Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 69 of 316
Found at i:20495239 original size:54 final size:54
Alignment explanation
Indices: 20495157--20495281 Score: 189
Period size: 54 Copynumber: 2.3 Consensus size: 54
20495147 GAATGACCAA
*
20495157 CTCACTTTACAATG-GAAATTATTGGTTGTTGGTGGAGGTTTAGTGACAACAAGC
1 CTCACTTTCCAA-GAGAAATTATTGGTTGTTGGTGGAGGTTTAGTGACAACAAGC
* * *
20495211 CTCACTTTCCAAGAGAAATTGTTGGTTGTTTGTGGAGGTTTAGTGGCAACAAGC
1 CTCACTTTCCAAGAGAAATTATTGGTTGTTGGTGGAGGTTTAGTGACAACAAGC
*
20495265 CTCACTTTCTAAGAGAA
1 CTCACTTTCCAAGAGAA
20495282 GTTTCTAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 1 0.02
54 64 0.98
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (54 bp):
CTCACTTTCCAAGAGAAATTATTGGTTGTTGGTGGAGGTTTAGTGACAACAAGC
Found at i:20495304 original size:54 final size:54
Alignment explanation
Indices: 20495157--20495315 Score: 155
Period size: 54 Copynumber: 2.9 Consensus size: 54
20495147 GAATGACCAA
* * * *
20495157 CTCACTTTACAATG-GAAATTATTGGTTGT-TGGTGGAGGTTTAGTGACAACAAGC
1 CTCACTTTCCAA-GAGAAATTGTTAGTTGTAT-GTGAAGGTTTAGTGACAACAAGC
* * * *
20495211 CTCACTTTCCAAGAGAAATTGTTGGTTGTTTGTGGAGGTTTAGTGGCAACAAGC
1 CTCACTTTCCAAGAGAAATTGTTAGTTGTATGTGAAGGTTTAGTGACAACAAGC
* * *
20495265 CTCACTTTCTAAGAGAAGTT-TCTAGTTGTCAT-TGAAGGTTCAGTGACAACA
1 CTCACTTTCCAAGAGAAATTGT-TAGTTGT-ATGTGAAGGTTTAGTGACAACA
20495316 GGCACAAACA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
53 2 0.02
54 87 0.96
55 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (54 bp):
CTCACTTTCCAAGAGAAATTGTTAGTTGTATGTGAAGGTTTAGTGACAACAAGC
Found at i:20498366 original size:21 final size:21
Alignment explanation
Indices: 20498328--20498367 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20498318 TTTATTAAGT
* * *
20498328 TAAATTTAAATTATTTTTTTA
1 TAAATTAAAATAAGTTTTTTA
20498349 TAAATTAAAATAAGTTTTT
1 TAAATTAAAATAAGTTTTT
20498368 GTCTTTATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TAAATTAAAATAAGTTTTTTA
Found at i:20500268 original size:38 final size:40
Alignment explanation
Indices: 20500217--20500299 Score: 134
Period size: 38 Copynumber: 2.1 Consensus size: 40
20500207 ATCATATGCA
20500217 TTTAATAATTTTATATTTC-AAAAA-AATAATATAATAGT
1 TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
* *
20500255 TTTAATAATTTTATATTTCAAAAAATAATAATTTCATAGT
1 TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
20500295 TTTAA
1 TTTAA
20500300 AATCATTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 19 0.46
39 5 0.12
40 17 0.41
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (40 bp):
TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
Found at i:20500301 original size:23 final size:23
Alignment explanation
Indices: 20500257--20500301 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20500247 ATAATAGTTT
*
20500257 TAATAATTTTATATTTCAAAAAA
1 TAATAATTTCATATTTCAAAAAA
*
20500280 TAATAATTTCATAGTTTTAAAA
1 TAATAATTTCATA-TTTCAAAA
20500302 TCATTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAATTTCATATTTCAAAAAA
Found at i:20504027 original size:49 final size:50
Alignment explanation
Indices: 20503922--20504097 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
20503912 CCATGGCAAC
* *
20503922 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGAAAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
20503972 AAGTGATAAGTAATAGCTTCGGCTACA-TTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
20504021 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
20504071 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
20504098 CTGATCAGTG
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
49 44 0.39
50 47 0.41
51 23 0.20
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:20504111 original size:31 final size:31
Alignment explanation
Indices: 20504073--20504190 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
20504063 ACAAATGACA
*
20504073 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
20504104 AGTGAAAAGTGGTAGCTTCGGCTATATGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
20504135 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
20504166 AGTGAATAGTGGTAGCTTCAGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
20504191 ATGTGACAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:20504262 original size:47 final size:46
Alignment explanation
Indices: 20504209--20504380 Score: 173
Period size: 47 Copynumber: 3.7 Consensus size: 46
20504199 AGTGATTTCT
* * *
20504209 GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTAC
1 GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATAC
* * * * * *
20504255 TGTATAAGACCATATCTTGGAAATGGCATCAGTGAGATATGTGATTC
1 -GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATAC
* * * *
20504302 GTGTAAGACCATAGCTGGGCTATGGCGTCGATATGTGATATGTGATTAC
1 GTATAAGACCATAGCTGGGATATGGCATCG--GTGTGATATGTGA-TAC
* *
20504351 GTGTAAGACCATAGCTGGGCTATGGCATCG
1 GTATAAGACCATAGCTGGGATATGGCATCG
20504381 ATAGATGAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 23 0.22
47 39 0.38
48 11 0.11
49 31 0.30
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (46 bp):
GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATAC
Found at i:20508923 original size:11 final size:11
Alignment explanation
Indices: 20508907--20508954 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
20508897 ATTAGATAAA
20508907 TAATATTTTAT
1 TAATATTTTAT
20508918 TAATATTTTAAT
1 TAATATTTT-AT
* *
20508930 GAGATATTTTAC
1 TA-ATATTTTAT
20508942 TAATATTTTAT
1 TAATATTTTAT
20508953 TA
1 TA
20508955 TAAATAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 19 0.61
12 5 0.16
13 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (11 bp):
TAATATTTTAT
Found at i:20511649 original size:33 final size:33
Alignment explanation
Indices: 20511630--20511758 Score: 208
Period size: 33 Copynumber: 3.9 Consensus size: 33
20511620 TTATGTACAC
*
20511630 TTTGTGTATACCATATGAAAAGGAAAGGTATAC
1 TTTGTGTATACCATATGAAAAGGAAAGGTATAA
*
20511663 TTTGTGTATACCATATGAATAGGAAAGGTA-AA
1 TTTGTGTATACCATATGAAAAGGAAAGGTATAA
20511695 TGTTGTGTATACCATATGAAAAGGAAAGGTATAA
1 T-TTGTGTATACCATATGAAAAGGAAAGGTATAA
20511729 TTTGTGTATACCACT-TGAAAAGGAAAGGTA
1 TTTGTGTATACCA-TATGAAAAGGAAAGGTA
20511759 CACTATATGT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.02
33 84 0.93
34 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (33 bp):
TTTGTGTATACCATATGAAAAGGAAAGGTATAA
Found at i:20511782 original size:32 final size:32
Alignment explanation
Indices: 20511609--20511783 Score: 110
Period size: 33 Copynumber: 5.3 Consensus size: 32
20511599 AAATGGTACA
** * * *
20511609 ACTTGAAAAGGTTATGTACACTTTGTGTATAC
1 ACTTGAAAAGGAAAGGTACAATATGTGTATAC
* * *
20511641 -CATATGAAAAGGAAAGGTATACTTTGTGTATAC
1 AC-T-TGAAAAGGAAAGGTACAATATGTGTATAC
* *
20511674 -CATATGAATAGGAAAGGTA-AATGTTGTGTATAC
1 AC-T-TGAAAAGGAAAGGTACAAT-ATGTGTATAC
* *
20511707 -CATATGAAAAGGAAAGGTATAATTTGTGTATACC
1 AC-T-TGAAAAGGAAAGGTACAATATGTGTATA-C
20511741 ACTTGAAAAGGAAAGGTACACTATATGTGTA-A-
1 ACTTGAAAAGGAAAGGTACA--ATATGTGTATAC
20511773 ACTTGAAAAGG
1 ACTTGAAAAGG
20511784 TTAATGTGCA
Statistics
Matches: 126, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.01
32 14 0.11
33 96 0.76
34 6 0.05
35 9 0.07
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (32 bp):
ACTTGAAAAGGAAAGGTACAATATGTGTATAC
Found at i:20511829 original size:33 final size:33
Alignment explanation
Indices: 20511743--20511829 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 33
20511733 TGTATACCAC
* * * * *
20511743 TTGAAAAGG-AAAGGTACACTATATGTGTAAAC
1 TTGAAAAGGTTAATGTACACTTTAAGTGTAAAA
*
20511775 TTGAAAAGGTTAATGTGCACTTTAAGTGTACAAA
1 TTGAAAAGGTTAATGTACACTTTAAGTGTA-AAA
20511809 TTGAAAAAGG-T-ATGTACACTT
1 TTG-AAAAGGTTAATGTACACTT
20511830 CGTGTGTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 9 0.20
33 24 0.53
34 6 0.13
35 6 0.13
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (33 bp):
TTGAAAAGGTTAATGTACACTTTAAGTGTAAAA
Found at i:20511870 original size:33 final size:33
Alignment explanation
Indices: 20511767--20511883 Score: 103
Period size: 33 Copynumber: 3.5 Consensus size: 33
20511757 TACACTATAT
* **
20511767 GTGTA-AACTTGAAAAGGTTAATGTGCACTTTAA
1 GTGTACAACTTGAAAAGG-GAATGTGCACTTCGA
* * * * *
20511800 GTGTACAAATTGAAAAAGGTATGTACACTTCGT
1 GTGTACAACTTGAAAAGGGAATGTGCACTTCGA
*
20511833 GTGTA-ACACTTGAAAAGGGAATGTGCACCTCGA
1 GTGTACA-ACTTGAAAAGGGAATGTGCACTTCGA
* *
20511866 GTGTACGACTAGAAAAGG
1 GTGTACAACTTGAAAAGG
20511884 AAAAGTCCAT
Statistics
Matches: 65, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
32 1 0.02
33 54 0.83
34 10 0.15
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (33 bp):
GTGTACAACTTGAAAAGGGAATGTGCACTTCGA
Found at i:20524721 original size:16 final size:16
Alignment explanation
Indices: 20524700--20524754 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
20524690 GCGATAGACA
20524700 AAGTAATGTAACACAG
1 AAGTAATGTAACACAG
**
20524716 AAGTAATGT-TGACA-
1 AAGTAATGTAACACAG
* **
20524730 AAGCAATGTAACATTG
1 AAGTAATGTAACACAG
20524746 AAGTAATGT
1 AAGTAATGT
20524755 TCAATCCAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
16 17 0.59
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (16 bp):
AAGTAATGTAACACAG
Found at i:20524732 original size:30 final size:30
Alignment explanation
Indices: 20524696--20524755 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20524686 AAATGCGATA
*
20524696 GACAAAGTAATGTAACACAGAAGTAATGTT
1 GACAAAGCAATGTAACACAGAAGTAATGTT
**
20524726 GACAAAGCAATGTAACATTGAAGTAATGTT
1 GACAAAGCAATGTAACACAGAAGTAATGTT
20524756 CAATCCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (30 bp):
GACAAAGCAATGTAACACAGAAGTAATGTT
Found at i:20532230 original size:38 final size:38
Alignment explanation
Indices: 20532179--20532256 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
20532169 GTTTGAATCG
20532179 TTCTCTAAAACGGAAGAGGAAACAAACAGATTTGGTAC
1 TTCTCTAAAACGGAAGAGGAAACAAACAGATTTGGTAC
20532217 TTCTCTAAAACGGAAGAGGAAACAAACAGATTTGGTAC
1 TTCTCTAAAACGGAAGAGGAAACAAACAGATTTGGTAC
20532255 TT
1 TT
20532257 GCTGCTCCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (38 bp):
TTCTCTAAAACGGAAGAGGAAACAAACAGATTTGGTAC
Found at i:20535196 original size:41 final size:41
Alignment explanation
Indices: 20535134--20535289 Score: 208
Period size: 41 Copynumber: 3.8 Consensus size: 41
20535124 AATCATCACA
*
20535134 AAAGG-TGAGCAATAGCGGCGTTTTTGGTCCAAACGACGCT
1 AAAGGTTGAGCAATAGTGGCGTTTTTGGTCCAAACGACGCT
* * *
20535174 AAAGGTTGAGCAATAGTGGCGTTTTTTGTCTAAACGCCGCT
1 AAAGGTTGAGCAATAGTGGCGTTTTTGGTCCAAACGACGCT
* * *
20535215 AAAGGTTGAGCTATAGTGGCGTTTTTTTGTTCAAAC-ACCGCT
1 AAAGGTTGAGCAATAGTGGCG-TTTTTGGTCCAAACGA-CGCT
*
20535257 AAATGTTGAGCAATAGTGGCGTTTTTGGTCCAA
1 AAAGGTTGAGCAATAGTGGCGTTTTTGGTCCAA
20535290 GCGCCACGAA
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
40 5 0.05
41 61 0.60
42 35 0.35
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (41 bp):
AAAGGTTGAGCAATAGTGGCGTTTTTGGTCCAAACGACGCT
Found at i:20535764 original size:8 final size:8
Alignment explanation
Indices: 20535743--20535859 Score: 56
Period size: 8 Copynumber: 15.6 Consensus size: 8
20535733 TGGCTTTCTC
20535743 TAAACCC-
1 TAAACCCT
20535750 T-AACCCT
1 TAAACCCT
20535757 TAAACCCT
1 TAAACCCT
20535765 TAAACCGC-
1 TAAACC-CT
*
20535773 TAAACCTT
1 TAAACCCT
*
20535781 TAAA-TCT
1 TAAACCCT
*
20535788 CAAACCC-
1 TAAACCCT
* *
20535795 GAAA-TCT
1 TAAACCCT
20535802 TAAACCC-
1 TAAACCCT
*
20535809 TAAACCCC
1 TAAACCCT
*
20535817 TAAACCAT
1 TAAACCCT
* *
20535825 TGAA-CCA
1 TAAACCCT
20535832 T-AA-CCT
1 TAAACCCT
20535838 CTAAACCCT
1 -TAAACCCT
*
20535847 TAAACCCC
1 TAAACCCT
20535855 TAAAC
1 TAAAC
20535860 TACAGACCCC
Statistics
Matches: 83, Mismatches: 16, Indels: 21
0.69 0.13 0.17
Matches are distributed among these distances:
6 10 0.12
7 22 0.27
8 47 0.57
9 4 0.05
ACGTcount: A:0.40, C:0.36, G:0.03, T:0.21
Consensus pattern (8 bp):
TAAACCCT
Found at i:20535822 original size:15 final size:15
Alignment explanation
Indices: 20535742--20535822 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 15
20535732 ATGGCTTTCT
20535742 CTAAACCCT-AACCC
1 CTAAACCCTAAACCC
* *
20535756 TTAAACCCTTAAACCG
1 CTAAACCC-TAAACCC
* * *
20535772 CTAAACCTTTAAATCT
1 CTAAACC-CTAAACCC
* *
20535788 C-AAACCCGAAA-TC
1 CTAAACCCTAAACCC
*
20535801 TTAAACCCTAAACCC
1 CTAAACCCTAAACCC
20535816 CTAAACC
1 CTAAACC
20535823 ATTGAACCAT
Statistics
Matches: 48, Mismatches: 14, Indels: 9
0.68 0.20 0.13
Matches are distributed among these distances:
14 19 0.40
15 13 0.27
16 16 0.33
ACGTcount: A:0.40, C:0.37, G:0.02, T:0.21
Consensus pattern (15 bp):
CTAAACCCTAAACCC
Found at i:20536668 original size:118 final size:115
Alignment explanation
Indices: 20536315--20536805 Score: 589
Period size: 118 Copynumber: 4.3 Consensus size: 115
20536305 AGCTTTGTTT
* * * * * *
20536315 TTAGTGGCGTTTTGACTAAAACGTCGCAAAAGGATAGCCGA-TAGTGGCGTTTTCAC-AAAAAAT
1 TTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATCC-ATTAGTGGCATTTTCACAAAAAAAC
* ** * *
20536378 GTCATGAATATGTTTTAAGA-GTGCAAAACACCACCGTTTTTATCTGCCTA
65 GCCGCGAATATGTTTTAAGATGTGCAAAACACTACAGTTTTTATCTGCCTA
* *
20536428 TTAGTGGCATTTTTACTAAAATGCCGCAAAAGGATATCCATTAGTGGCGTTTTCACAAAAAAACG
1 TTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATCCATTAGTGGCATTTTCACAAAAAAACG
* *
20536493 CCGCGAATATGTTTTAAGAGTGTGCAAAACGC-AGCTGTTTTTATCTGCCTA
66 CCGCGAATATGTTTTAAGA-TGTGCAAAACACTA-CAGTTTTTATCTGCCTA
* **
20536544 TTAGTGGTGTTTTTACTAAAATGCTACAAAAGGATATCCATTAGTGGCATTTTCACAAAAAAAAA
1 TTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATCCATTAGTGGCATTTTCAC--AAAAAAA
* * *
20536609 CGCCGCGAATATGTTTTAAGAGTGTGCAAAACGCTGCGGTTTTTATCTGCCTA
64 CGCCGCGAATATGTTTTAAGA-TGTGCAAAACACTACAGTTTTTATCTGCCTA
* * * * *
20536662 TCAGTGGCGCTTTTACTAAAACGCCGCAAAAGGATATCCTTTAGTGGCATTTTCAC-ATAAAACG
1 TTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATCCATTAGTGGCATTTTCACAAAAAAACG
* * * *
20536726 CTGCGAA-ATGGCTTTAAGATGTGCAAAACACTACAGTTTTTATCTGCTTT
66 CCGCGAATAT-GTTTTAAGATGTGCAAAACACTACAGTTTTTATCTGCCTA
* *
20536776 TTAGTGGCGTTTTTACTAAAACGTCGCAAA
1 TTAGTGGCGTTTTTACTAAAATGCCGCAAA
20536806 TATAGATTAT
Statistics
Matches: 333, Mismatches: 36, Indels: 17
0.86 0.09 0.04
Matches are distributed among these distances:
112 1 0.00
113 49 0.15
114 78 0.23
115 22 0.07
116 77 0.23
118 106 0.32
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (115 bp):
TTAGTGGCGTTTTTACTAAAATGCCGCAAAAGGATATCCATTAGTGGCATTTTCACAAAAAAACG
CCGCGAATATGTTTTAAGATGTGCAAAACACTACAGTTTTTATCTGCCTA
Found at i:20538138 original size:13 final size:14
Alignment explanation
Indices: 20538122--20538157 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
20538112 CAATCTCATA
20538122 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
20538135 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
20538148 TCTC-ATTTCA
1 TCTCAATTTCA
20538158 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:20538147 original size:18 final size:19
Alignment explanation
Indices: 20538109--20538149 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
20538099 TGGTTCATGT
20538109 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
20538128 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
20538146 TTTC
1 TTTC
20538150 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:20538317 original size:30 final size:30
Alignment explanation
Indices: 20538281--20538374 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
20538271 ATCCAACCCA
20538281 AACACACCCGGAATATTATAAATCCTCCAT
1 AACACACCCGGAATATTATAAATCCTCCAT
** * *
20538311 AACACA-CTAGTATATCAT--ATCCTCCCA-
1 AACACACCCGGAATATTATAAATCCT-CCAT
20538338 AACACACCCGGAATATTATAAATCCTCCAT
1 AACACACCCGGAATATTATAAATCCTCCAT
20538368 AACACAC
1 AACACAC
20538375 TAGTATATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
27 11 0.22
28 11 0.22
29 11 0.22
30 18 0.35
ACGTcount: A:0.40, C:0.32, G:0.05, T:0.22
Consensus pattern (30 bp):
AACACACCCGGAATATTATAAATCCTCCAT
Found at i:20538335 original size:27 final size:27
Alignment explanation
Indices: 20538302--20538401 Score: 105
Period size: 27 Copynumber: 3.6 Consensus size: 27
20538292 AATATTATAA
20538302 ATCCT-CCATAACACACTAGTATATCAT
1 ATCCTCCCA-AACACACTAGTATATCAT
** * *
20538329 ATCCTCCCAAACACACCCGGAATATTAT
1 ATCCTCCCAAACACA-CTAGTATATCAT
20538357 AAATCCT-CCATAACACACTAGTATATCAT
1 --ATCCTCCCA-AACACACTAGTATATCAT
20538386 ATCCTCCCAAACACAC
1 ATCCTCCCAAACACAC
20538402 CAATAATGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
27 23 0.39
28 14 0.24
29 11 0.19
30 11 0.19
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.24
Consensus pattern (27 bp):
ATCCTCCCAAACACACTAGTATATCAT
Found at i:20538351 original size:57 final size:57
Alignment explanation
Indices: 20538277--20538402 Score: 252
Period size: 57 Copynumber: 2.2 Consensus size: 57
20538267 GAATATCCAA
20538277 CCCAAACACACCCGGAATATTATAAATCCTCCATAACACACTAGTATATCATATCCT
1 CCCAAACACACCCGGAATATTATAAATCCTCCATAACACACTAGTATATCATATCCT
20538334 CCCAAACACACCCGGAATATTATAAATCCTCCATAACACACTAGTATATCATATCCT
1 CCCAAACACACCCGGAATATTATAAATCCTCCATAACACACTAGTATATCATATCCT
20538391 CCCAAACACACC
1 CCCAAACACACC
20538403 AATAATGCAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 69 1.00
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.22
Consensus pattern (57 bp):
CCCAAACACACCCGGAATATTATAAATCCTCCATAACACACTAGTATATCATATCCT
Found at i:20538865 original size:15 final size:15
Alignment explanation
Indices: 20538845--20538891 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
20538835 TATATTATAT
20538845 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
20538860 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
20538875 TTCAATCAATATAAA
1 TTCAATCAATATAAA
20538890 TT
1 TT
20538892 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:20539853 original size:23 final size:23
Alignment explanation
Indices: 20539802--20539856 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
20539792 TCGTCCCTGC
*
20539802 TATTCTGTTTCTTTCTTTCTTTT
1 TATTCTTTTTCTTTCTTTCTTTT
*
20539825 TATTCTTTTTGTTTCTTTC-TTT
1 TATTCTTTTTCTTTCTTTCTTTT
20539847 TATTTCTTTT
1 TA-TTCTTTT
20539857 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.05, C:0.15, G:0.04, T:0.76
Consensus pattern (23 bp):
TATTCTTTTTCTTTCTTTCTTTT
Found at i:20541783 original size:9 final size:9
Alignment explanation
Indices: 20541769--20541913 Score: 141
Period size: 9 Copynumber: 16.1 Consensus size: 9
20541759 ATTCCTTTCT
20541769 TAACTTACA
1 TAACTTACA
20541778 TAACTTACA
1 TAACTTACA
* *
20541787 TAA-ATATA
1 TAACTTACA
* *
20541795 TATCATATCA
1 TAACTTA-CA
20541805 TAACTTACA
1 TAACTTACA
*
20541814 TAACTTATA
1 TAACTTACA
20541823 TAACTTACA
1 TAACTTACA
*
20541832 TAATTTACA
1 TAACTTACA
20541841 TAACTTACA
1 TAACTTACA
* *
20541850 TAA-ATATA
1 TAACTTACA
* *
20541858 TATCATATCA
1 TAACTTA-CA
20541868 TAACTTACA
1 TAACTTACA
20541877 TAACTTACA
1 TAACTTACA
* *
20541886 CAATTTACA
1 TAACTTACA
20541895 TAACTTACA
1 TAACTTACA
*
20541904 TAAATTACA
1 TAACTTACA
20541913 T
1 T
20541914 GATTTAATTC
Statistics
Matches: 111, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
8 10 0.09
9 89 0.80
10 12 0.11
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TAACTTACA
Found at i:20541872 original size:63 final size:63
Alignment explanation
Indices: 20541769--20541913 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
20541759 ATTCCTTTCT
* *
20541769 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTATATAACTTACA
1 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
* *
20541832 TAATTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAATTTACA
1 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
*
20541895 TAACTTACATAAATTACAT
1 TAACTTACATAACTTACAT
20541914 GATTTAATTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 76 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (63 bp):
TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
Found at i:20545813 original size:45 final size:45
Alignment explanation
Indices: 20545718--20545815 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
20545708 GTAGCAGTAG
* * *
20545718 CAGTAACAGTAACGGTATTCAACACACAAAGTGCTGAATCTATAA
1 CAGTAACAGTAACAGTATTCAACACACAAAATGCTGAATCGATAA
* * * *
20545763 TAGTAACGGTAACAGTATTCGACACACAAAATG-TCGAATCGGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAATGCT-GAATCGATAA
20545808 CAGTAACA
1 CAGTAACA
20545816 ATAGTCGGCA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAATGCTGAATCGATAA
Found at i:20547429 original size:20 final size:19
Alignment explanation
Indices: 20547402--20547443 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
20547392 ATATAAAACC
20547402 ATAACAATTA-ATAATTATA
1 ATAACAATTATATAA-TATA
20547421 ATAATCAATTATATAATATA
1 ATAA-CAATTATATAATATA
20547441 ATA
1 ATA
20547444 TAATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAACAATTATATAATATA
Found at i:20547441 original size:5 final size:5
Alignment explanation
Indices: 20547431--20547461 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
20547421 ATAATCAATT
20547431 ATATA ATATA ATATA ATATA ATAT- ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA AT
20547462 CTAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:20550812 original size:43 final size:43
Alignment explanation
Indices: 20550751--20551104 Score: 390
Period size: 43 Copynumber: 8.3 Consensus size: 43
20550741 TGACTTGTAG
** * *
20550751 TAGCGGCGTTTGTAG-AGAAAGCGTTGATAAAGGTCACGATCTA
1 TAGCGGCGTTTGTAGTA-AAAGCGCCGCTAAAGGTCACGTTCTA
* * *
20550794 TAGCGGCGTTTGTAG-AGAAAGCGCCACTAAAGGTCATGTTTTA
1 TAGCGGCGTTTGTAGTA-AAAGCGCCGCTAAAGGTCACGTTCTA
* * *
20550837 TAGCGACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
* *
20550880 TAGCGGCATTTGTAG-AAAAGCGCCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
* * *
20550922 TAGCCGCGTTTGTAGTAAAAACGTCGCTAAAGGTCACGTTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
* * * * * * *
20550965 CAGCGGTGTTAGTAGTAAAACCGCCACTAAAGGTTACATTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
* * *
20551008 TAGCGGCATTTGTAGTAAAAGCACCGCTAAAGGTCACGATCTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
* * * * *
20551051 TAACGGCCTTTGTAGTAAAAGCGTCGCTAAAGGTCATGTTTTA
1 TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
*
20551094 TAGTGGCGTTT
1 TAGCGGCGTTT
20551105 TTTCAAATAA
Statistics
Matches: 257, Mismatches: 52, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
42 38 0.15
43 218 0.85
44 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGGTCACGTTCTA
Found at i:20551041 original size:171 final size:172
Alignment explanation
Indices: 20550751--20551096 Score: 446
Period size: 171 Copynumber: 2.0 Consensus size: 172
20550741 TGACTTGTAG
* * * * * *
20550751 TAGCGGCGTTTGTAGAGAAAGCGTTGATAAAGGTCACGATCTATAGCGGCGTTTGTAGAGAAAGC
1 TAGCCGCGTTTGTAGAGAAAACGTCGATAAAGGTCACGATCTACAGCGGCGTTAGTAGAGAAACC
** * * ** *
20550816 GCCACTAAAGGTCATGTTTTATAGCGACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTAT
66 GCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATCTAT
*
20550881 AGCGGCATTTGTAG-AAAAGCGCCGCTAAAGGTCATGTTCTA
131 AACGGCATTTGTAGTAAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
20550922 TAGCCGCGTTTGTAGTA-AAAACGTCGCTAAAGGTCACGTTCTACAGCGGTGTTAGTAGTA-AAA
1 TAGCCGCGTTTGTAG-AGAAAACGTCGATAAAGGTCACGATCTACAGCGGCGTTAGTAG-AGAAA
* * *
20550985 CCGCCACTAAAGGTTACATTCTATAGCGGCATTTGTAGTAAAAGCACCGCTAAAGGTCACGATCT
64 CCGCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATCT
* * *
20551050 ATAACGGCCTTTGTAGTAAAAGCGTCGCTAAAGGTCATGTTTTA
129 ATAACGGCATTTGTAGTAAAAGCGCCGCTAAAGGTCATGTTCTA
20551094 TAG
1 TAG
20551097 TGGCGTTTTT
Statistics
Matches: 149, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
171 119 0.80
172 30 0.20
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (172 bp):
TAGCCGCGTTTGTAGAGAAAACGTCGATAAAGGTCACGATCTACAGCGGCGTTAGTAGAGAAACC
GCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATCTAT
AACGGCATTTGTAGTAAAAGCGCCGCTAAAGGTCATGTTCTA
Found at i:20559893 original size:33 final size:35
Alignment explanation
Indices: 20559856--20559927 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
20559846 TAATATAAAT
* * * *
20559856 ATAAGTAGTTCCTTAAC-AAGCTTTTAAGCA-AAC
1 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
20559889 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
1 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
20559924 ATAA
1 ATAA
20559928 CAGGAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 15 0.45
34 11 0.33
35 7 0.21
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (35 bp):
ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
Found at i:20562664 original size:17 final size:18
Alignment explanation
Indices: 20562632--20562665 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20562622 TCAACTTAAA
20562632 AAATAAAGACAAATACAG
1 AAATAAAGACAAATACAG
*
20562650 AAATAAA-ATAAATACA
1 AAATAAAGACAAATACA
20562666 TAAGTAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (18 bp):
AAATAAAGACAAATACAG
Found at i:20562783 original size:3 final size:3
Alignment explanation
Indices: 20562775--20562799 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20562765 AAATAAATGA
20562775 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
20562800 TGTACAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20562880 original size:15 final size:14
Alignment explanation
Indices: 20562862--20562905 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
20562852 CAAATAGATG
*
20562862 AATAGATAATAATAT
1 AATA-ATAATAATAA
20562877 AATAATAGATAATAA
1 AATAATA-ATAATAA
*
20562892 AATACTAATAATAA
1 AATAATAATAATAA
20562906 TGAAGGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:20562883 original size:18 final size:18
Alignment explanation
Indices: 20562862--20562906 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
20562852 CAAATAGATG
*
20562862 AATAGATAATAATATAAT
1 AATAGATAATAAAATAAT
*
20562880 AATAGATAATAAAATACT
1 AATAGATAATAAAATAAT
20562898 AATA-ATAAT
1 AATAGATAAT
20562907 GAAGGCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
AATAGATAATAAAATAAT
Found at i:20565508 original size:12 final size:12
Alignment explanation
Indices: 20565493--20565524 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20565483 CCCGGCTAAG
20565493 TATTAATTTTTA
1 TATTAATTTTTA
20565505 TATTAA-TTTTA
1 TATTAATTTTTA
20565516 TA-TAATTTT
1 TATTAATTTT
20565525 GAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 10 0.53
12 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTAATTTTTA
Found at i:20565685 original size:30 final size:30
Alignment explanation
Indices: 20565651--20565707 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
20565641 TAACAAGCAG
20565651 ATGCCTCTAAAATAATAACAAAATTAACAA
1 ATGCCTCTAAAATAATAACAAAATTAACAA
*
20565681 ATGCCTTTAAAATAATAACAAAATTAA
1 ATGCCTCTAAAATAATAACAAAATTAA
20565708 TAAGAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (30 bp):
ATGCCTCTAAAATAATAACAAAATTAACAA
Found at i:20565765 original size:22 final size:22
Alignment explanation
Indices: 20565740--20565782 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20565730 TATCCAAACA
20565740 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* *
20565762 ATAATAGTAAAATAGTAGCAA
1 ATAACAATAAAATAGTAGCAA
20565783 AATAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:20565786 original size:11 final size:11
Alignment explanation
Indices: 20565748--20565787 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
20565738 CAATAACAAT
20565748 AAAATAGTAGC
1 AAAATAGTAGC
* * *
20565759 AACATAATAGT
1 AAAATAGTAGC
20565770 AAAATAGTAGC
1 AAAATAGTAGC
20565781 AAAATAG
1 AAAATAG
20565788 GAAAAAAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:20568262 original size:4 final size:4
Alignment explanation
Indices: 20568253--20568279 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20568243 GGCTTCAACC
20568253 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
20568280 AAGGCATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:20574235 original size:10 final size:10
Alignment explanation
Indices: 20574222--20574246 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20574212 ATATATAAAA
20574222 ATAAAATATT
1 ATAAAATATT
20574232 ATAAAATATT
1 ATAAAATATT
20574242 ATAAA
1 ATAAA
20574247 CTTAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATATT
Found at i:20584688 original size:16 final size:17
Alignment explanation
Indices: 20584667--20584706 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20584657 CTCCCCCTAA
**
20584667 AATTTTTATT-TTTATT
1 AATTTTTATTATAAATT
20584683 AATTTTTATTATAAATT
1 AATTTTTATTATAAATT
20584700 AATTTTT
1 AATTTTT
20584707 TAAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTATTATAAATT
Found at i:20596859 original size:14 final size:14
Alignment explanation
Indices: 20596840--20596876 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20596830 TAAAATATCC
20596840 AAATAATAACAAGA
1 AAATAATAACAAGA
* *
20596854 AAATAATAGCAATA
1 AAATAATAACAAGA
20596868 AAATAATAA
1 AAATAATAA
20596877 AATAACAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATAATAACAAGA
Found at i:20604218 original size:9 final size:9
Alignment explanation
Indices: 20604204--20604275 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
20604194 CAAGTATAAT
20604204 TAAGTTATG
1 TAAGTTATG
20604213 TAAGTTATG
1 TAAGTTATG
* * *
20604222 ATATGATATA
1 -TAAGTTATG
*
20604232 T-ATTTATG
1 TAAGTTATG
*
20604240 T-A-TTATT
1 TAAGTTATG
*
20604247 TAAGTTTTG
1 TAAGTTATG
*
20604256 TAAATTATG
1 TAAGTTATG
20604265 TAAGTTATG
1 TAAGTTATG
20604274 TA
1 TA
20604276 TTATGTACGA
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
7 5 0.11
8 6 0.13
9 30 0.64
10 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (9 bp):
TAAGTTATG
Found at i:20604422 original size:9 final size:9
Alignment explanation
Indices: 20604408--20604515 Score: 59
Period size: 9 Copynumber: 12.2 Consensus size: 9
20604398 TGTGTTAATT
20604408 TTATGTAAA
1 TTATGTAAA
*
20604417 TTATGTAAG
1 TTATGTAAA
20604426 TTATG-AAA
1 TTATGTAAA
*
20604434 TTTGATCTTTAAA
1 -TT-A--TGTAAA
* *
20604447 TTATGCAAG
1 TTATGTAAA
*
20604456 TCATGT--A
1 TTATGTAAA
20604463 TTATGTAAGA
1 TTATGTAA-A
20604473 -TATGT--A
1 TTATGTAAA
*
20604479 TTATGTAAG
1 TTATGTAAA
20604488 TTATGTAAA
1 TTATGTAAA
*
20604497 TTATGTAAG
1 TTATGTAAA
20604506 TTATG-AAA
1 TTATGTAAA
20604514 TT
1 TT
20604516 CGAACTTTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 23
0.67 0.13 0.21
Matches are distributed among these distances:
6 1 0.01
7 10 0.14
8 6 0.08
9 48 0.65
10 2 0.03
11 1 0.01
12 3 0.04
13 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (9 bp):
TTATGTAAA
Found at i:20604467 original size:16 final size:15
Alignment explanation
Indices: 20604446--20604506 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 15
20604436 TGATCTTTAA
*
20604446 ATTATGCAAGTCATGT
1 ATTATGTAAGT-ATGT
20604462 ATTATGTAAGATATGT
1 ATTATGTAAG-TATGT
20604478 ATTATGTAAGTTATGT
1 ATTATGTAAG-TATGT
20604494 AAATTATGTAAGT
1 --ATTATGTAAGT
20604507 TATGAAATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 28 0.70
17 2 0.05
18 10 0.25
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (15 bp):
ATTATGTAAGTATGT
Found at i:20604826 original size:40 final size:41
Alignment explanation
Indices: 20604782--20604868 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 41
20604772 TTAAATACAT
20604782 TTAAAACAAATATTAAAACAAGAAACAAA-TAAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATTAAAAAATATA
* * * * *
20604822 TTAAAACAATTCTTAAAACAATACACAAATTGAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATTAAAAAATATA
*
20604863 ATAAAA
1 TTAAAA
20604869 ATTGATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 25 0.62
41 15 0.38
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (41 bp):
TTAAAACAAATATTAAAACAAGAAACAAATTAAAAAATATA
Found at i:20604912 original size:23 final size:21
Alignment explanation
Indices: 20604884--20604926 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
20604874 TTATATTAAA
*
20604884 ATTAAAATTAAAATATAAATATG
1 ATTAAAAATAAAA-A-AAATATG
20604907 ATTAAAAATAAAAAAAATAT
1 ATTAAAAATAAAAAAAATAT
20604927 ATATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATTAAAAATAAAAAAAATATG
Found at i:20605325 original size:62 final size:62
Alignment explanation
Indices: 20605248--20605388 Score: 246
Period size: 62 Copynumber: 2.3 Consensus size: 62
20605238 AATTAAAGTG
* *
20605248 AAATAAAATAGAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATATTA
* *
20605310 AAATAAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAATATTA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATATTA
20605372 AAATAAAATAAAATATT
1 AAATAAAATAAAATATT
20605389 GAAATTATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (62 bp):
AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATATTA
Found at i:20605429 original size:99 final size:99
Alignment explanation
Indices: 20605310--20605681 Score: 611
Period size: 99 Copynumber: 3.8 Consensus size: 99
20605300 GGTAATGTTA
* * *
20605310 AAATAAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAATATTAAAA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
20605375 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
* *
20605409 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
20605474 TAAAATAAAACATTGAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
* * *
20605508 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
20605573 TAAAATAAAATATTAAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
* * *
20605607 AAAAAAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAAT-TTGAAA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT-AAA
20605671 ATAAAATAAAA
65 ATAAAATAAAA
20605682 GATAATAAAA
Statistics
Matches: 257, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
98 2 0.01
99 255 0.99
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.38
Consensus pattern (99 bp):
AAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
TAAAATAAAATATTGAAATTATTTTTCGTGATTC
Found at i:20608679 original size:12 final size:12
Alignment explanation
Indices: 20608662--20608687 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20608652 CAAGTTAAAT
20608662 TAAGTCACCAAA
1 TAAGTCACCAAA
20608674 TAAGTCACCAAA
1 TAAGTCACCAAA
20608686 TA
1 TA
20608688 TGCAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAGTCACCAAA
Found at i:20609978 original size:77 final size:77
Alignment explanation
Indices: 20609885--20610058 Score: 271
Period size: 77 Copynumber: 2.3 Consensus size: 77
20609875 TTTAGCGGCG
*
20609885 TTTTTCAAAAAGCGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTA
1 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACT-
20609950 TTTTTTGCGAC-A
65 TTTTTTGCGACGA
* *
20609962 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGATGTCGTTTTGTTCAACTT
1 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTT
* *
20610027 TTTTTGCGGCGC
66 TTTTTGCGACGA
*
20610039 TTTTT-AAAAAACGTCGCTAA
1 TTTTTCAAAAAACGCCGCTAA
20610059 TGCTTGATCT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 24 0.27
77 66 0.73
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (77 bp):
TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTT
TTTTTGCGACGA
Found at i:20611274 original size:14 final size:15
Alignment explanation
Indices: 20611241--20611275 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20611231 TTTTAAGGAA
20611241 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
20611256 AAAAATAAATGTTTT
1 AAAAATAAATATTGT
20611271 AAAAA
1 AAAAA
20611276 GCTTAGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:20613416 original size:5 final size:5
Alignment explanation
Indices: 20613406--20613436 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
20613396 TGTTTGGAGT
*
20613406 GAAGA GAAGA GAAGA GAAGG GAAGA GAAGA G
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA G
20613437 CGAGTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:20614693 original size:37 final size:37
Alignment explanation
Indices: 20614643--20614716 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
20614633 CTTGGGGCTA
20614643 TGTCAGGAGAAATTCAATTTTCAAATCAACTAATAAT
1 TGTCAGGAGAAATTCAATTTTCAAATCAACTAATAAT
20614680 TGTCAGGAGAAATTCAATTTTCAAATCAACTAATAAT
1 TGTCAGGAGAAATTCAATTTTCAAATCAACTAATAAT
20614717 GATTGTTCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (37 bp):
TGTCAGGAGAAATTCAATTTTCAAATCAACTAATAAT
Found at i:20620601 original size:20 final size:20
Alignment explanation
Indices: 20620572--20620616 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20620562 TGTCAGTCTT
* * *
20620572 ATGAATAGTGGAGTTAAGTC
1 ATGAACAGTGGAGTCAAATC
20620592 ATGAACAGTGGAGTCAAATC
1 ATGAACAGTGGAGTCAAATC
20620612 ATGAA
1 ATGAA
20620617 GAATGATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (20 bp):
ATGAACAGTGGAGTCAAATC
Found at i:20629312 original size:29 final size:28
Alignment explanation
Indices: 20629276--20629377 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
20629266 AGAAATACTA
20629276 ATATCATGGCTCGAAGCCAAATCTGCCG
1 ATATCATGGCTCGAAGCCAAATCTGCCG
* * *
20629304 ATATGCATGGCCCGAA---ATA-CT---A
1 ATAT-CATGGCTCGAAGCCAAATCTGCCG
*
20629326 ATATCATGGCTCGAAGCCAAATCAGCCG
1 ATATCATGGCTCGAAGCCAAATCTGCCG
20629354 ATATGCATGG-TCCGAAGCCAAATC
1 ATAT-CATGGCT-CGAAGCCAAATC
20629378 GATTTATCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
21 10 0.18
22 4 0.07
24 2 0.04
25 3 0.05
26 2 0.04
28 9 0.16
29 27 0.47
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (28 bp):
ATATCATGGCTCGAAGCCAAATCTGCCG
Found at i:20629330 original size:50 final size:50
Alignment explanation
Indices: 20629267--20629369 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
20629257 ACCTATCCCA
*
20629267 GAAATACTAATATCATGGCTCGAAGCCAAATCTGCCGATATGCATGGCCC
1 GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
*
20629317 GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGTCC
1 GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
20629367 GAA
1 GAA
20629370 GCCAAATCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (50 bp):
GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
Found at i:20630891 original size:20 final size:20
Alignment explanation
Indices: 20630866--20630958 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 20
20630856 ATGATATTAT
20630866 TTTAATATTTTAATATTAAA
1 TTTAATATTTTAATATTAAA
* *
20630886 TTTAAT-TTAATACTTATCTTAATA
1 TTTAATATT--T--TAATATTAA-A
* *
20630910 TTTTATTAATTTAATATTAAA
1 -TTTAATATTTTAATATTAAA
* * *
20630931 GTGAATATCTTAATATTAAA
1 TTTAATATTTTAATATTAAA
20630951 TTTAATAT
1 TTTAATAT
20630959 AATTTTTCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.51
21 2 0.04
22 7 0.13
23 7 0.13
24 2 0.04
25 5 0.09
26 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTAATATTTTAATATTAAA
Found at i:20631014 original size:16 final size:16
Alignment explanation
Indices: 20630981--20631015 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20630971 ATTTAATAAG
* *
20630981 ATTTAATATTATATTA
1 ATTTAATATTAAAGTA
20630997 ATTTAATATTAAAGTA
1 ATTTAATATTAAAGTA
20631013 ATT
1 ATT
20631016 AAGTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTAATATTAAAGTA
Found at i:20636178 original size:7 final size:7
Alignment explanation
Indices: 20636166--20636195 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20636156 TAGCCTATTA
20636166 ATTAGCC
1 ATTAGCC
20636173 ATTAGCC
1 ATTAGCC
20636180 ATTAGCC
1 ATTAGCC
20636187 ATTAGCC
1 ATTAGCC
20636194 AT
1 AT
20636196 GGCCAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (7 bp):
ATTAGCC
Found at i:20639992 original size:19 final size:19
Alignment explanation
Indices: 20639965--20640003 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
20639955 AAAATAATCT
20639965 TAAAAAATC-AAAATTTTA
1 TAAAAAATCTAAAATTTTA
20639983 TAAAATAATCTTAAAATTTTA
1 TAAAA-AATC-TAAAATTTTA
20640004 AATTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
21 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATCTAAAATTTTA
Found at i:20645356 original size:50 final size:51
Alignment explanation
Indices: 20645289--20645398 Score: 161
Period size: 50 Copynumber: 2.2 Consensus size: 51
20645279 CCATTTCAAT
20645289 CCTTTTCATAATTTCATGACATAGTTCATTTGAAT-TCATACCTTTCCTTTC
1 CCTTTTCATAATTTCATGACATAGTTCATTTGAATGT-ATACCTTTCCTTTC
* * *
20645340 CCTTTT-ATAATTTCATGACATAGTTTATTTGAATGTATACTTTTCCTTTA
1 CCTTTTCATAATTTCATGACATAGTTCATTTGAATGTATACCTTTCCTTTC
*
20645390 CTTTTTCAT
1 CCTTTTCAT
20645399 GGTCGTTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 44 0.83
51 9 0.17
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (51 bp):
CCTTTTCATAATTTCATGACATAGTTCATTTGAATGTATACCTTTCCTTTC
Found at i:20658268 original size:3 final size:3
Alignment explanation
Indices: 20658253--20658294 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
20658243 TAAGATATGA
*
20658253 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20658295 AAAAAGTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:20658978 original size:8 final size:8
Alignment explanation
Indices: 20658962--20659029 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 8
20658952 ACCAAAATTA
*
20658962 AATTCTAT
1 AATTTTAT
20658970 AATTTTAT
1 AATTTTAT
*
20658978 AATTGTA-
1 AATTTTAT
**
20658985 AA-AATAT
1 AATTTTAT
20658992 AATTTTAT
1 AATTTTAT
*
20659000 CATTTTAAT
1 AATTTT-AT
20659009 AA-TTTAT
1 AATTTTAT
*
20659016 ATTTTTAT
1 AATTTTAT
20659024 AATTTT
1 AATTTT
20659030 TAAATGATTA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
6 2 0.04
7 7 0.15
8 34 0.74
9 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (8 bp):
AATTTTAT
Found at i:20658995 original size:22 final size:24
Alignment explanation
Indices: 20658967--20659027 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
20658957 AATTAAATTC
20658967 TATAATTTTATAATTGTAA-AA-A
1 TATAATTTTATAATTGTAATAATA
* * *
20658989 TATAATTTTATCATTTTAATAATT
1 TATAATTTTATAATTGTAATAATA
*
20659013 TATATTTTTATAATT
1 TATAATTTTATAATT
20659028 TTTAAATGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TATAATTTTATAATTGTAATAATA
Found at i:20659025 original size:15 final size:16
Alignment explanation
Indices: 20658989--20659028 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
20658979 ATTGTAAAAA
20658989 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
20659006 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
20659021 TATAATTT
1 TATAATTT
20659029 TTAAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:20660594 original size:21 final size:21
Alignment explanation
Indices: 20660550--20660595 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
20660540 TTTCTTTTTG
*
20660550 AAAAAGAACAAAATGAATTAT
1 AAAAAGAACAAAATGAATCAT
*
20660571 AAAAA-AATAAAATGAATCACT
1 AAAAAGAACAAAATGAATCA-T
20660592 AAAA
1 AAAA
20660596 CTAAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAAGAACAAAATGAATCAT
Found at i:20662264 original size:17 final size:17
Alignment explanation
Indices: 20662242--20662277 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20662232 AAGAGTAGAT
20662242 TTTTAGTCTAAATATTA
1 TTTTAGTCTAAATATTA
* *
20662259 TTTTAGTTTAAATTTTA
1 TTTTAGTCTAAATATTA
20662276 TT
1 TT
20662278 ATTTATGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTAGTCTAAATATTA
Found at i:20662469 original size:15 final size:16
Alignment explanation
Indices: 20662449--20662490 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20662439 TTAATTATTT
20662449 TAAAAATTATA-AAAA
1 TAAAAATTATATAAAA
*
20662464 TAAAAATTA-ATATAA
1 TAAAAATTATATAAAA
20662479 TAAAAA-TATATA
1 TAAAAATTATATA
20662491 TTAACTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATTATATAAAA
Found at i:20662493 original size:21 final size:22
Alignment explanation
Indices: 20662457--20662511 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
20662447 TTTAAAAATT
* *
20662457 ATAAAAATAAAAATTAA-TATA
1 ATAAAAATATATATTAACTATA
* *
20662478 ATAAAAATATATATTAACTTTT
1 ATAAAAATATATATTAACTATA
20662500 AT-AAAATATATA
1 ATAAAAATATATA
20662512 ACATAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAATATATATTAACTATA
Found at i:20662746 original size:3 final size:3
Alignment explanation
Indices: 20662738--20662764 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20662728 CAAGGATTTC
20662738 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
20662765 TACCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20662905 original size:16 final size:16
Alignment explanation
Indices: 20662884--20662923 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20662874 TTTTCCTTTT
*
20662884 TTCACTCCCTCCCT-CC
1 TTCACTCCCT-CATGCC
20662900 TTCACTCCCTCATGCC
1 TTCACTCCCTCATGCC
20662916 TTCACTCC
1 TTCACTCC
20662924 ACAAAACGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.10, C:0.55, G:0.03, T:0.33
Consensus pattern (16 bp):
TTCACTCCCTCATGCC
Found at i:20671411 original size:3 final size:3
Alignment explanation
Indices: 20671405--20671429 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20671395 TTATTATTAT
20671405 TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC T
20671430 TCTTCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Found at i:20676674 original size:13 final size:14
Alignment explanation
Indices: 20676655--20676687 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20676645 GCCCAATACC
*
20676655 TAAAATAAAATAAA
1 TAAAATAAAAGAAA
20676669 -AAAATAAAAGAAA
1 TAAAATAAAAGAAA
20676682 TAAAAT
1 TAAAAT
20676688 CTAAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAAATAAAAGAAA
Found at i:20676718 original size:13 final size:13
Alignment explanation
Indices: 20676700--20676802 Score: 51
Period size: 13 Copynumber: 9.2 Consensus size: 13
20676690 AAATATCTTT
20676700 ACTCCACTAAACC
1 ACTCCACTAAACC
20676713 ACT-C-C--AACC
1 ACTCCACTAAACC
20676722 ACT---CTAA-CC
1 ACTCCACTAAACC
*
20676731 ACTCCACTAAATC
1 ACTCCACTAAACC
20676744 ACT-C-C--AACC
1 ACTCCACTAAACC
*
20676753 ACTTCACTAAACC
1 ACTCCACTAAACC
20676766 AC-CC-C--AACC
1 ACTCCACTAAACC
*
20676775 A-TCCTACTAAACT
1 ACTCC-ACTAAACC
20676788 ACTCCACTAAACC
1 ACTCCACTAAACC
20676801 AC
1 AC
20676803 CCAACCACTT
Statistics
Matches: 69, Mismatches: 5, Indels: 32
0.65 0.05 0.30
Matches are distributed among these distances:
8 1 0.01
9 25 0.36
10 2 0.03
11 5 0.07
12 7 0.10
13 26 0.38
14 3 0.04
ACGTcount: A:0.37, C:0.46, G:0.00, T:0.17
Consensus pattern (13 bp):
ACTCCACTAAACC
Found at i:20676746 original size:22 final size:22
Alignment explanation
Indices: 20676718--20676793 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
20676708 AAACCACTCC
*
20676718 AACCACTCTAACCACTCCACTA
1 AACCACTCCAACCACTCCACTA
* *
20676740 AATCACTCCAACCACTTCACTA
1 AACCACTCCAACCACTCCACTA
*
20676762 AACCACCCCAACCA-TCCTACTA
1 AACCACTCCAACCACTCC-ACTA
*
20676784 AACTACTCCA
1 AACCACTCCA
20676794 CTAAACCACC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 2 0.04
22 43 0.96
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCACTCCAACCACTCCACTA
Found at i:20677218 original size:3 final size:3
Alignment explanation
Indices: 20677207--20677286 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
20677197 TTTTATTTTT
* *
20677207 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TT- TCTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A
20677252 TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
20677287 ATATACCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:20677246 original size:18 final size:18
Alignment explanation
Indices: 20677211--20677290 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
20677201 ATTTTTTTAT
* *
20677211 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
20677230 TTTATATTATTATTATT-
1 TTTATATTATTATTATTA
* *
20677247 TCTCAT-GTATATATTATTA
1 T-TTATATTAT-TATTATTA
20677266 TTTATATTATTATTA-TA
1 TTTATATTATTATTATTA
20677283 TTATATAT
1 TT-TATAT
20677291 ACCCTCTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.16
18 34 0.68
19 8 0.16
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:20677273 original size:12 final size:12
Alignment explanation
Indices: 20677206--20677286 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
20677196 GTTTTATTTT
*
20677206 TTTATTTTATTA
1 TTTATATTATTA
* *
20677218 TTTTTACTATTA
1 TTTATATTATTA
20677230 TTTATATTATTA
1 TTTATATTATTA
* *
20677242 -TTAT-TTCTCA
1 TTTATATTATTA
20677252 TGTATATATTATTA
1 T-T-TATATTATTA
20677266 TTTATATTATTA
1 TTTATATTATTA
20677278 -TTATATTAT
1 TTTATATTAT
20677287 ATATACCCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 4 0.07
11 13 0.23
12 30 0.54
13 4 0.07
14 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:20680140 original size:19 final size:19
Alignment explanation
Indices: 20680118--20680164 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
20680108 CTTCCTTTCT
20680118 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTCCA-ACA
*
20680137 TTTGCATTACATTGCAACA
1 TTTGCATTACATTCCAACA
20680156 TTTGCATTA
1 TTTGCATTA
20680165 AACTTTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCAACA
Found at i:20680332 original size:24 final size:24
Alignment explanation
Indices: 20680297--20680347 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
20680287 TAGAAAGGAT
*
20680297 AGAACAAATACAAAG-GGAGATGCA
1 AGAACAAATAC-AAGCGCAGATGCA
*
20680321 AGAACAATTACAAGCGCAGATGCA
1 AGAACAAATACAAGCGCAGATGCA
20680345 AGA
1 AGA
20680348 GCAACTGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.51, C:0.16, G:0.24, T:0.10
Consensus pattern (24 bp):
AGAACAAATACAAGCGCAGATGCA
Found at i:20683868 original size:53 final size:52
Alignment explanation
Indices: 20683765--20683868 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 52
20683755 GTCCAAATAA
* * * *
20683765 ATTTTCTTCTTATTGCATTGCTATCTTTGATTAAATCATTCGTTTTGAGTTG
1 ATTTCCTTCTTATTGCATTGCTATCTTTGATTAAATCATCCATTTCGAGTTG
* *
20683817 ATTTCCTTCTTATTGCATTTG-TAATCTTTGATTAATTTATCCATTTCGAGTT
1 ATTTCCTTCTTATTGCA-TTGCT-ATCTTTGATTAAATCATCCATTTCGAGTT
20683869 ATGCTCCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
52 17 0.39
53 27 0.61
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (52 bp):
ATTTCCTTCTTATTGCATTGCTATCTTTGATTAAATCATCCATTTCGAGTTG
Found at i:20685191 original size:205 final size:205
Alignment explanation
Indices: 20684827--20685315 Score: 773
Period size: 205 Copynumber: 2.4 Consensus size: 205
20684817 ATCAGGCAGA
*
20684827 GAGCAGATCGAAGACATAGCTGATTTAGG-TTTCACGTGTTTACGTTGAAGCAAATCTAAGATGA
1 GAGCAAATCGAAGACATAGCTGATTT-GGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGA
* *
20684891 TTTGGAATTTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAG
65 TTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAG
* * * * *
20684956 ACACATAGCAGATCTAACCTTCAGATGTTTATACTTAAGTAGATCCAAGATGGTTTGGCATCCTT
130 ACACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTT
20685021 CTGCTTACAAG
195 CTGCTTACAAG
* * *
20685032 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGTAAATCTAAGATGAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
* * * * * *
20685097 TTGGCATCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGTATCTCCACTTCGATGGAGGGTAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
*
20685162 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTG
131 CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTC
20685227 TGCTTACAAG
196 TGCTTACAAG
* *
20685237 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCCAAGATAAT
1 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
*
20685302 TTGGCGTCTCTGTA
66 TTGGCATCTCTGTA
20685316 GCGGCGAAGA
Statistics
Matches: 259, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
204 2 0.01
205 257 0.99
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (205 bp):
GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGACGGAAGGCAGA
CACATAGCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTC
TGCTTACAAG
Found at i:20685633 original size:132 final size:132
Alignment explanation
Indices: 20685340--20686458 Score: 1828
Period size: 132 Copynumber: 8.5 Consensus size: 132
20685330 ATCGAAGATT
* *
20685340 GCAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGTAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
20685405 TTACAGTGAAGCAGATCGAAGATTTCAGCAT-GCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20685469 CA
131 CA
* * **
20685471 GCAGATTTGACATCCCTGTGCTTATAGGGAATAGATCGAAGATAATAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
20685536 TTACAGTAAAGCAGATCGAAGATTTTAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20685601 CA
131 CA
*
20685603 GCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
20685668 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20685733 CA
131 CA
* * * *
20685735 GCAGATTTGGTATCCCTGTGCTTATATGGAACAGATCAAAGATAGCAGATCTGACATTCTTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* *
20685800 TTACAGTGAAGCAGATCAAAGATTTCAGTATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20685865 CA
131 CA
* * *
20685867 GTAGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCAGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
20685932 TTACGGTGAAACAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
*
20685997 TA
131 CA
*
20685999 ACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* *
20686064 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTATGCTTATAGGGAAAAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20686129 CA
131 CA
*
20686131 GCAGATTTGGTATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
*
20686196 TTACAGTGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
20686261 CA
131 CA
* * *
20686263 ACAAATTTGGCATCCATGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * * *
20686328 TTACGGTGAAGCAGATCGAAGATTTCAGCATGGAATCCCTATGCTTATAGGGAACAAGTTGAAGA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
*
20686393 TA
131 CA
* * * * * * *
20686395 GCAGATTTGGCATCCTTGTGTTTATAGGGAACA-AGTTGAAGACAGCAGATTTGGCATCCCTGTG
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATTCCTGTG
20686459 TTTATGGGGA
Statistics
Matches: 917, Mismatches: 69, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
131 91 0.10
132 826 0.90
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (132 bp):
GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
CA
Found at i:20687922 original size:13 final size:14
Alignment explanation
Indices: 20687905--20687937 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20687895 GCCCAATACC
*
20687905 TAAAATAAAATAAA
1 TAAAATAAAAGAAA
20687919 -AAAATAAAAGAAA
1 TAAAATAAAAGAAA
20687932 TAAAAT
1 TAAAAT
20687938 CCAAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAAATAAAAGAAA
Found at i:20687973 original size:9 final size:9
Alignment explanation
Indices: 20687959--20688017 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
20687949 TACTCCACTA
20687959 AACCACTCC
1 AACCACTCC
*
20687968 AACCACTCT
1 AACCACTCC
20687977 AACCACTCCAC
1 AACCACT-C-C
*
20687988 TAAATCACTCC
1 --AACCACTCC
20687999 AACCACTCC
1 AACCACTCC
20688008 AACCACTCC
1 AACCACTCC
20688017 A
1 A
20688018 CTAAACCACC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 33 0.79
10 1 0.02
11 1 0.02
12 1 0.02
13 6 0.14
ACGTcount: A:0.36, C:0.49, G:0.00, T:0.15
Consensus pattern (9 bp):
AACCACTCC
Found at i:20687975 original size:22 final size:22
Alignment explanation
Indices: 20687950--20688052 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
20687940 AAATATCTTT
20687950 ACTCCACTAAACCACTCCAACC
1 ACTCCACTAAACCACTCCAACC
*
20687972 ACT---CT-AACCACTCC-ACTA
1 ACTCCACTAAACCACTCCAAC-C
* *
20687990 AAT-CACTCCAACCACTCCAACC
1 ACTCCACT-AAACCACTCCAACC
*
20688012 ACTCCACTAAACCACCCCAACC
1 ACTCCACTAAACCACTCCAACC
*
20688034 AC-CCTACTAAACTACTCCA
1 ACTCC-ACTAAACCACTCCA
20688053 CTAAACCACC
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.03
18 11 0.17
19 2 0.03
20 2 0.03
21 2 0.03
22 40 0.62
23 6 0.09
ACGTcount: A:0.36, C:0.49, G:0.00, T:0.16
Consensus pattern (22 bp):
ACTCCACTAAACCACTCCAACC
Found at i:20687985 original size:31 final size:31
Alignment explanation
Indices: 20687950--20688070 Score: 163
Period size: 31 Copynumber: 3.8 Consensus size: 31
20687940 AAATATCTTT
20687950 ACTCCACTAAACCACTCCAACCACTCTAACC
1 ACTCCACTAAACCACTCCAACCACTCTAACC
* *
20687981 ACTCCACTAAATCACTCCAACCACTCCAACC
1 ACTCCACTAAACCACTCCAACCACTCTAACC
* *
20688012 ACTCCACTAAACCACCCCAACCACCCTACTAAACT
1 ACTCCACTAAACCACTCCAACCA--CT-CT-AACC
20688047 ACTCCACTAAACCAC-CCAACCACT
1 ACTCCACTAAACCACTCCAACCACT
20688071 TCACTTGCCT
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
31 50 0.62
32 2 0.03
33 2 0.03
34 8 0.10
35 18 0.22
ACGTcount: A:0.36, C:0.49, G:0.00, T:0.15
Consensus pattern (31 bp):
ACTCCACTAAACCACTCCAACCACTCTAACC
Found at i:20688026 original size:13 final size:12
Alignment explanation
Indices: 20688008--20688064 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
20687998 CAACCACTCC
20688008 AACCACTCCACTA
1 AACCAC-CCACTA
20688021 AACCACCC-C--
1 AACCACCCACTA
20688030 AACCACCCTACTA
1 AACCACCC-ACTA
*
20688043 AACTACTCCACTA
1 AACCAC-CCACTA
20688056 AACCACCCA
1 AACCACCCA
20688065 ACCACTTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
9 8 0.22
11 2 0.05
12 5 0.14
13 20 0.54
14 2 0.05
ACGTcount: A:0.39, C:0.49, G:0.00, T:0.12
Consensus pattern (12 bp):
AACCACCCACTA
Found at i:20688481 original size:3 final size:3
Alignment explanation
Indices: 20688462--20688549 Score: 62
Period size: 3 Copynumber: 29.3 Consensus size: 3
20688452 GAACTTTGTT
* *
20688462 TTA TT- TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
20688505 TTA TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA
1 TTA TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
20688549 T
1 T
20688550 ATATACCCTC
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
2 9 0.13
3 51 0.74
4 7 0.10
5 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20688536 original size:12 final size:12
Alignment explanation
Indices: 20688470--20688549 Score: 76
Period size: 12 Copynumber: 6.8 Consensus size: 12
20688460 TTTTATTTTA
*
20688470 TTATTTTATTAT
1 TTATATTATTAT
* *
20688482 TTTTACTATTAT
1 TTATATTATTAT
20688494 TTATATTATTA-
1 TTATATTATTAT
* *
20688505 TTAT-TTCTCAT
1 TTATATTATTAT
20688516 GTATATATTATTAT
1 -T-TATATTATTAT
20688530 TTATATTATTA-
1 TTATATTATTAT
20688541 TTATATTAT
1 TTATATTAT
20688550 ATATACCCTC
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
10 4 0.07
11 13 0.24
12 29 0.53
13 4 0.07
14 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:20689942 original size:35 final size:35
Alignment explanation
Indices: 20689903--20689972 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
20689893 TGCCTCGAAA
* * *
20689903 CCTTTTTAGTTGAACTCCTTATCATTAATATTTTG
1 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
20689938 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
1 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
20689973 GAATTCATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (35 bp):
CCTTTTTAATTGAACACCTTATCATGAATATTTTG
Found at i:20690838 original size:9 final size:10
Alignment explanation
Indices: 20690804--20690836 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20690794 TTTATCTAAG
20690804 TTATATATAA
1 TTATATATAA
*
20690814 ATATATATAA
1 TTATATATAA
20690824 TTAT-TATAA
1 TTATATATAA
20690833 TTAT
1 TTAT
20690837 TAACCATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTATATATAA
Found at i:20692049 original size:20 final size:20
Alignment explanation
Indices: 20692026--20692072 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
20692016 GTATAATTAA
20692026 TATGTGTTTAATTTAATATG
1 TATGTGTTTAATTTAATATG
20692046 TATGTGTTTAATTTAATATG
1 TATGTGTTTAATTTAATATG
20692066 TATGTGT
1 TATGTGT
20692073 GGTAAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (20 bp):
TATGTGTTTAATTTAATATG
Found at i:20692509 original size:45 final size:44
Alignment explanation
Indices: 20692459--20692571 Score: 163
Period size: 45 Copynumber: 2.5 Consensus size: 44
20692449 CGACTACTGT
* *
20692459 TACTGTTGTCGTTACTGTTACTGATTCGACACTTTGTGTGTCGAA
1 TACTGTT-ACGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
* *
20692504 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAA
1 TACTGTTA-CGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
20692549 TACTGTTACTGTTACTGTTACTG
1 TACTGTTAC-GTTACTGTTACTG
20692572 CTACCGTTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 1 0.02
45 60 0.98
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (44 bp):
TACTGTTACGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
Found at i:20692560 original size:6 final size:6
Alignment explanation
Indices: 20692549--20692592 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
20692539 GTGTGTTGAA
* * *
20692549 TACTGT TACTGT TACTGT TACTGC TACCGT TAGTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
20692593 TAGGTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:20694678 original size:12 final size:13
Alignment explanation
Indices: 20694650--20694682 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20694640 TTATTTCTTT
20694650 TTCTCCATCTACC
1 TTCTCCATCTACC
*
20694663 TTCTCC-TCTTCC
1 TTCTCCATCTACC
20694675 TTCTCCAT
1 TTCTCCAT
20694683 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:20695782 original size:28 final size:28
Alignment explanation
Indices: 20695750--20695842 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
20695740 ATTTACTAGA
20695750 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
20695778 ATACCCCTATGTATACAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
20695806 ATACCCATATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
20695834 ATACCCCTA
1 ATACCCCTA
20695843 GGGTTAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:20695989 original size:28 final size:27
Alignment explanation
Indices: 20695948--20696037 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
20695938 AGGAAGCGTC
20695948 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
20695976 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
20696003 CTGGTGGCACTGCCACAAAATGTCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
20696032 CTGGTG
1 CTGGTG
20696038 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:20696056 original size:55 final size:56
Alignment explanation
Indices: 20695948--20696062 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
20695938 AGGAAGCGTC
* * *
20695948 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
20696003 CTGGTGGC-ACTGCCACAAAATGTCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
20696059 CTGG
1 CTGG
20696063 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:20699465 original size:32 final size:33
Alignment explanation
Indices: 20699385--20699465 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 33
20699375 ACATTGTCAG
*
20699385 TCCAACCAAACACACTAGATGCTCACACGAGCCAA
1 TCCAACC-AACACACTA-ATGCTCACAAGAGCCAA
** * * *
20699420 TCCCTCCAGCACACT-ATGCTCATAAGAGCTAA
1 TCCAACCAACACACTAATGCTCACAAGAGCCAA
20699452 TCCAACCAACACAC
1 TCCAACCAACACAC
20699466 CAAACAGAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
32 25 0.68
34 7 0.19
35 5 0.14
ACGTcount: A:0.37, C:0.38, G:0.10, T:0.15
Consensus pattern (33 bp):
TCCAACCAACACACTAATGCTCACAAGAGCCAA
Found at i:20702127 original size:7 final size:7
Alignment explanation
Indices: 20702115--20702143 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
20702105 TACATAAATG
20702115 TATATAA
1 TATATAA
20702122 TATATAA
1 TATATAA
20702129 TATATAA
1 TATATAA
20702136 TATATAA
1 TATATAA
20702143 T
1 T
20702144 TCTATACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:20703320 original size:22 final size:24
Alignment explanation
Indices: 20703295--20703338 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
20703285 TTTTAAATTT
20703295 AAAT-TTAATTATAAAA-ATATAG
1 AAATATTAATTATAAAACATATAG
*
20703317 AAATATTAGTTATAAAACATAT
1 AAATATTAATTATAAAACATAT
20703339 TTTTGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATATTAATTATAAAACATATAG
Found at i:20703626 original size:30 final size:31
Alignment explanation
Indices: 20703592--20703649 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
20703582 TTGATATCTG
* * *
20703592 AACTTGACTTTTTTTC-TAATTTGGTACGTA
1 AACTTAACATTTTTTCATAAGTTGGTACGTA
20703622 AACTTAACATTTTTTCATAAGTTGGTAC
1 AACTTAACATTTTTTCATAAGTTGGTAC
20703650 TTAATCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (31 bp):
AACTTAACATTTTTTCATAAGTTGGTACGTA
Found at i:20703696 original size:60 final size:60
Alignment explanation
Indices: 20703609--20703721 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
20703599 CTTTTTTTCT
* * * *
20703609 AATTTGGTACGTAAACTTAACATTTTTTCATAAGTTGGTACTTAATCTTTTTTAGGGTCC
1 AATTCGGTACCTAAACTCAACATTTTTTCATAAGTTAGTACTTAATCTTTTTTAGGGTCC
* * *
20703669 AATTCGGTACCTAAACTCAAC-TCTTTTTCCTTATTTAGTACTTAATCTTTTTT
1 AATTCGGTACCTAAACTCAACAT-TTTTTCATAAGTTAGTACTTAATCTTTTTT
20703722 CGTTCGATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (60 bp):
AATTCGGTACCTAAACTCAACATTTTTTCATAAGTTAGTACTTAATCTTTTTTAGGGTCC
Found at i:20718120 original size:9 final size:9
Alignment explanation
Indices: 20718093--20718129 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20718083 TGAGTTTTTG
20718093 AATTCGAAT
1 AATTCGAAT
* *
20718102 AACTCAAAT
1 AATTCGAAT
20718111 AATTCGAAT
1 AATTCGAAT
20718120 AATTCGAAT
1 AATTCGAAT
20718129 A
1 A
20718130 TTAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20719490 original size:18 final size:18
Alignment explanation
Indices: 20719467--20719503 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20719457 TATAGTTTGA
* *
20719467 TATTCGGTTTATTTGAAT
1 TATTCGGGTTATTCGAAT
20719485 TATTCGGGTTATTCGAAT
1 TATTCGGGTTATTCGAAT
20719503 T
1 T
20719504 CAAAAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (18 bp):
TATTCGGGTTATTCGAAT
Found at i:20722547 original size:7 final size:7
Alignment explanation
Indices: 20722537--20722561 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20722527 AGTCATTTCA
20722537 TATTTAG
1 TATTTAG
20722544 TATTTAG
1 TATTTAG
20722551 TATTTAG
1 TATTTAG
20722558 TATT
1 TATT
20722562 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20723669 original size:25 final size:24
Alignment explanation
Indices: 20723616--20723669 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
20723606 AAAAAGTTGT
20723616 TTTTAATATTTTAATAGTAAATTAA
1 TTTTAATATTTTAATAG-AAATTAA
20723641 TTTT-ATATTTTGAATA-AAATATAA
1 TTTTAATATTTT-AATAGAAAT-TAA
20723665 GTTTT
1 -TTTT
20723670 TTTTAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.15
24 10 0.38
25 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTTAATATTTTAATAGAAATTAA
Found at i:20726921 original size:125 final size:126
Alignment explanation
Indices: 20726723--20726972 Score: 349
Period size: 125 Copynumber: 2.0 Consensus size: 126
20726713 GGCCAATCAT
* * * * *
20726723 GAATTATTGTAGAAAAAGAGCGTCTACGTGAGAGTTTTTTTCAGAAATTTTGCTGACAATGCATC
1 GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
* * * *
20726788 CTGCTTGAAGTGTTTTTCACACCATTTGTTCAGAAACG-TTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTCACACCATTTATTCAAAAACGTTTTATCAAAATTATTTTTTCAA
* * * *
20726848 GAATTACTGTAGAAAAACAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTGCTGACAGTGCATC
1 GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
* * *
20726913 TTGCTTGAAGCGTTTTTGACACTATTTATTCAAAAACGTTTTATCAAAATTATTTTTTCA
66 CTGCTTGAAGCGTTTTTCACACCATTTATTCAAAAACGTTTTATCAAAATTATTTTTTCA
20726973 CGGTACAAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
125 88 0.81
126 20 0.19
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
CTGCTTGAAGCGTTTTTCACACCATTTATTCAAAAACGTTTTATCAAAATTATTTTTTCAA
Found at i:20727077 original size:30 final size:29
Alignment explanation
Indices: 20727043--20727128 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 29
20727033 AACCTTACAC
*
20727043 CCTAATTTAATTTATTTAAAACCCTAGAAT
1 CCTAATTTAATTTATTTAAAACCATA-AAT
*
20727073 CCTAATTTACTTAATTTATCTAAAAACCATAAAT
1 CCTAA--T--TTAATTTAT-TTAAAACCATAAAT
*
20727107 CCTAATTTAACTTATTTAAAAC
1 CCTAATTTAATTTATTTAAAAC
20727129 AACAATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
29 6 0.13
30 13 0.28
32 2 0.04
34 17 0.36
35 9 0.19
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (29 bp):
CCTAATTTAATTTATTTAAAACCATAAAT
Found at i:20727087 original size:34 final size:35
Alignment explanation
Indices: 20727049--20727124 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
20727039 ACACCCTAAT
* *
20727049 TTAATTTAT-TTAAAACCCTAGAATCCTAATTT-AC
1 TTAATTTATCTAAAAACCATA-AATCCTAATTTAAC
20727083 TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
1 TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
20727118 TT-ATTTA
1 TTAATTTA
20727125 AAACAACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.41, C:0.16, G:0.01, T:0.42
Consensus pattern (35 bp):
TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
Found at i:20727181 original size:17 final size:18
Alignment explanation
Indices: 20727155--20727191 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20727145 ACCCTAAACC
20727155 TAAAACCCTAATTT-ATT
1 TAAAACCCTAATTTAATT
*
20727172 TAAAATCCTAATTTAATT
1 TAAAACCCTAATTTAATT
20727190 TA
1 TA
20727192 TTTAAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAACCCTAATTTAATT
Found at i:20727189 original size:22 final size:22
Alignment explanation
Indices: 20727163--20727204 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20727153 CCTAAAACCC
*
20727163 TAATTTATTTAAAATCCTAATT
1 TAATTTATTTAAAACCCTAATT
20727185 TAATTTATTTAAAACCCTAA
1 TAATTTATTTAAAACCCTAA
20727205 AAAAATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTATTTAAAACCCTAATT
Found at i:20727327 original size:41 final size:41
Alignment explanation
Indices: 20727261--20727338 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
20727251 TTAACTTATT
*
20727261 TAAAACACTAATTTATTTAAATTATTTAAAAACTCTACACC
1 TAAAACACTAATTTACTTAAATTATTTAAAAACTCTACACC
* * *
20727302 TAAAACCCTAATTTACTTAATTTATTTAACAACTCTA
1 TAAAACACTAATTTACTTAAATTATTTAAAAACTCTA
20727339 AACCCTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (41 bp):
TAAAACACTAATTTACTTAAATTATTTAAAAACTCTACACC
Done.