9763150 original size:19 final size:20
Alignment explanation
Indices: 9763126--9763163 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9763116 CTATAAATAC
9763126 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
9763145 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
9763164 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:9769160 original size:21 final size:22
Alignment explanation
Indices: 9769122--9769162 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9769112 TACCTTTTGT
* *
9769122 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTAAATTTTCA
9769144 CACTTG-TCCCTTAAATTTT
1 CACTTGTTCCCTTAAATTTT
9769163 TCTACCTAGG
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:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (22 bp):
CACTTGTTCCCTTAAATTTTCA
Found at i:9777243 original size:22 final size:22
Alignment explanation
Indices: 9777201--9777241 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9777191 TACTTTTTAT
*
9777201 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
9777223 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
9777242 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:9777299 original size:11 final size:11
Alignment explanation
Indices: 9777255--9777293 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
9777245 ACCTAGGGTT
9777255 TTTGTTCTT-C
1 TTTGTTCTTCC
9777265 -TT-TTCTTCC
1 TTTGTTCTTCC
9777274 TTTGTTCTTCC
1 TTTGTTCTTCC
9777285 TTTGTTCTT
1 TTTGTTCTT
9777294 GTTTTGGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.19
9 3 0.12
10 2 0.08
11 16 0.62
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTGTTCTTCC
Found at i:9798398 original size:2 final size:2
Alignment explanation
Indices: 9798388--9798423 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
9798378 TATAACACAC
* *
9798388 AT AT CT AT AT AT GT 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
9798424 CCATCACCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9798522 original size:42 final size:42
Alignment explanation
Indices: 9798464--9798659 Score: 225
Period size: 42 Copynumber: 4.7 Consensus size: 42
9798454 CAGCTCATAT
* *
9798464 GCACTCCCACTAGCACATGGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
** * *
9798506 GCACTCTTACTCGCACATAGCAT-GGTCAACATCGGCTTATGT
1 GCACTCCCACTCGCACATAGC-TGGGTCAGCATCGGCTTATGC
* *
9798548 GCACTCCCCCTCGCACATAGCCGGGTCAGCATCGGCTTATGC
1 GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
* * * * *
9798590 TCACTCCCCCTCACACATAGTTGGGTCAGCATCGACTTATGC
1 GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
* *
9798632 ACACTCCTACTCGCACATAG-TCGGGTCA
1 GCACTCCCACTCGCACATAGCT-GGGTCA
9798660 ATATCATTAC
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 128 0.98
43 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (42 bp):
GCACTCCCACTCGCACATAGCTGGGTCAGCATCGGCTTATGC
Found at i:9801056 original size:101 final size:101
Alignment explanation
Indices: 9800936--9801143 Score: 299
Period size: 101 Copynumber: 2.1 Consensus size: 101
9800926 GAATGTGTTA
* *
9800936 ATACATTTTGGGAAAAATGGTCTTGGGTGCTCCTTGCTTCAAATGTATCAATACATAAGGGCAAT
1 ATACATTTTGAGAAAAATGGTCTTGGGTGCTCCTTACTTCAAATGTATCAATACATAAGGGCAAT
* * * *
9801001 GTATTGATACATGTTCATCTTTCTAGGAATGCATCG
66 ATATTAATACATGTTCATCTTTCCAAGAATGCATCG
* * * **
9801037 ATACATTTTGAGTAGAATGGTCTTGGGTGCTCCTTACTTCAAATGTATCGATACATTGGGGCAAT
1 ATACATTTTGAGAAAAATGGTCTTGGGTGCTCCTTACTTCAAATGTATCAATACATAAGGGCAAT
* *
9801102 ATATTAATACATGTTCATTTTTCCAAGAATGTATCG
66 ATATTAATACATGTTCATCTTTCCAAGAATGCATCG
9801138 ATACAT
1 ATACAT
9801144 CCTACCCAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (101 bp):
ATACATTTTGAGAAAAATGGTCTTGGGTGCTCCTTACTTCAAATGTATCAATACATAAGGGCAAT
ATATTAATACATGTTCATCTTTCCAAGAATGCATCG
Found at i:9803499 original size:39 final size:39
Alignment explanation
Indices: 9803405--9803501 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 39
9803395 AGGTAGTGTA
* * **
9803405 CAGTGTGAGAGAGCACACGCCGATGATATAGGCCATGTG
1 CAGTGTGGGAGAGCACATGATGATGATATAGGCCATGTG
* *
9803444 CAGTGTGGGAGAGCACATGATGATGATATATGCCGTGTG
1 CAGTGTGGGAGAGCACATGATGATGATATAGGCCATGTG
*
9803483 CGGTGTGGGA-ATGCACATG
1 CAGTGTGGGAGA-GCACATG
9803502 GCGGTGATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (39 bp):
CAGTGTGGGAGAGCACATGATGATGATATAGGCCATGTG
Found at i:9805329 original size:24 final size:24
Alignment explanation
Indices: 9805292--9805337 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
9805282 AAAAATCAAT
9805292 TTTCTTTCATTTT-CTCTTCTTTGA
1 TTTCTTTCATTTTCCT-TTCTTTGA
9805316 TTTCTATTCA-TTTCCTTTCTTT
1 TTTCT-TTCATTTTCCTTTCTTT
9805338 TCTTGCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTCTTTCATTTTCCTTTCTTTGA
Found at i:9810165 original size:43 final size:43
Alignment explanation
Indices: 9810117--9810293 Score: 189
Period size: 43 Copynumber: 4.1 Consensus size: 43
9810107 TTGTGTGATA
**
9810117 ATGATGACCCAGCTATGTGCGAAGT-GGGAGTGCACATGTGCTG
1 ATGATGACCCAGCTATGTGCG-AGTAGGGAGTGCACATAAGCTG
* **
9810160 ATGATGATCCAGCTATGTGCGAGTAGGGAGTGTGCATAAGCTG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCTG
* * * *
9810203 ATGAGGACCC-GACTATGTACGAGTAGGGAGTGTGA-ATAAGCCG
1 ATGATGACCCAG-CTATGTGCGAGTAGGGAGTG-CACATAAGCTG
* * * *
9810246 ATGATGACCCAACTATGTCCGAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCTG
9810289 ATGAT
1 ATGAT
9810294 AATGACCCGA
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
42 4 0.04
43 109 0.96
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCTG
Found at i:9813844 original size:21 final size:21
Alignment explanation
Indices: 9813793--9813847 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
9813783 AATCATCTGT
*
9813793 ACAAGGGTTCCTCTCAACTGC
1 ACAAGGGTTTCTCTCAACTGC
*
9813814 ACAAGGGTTTCTCTCAATTGC
1 ACAAGGGTTTCTCTCAACTGC
9813835 ACAAGGGTTTCTC
1 ACAAGGGTTTCTC
9813848 GTTAAAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (21 bp):
ACAAGGGTTTCTCTCAACTGC
Found at i:9814895 original size:20 final size:20
Alignment explanation
Indices: 9814872--9814911 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9814862 AGAAAAGCAA
9814872 GAAGCTACTGGAAAAATGAG
1 GAAGCTACTGGAAAAATGAG
* * *
9814892 GAAGTTGCTGGAGAAATGAG
1 GAAGCTACTGGAAAAATGAG
9814912 ATATTTATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.35, T:0.17
Consensus pattern (20 bp):
GAAGCTACTGGAAAAATGAG
Found at i:9819944 original size:42 final size:43
Alignment explanation
Indices: 9819804--9819936 Score: 218
Period size: 42 Copynumber: 3.1 Consensus size: 43
9819794 ACCATCCCAC
9819804 CATCATCAGCTCATGTGCACTTCCCAC-TCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCAC-TCCCACATCGCACATAGCTGGGT
* *
9819847 CATCATCAGCTCATGTGCACT-CCACATCGCACATAGCTAGGC
1 CATCATCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGT
9819889 CATCATCAGCTCATGTGCACTCCCACAT-GCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGT
9819931 CATCAT
1 CATCAT
9819937 TATCTCATAA
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
41 4 0.05
42 54 0.64
43 26 0.31
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (43 bp):
CATCATCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGT
Found at i:9821671 original size:30 final size:30
Alignment explanation
Indices: 9821630--9821698 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
9821620 AACCCTTTTT
* *
9821630 TTTTCATTTAATTGAAATTGTTCAAAAATG
1 TTTTAATTTAATTAAAATTGTTCAAAAATG
*
9821660 TTTTAATTTAATTAAAATTGTTCATAAATG
1 TTTTAATTTAATTAAAATTGTTCAAAAATG
9821690 TTTTAATTT
1 TTTTAATTT
9821699 CTTAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (30 bp):
TTTTAATTTAATTAAAATTGTTCAAAAATG
Found at i:9824434 original size:59 final size:59
Alignment explanation
Indices: 9824370--9824491 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 59
9824360 GGAATTATTT
* * *
9824370 TTAAGCCTTT-AAAAAGTAATGATGTTATACTTAATCCTTGAAATG-CAGAGAGGTTATGC
1 TTAAGCCTTTAAAAAAGTAATGAAGTTATACTTAATCCTTAAAAAGACA-A-AGGTTATGC
* * * *
9824429 TTAAGCTTTTAAAAAAGTAGTGAAGTTATGCTTGATCCTTAAAAAGACAAAGGTTATGC
1 TTAAGCCTTTAAAAAAGTAATGAAGTTATACTTAATCCTTAAAAAGACAAAGGTTATGC
9824488 TTAA
1 TTAA
9824492 TCCATGAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 22 0.41
60 30 0.56
61 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (59 bp):
TTAAGCCTTTAAAAAAGTAATGAAGTTATACTTAATCCTTAAAAAGACAAAGGTTATGC
Found at i:9824548 original size:37 final size:37
Alignment explanation
Indices: 9824477--9824568 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
9824467 TTAAAAAGAC
9824477 AAAGGTTATGCTTAATCCATGAAAAGAAGCAGTTTGT
1 AAAGGTTATGCTTAATCCATGAAAAGAAGCAGTTTGT
* *
9824514 AAAGCTTATGCTTAATCCATGAAAAGCAA-TAGTTTGT
1 AAAGGTTATGCTTAATCCATGAAAAG-AAGCAGTTTGT
* * *
9824551 CAAGGATATGCTTGATCC
1 AAAGGTTATGCTTAATCC
9824569 TTTAATAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
37 46 0.96
38 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (37 bp):
AAAGGTTATGCTTAATCCATGAAAAGAAGCAGTTTGT
Found at i:9834885 original size:20 final size:20
Alignment explanation
Indices: 9834860--9834899 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9834850 AGCAGGAGAA
9834860 GAAGCTGCTGGAAAAATGAG
1 GAAGCTGCTGGAAAAATGAG
*
9834880 GAAGCTGCTGGAGAAATGAG
1 GAAGCTGCTGGAAAAATGAG
9834900 ATATTTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.38, T:0.15
Consensus pattern (20 bp):
GAAGCTGCTGGAAAAATGAG
Found at i:9839625 original size:25 final size:25
Alignment explanation
Indices: 9839584--9839631 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
9839574 CACAAGCTTG
9839584 GAGTGAGGTATAAATTCCACTCTAA
1 GAGTGAGGTATAAATTCCACTCTAA
*
9839609 GAGTGAGGTGAT-GATTCCACTCT
1 GAGTGAGGT-ATAAATTCCACTCT
9839632 TATGATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (25 bp):
GAGTGAGGTATAAATTCCACTCTAA
Found at i:9839718 original size:32 final size:31
Alignment explanation
Indices: 9839648--9839707 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
9839638 GCATTGATGC
*
9839648 CCAAGGTGCAATGGGGTTTAAATATTGCCAA
1 CCAAGGTGCAATGGGGTTTAAACATTGCCAA
9839679 CCTAAGGTGCAATGGGGTTTAAACATTGC
1 CC-AAGGTGCAATGGGGTTTAAACATTGC
9839708 TGGTCCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
CCAAGGTGCAATGGGGTTTAAACATTGCCAA
Found at i:9847006 original size:57 final size:57
Alignment explanation
Indices: 9846943--9847052 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
9846933 TGTTGCCACT
** *
9846943 GCTGAAGGAGGAAAGGGCTGCTTGTAGCGAGGGTTGTCCCTTACGAGTGGAGCCGCC
1 GCTGAAGGAGGAAAGGGCTGCTTGTAGCGAGGGTCATCCCCTACGAGTGGAGCCGCC
* *
9847000 GCTGAAGGAGGAAAGGGCTGCTTGTAGTGAGGGTCATCCCCTATGAGTGGAGC
1 GCTGAAGGAGGAAAGGGCTGCTTGTAGCGAGGGTCATCCCCTACGAGTGGAGC
9847053 TCAACCGTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.40, T:0.20
Consensus pattern (57 bp):
GCTGAAGGAGGAAAGGGCTGCTTGTAGCGAGGGTCATCCCCTACGAGTGGAGCCGCC
Found at i:9850580 original size:35 final size:35
Alignment explanation
Indices: 9850513--9850629 Score: 141
Period size: 35 Copynumber: 3.4 Consensus size: 35
9850503 CAATTAGGCC
* * *
9850513 TAATTAAACAATTTTAATCAACTAGGCCCAATGACT
1 TAATTAAACAA-TTTAATTAAATAGGCACAATGACT
* * * *
9850549 TAATTAAACAATTTAATTAATTAAGCTCAATGATT
1 TAATTAAACAATTTAATTAAATAGGCACAATGACT
9850584 TAATTAAACAATTTAATTAAATAGGCAC-A--ACT
1 TAATTAAACAATTTAATTAAATAGGCACAATGACT
9850616 TAATTAAACAATTT
1 TAATTAAACAATTT
9850630 TAATCAAGTG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
32 16 0.22
34 1 0.01
35 44 0.61
36 11 0.15
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (35 bp):
TAATTAAACAATTTAATTAAATAGGCACAATGACT
Found at i:9855002 original size:35 final size:35
Alignment explanation
Indices: 9854963--9855104 Score: 167
Period size: 35 Copynumber: 4.1 Consensus size: 35
9854953 TTACTCAGCA
*
9854963 CATGTGCACTCCCTACACGCACAAGGCAATATCAT
1 CATGTGCACTCCCTACACGCACAAGGTAATATCAT
* * *
9854998 CATGTGCACACCCTACACGCATAAGGTAATATAAT
1 CATGTGCACTCCCTACACGCACAAGGTAATATCAT
* ***
9855033 CATGTGCACTCCCTACACGGACATTTTAATATCAT
1 CATGTGCACTCCCTACACGCACAAGGTAATATCAT
* * ***
9855068 CATGTGCACTTCCTACACACACATTTTAATATCAT
1 CATGTGCACTCCCTACACGCACAAGGTAATATCAT
9855103 CA
1 CA
9855105 CACGCACTCC
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 93 1.00
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (35 bp):
CATGTGCACTCCCTACACGCACAAGGTAATATCAT
Found at i:9855112 original size:35 final size:35
Alignment explanation
Indices: 9855038--9855114 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
9855028 ATAATCATGT
** ***
9855038 GCACTCCCTACACGGACATTTTAATATCATCATGT
1 GCACTCCCTACACACACATTTTAATATCATCACAC
*
9855073 GCACTTCCTACACACACATTTTAATATCATCACAC
1 GCACTCCCTACACACACATTTTAATATCATCACAC
9855108 GCACTCC
1 GCACTCC
9855115 TGCCCACATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.29
Consensus pattern (35 bp):
GCACTCCCTACACACACATTTTAATATCATCACAC
Done.