Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 32 of 106
Found at i:12406577 original size:29 final size:29
Alignment explanation
Indices: 12406545--12406607 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
12406535 ACTGATTCAT
12406545 GTACAACTTAC-TCTCTTGTACCTATTCTC
1 GTACAACTT-CTTCTCTTGTACCTATTCTC
*
12406574 GTACAACTTCTTCTCTTGTACCTATTCTT
1 GTACAACTTCTTCTCTTGTACCTATTCTC
12406603 GTACA
1 GTACA
12406608 CCTCTTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.43
Consensus pattern (29 bp):
GTACAACTTCTTCTCTTGTACCTATTCTC
Found at i:12414920 original size:190 final size:189
Alignment explanation
Indices: 12414597--12414945 Score: 527
Period size: 190 Copynumber: 1.8 Consensus size: 189
12414587 GGCGATATAA
* * * *
12414597 GGTGGTTGACATGATGATGTGGCATTGCCACGTCACCTCAACATGCTAACATCGTAGTGTCACAT
1 GGTGGTTGACATGATAACGTGGCACTGCCACGTCACCTCAACATGCTAACATAGTAGTGTCACAT
* * **
12414662 CATTATTTAAGTTCGAGTTATTGATGTGGCATTACCATGTCAACATATCAAAGTAAGGTGGGCAT
66 CACTATTTAAGTTCGAGTTATTGATGTGGCACTACCATGTCAACATATCAAAACAAGGTGGGCAT
*
12414727 TAAGGCTCCACGTCAACATGTCTAAATGACGTGGACATTTTTACTAACATGGTGGCATGG
131 TAAGG-TCCACGTCAACATGTCAAAATGACGTGGACATTTTTACTAACATGGTGGCATGG
* *
12414787 GGTGGTTGACATGATAACGTGGCACTGCCACGTCACCTCAATATGCTAACGTAGTAGTGTCACAT
1 GGTGGTTGACATGATAACGTGGCACTGCCACGTCACCTCAACATGCTAACATAGTAGTGTCACAT
* * ** *
12414852 CACTCTTTAAGTTCGAGTTATTGATGTGGCACTATCATGTCAATGTGTCAAAACAAGGTGGGCAT
66 CACTATTTAAGTTCGAGTTATTGATGTGGCACTACCATGTCAACATATCAAAACAAGGTGGGCAT
**
12414917 TAAGGTCTGCGTCAACATGTCAAAATGAC
131 TAAGGTCCACGTCAACATGTCAAAATGAC
12414946 ATGGCAATAT
Statistics
Matches: 141, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
189 21 0.15
190 120 0.85
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (189 bp):
GGTGGTTGACATGATAACGTGGCACTGCCACGTCACCTCAACATGCTAACATAGTAGTGTCACAT
CACTATTTAAGTTCGAGTTATTGATGTGGCACTACCATGTCAACATATCAAAACAAGGTGGGCAT
TAAGGTCCACGTCAACATGTCAAAATGACGTGGACATTTTTACTAACATGGTGGCATGG
Found at i:12415546 original size:23 final size:23
Alignment explanation
Indices: 12415514--12415568 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
12415504 GTTTAGAGTT
* *
12415514 TGTGAAACGGCATATTGGGAATG
1 TGTGACACGGCATAATGGGAATG
12415537 TGTGACACGGCATAATGGGAATG
1 TGTGACACGGCATAATGGGAATG
12415560 TGTGACACG
1 TGTGACACG
12415569 ACTGTGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.24
Consensus pattern (23 bp):
TGTGACACGGCATAATGGGAATG
Found at i:12415643 original size:47 final size:46
Alignment explanation
Indices: 12415587--12415765 Score: 243
Period size: 47 Copynumber: 3.8 Consensus size: 46
12415577 ATGGCAGGGT
* * *
12415587 TTAAAGTTTGTGACACGCCATTGAGGGAATCTATGACACGACAAAG
1 TTAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAATG
* * *
12415633 TTCAAAGTTTGTGACATGCCATGAAGGGAATCTGTGACACGACAGTG
1 TT-AAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAATG
*
12415680 TTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACA-TAGCAATG
1 TTAA-AGTTTGTGACACGCCATGGAGGGAATCTGTGACACGA-CAATG
*
12415727 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACA
1 -TTAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACA
12415766 TAGTAGGGTT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
46 5 0.04
47 110 0.93
48 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (46 bp):
TTAAAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAATG
Found at i:12415669 original size:23 final size:23
Alignment explanation
Indices: 12415642--12415765 Score: 72
Period size: 23 Copynumber: 5.3 Consensus size: 23
12415632 GTTCAAAGTT
*
12415642 TGTGACATGCCATGAAGGGAATC
1 TGTGACACGCCATGAAGGGAATC
* * *
12415665 TGTGACACGACAGTGTTAA--GAGTT
1 TGTGACACGCCA-TG--AAGGGAATC
*
12415689 TGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCATGAAGGGAATC
* * **** * *
12415712 TGTGACATAGCAATGTTTAGAGTT
1 TGTGACA-CGCCATGAAGGGAATC
*
12415736 TGTGACACGCCATGGAGGGAATC
1 TGTGACACGCCATGAAGGGAATC
12415759 TGTGACA
1 TGTGACA
12415766 TAGTAGGGTT
Statistics
Matches: 71, Mismatches: 24, Indels: 12
0.66 0.22 0.11
Matches are distributed among these distances:
21 1 0.01
23 37 0.52
24 31 0.44
26 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (23 bp):
TGTGACACGCCATGAAGGGAATC
Found at i:12415781 original size:47 final size:47
Alignment explanation
Indices: 12415570--12415799 Score: 239
Period size: 47 Copynumber: 4.9 Consensus size: 47
12415560 TGTGACACGA
* * * *
12415570 CTGTGACATGGCAGGGTTTAAAGTTTGTGACACGCCATTGAGGGAAT
1 CTGTGACATAGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * ** * * *
12415617 CTATGACA-CGACAAAGTTCAAAGTTTGTGACATGCCATGAAGGGAAT
1 CTGTGACATAG-CAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * *
12415664 CTGTGACA-CGACAGTGTTAAGAGTTTGTGACACGCCATGGAGGGAAT
1 CTGTGACATAG-CAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
** *
12415711 CTGTGACATAGCAATGTTTAGAGTTTGTGACACGCCATGGAGGGAAT
1 CTGTGACATAGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * * *
12415758 CTGTGACATAGTAGGGTTCAGAGTTTGTCAGACTCCATGGAG
1 CTGTGACATAGCAGGGTTCAGAGTTTGTGACACGCCATGGAG
12415800 ATTTGTGACA
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 154 0.99
48 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (47 bp):
CTGTGACATAGCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
Found at i:12415781 original size:94 final size:94
Alignment explanation
Indices: 12415570--12415799 Score: 268
Period size: 94 Copynumber: 2.4 Consensus size: 94
12415560 TGTGACACGA
* * *
12415570 CTGTGACATGGCAGGGTTTAA-AGTTTGTGACACGCCATTGAGGGAATCTATGACACGACAAAGT
1 CTGTGACATAGCAGGG-TTAAGAGTTTGTGACACGCCATGGAGGGAATCTATGACAAGACAAAGT
*
12415634 TCAAAGTTTGTGACATGCCATGAAGGGAAT
65 TCAAAGTTTGTGACACGCCATGAAGGGAAT
* * * *
12415664 CTGTGACA-CGACAGTGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATAG-CAATG
1 CTGTGACATAG-CAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTATGACA-AGACAAAG
* * *
12415727 TTTAGAGTTTGTGACACGCCATGGAGGGAAT
64 TTCAAAGTTTGTGACACGCCATGAAGGGAAT
* * * * *
12415758 CTGTGACATAGTAGGGTTCAGAGTTTGTCAGACTCCATGGAG
1 CTGTGACATAGCAGGGTTAAGAGTTTGTGACACGCCATGGAG
12415800 ATTTGTGACA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
93 5 0.04
94 108 0.94
95 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (94 bp):
CTGTGACATAGCAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTATGACAAGACAAAGTT
CAAAGTTTGTGACACGCCATGAAGGGAAT
Found at i:12416498 original size:31 final size:31
Alignment explanation
Indices: 12416453--12416718 Score: 358
Period size: 31 Copynumber: 8.6 Consensus size: 31
12416443 GTGTCAGCGT
*
12416453 TGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* * * *
12416484 TAGCGTATAACAACATTTGACTTGATACGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
** * *
12416515 TGGCGTGTAATGACATTTGACTTGATACGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
12416546 TGGCGTGTAACAACATTTTACATT-ATACGCA
1 TGGCGTGTAACAACATTTTAC-TTGATATGCA
* *
12416577 TGACATGTAACAACATTTTACGTT-ATATGCA
1 TGGCGTGTAACAACATTTTAC-TTGATATGCA
12416608 TGGCGTGTAACAACATTTTACGTT-ATATGCA
1 TGGCGTGTAACAACATTTTAC-TTGATATGCA
12416639 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
12416670 TGGCGTGTAATAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
12416701 TGGCATGTAACAACATTT
1 TGGCGTGTAACAACATTT
12416719 ATTTCTTTCT
Statistics
Matches: 214, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
30 2 0.01
31 210 0.98
32 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:12417990 original size:31 final size:31
Alignment explanation
Indices: 12417952--12418091 Score: 183
Period size: 31 Copynumber: 4.5 Consensus size: 31
12417942 TTTGTCAGTC
12417952 ATGTTGTTACACACCATGCATAT-AATGTAAA
1 ATGTTGTTACACACCATGCATATCAA-GTAAA
* * *
12417983 ATGTTGTTACACGCCATGCGTATCAAGTCAA
1 ATGTTGTTACACACCATGCATATCAAGTAAA
12418014 ATGTTGTTACACACCATGCATATCAAGTAAA
1 ATGTTGTTACACACCATGCATATCAAGTAAA
* *** *
12418045 ATGTTGTTATATGTCATGCATATCAAGTCAA
1 ATGTTGTTACACACCATGCATATCAAGTAAA
*
12418076 ATGTTGTTATACACCA
1 ATGTTGTTACACACCA
12418092 ATACTGATAC
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 92 0.98
32 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (31 bp):
ATGTTGTTACACACCATGCATATCAAGTAAA
Found at i:12418049 original size:62 final size:62
Alignment explanation
Indices: 12417952--12418091 Score: 219
Period size: 62 Copynumber: 2.3 Consensus size: 62
12417942 TTTGTCAGTC
*
12417952 ATGTTGTTACACACCATGCATATAATGTAAAATGTTGTTACACGCCATGCGTATCAAGTCAA
1 ATGTTGTTACACACCATGCATATAATGTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
* * *
12418014 ATGTTGTTACACACCATGCATATCAA-GTAAAATGTTGTTATATGTCATGCATATCAAGTCAA
1 ATGTTGTTACACACCATGCATAT-AATGTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
*
12418076 ATGTTGTTATACACCA
1 ATGTTGTTACACACCA
12418092 ATACTGATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 70 0.97
63 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (62 bp):
ATGTTGTTACACACCATGCATATAATGTAAAATGTTGTTACACGCCATGCATATCAAGTCAA
Found at i:12422443 original size:21 final size:21
Alignment explanation
Indices: 12422419--12422459 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12422409 GATTTTGAAT
* * *
12422419 TTTCCTTTTTTTTTTTTATTG
1 TTTCCCTTCTTTTGTTTATTG
12422440 TTTCCCTTCTTTTGTTTATT
1 TTTCCCTTCTTTTGTTTATT
12422460 TAGATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTCCCTTCTTTTGTTTATTG
Found at i:12427634 original size:28 final size:28
Alignment explanation
Indices: 12427600--12427656 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12427590 TCATTACAAG
12427600 TTAGTAATAATTTTCTTCTTCATTAGCA
1 TTAGTAATAATTTTCTTCTTCATTAGCA
12427628 TTAGTAATAATTTTCTTCTTCATTAGCA
1 TTAGTAATAATTTTCTTCTTCATTAGCA
12427656 T
1 T
12427657 ACTTGGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (28 bp):
TTAGTAATAATTTTCTTCTTCATTAGCA
Found at i:12432290 original size:2 final size:2
Alignment explanation
Indices: 12432279--12432325 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
12432269 GGCGCCATCA
12432279 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12432320 AG AT AT
1 AT AT AT
12432326 TCCTCCACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12446440 original size:74 final size:74
Alignment explanation
Indices: 12446313--12446474 Score: 182
Period size: 74 Copynumber: 2.2 Consensus size: 74
12446303 AGAGATCTCT
* * * * * * * *
12446313 TAATTGGTTAGAGCCTCATGTAATTGGTTAACGAAGAGCATATAGCAACAAGACAGTACATGATA
1 TAATCGGTTAGAGCCTCATGCAATTAGTTAACGAAGAACACATAGCAACAAGACAATACAAGACA
12446378 GAGAAGCTG
66 GAGAAGCTG
* * * * *
12446387 TAATCGGTTAGAGCCTCATGCAATTAGTTAATGCAA-AACACATAGTAATAAGACAATGCAAGGC
1 TAATCGGTTAGAGCCTCATGCAATTAGTTAACG-AAGAACACATAGCAACAAGACAATACAAGAC
12446451 AGAGAAGCTG
65 AGAGAAGCTG
*
12446461 TAATCAGTTAGAGC
1 TAATCGGTTAGAGC
12446475 TGCCTGTAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 71 0.97
75 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (74 bp):
TAATCGGTTAGAGCCTCATGCAATTAGTTAACGAAGAACACATAGCAACAAGACAATACAAGACA
GAGAAGCTG
Found at i:12454673 original size:18 final size:18
Alignment explanation
Indices: 12454647--12454682 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12454637 CTCAAGGAGA
*
12454647 AGAAAAAGAAAGAGAAAG
1 AGAAAAAGAAAGAAAAAG
*
12454665 AGAAGAAGAAAGAAAAAG
1 AGAAAAAGAAAGAAAAAG
12454683 GGAGCAGCAG
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAGAAAAAG
Found at i:12454727 original size:12 final size:12
Alignment explanation
Indices: 12454704--12454742 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
12454694 GGTGCCGAAG
12454704 AGAAAAAGAAGAA
1 AGAAAAA-AAGAA
12454717 AGAAAAAAAGAA
1 AGAAAAAAAGAA
*
12454729 AGAAGAAAGAGAA
1 AGAA-AAAAAGAA
12454742 A
1 A
12454743 AAGAGCAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:12454732 original size:19 final size:19
Alignment explanation
Indices: 12454708--12454746 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12454698 CCGAAGAGAA
12454708 AAAGAAGAAAGAAAAAAAG
1 AAAGAAGAAAGAAAAAAAG
*
12454727 AAAGAAGAAAGAGAAAAAG
1 AAAGAAGAAAGAAAAAAAG
12454746 A
1 A
12454747 GCAGCGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAGAAGAAAGAAAAAAAG
Found at i:12454774 original size:60 final size:61
Alignment explanation
Indices: 12454641--12454805 Score: 169
Period size: 60 Copynumber: 2.7 Consensus size: 61
12454631 CAACATCTCA
* * * * *
12454641 AGGAGAAGAAAAAGAAAGAGAAAGAG-AAGAAGAAAGA-AAAAGGGAGCAGCAGCGGTGCCG
1 AGGAGAAGAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAA-AGAGCAGCAGCGATGCCG
* * *
12454701 AAGAGAAAAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGC-GAC-ATGTCG
1 AGGAGAAGAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGCAG-CGATGCCG
* *
12454761 AGGAGAAGAAGAAGAAAAAATAAAAAGAAA-AAGGAAGAAGAAAAA
1 AGGAGAAGAAGAAGAAAGAA-AAAAAGAAAGAAGAAAG-AGAAAAA
12454806 AGAAAGAAGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
60 49 0.56
61 35 0.40
62 4 0.05
ACGTcount: A:0.62, C:0.05, G:0.30, T:0.02
Consensus pattern (61 bp):
AGGAGAAGAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGCAGCGATGCCG
Found at i:12454790 original size:13 final size:13
Alignment explanation
Indices: 12454766--12454829 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
12454756 TGTCGAGGAG
*
12454766 AAGAAGAAGAAAA
1 AAGAAAAAGAAAA
*
12454779 AATAAAAAGAAAA
1 AAGAAAAAGAAAA
* *
12454792 AGGAAGAAGAAAA
1 AAGAAAAAGAAAA
12454805 AAGAAAGAAG-AAA
1 AAGAAA-AAGAAAA
*
12454818 AAGAAGAAGAAA
1 AAGAAAAAGAAA
12454830 GAGAAAAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 3 0.07
13 35 0.85
14 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:12454797 original size:26 final size:26
Alignment explanation
Indices: 12454766--12454829 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
12454756 TGTCGAGGAG
*
12454766 AAGAAGAAGAAAAAATAAA-AAGAAA
1 AAGAAGAAGAAAAAAGAAAGAAGAAA
12454791 AAGGAAGAAGAAAAAAGAAAGAAGAAA
1 AA-GAAGAAGAAAAAAGAAAGAAGAAA
12454818 AAGAAGAAGAAA
1 AAGAAGAAGAAA
12454830 GAGAAAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 2 0.06
26 26 0.72
27 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (26 bp):
AAGAAGAAGAAAAAAGAAAGAAGAAA
Found at i:12454834 original size:6 final size:7
Alignment explanation
Indices: 12454764--12454835 Score: 66
Period size: 7 Copynumber: 11.1 Consensus size: 7
12454754 CATGTCGAGG
12454764 AGAAG-A
1 AGAAGAA
12454770 AGAAGAA
1 AGAAGAA
* *
12454777 AAAATAA
1 AGAAGAA
12454784 A-AAGAA
1 AGAAGAA
*
12454790 A-AAGGA
1 AGAAGAA
12454796 AGAAGAA
1 AGAAGAA
*
12454803 AAAAGAA
1 AGAAGAA
12454810 AGAAGAA
1 AGAAGAA
12454817 A-AAG-A
1 AGAAGAA
12454822 AGAAGAA
1 AGAAGAA
12454829 AG-AGAA
1 AGAAGAA
12454835 A
1 A
12454836 AGGAGCAGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
5 2 0.04
6 26 0.47
7 27 0.49
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (7 bp):
AGAAGAA
Found at i:12454837 original size:7 final size:6
Alignment explanation
Indices: 12454766--12454836 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
12454756 TGTCGAGGAG
* * *
12454766 AAGAAG AAGAAAA AATAAA AAGAAA AAGGAAG AAGAAAA AAGAAA GAAGAAA
1 AAGAAA AAG-AAA AAGAAA AAGAAA AA-GAAA AAG-AAA AAGAAA -AAGAAA
* *
12454818 AAGAAG AAGAAA GAGAAA A
1 AAGAAA AAGAAA AAGAAA A
12454837 GGAGCAGCAG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
6 32 0.62
7 20 0.38
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:12454837 original size:26 final size:24
Alignment explanation
Indices: 12454766--12454829 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 24
12454756 TGTCGAGGAG
*
12454766 AAGAAGAAGAAAAAATAAAAAGAAA
1 AAGAAGAAGAAAAAA-AAGAAGAAA
12454791 AAGGAAGAAGAAAAAAGAAAGAAGAAA
1 AA-GAAGAAG-AAAAA-AAAGAAGAAA
12454818 AAGAAGAAGAAA
1 AAGAAGAAGAAA
12454830 GAGAAAAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 5 0.14
26 14 0.40
27 15 0.43
28 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (24 bp):
AAGAAGAAGAAAAAAAAGAAGAAA
Found at i:12454842 original size:93 final size:96
Alignment explanation
Indices: 12454707--12454891 Score: 249
Period size: 93 Copynumber: 2.0 Consensus size: 96
12454697 GCCGAAGAGA
*
12454707 AAAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGC-GACATGTCGAGGAGAAGAA
1 AAAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGCAG-CATGTCGAGG-GAAAAA
*
12454771 GAAGA-A-AAAATAAAA-AG-AAAAAGGAAGAAG
64 AAAGAGAGAAAA-AAAAGAGAAAAAAGGAAGAAG
* *
12454801 AAAA-AAGAAAGAAGAAAAAG-AAGAAGAAAGAGAAAAGGAGCAGCAGCGTGTCGAGGGAAAAAA
1 AAAAGAAGAAAGAA-AAAAAGAAAGAAGAAAGAGAAAAAGAGCAGCAGCATGTCGAGGGAAAAAA
12454864 AAGAGAGAAAAAAAAGAGAAAAAAGGAA
65 AAGAGAGAAAAAAAAGAGAAAAAAGGAA
12454892 AAAAAATATA
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
92 9 0.11
93 46 0.57
94 17 0.21
95 9 0.11
ACGTcount: A:0.65, C:0.04, G:0.28, T:0.03
Consensus pattern (96 bp):
AAAAGAAGAAAGAAAAAAAGAAAGAAGAAAGAGAAAAAGAGCAGCAGCATGTCGAGGGAAAAAAA
AGAGAGAAAAAAAAGAGAAAAAAGGAAGAAG
Found at i:12454875 original size:13 final size:13
Alignment explanation
Indices: 12454857--12454887 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12454847 CGTGTCGAGG
12454857 GAAAAAAAAGAGA
1 GAAAAAAAAGAGA
12454870 GAAAAAAAAGAGA
1 GAAAAAAAAGAGA
12454883 -AAAAA
1 GAAAAA
12454888 GGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAGAGA
Found at i:12454876 original size:11 final size:11
Alignment explanation
Indices: 12454860--12454896 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12454850 GTCGAGGGAA
12454860 AAAAAAGAGAG
1 AAAAAAGAGAG
*
12454871 AAAAAAAAGAG
1 AAAAAAGAGAG
12454882 AAAAAAG-GA-
1 AAAAAAGAGAG
12454891 AAAAAA
1 AAAAAA
12454897 ATATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:12455599 original size:60 final size:59
Alignment explanation
Indices: 12455506--12455802 Score: 409
Period size: 60 Copynumber: 5.0 Consensus size: 59
12455496 TTTGATTTAA
*
12455506 AAAGGGGGACCTGAAGCTCCGATTCATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
* * *
12455566 AAAGGGGGACTTGAAGCCCCGATTCATATTGGGTGGCGTGGGTAGTTCCTATGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATT-GGTGGCGTGGGTAGTTCCCACGAGTAGGT
* * * * * *
12455626 AAAGGGAGACTTGAAG-CCCGATTTATGTATGATGGCATGGGTAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATAT-TGGTGGCGTGGGTAGTTCCCACGAGTAGGT
* * * *
12455685 AAAGGGGGACCTGAAGTCCCGATTTATGTATGGTGGCGTGGGTAGTTCCCACAAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATAT-TGGTGGCGTGGGTAGTTCCCACGAGTAGGT
*
12455745 AAAGGGGGACCTGAAGCCCCGATTCATA-TGGTGGCGTGGGCAGTTCCCACGAGTAGGT
1 AAAGGGGGACCTGAAGCCCCGATTCATATTGGTGGCGTGGGTAGTTCCCACGAGTAGGT
12455803 GATGATGTCT
Statistics
Matches: 214, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
58 28 0.13
59 49 0.23
60 137 0.64
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (59 bp):
AAAGGGGGACCTGAAGCCCCGATTCATATTGGTGGCGTGGGTAGTTCCCACGAGTAGGT
Found at i:12455742 original size:119 final size:118
Alignment explanation
Indices: 12455506--12455802 Score: 391
Period size: 119 Copynumber: 2.5 Consensus size: 118
12455496 TTTGATTTAA
* * *
12455506 AAAGGGGGACCTGAAGCTCCGATTCATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
1 AAAGGGAGACCTGAAGCCCCGATTCATA-T-GATGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
* * **
12455571 GGGACTTGAAGCCCCGATTCATATTGGGTGGCGTGGGTAGTTCCTATGAGTAGGT
64 GGGACCTGAAGCCCCGATTCATATTGGGTGGCGTGGGTAGTTCCCACAAGTAGGT
* * *
12455626 AAAGGGAGACTTGAAG-CCCGATTTATGTATGATGGCATGGGTAGTTCCCACGAGTAGGTAAAGG
1 AAAGGGAGACCTGAAGCCCCGATTCA--TATGATGGCGTGGGTAGTTCCCACGAGTAGGTAAAGG
* * *
12455690 GGGACCTGAAGTCCCGATTTATGTAT-GGTGGCGTGGGTAGTTCCCACAAGTAGGT
64 GGGACCTGAAGCCCCGATTCATAT-TGGGTGGCGTGGGTAGTTCCCACAAGTAGGT
* * *
12455745 AAAGGGGGACCTGAAGCCCCGATTCATATGGTGGCGTGGGCAGTTCCCACGAGTAGGT
1 AAAGGGAGACCTGAAGCCCCGATTCATATGATGGCGTGGGTAGTTCCCACGAGTAGGT
12455803 GATGATGTCT
Statistics
Matches: 154, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
118 29 0.19
119 99 0.64
120 24 0.16
121 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (118 bp):
AAAGGGAGACCTGAAGCCCCGATTCATATGATGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGG
GACCTGAAGCCCCGATTCATATTGGGTGGCGTGGGTAGTTCCCACAAGTAGGT
Found at i:12457667 original size:2 final size:2
Alignment explanation
Indices: 12457660--12457694 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
12457650 TGATCATGAA
*
12457660 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12457695 AAGGTTATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12462503 original size:18 final size:18
Alignment explanation
Indices: 12462477--12462512 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12462467 CTCGGGGAGA
*
12462477 AGAAAAAGAAAGAGAAAG
1 AGAAAAAGAAAGAAAAAG
*
12462495 AGAAGAAGAAAGAAAAAG
1 AGAAAAAGAAAGAAAAAG
12462513 GGAGCAGTAG
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAGAAAAAG
Found at i:12472051 original size:74 final size:74
Alignment explanation
Indices: 12471907--12472068 Score: 182
Period size: 74 Copynumber: 2.2 Consensus size: 74
12471897 TGAGATCTCC
* * * * * **
12471907 TAATCGGTTAAAGCCTCTTGTAATTGGTTAACGAAGAGCACATAGTAGCAAGACAATACACGGTA
1 TAATCGGTTAAAGCCTATTGTAATTAGTTAACGAAGAACACACAGTAGCAAGACAATACAAGCCA
12471972 AAAAAACTA
66 AAAAAACTA
* * *
12471981 TAATTGGTTAAAGCCTATTGTAATTAGTTAACGCAA-AACACACAGTAGTAAGACAATGCAAGCC
1 TAATCGGTTAAAGCCTATTGTAATTAGTTAACG-AAGAACACACAGTAGCAAGACAATACAAGCC
* *
12472045 AGAAAAATTA
65 AAAAAAACTA
* *
12472055 TACTCAGTTAAAGC
1 TAATCGGTTAAAGC
12472069 TGCCTGTAGC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 70 0.97
75 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (74 bp):
TAATCGGTTAAAGCCTATTGTAATTAGTTAACGAAGAACACACAGTAGCAAGACAATACAAGCCA
AAAAAACTA
Found at i:12478077 original size:55 final size:55
Alignment explanation
Indices: 12477986--12478171 Score: 205
Period size: 55 Copynumber: 3.4 Consensus size: 55
12477976 GTTAGCGCTA
* * * * *
12477986 TTTTAGAGTGTCATGGCTGTTCCTGGCGTGTTGTGGGTTAACTAGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCTTGGTGTGTCGTGGGTTAACTAGTTTTTTGGGT
* * * * * *
12478041 TGTTAACGTGTCACGGCTGTTCTTGGTGTGTCGTGGGTTAA-TTGAATTTATGAGT
1 TTTTAGCGTGTCACGGCTGTTCTTGGTGTGTCGTGGGTTAACTAG-TTTTTTGGGT
* * * *
12478096 TTTTGGCGTATCACGGCTGTTCTTGGCT-TGTCGTGGGTTAACTGGTTTTTTGGAT
1 TTTTAGCGTGTCACGGCTGTTCTTGG-TGTGTCGTGGGTTAACTAGTTTTTTGGGT
12478151 TTTTAGCGTGTCACGGCTGTT
1 TTTTAGCGTGTCACGGCTGTT
12478172 GGTGTAACGA
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
54 2 0.02
55 101 0.95
56 3 0.03
ACGTcount: A:0.12, C:0.13, G:0.31, T:0.44
Consensus pattern (55 bp):
TTTTAGCGTGTCACGGCTGTTCTTGGTGTGTCGTGGGTTAACTAGTTTTTTGGGT
Found at i:12478233 original size:23 final size:23
Alignment explanation
Indices: 12478201--12478279 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
12478191 TTACAATGAT
*
12478201 TGGCGTGTCACAATAGTGATGCA
1 TGGCGTGTCACGATAGTGATGCA
* * *
12478224 TGTCTTGTCACGACAGTGATGCA
1 TGGCGTGTCACGATAGTGATGCA
* *
12478247 TGGCGTGTCACGATACTAATGCA
1 TGGCGTGTCACGATAGTGATGCA
12478270 TGGCGTGTCA
1 TGGCGTGTCA
12478280 TGACATTTGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (23 bp):
TGGCGTGTCACGATAGTGATGCA
Found at i:12478303 original size:31 final size:31
Alignment explanation
Indices: 12478265--12478347 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
12478255 CACGATACTA
**
12478265 ATGCATGGCGTGTCATGACATTTGAC-TTGAT
1 ATGCATGGCGTGTCACAACATTTGACGTT-AT
* *
12478296 ATGCATGGCGTGTTACAACATTTTACGTTAT
1 ATGCATGGCGTGTCACAACATTTGACGTTAT
* *
12478327 ATGCATGGTGTGTAACAACAT
1 ATGCATGGCGTGTCACAACAT
12478348 GACTGACAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 43 0.96
32 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACGTTAT
Found at i:12482581 original size:31 final size:31
Alignment explanation
Indices: 12482537--12482829 Score: 338
Period size: 31 Copynumber: 9.5 Consensus size: 31
12482527 AATAAGGAAT
* *
12482537 AAATG-TGAGACACGCCATGCAAAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
** *
12482567 AAATGTTGTGACACGCCATGCATAGGAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
12482598 AAACGTTGTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
12482629 AATTGTTCTGACACGCCATGCATAATAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
12482660 AAACGTTGTGACATGCCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
12482691 AATTGTTTTGACACACTATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
12482722 AATTGTTCTGACACGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
12482753 AAATATTGTGACACGCCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
12482784 AATTGTTCTGAC-CTGCCATGCATAACAAGTA
1 AAATGTTGTGACAC-GCCATGCATAACAAGTA
*
12482815 AAATGTTGTCACACG
1 AAATGTTGTGACACG
12482830 TTAACGCTGA
Statistics
Matches: 216, Mismatches: 44, Indels: 5
0.82 0.17 0.02
Matches are distributed among these distances:
30 6 0.03
31 209 0.97
32 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:12482829 original size:93 final size:93
Alignment explanation
Indices: 12482545--12482821 Score: 396
Period size: 93 Copynumber: 3.0 Consensus size: 93
12482535 ATAAATGTGA
* * ** * *
12482545 GACACGCCATGCAAAACAAGTAAAATGTTGTGACACGCCATGCATAGGAAGTTAAA-CGTTGTGA
1 GACACGCCATGCATAACAAGTTAAATGTTGTGACACGCCATGCATAACAA-TTAAATTGTTCTGA
12482609 CACGCCATGCATAACAAGTAAATTGTTCT
65 CACGCCATGCATAACAAGTAAATTGTTCT
* * * *
12482638 GACACGCCATGCATAATAAGTTAAACGTTGTGACATGCCATGCATAACAATTAAATTGTTTTGAC
1 GACACGCCATGCATAACAAGTTAAATGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
* *
12482703 ACACTATGCATAACAAGTAAATTGTTCT
66 ACGCCATGCATAACAAGTAAATTGTTCT
*
12482731 GACACGCCATGCATAACAAGTTAAATATTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
1 GACACGCCATGCATAACAAGTTAAATGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
*
12482796 -CTGCCATGCATAACAAGTAAAATGTT
66 AC-GCCATGCATAACAAGTAAATTGTT
12482822 GTCACACGTT
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
92 6 0.04
93 157 0.96
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (93 bp):
GACACGCCATGCATAACAAGTTAAATGTTGTGACACGCCATGCATAACAATTAAATTGTTCTGAC
ACGCCATGCATAACAAGTAAATTGTTCT
Found at i:12483241 original size:31 final size:31
Alignment explanation
Indices: 12483129--12483311 Score: 116
Period size: 31 Copynumber: 5.9 Consensus size: 31
12483119 GTTGAGTGGA
* * * **
12483129 AGCAGATTTATGGGCTAACACGCTGAGTGAA
1 AGCAGATTTATGGGGTGACACGCTGACTGCT
* * * *
12483160 AGTAGATTTATGGGCTGACACGCTGAGTGTT
1 AGCAGATTTATGGGGTGACACGCTGACTGCT
** * ** *
12483191 AGTGGATTTACGGCATGACACGCTGACTTCT
1 AGCAGATTTATGGGGTGACACGCTGACTGCT
* * * *
12483222 TGCAGATTTATGGGGTGACACGTTGAGTGCA
1 AGCAGATTTATGGGGTGACACGCTGACTGCT
* * * *
12483253 AGCAGATGTATGTTGG-GACACGCTGAGTGGT
1 AGCAGATTTATG-GGGTGACACGCTGACTGCT
* * *
12483284 AGCATATTTATGGCGTCACACGCTGACT
1 AGCAGATTTATGGGGTGACACGCTGACT
12483312 TCTTGCTATT
Statistics
Matches: 117, Mismatches: 33, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
30 1 0.01
31 114 0.97
32 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (31 bp):
AGCAGATTTATGGGGTGACACGCTGACTGCT
Found at i:12483293 original size:93 final size:92
Alignment explanation
Indices: 12483130--12483317 Score: 225
Period size: 93 Copynumber: 2.0 Consensus size: 92
12483120 TTGAGTGGAA
* * * **
12483130 GCAGATTTATGGGCTAACACGCTGAGTGAAAGTAGATTTATGGGCTGACACGCTGAGTGTTAGTG
1 GCAGATTTATGGGCTAACACGCTGAGTGAAAGCAGATGTATGGGC-GACACGCTGAGTGGTAGCA
*
12483195 GATTTACGGCATGACACGCTGACTTCTT
65 GATTTACGGCATCACACGCTGACTTCTT
* * * *
12483223 GCAGATTTATGGGGTGACACGTTGAGTGCAAGCAGATGTATGTTGG-GACACGCTGAGTGGTAGC
1 GCAGATTTATGGGCTAACACGCTGAGTGAAAGCAGATGTATG--GGCGACACGCTGAGTGGTAGC
* * *
12483287 ATATTTATGGCGTCACACGCTGACTTCTT
64 AGATTTACGGCATCACACGCTGACTTCTT
12483316 GC
1 GC
12483318 TATTGTGTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
93 78 0.98
95 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (92 bp):
GCAGATTTATGGGCTAACACGCTGAGTGAAAGCAGATGTATGGGCGACACGCTGAGTGGTAGCAG
ATTTACGGCATCACACGCTGACTTCTT
Found at i:12483422 original size:15 final size:15
Alignment explanation
Indices: 12483397--12483442 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
12483387 TATAGGCAAA
12483397 AAAATTAATTGTGTAT
1 AAAA-TAATTGTGTAT
12483413 AAAATAA-T-TGTAT
1 AAAATAATTGTGTAT
*
12483426 AAAGTATATTGTGTAT
1 AAAATA-ATTGTGTAT
12483442 A
1 A
12483443 CAGAAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 4 0.15
16 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (15 bp):
AAAATAATTGTGTAT
Found at i:12483477 original size:14 final size:15
Alignment explanation
Indices: 12483457--12483503 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
12483447 AAGAATTAAT
*
12483457 TTTGTATACAATGAA
1 TTTGTATACAATAAA
*
12483472 -TTGTATAAAATAAA
1 TTTGTATACAATAAA
12483486 TTATGTATACAA-AAA
1 TT-TGTATACAATAAA
12483501 TTT
1 TTT
12483504 TGTGCATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 13 0.48
15 6 0.22
16 8 0.30
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (15 bp):
TTTGTATACAATAAA
Found at i:12483477 original size:52 final size:51
Alignment explanation
Indices: 12483370--12483528 Score: 150
Period size: 52 Copynumber: 3.2 Consensus size: 51
12483360 AAAATTCTTG
* * *
12483370 GTATCAAATTAATTATGTATAGGCA-AAAAAATTAATTGTGTATAAAATAATT
1 GTATAAAATAAATTATGTATA--CAGAAAGAATTAATTGTGTATAAAATAATT
* * * * *
12483422 GTATAAAGTATATTGTGTATACAGAAAGAATTAATTTTGTATACAATGAATT
1 GTATAAAATAAATTATGTATACAGAAAGAATTAATTGTGTATAAAAT-AATT
*
12483474 GTATAAAATAAATTATGTATAC--AAA-AATT--TTGTGCATAAAATTAATT
1 GTATAAAATAAATTATGTATACAGAAAGAATTAATTGTGTATAAAA-TAATT
*
12483521 ATATAAAA
1 GTATAAAA
12483529 GACAAGGGCC
Statistics
Matches: 89, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
47 20 0.22
48 1 0.01
49 4 0.04
50 5 0.06
51 20 0.22
52 39 0.44
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (51 bp):
GTATAAAATAAATTATGTATACAGAAAGAATTAATTGTGTATAAAATAATT
Found at i:12485097 original size:31 final size:31
Alignment explanation
Indices: 12485059--12485418 Score: 441
Period size: 31 Copynumber: 11.6 Consensus size: 31
12485049 AACCATAAAC
* *
12485059 AGTAAAATGTTGTGACACGCCGTGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
*
12485090 AGTAAAATGTTGTGACACGCCATGCAAAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
*
12485121 AGTAAAATGTTGTGACATGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * *
12485152 AGTTAAACGTTGTGACACCCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * *
12485183 AGTTAAACGTTGTGACACCCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
12485214 AGTAAAATGTTGTGACACGCCATGCATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
12485245 AGTTAAACGTTGTGACATGCCAAGGATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * * *
12485276 AGCAAATTGTTGTGACAAGCCAAGGATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * *
12485307 AGCAAAATGTTCTGACACGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* * * *
12485338 ACTCAAACGTTGTGACACGCCATGAATAACA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
12485369 AGTAAAATGTTGTGACATGCCATGCATATCA
1 AGTAAAATGTTGTGACACGCCATGCATAACA
* *
12485400 AGTCAAATGTTGTCACACG
1 AGTAAAATGTTGTGACACG
12485419 GTAAGGTTGA
Statistics
Matches: 285, Mismatches: 44, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 285 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (31 bp):
AGTAAAATGTTGTGACACGCCATGCATAACA
Found at i:12486068 original size:156 final size:156
Alignment explanation
Indices: 12485784--12486153 Score: 463
Period size: 156 Copynumber: 2.4 Consensus size: 156
12485774 AATTGCAATA
*
12485784 ACATATATAACTATGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
*
12485849 AATATCCTAACCGACGGCTCGTTAGCAGTCTACAGTGGAACCGAACCGATCGGTGCTTGAGGACA
66 AATATCCTAACCGACGGCTCGTTAGCAGTCTACAGTGGAACCGAACCGATCAGTGCTTGAGGACA
*
12485914 TGTTGTCGCTTTAACAAACTGTAATT
131 TGTCGTCGCTTTAACAAACTGTAATT
*
12485940 ACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
* * * * * * ** * * *
12486005 AATATCCTTACCGCCGGCTCGTTAGCTGTCTGCGGTTGAGTCGGACTGATCAGTGCTTGAGGACC
66 AATATCCTAACCGACGGCTCGTTAGCAGTCTACAGTGGAACCGAACCGATCAGTGCTTGAGGACA
* ***
12486070 TGTCGTCGTTTTTGTAAACTGTAATT
131 TGTCGTCGCTTTAACAAACTGTAATT
* * * * * * * * **
12486096 ACAGAAATTACTGTGTTACTCGATAAACATATGTGAGAA-TGTAGAACACAAACCGTTA
1 ACATATATAACTGTGTTATTCAATAATCATATATG-GAATTGTTGAACATTAACCGTTA
12486154 AAACCGATCT
Statistics
Matches: 183, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
156 180 0.98
157 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (156 bp):
ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
AATATCCTAACCGACGGCTCGTTAGCAGTCTACAGTGGAACCGAACCGATCAGTGCTTGAGGACA
TGTCGTCGCTTTAACAAACTGTAATT
Found at i:12487155 original size:43 final size:43
Alignment explanation
Indices: 12487102--12487297 Score: 243
Period size: 43 Copynumber: 4.6 Consensus size: 43
12487092 TTCCCAGATC
***
12487102 ATGCGCACTCCCTACTCGCACATGGTTAGGTCATCACTGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACTGGGTT
* *** * *
12487145 ATGCACACTCCCTACTCGCACATGGTTATGTCATCATTGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACTGGGTT
* * *
12487188 ATGCACACTCCCTACTCGCACATAACCAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACTGGGTT
*
12487231 ATGCGCACTCCCTACTCGCACATAACT-GAGTCATCA-TCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACTAG-GTCATCACT-GGGTT
12487274 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
12487298 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 136 0.99
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACTGGGTT
Found at i:12487204 original size:86 final size:86
Alignment explanation
Indices: 12487102--12487297 Score: 268
Period size: 86 Copynumber: 2.3 Consensus size: 86
12487092 TTCCCAGATC
**** *
12487102 ATGCGCACTCCCTACTCGCACATGGTTAGGTCATCACTGGGTTATGCACACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGCACACTCCCTACTCGCACA
** * * *
12487167 T-GGTTATGTCATCATTGGGTT
66 TAACTGA-GTCATCATCGGCTT
* *
12487188 ATGCACACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGCGCACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGCACACTCCCTACTCGCACA
12487253 TAACTGAGTCATCATCGGCTT
66 TAACTGAGTCATCATCGGCTT
12487274 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
12487298 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 94 0.98
87 2 0.02
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (86 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCACCGGGTTATGCACACTCCCTACTCGCACA
TAACTGAGTCATCATCGGCTT
Found at i:12490864 original size:31 final size:31
Alignment explanation
Indices: 12490693--12490847 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
12490683 AAATAAGGAA
* * *
12490693 TAAATGTTGTGACACGCCATGCATAGCAAGC
1 TAAACGTTGTGACACGCCATGCATAACAAGT
* *
12490724 AAAATGTTGTGACACGCCATGCATAACAAGT
1 TAAACGTTGTGACACGCCATGCATAACAAGT
*
12490755 TAAACGTTGTGACATGCCATGCATAACAAGT
1 TAAACGTTGTGACACGCCATGCATAACAAGT
*
12490786 TAAACGTTGTGACATGCCATGCATAACAAGT
1 TAAACGTTGTGACACGCCATGCATAACAAGT
12490817 TAAACGTTGTGACACGCCATGCATAACAAGT
1 TAAACGTTGTGACACGCCATGCATAACAAGT
12490848 AAAATGCTGT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 117 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (31 bp):
TAAACGTTGTGACACGCCATGCATAACAAGT
Found at i:12491401 original size:53 final size:53
Alignment explanation
Indices: 12491333--12491452 Score: 168
Period size: 53 Copynumber: 2.3 Consensus size: 53
12491323 TCTATTTCAA
* * * *
12491333 ACCATGACGTGTCAGCTGCTCAAGCACTGTCGTGTCACACACTCTAAACCATG
1 ACCATGGCGTGTCAGCTGCTCAAGCAATGCCATGTCACACACTCTAAACCATG
** *
12491386 ACCATGGCGTGTCAGCTTTTCAAGTAATGCCATGTCACACACTCTAAACCATG
1 ACCATGGCGTGTCAGCTGCTCAAGCAATGCCATGTCACACACTCTAAACCATG
*
12491439 ACCATGGCATGTCA
1 ACCATGGCGTGTCA
12491453 CCAACTCTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (53 bp):
ACCATGGCGTGTCAGCTGCTCAAGCAATGCCATGTCACACACTCTAAACCATG
Found at i:12491522 original size:47 final size:47
Alignment explanation
Indices: 12491440--12491712 Score: 280
Period size: 47 Copynumber: 5.8 Consensus size: 47
12491430 TAAACCATGA
* * * * *
12491440 CCATGGCATGTCACCAACTCTAAACTCTGATGTGTCACAGATTCCCT
1 CCATGGCGTCTCACCAACTCTGAACGCTGACGTGTCACAGATTCCCT
*
12491487 CCATGGCGTCTCACGAACTCTGAACGCTGACGTGTCACAGATTCCCT
1 CCATGGCGTCTCACCAACTCTGAACGCTGACGTGTCACAGATTCCCT
** * * * * *
12491534 TAATGCCGTGTCACCAACTCTTAACTCTGACGTGTCACAAATTCCCT
1 CCATGGCGTCTCACCAACTCTGAACGCTGACGTGTCACAGATTCCCT
* *
12491581 CCATGGCGTCTCACCAACTCTGAACG-TTAGTGTGTCACAGATTCCCT
1 CCATGGCGTCTCACCAACTCTGAACGCTGA-CGTGTCACAGATTCCCT
* ** * * * * *
12491628 CCATGCCGAGTCAACAACTCTTAACTCT-AGCGTGTCACAAATTTCCT
1 CCATGGCGTCTCACCAACTCTGAACGCTGA-CGTGTCACAGATTCCCT
* * *
12491675 CAATGGCGTCTCACCAACTCTGAACGTTGGCGTGTCAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGACGTGTCAC
12491713 CAACTCTTAA
Statistics
Matches: 182, Mismatches: 41, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
46 2 0.01
47 179 0.98
48 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (47 bp):
CCATGGCGTCTCACCAACTCTGAACGCTGACGTGTCACAGATTCCCT
Found at i:12491561 original size:94 final size:93
Alignment explanation
Indices: 12491448--12491712 Score: 370
Period size: 94 Copynumber: 2.8 Consensus size: 93
12491438 GACCATGGCA
* * * *
12491448 TGTCACCAACTCTAAACTCTGATGTGTCACAGATTCCCTCCATGGCGTCTCACGAACTCTGAACG
1 TGTCACCAACTCTTAACTCTGACGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACG
*
12491513 CTGACGTGTCACAGATTCCCTTAATGCCG
66 -TGACGTGTCACAGATTCCCTCAATGCCG
12491542 TGTCACCAACTCTTAACTCTGACGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACG
1 TGTCACCAACTCTTAACTCTGACGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACG
* * *
12491607 TTAGTGTGTCACAGATTCCCTCCATGCCG
66 TGA-CGTGTCACAGATTCCCTCAATGCCG
* * * *
12491636 AGTCAACAACTCTTAACTCT-AGCGTGTCACAAATTTCCTCAATGGCGTCTCACCAACTCTGAAC
1 TGTCACCAACTCTTAACTCTGA-CGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAAC
*
12491700 GTTGGCGTGTCAC
65 G-TGACGTGTCAC
12491713 CAACTCTTAA
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
93 3 0.02
94 149 0.97
95 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (93 bp):
TGTCACCAACTCTTAACTCTGACGTGTCACAAATTCCCTCCATGGCGTCTCACCAACTCTGAACG
TGACGTGTCACAGATTCCCTCAATGCCG
Found at i:12491694 original size:141 final size:141
Alignment explanation
Indices: 12491440--12491712 Score: 331
Period size: 141 Copynumber: 1.9 Consensus size: 141
12491430 TAAACCATGA
* * *
12491440 CCATGGCATGTCACCAACTCTAAACTCTGATGTGTCACAGATTCCCTCCATGGCGTCTCACGAAC
1 CCATGGCATCTCACCAACTCTAAACTCTGATGTGTCACAGATTCCCTCCATGCCGACTCACGAAC
* * * *
12491505 TCTGAACGCTGACGTGTCACAGATTCCCTTAATGCCGTGTCACCAACTCTTAAC-TCTGACGTGT
66 TCTGAACGCTGACGTGTCACAAATTCCCTCAATGCCGTCTCACCAACTCTGAACGT-TGACGTGT
12491569 CACAAATTCCCT
130 CACAAATTCCCT
* * *
12491581 CCATGGCGTCTCACCAACTCTGAACGT-T-AGTGTGTCACAGATTCCCTCCATGCCGAGTCAAC-
1 CCATGGCATCTCACCAACTCTAAAC-TCTGA-TGTGTCACAGATTCCCTCCATGCCGACTC-ACG
* * * * *
12491643 AACTCTTAACTCT-AGCGTGTCACAAATTTCCTCAATGGCGTCTCACCAACTCTGAACGTTGGCG
63 AACTCTGAACGCTGA-CGTGTCACAAATTCCCTCAATGCCGTCTCACCAACTCTGAACGTTGACG
12491707 TGTCAC
127 TGTCAC
12491713 CAACTCTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
140 2 0.02
141 106 0.95
142 4 0.04
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (141 bp):
CCATGGCATCTCACCAACTCTAAACTCTGATGTGTCACAGATTCCCTCCATGCCGACTCACGAAC
TCTGAACGCTGACGTGTCACAAATTCCCTCAATGCCGTCTCACCAACTCTGAACGTTGACGTGTC
ACAAATTCCCT
Found at i:12491706 original size:24 final size:24
Alignment explanation
Indices: 12491678--12491736 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
12491668 ATTTCCTCAA
12491678 TGGCGTCTCACCAACTCTGAACGT
1 TGGCGTCTCACCAACTCTGAACGT
* * *
12491702 TGGCGTGTCACCAACTCTTAACTT
1 TGGCGTCTCACCAACTCTGAACGT
*
12491726 TGGCATCTCAC
1 TGGCGTCTCAC
12491737 AGATTCCCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.19, T:0.29
Consensus pattern (24 bp):
TGGCGTCTCACCAACTCTGAACGT
Found at i:12491758 original size:71 final size:71
Alignment explanation
Indices: 12491631--12491783 Score: 189
Period size: 71 Copynumber: 2.2 Consensus size: 71
12491621 ATTCCCTCCA
* * * * * *
12491631 TGCCGAGTCAACAACTCTTAACTCTAGCGTGTCACAAATTTCCTCAATGGCGTCTCACCAACTCT
1 TGCCGTGTCACCAACTCTTAACTCTAGCATCTCACAAATTCCCTCAATGACGTCTCACCAACTCT
*
12491696 GAACGT
66 GAACGG
* * * * *
12491702 TGGCGTGTCACCAACTCTTAACTTTGGCATCTCACAGATTCCCTCTATGACGTCTCACCAACTCT
1 TGCCGTGTCACCAACTCTTAACTCTAGCATCTCACAAATTCCCTCAATGACGTCTCACCAACTCT
*
12491767 GAGCGG
66 GAACGG
12491773 TGCCGTGTCAC
1 TGCCGTGTCAC
12491784 AGCCATGTCA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (71 bp):
TGCCGTGTCACCAACTCTTAACTCTAGCATCTCACAAATTCCCTCAATGACGTCTCACCAACTCT
GAACGG
Found at i:12507657 original size:1 final size:1
Alignment explanation
Indices: 12507651--12507681 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
12507641 TTGTACACCA
12507651 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12507682 TCAATTGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:12508225 original size:17 final size:19
Alignment explanation
Indices: 12508188--12508226 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12508178 TGCAATTTTT
*
12508188 TTTTTTTCATTTTTCTAAC
1 TTTTTTTCATTTTACTAAC
12508207 TTTTTTTC-TTTTACT-AC
1 TTTTTTTCATTTTACTAAC
12508224 TTT
1 TTT
12508227 CTCAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTTCATTTTACTAAC
Found at i:12509276 original size:301 final size:295
Alignment explanation
Indices: 12508618--12509215 Score: 822
Period size: 301 Copynumber: 2.0 Consensus size: 295
12508608 CTAATGTGTT
* ** * * * ** * * *
12508618 CTTCTAAAAACCAAAAAATTCATTACGACAAACACCAAATTACACCAATCAATTCATAAACCTGA
1 CTTCTAAAAACCATAAAATTCAAAACAACAAACACAAAATAACAAAAATCAATACATAAATCGGA
*
12508683 CATTCATCCATCTTTCAGTTATATGATATCTCTCCTATTGTATAGTTAATAAATTTGTACCTGGC
66 CATTCATCCATCTTTCAGTTATATGATATCTCTCCTATTGCATAGTTAATAAATTTGTACCTGGC
* *
12508748 ATGATCGAAGAGCTAGCCATCAGCCAATGACAGATCTAGACATTGAGTCTTGGGGAGGCCATACT
131 ATGATCGAAGAGCTAGCCATCAGCCAATGACAGATCTAGACATTGAGTCTCGGGGAAGCCATACT
* *
12508813 AAACCTAGACTTTGTTTCATAAATAAACCTATTATATTTACTAATATAAAAGAAAATAGAAATAT
196 AAACCTAGACTTTGTTTCATAAATAAACCAATTATATTTACCAATATAAAAGAAAATAGAAATAT
*** * ***
12508878 AGATGTAAGCAAAATCGGCTACTGATGCTTATGTGTT
261 AGATGTAAGCAAAATC-GCTAC-GAAAATAATGTAAA
** * ** *
12508915 CTTCTAAAAACCATAAAATTCATTACAACAAACACAAAATTACACCAATCAATTCATAAATCGGA
1 CTTCTAAAAACCATAAAATTCAAAACAACAAACACAAAATAACAAAAATCAATACATAAATCGGA
* *
12508980 CATTCATCCATCTTTCAGTTATATGATATCTCTTCCTTCAATTGCATGGTTAATAAATTTGTGCC
66 CATTCATCCATCTTTCAGTTATATGATATCTC-TCC-T--ATTGCATAGTTAATAAATTTGTACC
12509045 TGGCATGATCGAAGAGCTAGCCATCAGCCAATGACAGATCTAGACATTGAGTCTCGGGGAAGCCA
127 TGGCATGATCGAAGAGCTAGCCATCAGCCAATGACAGATCTAGACATTGAGTCTCGGGGAAGCCA
12509110 TACTAAACCTAGACTTTGTTTCATAAATAAACCCAATTATATTTACCAATATAAAAGAAAATAGA
192 TACTAAACCTAGACTTTGTTTCATAAATAAA-CCAATTATATTTACCAATATAAAAGAAAATAGA
*
12509175 AATATAGATGTGAGCAAAATC-CTA-GAAAATAATGTCAAA
256 AATATAGATGTAAGCAAAATCGCTACGAAAATAATGT-AAA
12509214 CT
1 CT
12509216 CAGATAATTT
Statistics
Matches: 275, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
297 92 0.33
298 10 0.04
299 3 0.01
300 3 0.01
301 116 0.42
302 51 0.19
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (295 bp):
CTTCTAAAAACCATAAAATTCAAAACAACAAACACAAAATAACAAAAATCAATACATAAATCGGA
CATTCATCCATCTTTCAGTTATATGATATCTCTCCTATTGCATAGTTAATAAATTTGTACCTGGC
ATGATCGAAGAGCTAGCCATCAGCCAATGACAGATCTAGACATTGAGTCTCGGGGAAGCCATACT
AAACCTAGACTTTGTTTCATAAATAAACCAATTATATTTACCAATATAAAAGAAAATAGAAATAT
AGATGTAAGCAAAATCGCTACGAAAATAATGTAAA
Found at i:12511069 original size:9 final size:9
Alignment explanation
Indices: 12511055--12511079 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12511045 AAAACAACTC
12511055 CAAATTCCT
1 CAAATTCCT
12511064 CAAATTCCT
1 CAAATTCCT
12511073 CAAATTC
1 CAAATTC
12511080 TGGTAAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (9 bp):
CAAATTCCT
Found at i:12511559 original size:31 final size:31
Alignment explanation
Indices: 12511521--12511579 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
12511511 GGCTTAACCA
* *
12511521 TAAACAAGATCATGCGGCAAGTATATAACTG
1 TAAACAAGAACATGCGACAAGTATATAACTG
*
12511552 TAAACAAGAACATGTGACAAGTATATAA
1 TAAACAAGAACATGCGACAAGTATATAA
12511580 AACCACTGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (31 bp):
TAAACAAGAACATGCGACAAGTATATAACTG
Found at i:12524914 original size:2 final size:2
Alignment explanation
Indices: 12524907--12524938 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12524897 CAAGAAAGAA
*
12524907 AG AG AG AG AA AG 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
12524939 GTTGGCGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12524918 original size:10 final size:10
Alignment explanation
Indices: 12524903--12524935 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
12524893 AAAGCAAGAA
12524903 AGAAAGAGAG
1 AGAAAGAGAG
12524913 AGAAAGAGAG
1 AGAAAGAGAG
*
12524923 AGAGAGAGAG
1 AGAAAGAGAG
12524933 AGA
1 AGA
12524936 GAGGTTGGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:12524918 original size:14 final size:14
Alignment explanation
Indices: 12524899--12524929 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12524889 AGGGAAAGCA
12524899 AGAAAGAAAGAGAG
1 AGAAAGAAAGAGAG
*
12524913 AGAAAGAGAGAGAG
1 AGAAAGAAAGAGAG
12524927 AGA
1 AGA
12524930 GAGAGAGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAGAG
Found at i:12528912 original size:36 final size:36
Alignment explanation
Indices: 12528871--12528946 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
12528861 AAGGAAGTTA
12528871 AACAAGTGAATAAAATAAAAAGAATGATTGGAAAAG
1 AACAAGTGAATAAAATAAAAAGAATGATTGGAAAAG
*
12528907 AACAAGTGAATAAAATAGAAAGAATGATTGGAAAAG
1 AACAAGTGAATAAAATAAAAAGAATGATTGGAAAAG
12528943 AACA
1 AACA
12528947 TGTGCGGTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.16
Consensus pattern (36 bp):
AACAAGTGAATAAAATAAAAAGAATGATTGGAAAAG
Found at i:12528944 original size:18 final size:18
Alignment explanation
Indices: 12528889--12528944 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
12528879 AATAAAATAA
12528889 AAAGAATGATTGGAAAAG
1 AAAGAATGATTGGAAAAG
* * *
12528907 AACA-AGTGAAT-AAAATAG
1 AA-AGAATGATTGGAAA-AG
12528925 AAAGAATGATTGGAAAAG
1 AAAGAATGATTGGAAAAG
12528943 AA
1 AA
12528945 CATGTGCGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (18 bp):
AAAGAATGATTGGAAAAG
Found at i:12529669 original size:16 final size:16
Alignment explanation
Indices: 12529650--12529685 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12529640 GTGCCTTGTT
*
12529650 AAAACCTTATAAGAAA
1 AAAACCTCATAAGAAA
*
12529666 AAAACCTCATGAGAAA
1 AAAACCTCATAAGAAA
12529682 AAAA
1 AAAA
12529686 ATCTGAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.14, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAACCTCATAAGAAA
Found at i:12532648 original size:25 final size:25
Alignment explanation
Indices: 12532620--12532669 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12532610 ATGGACTTCT
*
12532620 CCCATTTCTTT-TTAATTGGATCATG
1 CCCA-TTCTTTCTTAATTGGACCATG
*
12532645 CCCATTCTTTCTTTATTGGACCATG
1 CCCATTCTTTCTTAATTGGACCATG
12532670 TCCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.46
Consensus pattern (25 bp):
CCCATTCTTTCTTAATTGGACCATG
Found at i:12532756 original size:4 final size:5
Alignment explanation
Indices: 12532714--12532754 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
12532704 TTCCTTGTTA
12532714 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
12532755 CTCTCTCACC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:12540094 original size:19 final size:19
Alignment explanation
Indices: 12540070--12540107 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12540060 CCATTTGACT
*
12540070 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
12540089 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
12540108 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:12540314 original size:28 final size:29
Alignment explanation
Indices: 12540273--12540332 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
12540263 GTCTATGGGC
* *
12540273 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
12540301 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
12540331 AA
1 AA
12540333 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:12543104 original size:18 final size:18
Alignment explanation
Indices: 12543070--12543104 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12543060 TTATAAGTCT
* *
12543070 TTATCCACTTTTGATGGA
1 TTATCCACTTCTCATGGA
12543088 TTATCCACTTCTCATGG
1 TTATCCACTTCTCATGG
12543105 GTTAATGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (18 bp):
TTATCCACTTCTCATGGA
Found at i:12545508 original size:72 final size:72
Alignment explanation
Indices: 12545390--12545638 Score: 320
Period size: 72 Copynumber: 3.4 Consensus size: 72
12545380 AACAGAATTG
** * *
12545390 ACTTAGTCGACCAAGATGTGAGTTAGTTGACTAAATGCTCTCTGCCAAAATCTGGACTTCAATAC
1 ACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGGACTTCAAGAC
*
12545455 GGAACCA
66 AGAACCA
** * * *
12545462 ACTTAGTCGATTAAGAAATGAGTTAGTCGACTAAATGCTTTTTGCCAAAATTTGGACTTCAAGAC
1 ACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGGACTTCAAGAC
12545527 AGAACCA
66 AGAACCA
* * * ***
12545534 ACTTAGTCGACCAAGAAATAAGTTAGTCGACTAAATGCTCTCTGCCAGAATCTATGACCAAAAGA
1 ACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCT-GGACTTCAAGA
12545599 CAGAACCA
65 CAGAACCA
*
12545607 ACTTAGTCGACCAAGAAGA-AAGTTAGTCGACT
1 ACTTAGTCGACCAAGAA-ATGAGTTAGTCGACT
12545639 GAGAGCTCTT
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
72 108 0.70
73 45 0.29
74 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (72 bp):
ACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATGCTCTCTGCCAAAATCTGGACTTCAAGAC
AGAACCA
Found at i:12549932 original size:32 final size:32
Alignment explanation
Indices: 12549896--12550000 Score: 95
Period size: 35 Copynumber: 3.2 Consensus size: 32
12549886 TCGCAATGGT
*
12549896 TTTTCACGAGATCAACCAAAACCCAAAATAGC
1 TTTTCACAAGATCAACCAAAACCCAAAATAGC
* * * * *
12549928 TTTTCA-AAGGCTCAACCACAACCTTTAACAATGGT
1 TTTTCACAA-GATCAACCAAAACC--CAA-AATAGC
*
12549963 TTTTCACAAGATCAACCAAAACCCAAAACTAAC
1 TTTTCACAAGATCAACCAAAACCCAAAA-TAGC
12549996 TTTTC
1 TTTTC
12550001 TAAGGCTAAG
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
31 1 0.02
32 20 0.36
33 8 0.15
34 2 0.04
35 22 0.40
36 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (32 bp):
TTTTCACAAGATCAACCAAAACCCAAAATAGC
Found at i:12549940 original size:67 final size:68
Alignment explanation
Indices: 12549859--12550007 Score: 219
Period size: 67 Copynumber: 2.2 Consensus size: 68
12549849 TTTTACAATG
* * * ** *
12549859 GCTTTTTATAGGCTCAGCCACAACCTTTCGCAATGGTTTTTCACGAGATCAACCAAAACCCAAAA
1 GCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCCAAAA
12549924 -TA
66 CTA
12549926 GCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCCAAAA
1 GCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCCAAAA
12549991 CTA
66 CTA
* *
12549994 ACTTTTCTAAGGCT
1 GCTTTTCAAAGGCT
12550008 AAGTTAGAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 59 0.81
68 14 0.19
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (68 bp):
GCTTTTCAAAGGCTCAACCACAACCTTTAACAATGGTTTTTCACAAGATCAACCAAAACCCAAAA
CTA
Found at i:12549978 original size:35 final size:35
Alignment explanation
Indices: 12549880--12549985 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 35
12549870 GCTCAGCCAC
** *
12549880 AACCTTTCGCAATGGTTTTTCACGAGATCAACCAA
1 AACCTTTAACAATGGTTTTTCACAAGATCAACCAA
* * * * *
12549915 AACC--CAA-AATAGCTTTTCA-AAGGCTCAACCAC
1 AACCTTTAACAATGGTTTTTCACAA-GATCAACCAA
12549947 AACCTTTAACAATGGTTTTTCACAAGATCAACCAA
1 AACCTTTAACAATGGTTTTTCACAAGATCAACCAA
12549982 AACC
1 AACC
12549986 CAAAACTAAC
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
31 1 0.02
32 22 0.42
34 2 0.04
35 26 0.49
36 2 0.04
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (35 bp):
AACCTTTAACAATGGTTTTTCACAAGATCAACCAA
Found at i:12557818 original size:28 final size:29
Alignment explanation
Indices: 12557758--12557823 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
12557748 GAGCAAATTT
* ** *
12557758 TGAAAAATTACACTTTTGCGCCCGTAAAG
1 TGAAAAATTACACTTTTACGCCCAAAAAA
*
12557787 TGAAAAATTACATTTTTAC-CCCAAAAAA
1 TGAAAAATTACACTTTTACGCCCAAAAAA
12557815 TGAAAAATT
1 TGAAAAATT
12557824 GCCTATAGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (29 bp):
TGAAAAATTACACTTTTACGCCCAAAAAA
Found at i:12558595 original size:74 final size:72
Alignment explanation
Indices: 12558411--12558626 Score: 208
Period size: 74 Copynumber: 3.0 Consensus size: 72
12558401 AAATTCAAAT
* * *
12558411 TTTCTGACAGT-GTGCTCTTAGTCGACTAA-CATATGTCTTAGTCGATTAAGTTGC-CTTTGTCT
1 TTTCTGACAGTAG-GCTTTTAGTCGACTAACCATCT-TCTTAGTCGATTAAGTT-CTTTTTGTCT
*
12558473 T-TGAACCCAG
63 TGT-AATCCAG
** * * *
12558483 TTTCTGGTAGTAAGCTTTTACTCGACTAACAATACTTCTTAGTCGATTAAGTTCTTTTTGTCTTG
1 TTTCTGACAGTAGGCTTTTAGTCGACTAACCAT-CTTCTTAGTCGATTAAGTTCTTTTTGTCTTG
12558548 TAATCCAG
65 TAATCCAG
* * * *
12558556 ATTTCTGACAGTAGGCTTTTAGTTGACTAACCATCCTTCTTGGTCGACTAAG-TCTTTTCTGTTT
1 -TTTCTGACAGTAGGCTTTTAGTCGACTAACCAT-CTTCTTAGTCGATTAAGTTCTTTT-TGTCT
12558620 TGTAATC
63 TGTAATC
12558627 TACTCTTGAA
Statistics
Matches: 118, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
72 24 0.20
73 39 0.33
74 55 0.47
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (72 bp):
TTTCTGACAGTAGGCTTTTAGTCGACTAACCATCTTCTTAGTCGATTAAGTTCTTTTTGTCTTGT
AATCCAG
Found at i:12559706 original size:38 final size:40
Alignment explanation
Indices: 12559635--12559741 Score: 93
Period size: 40 Copynumber: 2.8 Consensus size: 40
12559625 TCCACTATAA
* *
12559635 ACTACC-TATC-A-AGGAGCAAGCATAACCTTTCACAA-AC
1 ACTACCTTATCAAGAGGAGAAAGCACAACC-TTCACAACAC
*
12559672 ACTACCTTATCAAGAGGAGAAAGCACAACC-TCACAACGTC
1 ACTACCTTATCAAGAGGAGAAAGCACAACCTTCACAAC-AC
* **
12559712 ACTACCTTTTC-A-AGGTTAAAGCACAACCTT
1 ACTACCTTATCAAGAGGAGAAAGCACAACCTT
12559742 TAATGAAGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
37 6 0.10
38 24 0.41
39 3 0.05
40 25 0.43
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (40 bp):
ACTACCTTATCAAGAGGAGAAAGCACAACCTTCACAACAC
Found at i:12571621 original size:31 final size:31
Alignment explanation
Indices: 12571578--12571641 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
12571568 TTCTAAAAAG
*
12571578 TAAAAAATTTAGAACAAAAATTTATTTGCTT
1 TAAAAAAATTAGAACAAAAATTTATTTGCTT
*
12571609 TAAAAAAATTAGAATAAAAATTTATTTGCTT
1 TAAAAAAATTAGAACAAAAATTTATTTGCTT
12571640 TA
1 TA
12571642 CTCTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (31 bp):
TAAAAAAATTAGAACAAAAATTTATTTGCTT
Found at i:12575662 original size:19 final size:17
Alignment explanation
Indices: 12575638--12575737 Score: 69
Period size: 18 Copynumber: 5.6 Consensus size: 17
12575628 TTAAAATTGT
*
12575638 TTAATTAAGTTGTGTCTAA
1 TTAATTAAATTGT-T-TAA
12575657 TTAATTAAATTGTTTAA
1 TTAATTAAATTGTTTAA
* * *
12575674 TTAAAT-CATTAGGCTTAA
1 TTAATTAAATT--GTTTAA
*
12575692 TTAATTAAATTATTTAA
1 TTAATTAAATTGTTTAA
* *
12575709 TTAAGT-CATTAGTCTTAA
1 TTAATTAAATT-GT-TTAA
12575727 TTAATTAAATT
1 TTAATTAAATT
12575738 AAACAATTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
16 6 0.10
17 18 0.29
18 20 0.32
19 18 0.29
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (17 bp):
TTAATTAAATTGTTTAA
Found at i:12575842 original size:107 final size:106
Alignment explanation
Indices: 12575653--12575879 Score: 303
Period size: 107 Copynumber: 2.1 Consensus size: 106
12575643 TAAGTTGTGT
* * *
12575653 CTAATTAATTAAA-TTGTTTAATTAAATCATTAGGCTTAATTAATTAAATTATTTAATTAAGTCA
1 CTAATTGATTAAATTTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTATTTAATTAAATCA
*
12575717 TTAGTCTTAATTAATTAAATTAAACAATTAAGTTATTGGGC
66 TTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGGGC
* * * * *
12575758 CTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATT
1 CTAATTGATTAAATTTGTTTAATTAAATCATTAGGCCTAATTAATT-AAATTATTTAATTAAATC
* ****
12575823 ATTGGGCTTAATTAATTAAATTGTTTAATTAAGTTATTGGGC
65 ATTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGGGC
*
12575865 CTAATCGATTAAATT
1 CTAATTGATTAAATT
12575880 AAACAATTAA
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 12 0.11
106 28 0.27
107 65 0.62
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (106 bp):
CTAATTGATTAAATTTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTATTTAATTAAATCA
TTAGGCTTAATTAATTAAATTAAACAATTAAGTTATTGGGC
Found at i:12575854 original size:142 final size:138
Alignment explanation
Indices: 12575624--12575899 Score: 390
Period size: 142 Copynumber: 2.0 Consensus size: 138
12575614 TCTCAAACAC
* *
12575624 TTGATTAAAATTGTTTAATTAAGTTGTGTCTAATTAATTAAATTGTTTAATTAAATCATTAGGCT
1 TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCT
* * * *
12575689 TAATTAATTAAATTATTTAATTAAGTCATTAGTCTTAATTAATTAAATTAAACAATTAAGTTATT
66 TAATTAATTAAATTATTTAATTAAGTCATTAGGCCTAATCAATTAAATTAAACAATTAAATTATT
12575754 GGGCCTAA
131 GGGCCTAA
* * * *
12575762 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTG
1 TTGATTAAAATTGTTTAATTAAG---TTGGGCCTAATTAATT-AAATTGTTTAATTAAATCATTA
* * * *
12575827 GGCTTAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATCGATTAAATTAAACAATTAAAT
62 GGCTTAATTAATTAAATTATTTAATTAAGTCATTAGGCCTAATCAATTAAATTAAACAATTAAAT
12575892 TATTGGGC
127 TATTGGGC
12575900 TTCTTAAGGA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
138 22 0.18
141 13 0.11
142 85 0.71
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.44
Consensus pattern (138 bp):
TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTGTTTAATTAAATCATTAGGCT
TAATTAATTAAATTATTTAATTAAGTCATTAGGCCTAATCAATTAAATTAAACAATTAAATTATT
GGGCCTAA
Found at i:12575899 original size:35 final size:35
Alignment explanation
Indices: 12575624--12575879 Score: 257
Period size: 35 Copynumber: 7.3 Consensus size: 35
12575614 TCTCAAACAC
* *
12575624 TTGATTAAAATTGTTTAATTAAG---TTGTGTCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* * * * *
12575657 TTAATTAAATTGTTTAATTAAATCATTAGGCTTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * * * * *
12575692 TTAATTAAATTATTTAATTAAGTCATTAGTCTTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* ****
12575727 TTAATTAAATTAAACAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
12575762 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
12575798 TTGATTAAAATTGTTTAATTAAATTATTGGGCTTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
*
12575834 TTAATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
12575869 TCGATTAAATT
1 TTGATTAAATT
12575880 AAACAATTAA
Statistics
Matches: 188, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
32 15 0.08
33 5 0.03
35 110 0.59
36 55 0.29
37 3 0.02
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:12580338 original size:25 final size:25
Alignment explanation
Indices: 12580260--12580341 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
12580250 AGCAATCATT
12580260 CCATCTCACCCAGCTCATGTGCATC
1 CCATCTCACCCAGCTCATGTGCATC
* * * ** *
12580285 CCACCACATCGTGCACATAGTCAGACATC
1 CCATCTCACCCAGCTCAT-GT--G-CATC
12580314 CCATCTCACCCAGCTCATGTGCATC
1 CCATCTCACCCAGCTCATGTGCATC
12580339 CCA
1 CCA
12580342 CCACATCGTG
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 19 0.46
26 3 0.07
28 3 0.07
29 16 0.39
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.21
Consensus pattern (25 bp):
CCATCTCACCCAGCTCATGTGCATC
Found at i:12584364 original size:491 final size:491
Alignment explanation
Indices: 12583442--12584427 Score: 1729
Period size: 491 Copynumber: 2.0 Consensus size: 491
12583432 TAATTGGATG
12583442 AAGTCCATGAGATTAATATGCCTTGCAAGGAAACTGTAATGGGTTGCAGTTATGAGATCCTTATG
1 AAGTCCATGAGATTAATATGCCTTGCAAGGAAACTGTAATGGGTTGCAGTTATGAGATCCTTATG
*
12583507 CATCAAAGCATAATCTCAAAATGTTCTTGGTCAATGTATCATTGAGACTGGACATCAATGATACT
66 CATCAAAGCATAATCTCAAAATGTTCCTGGTCAATGTATCATTGAGACTGGACATCAATGATACT
* * *
12583572 TAAAGACTGGTACATTTTATATTCCTTACTTGAGAAGTAAGCAACCGATCTCATAGCTTAAAGTA
131 TAAAGACTAGTACATTCTATATTCCTTACTTAAGAAGTAAGCAACCGATCTCATAGCTTAAAGTA
* * * *
12583637 TAGAGATACTTGGAACTAGAATGTAGGTGTTTGCCTAGGAGAGCAAGTTCATTGAACATGACCCG
196 TAGAGATACTAGGAACTAGAATGTAAGTGCTTGCCTAGGAGAGCAAGTTCACTGAACATGACCCG
* *
12583702 CCATGAGAAATGCATTTGGTATTTCACTCAAATCTCTATGCAATACTTCTCATGTGTCAGTTGTG
261 CCATGAGAAATGCATTTGGTATTTAACTCAAATCTCTATGCAATACTTCTCATGTGTCAGATGTG
*
12583767 TAAATACTCCCCAGACTTGAGACACCAAGTTGTTTTATGTGTGGAATGCTATGCTTTGATTTCAT
326 TAAATACTCCCCAAACTTGAGACACCAAGTTGTTTTATGTGTGGAATGCTATGCTTTGATTTCAT
*
12583832 CTCTACGAGTGCCTAACCAAGGATGCCAAAACAGAATGCTTTTAAGTATAGTATGAAGCATGTGA
391 CTCTACGAGTGCCTAACCAAGGATGCCAAAACAGAATGCTTTTAAGTATAGTATAAAGCATGTGA
*
12583897 AGGCAAATGAGTGGTCAAGATAGGAATCATCACCTC
456 AGGCAAATGAGTGGTCAAGATAGGAATCATCACCCC
*
12583933 AAGTCCATGAGATTAATATGCCTTGCAAGGGAACTGTAATGGGTTGCAGTTATGAGATCCTTATG
1 AAGTCCATGAGATTAATATGCCTTGCAAGGAAACTGTAATGGGTTGCAGTTATGAGATCCTTATG
* *
12583998 CATCAAAGCGTAATCTTAAAATGTTCCTGGTCAATGTATCATTGAGACTGGACATCAATGATACT
66 CATCAAAGCATAATCTCAAAATGTTCCTGGTCAATGTATCATTGAGACTGGACATCAATGATACT
* *
12584063 TAGAGACTAGTACATTCTATGTTCCTTACTTAAGAAGTAAGCAACCGATCTCATAGCTTAAAGTA
131 TAAAGACTAGTACATTCTATATTCCTTACTTAAGAAGTAAGCAACCGATCTCATAGCTTAAAGTA
*
12584128 TAGAGATACTAGGAACTAGAATGTAAGTGCTTGCCTATGAGAGCAAGTTCACTGAACATGACCCG
196 TAGAGATACTAGGAACTAGAATGTAAGTGCTTGCCTAGGAGAGCAAGTTCACTGAACATGACCCG
* * *
12584193 CCATGAGAAGTGCATTTGGTATTTAACTCAAGTGTCTATGCAATACTTCTCATGTGTCAGATGTG
261 CCATGAGAAATGCATTTGGTATTTAACTCAAATCTCTATGCAATACTTCTCATGTGTCAGATGTG
*
12584258 TAAATACTCCCCAAACTTGAGACACCAAGTTGTTTTATGTGTGGAGTGCTATGCTTTGATTTCAT
326 TAAATACTCCCCAAACTTGAGACACCAAGTTGTTTTATGTGTGGAATGCTATGCTTTGATTTCAT
* * **
12584323 CTCTACGGGTGCCTAACCAAGGATGCCAAAACAGGATGCTTTTGGGTATAGTATAAAGCATGTGA
391 CTCTACGAGTGCCTAACCAAGGATGCCAAAACAGAATGCTTTTAAGTATAGTATAAAGCATGTGA
12584388 AGGCAAATGAGTGGTCAAGATAGGAATCATCACCCC
456 AGGCAAATGAGTGGTCAAGATAGGAATCATCACCCC
12584424 AAGT
1 AAGT
12584428 GATGCAAGGG
Statistics
Matches: 468, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
491 468 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (491 bp):
AAGTCCATGAGATTAATATGCCTTGCAAGGAAACTGTAATGGGTTGCAGTTATGAGATCCTTATG
CATCAAAGCATAATCTCAAAATGTTCCTGGTCAATGTATCATTGAGACTGGACATCAATGATACT
TAAAGACTAGTACATTCTATATTCCTTACTTAAGAAGTAAGCAACCGATCTCATAGCTTAAAGTA
TAGAGATACTAGGAACTAGAATGTAAGTGCTTGCCTAGGAGAGCAAGTTCACTGAACATGACCCG
CCATGAGAAATGCATTTGGTATTTAACTCAAATCTCTATGCAATACTTCTCATGTGTCAGATGTG
TAAATACTCCCCAAACTTGAGACACCAAGTTGTTTTATGTGTGGAATGCTATGCTTTGATTTCAT
CTCTACGAGTGCCTAACCAAGGATGCCAAAACAGAATGCTTTTAAGTATAGTATAAAGCATGTGA
AGGCAAATGAGTGGTCAAGATAGGAATCATCACCCC
Found at i:12588512 original size:10 final size:10
Alignment explanation
Indices: 12588497--12588546 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
12588487 ATAACTCTTC
12588497 TTAAAGTAAA
1 TTAAAGTAAA
*
12588507 TTAAAGCAAA
1 TTAAAGTAAA
*
12588517 ATAAAGTAAA
1 TTAAAGTAAA
*
12588527 TTAAAGCAAA
1 TTAAAGTAAA
*
12588537 ATAAAGTAAA
1 TTAAAGTAAA
12588547 CTTACACTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.22
Consensus pattern (10 bp):
TTAAAGTAAA
Found at i:12588523 original size:20 final size:20
Alignment explanation
Indices: 12588498--12588546 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
12588488 TAACTCTTCT
12588498 TAAAGTAAATTAAAGCAAAA
1 TAAAGTAAATTAAAGCAAAA
12588518 TAAAGTAAATTAAAGCAAAA
1 TAAAGTAAATTAAAGCAAAA
12588538 TAAAGTAAA
1 TAAAGTAAA
12588547 CTTACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.20
Consensus pattern (20 bp):
TAAAGTAAATTAAAGCAAAA
Found at i:12596976 original size:21 final size:21
Alignment explanation
Indices: 12596952--12597007 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
12596942 TCTGTTTCAA
12596952 ATGTATCGATACATGTTCATG
1 ATGTATCGATACATGTTCATG
12596973 ATGTATCGATACATGTTCATG
1 ATGTATCGATACATGTTCATG
*
12596994 ATGTATCAATACAT
1 ATGTATCGATACAT
12597008 ATGGTCATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (21 bp):
ATGTATCGATACATGTTCATG
Found at i:12598140 original size:80 final size:80
Alignment explanation
Indices: 12598043--12598218 Score: 212
Period size: 80 Copynumber: 2.2 Consensus size: 80
12598033 ATGTTCGATG
* * * * **
12598043 TATGAGTTCCATTTATGAGATTATGACATGTATGTCATGAGATGTACATGTTAAGCATA-TCATG
1 TATGAGTT--ATTTATGAGATTATGAAATGCATGCCATGAGATGTACATGTTAAG-ATAGCCAAA
12598107 TACACTATGGGCTAAGCA
63 TACACTATGGGCTAAGCA
** *
12598125 TATGAGTTATTTATGAGATTATGAAATGCATGCCATGAGATGTATGTGTTGAGATAGCCAAATAC
1 TATGAGTTATTTATGAGATTATGAAATGCATGCCATGAGATGTACATGTTAAGATAGCCAAATAC
12598190 ACTATGGGCTAAGCA
66 ACTATGGGCTAAGCA
*
12598205 TGATGA-TGATTTAT
1 T-ATGAGTTATTTAT
12598219 AAAAAAAGGT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.04
80 67 0.82
81 4 0.05
82 8 0.10
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (80 bp):
TATGAGTTATTTATGAGATTATGAAATGCATGCCATGAGATGTACATGTTAAGATAGCCAAATAC
ACTATGGGCTAAGCA
Found at i:12604528 original size:16 final size:16
Alignment explanation
Indices: 12604504--12604539 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12604494 TTTGTTTCAG
*
12604504 ATTTTTATTTTTTATT
1 ATTTATATTTTTTATT
*
12604520 ATTTATATTTTTTCTT
1 ATTTATATTTTTTATT
12604536 ATTT
1 ATTT
12604540 TTTTTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTATATTTTTTATT
Found at i:12604541 original size:32 final size:31
Alignment explanation
Indices: 12604504--12604566 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
12604494 TTTGTTTCAG
12604504 ATTTTTATTT-TTTATTATTTATATTT-TTTCTT
1 ATTTTT-TTTATTT-TTATTT-TATTTATTTCTT
12604536 ATTTTTTTTAGTTTTTATTTTATTTATTTCT
1 ATTTTTTTTA-TTTTTATTTTATTTATTTCT
12604567 ATCATTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
31 8 0.29
32 17 0.61
33 3 0.11
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (31 bp):
ATTTTTTTTATTTTTATTTTATTTATTTCTT
Found at i:12615412 original size:2 final size:2
Alignment explanation
Indices: 12615400--12615453 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
12615390 TTCGTATTAC
12615400 TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
12615441 CA TA TA TA TA TA T
1 TA TA TA TA TA TA T
12615454 GGTTATTTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12615420 original size:15 final size:15
Alignment explanation
Indices: 12615400--12615451 Score: 77
Period size: 15 Copynumber: 3.3 Consensus size: 15
12615390 TTCGTATTAC
12615400 TATATTATATATATA
1 TATATTATATATATA
12615415 TATATTATATATATA
1 TATATTATATATATA
*
12615430 TAGTATATATACATATA
1 TA-TAT-TATATATATA
12615447 TATAT
1 TATAT
12615452 ATGGTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 17 0.50
16 6 0.18
17 11 0.32
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:12615423 original size:13 final size:12
Alignment explanation
Indices: 12615400--12615453 Score: 76
Period size: 11 Copynumber: 4.6 Consensus size: 12
12615390 TTCGTATTAC
12615400 TATAT-TATATA
1 TATATATATATA
12615411 TATATATAT-TA
1 TATATATATATA
12615422 TATATATATAGTA
1 TATATATATA-TA
*
12615435 TATATACATATA
1 TATATATATATA
12615447 TATATAT
1 TATATAT
12615454 GGTTATTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 16 0.42
12 11 0.29
13 11 0.29
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
TATATATATATA
Found at i:12617406 original size:2 final size:2
Alignment explanation
Indices: 12617399--12617432 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12617389 AAAATTATCA
12617399 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
12617433 NTGTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12617571 original size:2 final size:2
Alignment explanation
Indices: 12617559--12617599 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
12617549 TTTTAATTAA
12617559 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12617600 TCAAAAGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12622864 original size:21 final size:21
Alignment explanation
Indices: 12622838--12622889 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
12622828 ATGCAAGGAA
12622838 CCTCATCGAGTAGCTAATTGT
1 CCTCATCGAGTAGCTAATTGT
12622859 CCTCATCGAGTAGCTAATTGT
1 CCTCATCGAGTAGCTAATTGT
12622880 CCTCATCGAG
1 CCTCATCGAG
12622890 CAACTCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (21 bp):
CCTCATCGAGTAGCTAATTGT
Found at i:12627398 original size:21 final size:22
Alignment explanation
Indices: 12627361--12627403 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
12627351 ATTTTATGAT
*
12627361 TTAATTTATAAATTAAA-ATTA
1 TTAATTTATAAAGTAAAGATTA
12627382 TTAATTTGAT-AAGTAAAGATTA
1 TTAATTT-ATAAAGTAAAGATTA
12627404 AACACATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAATTTATAAAGTAAAGATTA
Found at i:12627484 original size:22 final size:22
Alignment explanation
Indices: 12627441--12627492 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
12627431 AATATTATTG
**
12627441 ATAATTAAATTATTAATCTTAT
1 ATAATTAAATTATTAAAATTAT
12627463 ATAATTAAA-TATATAAAATTAT
1 ATAATTAAATTAT-TAAAATTAT
12627485 -TAAATTAA
1 AT-AATTAA
12627493 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTAAATTATTAAAATTAT
Found at i:12648884 original size:31 final size:31
Alignment explanation
Indices: 12648846--12648907 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12648836 AAAGATGCCA
12648846 TAAAATGAAATATTACAAATAAGTCATGAAT
1 TAAAATGAAATATTACAAATAAGTCATGAAT
*
12648877 TAAAATGAAATATTACAAATGAGTCATGAAT
1 TAAAATGAAATATTACAAATAAGTCATGAAT
12648908 AATTGGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.29
Consensus pattern (31 bp):
TAAAATGAAATATTACAAATAAGTCATGAAT
Found at i:12651659 original size:2 final size:2
Alignment explanation
Indices: 12651652--12651698 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
12651642 TCCGAACTCG
* *
12651652 TA TA TA TA TA TA TA TA TA TG TA TA TA TT TA TA TA -A TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12651692 TA TA TA T
1 TA TA TA T
12651699 TTTTAGGGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12651699 original size:20 final size:20
Alignment explanation
Indices: 12651651--12651700 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
12651641 ATCCGAACTC
*
12651651 GTATATATATATATATATAT
1 GTATATATTTATATATATAT
12651671 GTATATATTTATATAATATAT
1 GTATATATTTATAT-ATATAT
12651692 -TATATATTT
1 GTATATATTT
12651701 TTAGGGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
GTATATATTTATATATATAT
Found at i:12656554 original size:26 final size:26
Alignment explanation
Indices: 12656525--12656574 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12656515 TTGGTGAGTG
12656525 ATCCACATAT-GATGGTAAAATTATCT
1 ATCCACATATAG-TGGTAAAATTATCT
* *
12656551 ATCCACTTCTAGTGGTAAAATTAT
1 ATCCACATATAGTGGTAAAATTAT
12656575 TCTTAGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (26 bp):
ATCCACATATAGTGGTAAAATTATCT
Found at i:12657572 original size:26 final size:26
Alignment explanation
Indices: 12657512--12657573 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12657502 ACCATATACC
*
12657512 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
12657538 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
12657564 CATCATCATC
1 CATCATCATC
12657574 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:12657866 original size:42 final size:42
Alignment explanation
Indices: 12657808--12657931 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 42
12657798 ATGGGGGCAA
* *
12657808 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
* *
12657850 CAACGGCTTATATGCACTCCTACTCGCACATAGTCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
12657892 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
12657932 CAAATCAACA
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:0.23, C:0.34, G:0.22, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:12663216 original size:17 final size:17
Alignment explanation
Indices: 12663194--12663226 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12663184 TAAATATAAG
12663194 AGAAAGTATATAGAGAA
1 AGAAAGTATATAGAGAA
*
12663211 AGAAAGTATTTAGAGA
1 AGAAAGTATATAGAGA
12663227 GAGTAAGAAG
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:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (17 bp):
AGAAAGTATATAGAGAA
Found at i:12664384 original size:4 final size:4
Alignment explanation
Indices: 12664375--12664403 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
12664365 AATATAAACT
12664375 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
12664404 GTGTGTGTGT
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:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:12664408 original size:2 final size:2
Alignment explanation
Indices: 12664401--12664443 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
12664391 TATGTATGTA
* * *
12664401 TG TG TG TG TG TG TG TG TG TG TG CG CG TT TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12664443 T
1 T
12664444 AATTTTGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.05, G:0.47, T:0.49
Consensus pattern (2 bp):
TG
Found at i:12669400 original size:28 final size:27
Alignment explanation
Indices: 12669364--12669416 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12669354 ATATCCTGGT
*
12669364 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
12669391 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
12669417 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:12669486 original size:20 final size:20
Alignment explanation
Indices: 12669461--12669506 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12669451 CTTCTAAACC
12669461 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
12669481 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
12669501 TCAAAT
1 TCAAAT
12669507 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:12681105 original size:42 final size:42
Alignment explanation
Indices: 12681059--12681160 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
12681049 GTAAGAGTAA
12681059 GAGTGCACATAAGCCGTTGCTGACCCGACTATGTGCGAATGG
1 GAGTGCACATAAGCCGTTGCTGACCCGACTATGTGCGAATGG
* * *
12681101 GAGTGCACATAAGCCGTTGCTGACCGGGCTATGTGCGAGTGG
1 GAGTGCACATAAGCCGTTGCTGACCCGACTATGTGCGAATGG
*
12681143 GAGTGCGCATAAGCCGTT
1 GAGTGCACATAAGCCGTT
12681161 ACATATGAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.22
Consensus pattern (42 bp):
GAGTGCACATAAGCCGTTGCTGACCCGACTATGTGCGAATGG
Found at i:12687368 original size:42 final size:42
Alignment explanation
Indices: 12687309--12687433 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
12687299 GTTGATGTGG
*
12687309 ACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTA
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTA
* *
12687351 ACCCGGCTATGTGCGAGT-GAGAGTGCACATACGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAG-GAGTGCACATAAGCCGTTGCTA
* * * * **
12687393 ACCCTAGCTATGTACAAGTAGGGGTGTGCATAAGCCGTTGC
1 ACCC-GGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
12687434 ATATGAGATG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 41 0.59
43 27 0.39
44 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTA
Found at i:12687481 original size:2 final size:2
Alignment explanation
Indices: 12687474--12687505 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12687464 ATGATGATTG
12687474 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
12687506 NNNNNNNNNN
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:12687664 original size:2 final size:2
Alignment explanation
Indices: 12687657--12687710 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
12687647 GTACATGATG
12687657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12687699 AT AT AC AT AT AT
1 AT AT AT AT AT AT
12687711 GGTATACGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12690727 original size:42 final size:42
Alignment explanation
Indices: 12690668--12690793 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
12690658 GTAATTATAT
* *
12690668 TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
1 TGACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
* *
12690710 TGACCTGGCTATGTGCGAGTGGGTGTGCACATAAGCCGTTGT
1 TGACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
*
12690752 TGA-CTCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGTTGC
1 TGACCT-GGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
12690794 ATATGAGATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
41 2 0.03
42 74 0.97
ACGTcount: A:0.18, C:0.21, G:0.36, T:0.25
Consensus pattern (42 bp):
TGACCTGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
Found at i:12690844 original size:2 final size:2
Alignment explanation
Indices: 12690837--12690866 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12690827 ATGATGATTG
*
12690837 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12690867 GGTATATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12690967 original size:2 final size:2
Alignment explanation
Indices: 12690960--12690991 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12690950 TTTTAGCNTG
*
12690960 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12690992 GGTATATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12691055 original size:125 final size:124
Alignment explanation
Indices: 12690837--12691081 Score: 472
Period size: 125 Copynumber: 2.0 Consensus size: 124
12690827 ATGATGATTG
12690837 ATATATATATATATATATATATACATATATGGTATATGGTTATAATGCAAAAAAGTGAGAATTTG
1 ATATATATATATATATATATATACATATATGGTATATGGTTATAATGCAAAAAAGTGAGAATTTG
12690902 AATTGTTGAAATTTGGGAGTTTGTATGTATTACATGTTGCTTTTGTCATTTTAGCNTGAT
66 AATTGTTGAAATTTGGGAGTTTGTATGTATTACATGTTGCTTTTGTCATTTTAGC-TGAT
*
12690962 ATATATATATATATATATATATACATATATGGTATATGGTTATAATGCAAAAATGTGAGAATTTG
1 ATATATATATATATATATATATACATATATGGTATATGGTTATAATGCAAAAAAGTGAGAATTTG
12691027 AATTGTTGAAATTTGGGAGTTTGTATGTATTACATGTTGCTTTTGTCATTTTAGC
66 AATTGTTGAAATTTGGGAGTTTGTATGTATTACATGTTGCTTTTGTCATTTTAGC
12691082 AGGATGGCTT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 119 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (124 bp):
ATATATATATATATATATATATACATATATGGTATATGGTTATAATGCAAAAAAGTGAGAATTTG
AATTGTTGAAATTTGGGAGTTTGTATGTATTACATGTTGCTTTTGTCATTTTAGCTGAT
Found at i:12702082 original size:28 final size:28
Alignment explanation
Indices: 12702047--12702121 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
12702037 TTGAAACATA
12702047 GGGG-CAAAACGGTAATTTTATCATCCC
1 GGGGTCAAAACGGTAATTTTATCATCCC
* * * *
12702074 GGGGTCAAAATGATAATTTTGTCATCTC
1 GGGGTCAAAACGGTAATTTTATCATCCC
* *
12702102 GGGTTCAAAACCGTAATTTT
1 GGGGTCAAAACGGTAATTTT
12702122 CACCATCCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 4 0.10
28 35 0.90
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (28 bp):
GGGGTCAAAACGGTAATTTTATCATCCC
Found at i:12707620 original size:2 final size:2
Alignment explanation
Indices: 12707613--12707647 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12707603 GTTCTAACAA
* *
12707613 AT AT AT AT AT AT AT AT AT AT CT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12707648 ATGTTCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12709877 original size:16 final size:16
Alignment explanation
Indices: 12709856--12709901 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
12709846 TCCATTTTCC
12709856 TCTCCTTTCTTTCCTT
1 TCTCCTTTCTTTCCTT
*
12709872 TCTCCTTTCTTCTTTCTTT
1 TCTCC--T-TTCTTTCCTT
12709891 TCTCCTTTCTT
1 TCTCCTTTCTT
12709902 CTTTCCCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 1 0.04
19 14 0.54
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTCCTTTCTTTCCTT
Found at i:12709879 original size:7 final size:7
Alignment explanation
Indices: 12709856--12709912 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
12709846 TCCATTTTCC
12709856 TCTCCTT
1 TCTCCTT
12709863 TCTTTCCTT
1 TC--TCCTT
12709872 TCTCCTT
1 TCTCCTT
*
12709879 TCTTCTT
1 TCTCCTT
12709886 TCT--TT
1 TCTCCTT
12709891 TCTCCTT
1 TCTCCTT
*
12709898 TCTTCTT
1 TCTCCTT
*
12709905 TCCCCTT
1 TCTCCTT
12709912 T
1 T
12709913 GGTTTTTGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 5 0.12
7 30 0.71
9 7 0.17
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (7 bp):
TCTCCTT
Found at i:12709884 original size:19 final size:19
Alignment explanation
Indices: 12709862--12709907 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
12709852 TTCCTCTCCT
12709862 TTCTTTCCTTTCTCCTTTC
1 TTCTTTCCTTTCTCCTTTC
*
12709881 TTCTTTCTTTTCTCCTTTC
1 TTCTTTCCTTTCTCCTTTC
12709900 TTCTTTCC
1 TTCTTTCC
12709908 CCTTTGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCTTTCCTTTCTCCTTTC
Done.