Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 85 of 206
Found at i:24299162 original size:40 final size:40
Alignment explanation
Indices: 24299091--24299325 Score: 222
Period size: 41 Copynumber: 5.8 Consensus size: 40
24299081 CTTTCGGGGC
* *
24299091 TTTAGCGGCGTTTTTGAAAATGCGCCACTAATGCTTAGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTT-GGGA
* * * *
24299132 TTTAGC-GCGTTTTTGGAAAAGCGCTGCTAATGCTCTGTGT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-TGGGA
* * * * * *
24299172 TTTAGCGGCATTTTTTAAAAAGCGTCGCTAAAGCTCGGGGT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCT-TGGGA
* * *
24299213 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCGGTA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTGGGA
* * *
24299253 TTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTGGGTGC
1 -TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTGG-GA
* *
24299295 TTTAGTGGCGCTTTTTCAAAAA-CGCCGCTAA
1 TTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAA
24299326 ATTTTTTTAT
Statistics
Matches: 160, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
40 34 0.21
41 116 0.73
42 10 0.06
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTGGGA
Found at i:24299244 original size:82 final size:81
Alignment explanation
Indices: 24299091--24299325 Score: 276
Period size: 82 Copynumber: 2.9 Consensus size: 81
24299081 CTTTCGGGGC
* * * * *
24299091 TTTAGCGGCGTTTTTGAAAATGCGCCACTAATGCTTAGGGATTTAGC-GCGTTTTTGGAAAAGCG
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGC-TGGGGATTTAGCGGCGTTTTTGAAAAAGCG
* * *
24299155 CTGCTAATGCTCTGTGT
65 CCGCTAATGCTCGGTAT
* * * *
24299172 TTTAGCGGCATTTTTTAAAAAGCGTCGCTAAAGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAGCG
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCT-GGGGATTTAGCGGCGTTTTTGAAAAAGCG
*
24299237 CCACTAATGCTCGGTAT
65 CCGCTAATGCTCGGTAT
* * *
24299254 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTGGGTGCTTTAGTGGCGCTTTTTCAAAAA-C
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTGGG-GATTTAGCGGCG-TTTTTGAAAAAGC
24299318 GCCGCTAA
64 GCCGCTAA
24299326 ATTTTTTTAT
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 40 0.31
82 79 0.61
83 10 0.08
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (81 bp):
TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTGGGGATTTAGCGGCGTTTTTGAAAAAGCGC
CGCTAATGCTCGGTAT
Found at i:24299691 original size:15 final size:14
Alignment explanation
Indices: 24299671--24299722 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
24299661 ACTATTTTAA
24299671 GGTTTAAGGAGTAT
1 GGTTTAAGGAGTAT
* *
24299685 GGGTTTAGGGATTAT
1 -GGTTTAAGGAGTAT
* * *
24299700 GGATTAGGGATTAT
1 GGTTTAAGGAGTAT
24299714 GGTTTAAGG
1 GGTTTAAGG
24299723 GTTGGGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (14 bp):
GGTTTAAGGAGTAT
Found at i:24299708 original size:14 final size:14
Alignment explanation
Indices: 24299689--24299715 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24299679 GAGTATGGGT
24299689 TTAGGGATTATGGA
1 TTAGGGATTATGGA
24299703 TTAGGGATTATGG
1 TTAGGGATTATGG
24299716 TTTAAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:24299740 original size:21 final size:21
Alignment explanation
Indices: 24299666--24299745 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
24299656 GAGTTACTAT
24299666 TTTAAGGTTTAAGGAGTATGGG-
1 TTTAAGGTTTAAGG-GT-TGGGA
* * * *
24299688 TTTAGGGATTATGGATTAGGGA
1 TTTAAGGTTTAAGGGTT-GGGA
*
24299710 -TTATGGTTTAAGGGTTGGGA
1 TTTAAGGTTTAAGGGTTGGGA
*
24299730 TTTAAGGTTTAGGGGT
1 TTTAAGGTTTAAGGGT
24299746 AAGGGCTTAG
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.11
21 29 0.64
22 11 0.24
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.39
Consensus pattern (21 bp):
TTTAAGGTTTAAGGGTTGGGA
Found at i:24300060 original size:15 final size:15
Alignment explanation
Indices: 24300014--24300063 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
24300004 TTTAAAGGTT
24300014 GGGATTTAAGG-TTTA
1 GGGATTT-AGGATTTA
* * *
24300029 GGG-GTTAAGAGTTA
1 GGGATTTAGGATTTA
24300043 GGGATTTAGGATTTA
1 GGGATTTAGGATTTA
24300058 GGGATT
1 GGGATT
24300064 CAGGGGTCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 17 0.63
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (15 bp):
GGGATTTAGGATTTA
Found at i:24300575 original size:40 final size:40
Alignment explanation
Indices: 24300481--24300596 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
24300471 AAAAGGCATT
* **
24300481 AAAAAACGCCGCTATAGATCGAACATTAGCGGCATTTCTTC
1 AAAAAA-GCCGCTATAGATCGAGCATTAGCGGTGTTTCTTC
24300522 --AAAAGCACTGCTATAGATCGAGCATTAGCGGTGTTTCTTC
1 AAAAAAGC-C-GCTATAGATCGAGCATTAGCGGTGTTTCTTC
* *
24300562 AAAAAAGCCGCTATAGATTGAGCTTTAGCGGTGTT
1 AAAAAAGCCGCTATAGATCGAGCATTAGCGGTGTT
24300597 ATTTTAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 52 0.79
41 1 0.02
42 6 0.09
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (40 bp):
AAAAAAGCCGCTATAGATCGAGCATTAGCGGTGTTTCTTC
Found at i:24300606 original size:40 final size:39
Alignment explanation
Indices: 24300479--24300612 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 39
24300469 ATAAAAGGCA
* ** *
24300479 TTAAAAAACGCCGCTATAGATCGAACATTAGCGGCATTTC
1 TTAAAAAA-GCCGCTATAGATCGAGCATTAGCGGTGTTTT
*
24300519 TT-CAAAAGCACTGCTATAGATCGAGCATTAGCGGTGTTTCT
1 TTAAAAAAGC-C-GCTATAGATCGAGCATTAGCGGTGTTT-T
* * *
24300560 TCAAAAAAGCCGCTATAGATTGAGCTTTAGCGGTGTTATT
1 TTAAAAAAGCCGCTATAGATCGAGCATTAGCGGTGTT-TT
*
24300600 TTAAAAACGCCGC
1 TTAAAAAAGCCGC
24300613 AAAAAATAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.03
39 5 0.06
40 62 0.79
41 3 0.04
42 6 0.08
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (39 bp):
TTAAAAAAGCCGCTATAGATCGAGCATTAGCGGTGTTTT
Found at i:24304985 original size:43 final size:43
Alignment explanation
Indices: 24304938--24305164 Score: 258
Period size: 43 Copynumber: 5.3 Consensus size: 43
24304928 TCATTTTTTA
* * *
24304938 TAGCGGCTTTTATGGCAAAAGCGCTGCTAAAGGTCATGATCTT
1 TAGCGGCTTTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
* * * *
24304981 TAGCGGCATTTGTAGTATAAGCGCCGCTAAAGGCCATGATCTT
1 TAGCGGCTTTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
* *
24305024 TAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGATCTT
1 TAGCGGCTTTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
* * * *
24305067 TAGCGG-TATTTGCGGTAGAAGCGCCGCTAAAGACCATGATCTT
1 TAGCGGCT-TTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
* * * * * *
24305110 TAGCGGCGTTTGTGTCAGAAGCACTGCTAAAGACCATGATCTT
1 TAGCGGCTTTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
24305153 TAGCGGCGTTTT
1 TAGCGGC-TTTT
24305165 AACGCCGCTA
Statistics
Matches: 156, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
43 153 0.98
44 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (43 bp):
TAGCGGCTTTTGTGGCAAAAGCGCCGCTAAAGGCCATGATCTT
Found at i:24305045 original size:86 final size:86
Alignment explanation
Indices: 24304938--24305159 Score: 327
Period size: 86 Copynumber: 2.6 Consensus size: 86
24304928 TCATTTTTTA
* * * *
24304938 TAGCGGCTTTTATGGCAAAAGCGCTGCTAAAGGTCATGATCTTTAGCGGCATTTGTAGTATAAGC
1 TAGCGGCGTTTGTGGCAAAAGCGCTGCTAAAGGTCATGATCTTTAGCGGCATTTGCAGTAGAAGC
*
24305003 GCCGCTAAAGGCCATGATCTT
66 GCCGCTAAAGACCATGATCTT
* * *
24305024 TAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGTATTTGCGGTAGAAGC
1 TAGCGGCGTTTGTGGCAAAAGCGCTGCTAAAGGTCATGATCTTTAGCGGCATTTGCAGTAGAAGC
24305089 GCCGCTAAAGACCATGATCTT
66 GCCGCTAAAGACCATGATCTT
* * * **
24305110 TAGCGGCGTTTGTGTCAGAAGCACTGCTAAAGACCATGATCTTTAGCGGC
1 TAGCGGCGTTTGTGGCAAAAGCGCTGCTAAAGGTCATGATCTTTAGCGGC
24305160 GTTTTAACGC
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 121 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGCAAAAGCGCTGCTAAAGGTCATGATCTTTAGCGGCATTTGCAGTAGAAGC
GCCGCTAAAGACCATGATCTT
Found at i:24307649 original size:16 final size:16
Alignment explanation
Indices: 24307630--24307684 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
24307620 ATTTTATGAA
24307630 AATTTTTATATTTTTT
1 AATTTTTATATTTTTT
24307646 AA-TTTTA-ATTTTGATT
1 AATTTTTATATTTT--TT
*
24307662 TATTTTT-TATTTTTGT
1 AATTTTTATATTTTT-T
24307678 AATTTTT
1 AATTTTT
24307685 GAATTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 12 0.38
17 9 0.28
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
AATTTTTATATTTTTT
Found at i:24307692 original size:27 final size:27
Alignment explanation
Indices: 24307614--24307693 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
24307604 CTCGAAACTT
*
24307614 TTTTTTATTTTATGAAAATTTTT--A-TA
1 TTTTTTATTTT-TG-TAATTTTTGAATTA
* *
24307640 TTTTTTA-ATTT-TAA-TTTTGATTTA
1 TTTTTTATTTTTGTAATTTTTGAATTA
24307664 TTTTTTATTTTTGTAATTTTTGAATTA
1 TTTTTTATTTTTGTAATTTTTGAATTA
24307691 TTT
1 TTT
24307694 ATTGATGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
21 4 0.09
22 2 0.05
24 10 0.23
25 5 0.12
26 10 0.23
27 12 0.28
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTTTTATTTTTGTAATTTTTGAATTA
Found at i:24309315 original size:14 final size:14
Alignment explanation
Indices: 24309296--24309325 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24309286 AAATATTTCC
24309296 ATATTAAAGAATGT
1 ATATTAAAGAATGT
*
24309310 ATATTAAAGCATGT
1 ATATTAAAGAATGT
24309324 AT
1 AT
24309326 TCTTGGCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (14 bp):
ATATTAAAGAATGT
Found at i:24314827 original size:50 final size:51
Alignment explanation
Indices: 24314701--24314948 Score: 234
Period size: 50 Copynumber: 4.8 Consensus size: 51
24314691 TGATAATAAC
* ** * * *
24314701 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGT-A-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * ** **
24314750 CTGCCAATGCCATATCCCAGATTTGGTCTTACATGGGAGTTCTCATATCAG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* ** *
24314801 -TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTC-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* *
24314850 ATGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTTAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC---A-G
* * *
24314906 ATTCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
24314949 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
49 39 0.24
50 80 0.50
51 2 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (51 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:24316571 original size:7 final size:7
Alignment explanation
Indices: 24316559--24316592 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
24316549 TAAGATGAAA
24316559 AGAAAAG
1 AGAAAAG
24316566 AGAAAAG
1 AGAAAAG
24316573 AGAAAAG
1 AGAAAAG
24316580 AGAAAAG
1 AGAAAAG
24316587 AGAAAA
1 AGAAAA
24316593 AGTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:24316899 original size:164 final size:162
Alignment explanation
Indices: 24316718--24317046 Score: 631
Period size: 164 Copynumber: 2.0 Consensus size: 162
24316708 GAAGAAGAGA
24316718 AAAGAGAGAAAAGAAGGAATGAATAGATAAGAATAGTGGTGCAAAATGAAAGATGGTGAAAAGTG
1 AAAGAGAGAAAAGAAGGAATGAATAGATAAGAATAGTGGTGCAAAATGAAAGATGGTGAAAAGTG
*
24316783 GTGGCACAAGGTGGTTTTCGTGGTGGTGGTATGGTGGTTATGGGTGGTATGGTGGAGGAGAAGCG
66 GTGGCACAAGGTGGTTTTCGTGGTGGTGGT-TGGTGGTTATGGGCGGTATGGTGGAGGAGAAGCG
24316848 TTGATCAACACACAACAATAAATAAAATAAAAT
130 TTGATCAACACACAACAATAAATAAAATAAAAT
24316881 AAAGATGAGAAAAGAAGGAATGAATAGATAAGAATAGTGGTGCAAAATGAAAGATGGTGAAAAGT
1 AAAGA-GAGAAAAGAAGGAATGAATAGATAAGAATAGTGGTGCAAAATGAAAGATGGTGAAAAGT
24316946 GGTGGCACAAGGTGGTTTTCGTGGTGGTGGTTGGTGGTTATGGGCGGTATGGTGGAGGAGAAGCG
65 GGTGGCACAAGGTGGTTTTCGTGGTGGTGGTTGGTGGTTATGGGCGGTATGGTGGAGGAGAAGCG
24317011 TTGATCAACACACAACAATAAATAAAATAAAAT
130 TTGATCAACACACAACAATAAATAAAATAAAAT
24317044 AAA
1 AAA
24317047 AATGGTGGAG
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
163 74 0.45
164 90 0.55
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.22
Consensus pattern (162 bp):
AAAGAGAGAAAAGAAGGAATGAATAGATAAGAATAGTGGTGCAAAATGAAAGATGGTGAAAAGTG
GTGGCACAAGGTGGTTTTCGTGGTGGTGGTTGGTGGTTATGGGCGGTATGGTGGAGGAGAAGCGT
TGATCAACACACAACAATAAATAAAATAAAAT
Found at i:24319629 original size:17 final size:17
Alignment explanation
Indices: 24319609--24319662 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
24319599 TAGCCTTGGC
24319609 ATTGTCTCTCGGTGCAT
1 ATTGTCTCTCGGTGCAT
*
24319626 ATTGTCTCTCGGTGCAC
1 ATTGTCTCTCGGTGCAT
24319643 ATTGTCTCTCGGTGCAT
1 ATTGTCTCTCGGTGCAT
24319660 ATT
1 ATT
24319663 TCTTGATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (17 bp):
ATTGTCTCTCGGTGCAT
Found at i:24320271 original size:29 final size:29
Alignment explanation
Indices: 24320114--24320321 Score: 144
Period size: 29 Copynumber: 7.3 Consensus size: 29
24320104 TTTAGATTCT
* * * *
24320114 GCCACGAAGGCGTCCTTTTAATAGAG-TA
1 GCCACAAAGGCATCCATTTAACAGAGATA
* * * *
24320142 TGCCAC-AAGGCATTCC-CTTAATAGCGATG
1 -GCCACAAAGGCA-TCCATTTAACAGAGATA
* * *
24320171 GCTACAAAGGCATCCTTTTAACAAAGATA
1 GCCACAAAGGCATCCATTTAACAGAGATA
* * *
24320200 GCCACAAATGCACCCTTTTAACAGAGATA
1 GCCACAAAGGCATCCATTTAACAGAGATA
* * *
24320229 GTCACAAAGGCATTCATTTAACTGAGATA
1 GCCACAAAGGCATCCATTTAACAGAGATA
* *
24320258 GCTACAAAGG----CATTTAACGGAGATA
1 GCCACAAAGGCATCCATTTAACAGAGATA
* *
24320283 GCCACAAA-GCTATTCATTTAACAGGGATA
1 GCCACAAAGGC-ATCCATTTAACAGAGATA
24320312 GCCACAAAGG
1 GCCACAAAGG
24320322 TTGATAACAG
Statistics
Matches: 143, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
24 1 0.01
25 21 0.15
28 20 0.14
29 100 0.70
30 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (29 bp):
GCCACAAAGGCATCCATTTAACAGAGATA
Found at i:24320280 original size:25 final size:25
Alignment explanation
Indices: 24320216--24320291 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
24320206 AATGCACCCT
* *
24320216 TTTAACAGAGATAGTCACAAAGGCATTCA
1 TTTAACGGAGATAGCCACAAAGG----CA
* *
24320245 TTTAACTGAGATAGCTACAAAGGCA
1 TTTAACGGAGATAGCCACAAAGGCA
24320270 TTTAACGGAGATAGCCACAAAG
1 TTTAACGGAGATAGCCACAAAG
24320292 CTATTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 22 0.52
29 20 0.48
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
TTTAACGGAGATAGCCACAAAGGCA
Found at i:24320298 original size:54 final size:54
Alignment explanation
Indices: 24320174--24320321 Score: 163
Period size: 54 Copynumber: 2.7 Consensus size: 54
24320164 AGCGATGGCT
* * * * *
24320174 ACAAAGGCATCCTTTTAACAAAGATAGCCACAAATGCACCCTTTTAACAGAGATAGTC
1 ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCA----TTTAACAGAGATAGCC
* * *
24320232 ACAAAGGCATTCATTTAACTGAGATAGCTACAAAGGCATTTAACGGAGATAGCC
1 ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCATTTAACAGAGATAGCC
*
24320286 ACAAA-GCTATTCATTTAACAGGGATAGCCACAAAGG
1 ACAAAGGC-ATTCATTTAACAGAGATAGCCACAAAGG
24320322 TTGATAACAG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.03
54 44 0.56
58 32 0.41
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (54 bp):
ACAAAGGCATTCATTTAACAGAGATAGCCACAAAGGCATTTAACAGAGATAGCC
Found at i:24320379 original size:29 final size:28
Alignment explanation
Indices: 24320339--24320433 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
24320329 CAGATAGTAA
* *
24320339 CCACAAAAGCTTTCTTATAATAGAGATCT
1 CCACAAAGGCTTTCTT-TAATAGAGATCG
* *
24320368 CCATAAAGGCTTCCATTTAATAGAGATCG
1 CCACAAAGGCTTTC-TTTAATAGAGATCG
* *
24320397 CCACAATGGCTTTCTTT--CAGAGA-CAG
1 CCACAAAGGCTTTCTTTAATAGAGATC-G
24320423 CCACAAAGGCT
1 CCACAAAGGCT
24320434 CACTTATACG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 16 0.29
28 3 0.05
29 33 0.60
30 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (28 bp):
CCACAAAGGCTTTCTTTAATAGAGATCG
Found at i:24333596 original size:18 final size:17
Alignment explanation
Indices: 24333575--24333608 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24333565 TTTCAAGATT
*
24333575 TTTTTAATTTTTGTATTC
1 TTTTCAATTTTT-TATTC
24333593 TTTTCAATTTTTTATT
1 TTTTCAATTTTTTATT
24333609 TTAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTCAATTTTTTATTC
Found at i:24337961 original size:19 final size:19
Alignment explanation
Indices: 24337939--24338002 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
24337929 TTTGTTTATG
24337939 TTAGAAATATTTGTATTCT
1 TTAGAAATATTTGTATTCT
* * *
24337958 TTAGAATTTTTTGTATTGCA
1 TTAGAAATATTTGTATT-CT
* *
24337978 TTAGAAATATTGGTATCCT
1 TTAGAAATATTTGTATTCT
24337997 TTAGAA
1 TTAGAA
24338003 TTTTTGGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 22 0.61
20 14 0.39
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.48
Consensus pattern (19 bp):
TTAGAAATATTTGTATTCT
Found at i:24338009 original size:19 final size:19
Alignment explanation
Indices: 24337951--24338013 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
24337941 AGAAATATTT
* *
24337951 GTATTCTTTAGAATTTTTT
1 GTATCCTTTAGAATTTTTG
* * * *
24337970 GTATTGCATTAGAAATATTG
1 GTA-TCCTTTAGAATTTTTG
24337990 GTATCCTTTAGAATTTTTG
1 GTATCCTTTAGAATTTTTG
24338009 GTATC
1 GTATC
24338014 ACTATAATTC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (19 bp):
GTATCCTTTAGAATTTTTG
Found at i:24345662 original size:14 final size:14
Alignment explanation
Indices: 24345643--24345690 Score: 96
Period size: 14 Copynumber: 3.4 Consensus size: 14
24345633 TGTATCATTC
24345643 GAATTCGATATAGT
1 GAATTCGATATAGT
24345657 GAATTCGATATAGT
1 GAATTCGATATAGT
24345671 GAATTCGATATAGT
1 GAATTCGATATAGT
24345685 GAATTC
1 GAATTC
24345691 TCTTTTCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (14 bp):
GAATTCGATATAGT
Found at i:24352497 original size:13 final size:13
Alignment explanation
Indices: 24352460--24352500 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
24352450 TTTTGCTTTA
24352460 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
24352473 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
24352486 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
24352499 CT
1 CT
24352501 TTGCTTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:24356767 original size:11 final size:11
Alignment explanation
Indices: 24356741--24356781 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
24356731 AAAAATTAGC
*
24356741 AGAAGAGAAGGA
1 AGAAGA-AAGGG
24356753 AGAAGAAAGGG
1 AGAAGAAAGGG
24356764 AGAAGAAA-GG
1 AGAAGAAAGGG
24356774 AGAAGAAA
1 AGAAGAAA
24356782 AAAAAGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 10 0.36
11 12 0.43
12 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (11 bp):
AGAAGAAAGGG
Found at i:24356886 original size:17 final size:16
Alignment explanation
Indices: 24356855--24356889 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
24356845 TATTGTGTAG
24356855 TTTGTTTATTGTTAAT
1 TTTGTTTATTGTTAAT
*
24356871 TTTGTGTTATTTTTAAT
1 TTTGT-TTATTGTTAAT
24356888 TT
1 TT
24356890 ATTTTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.71
Consensus pattern (16 bp):
TTTGTTTATTGTTAAT
Found at i:24359299 original size:19 final size:19
Alignment explanation
Indices: 24359272--24359310 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
24359262 CGTGCAATGA
24359272 GCTACAGGGATGGATAGCC
1 GCTACAGGGATGGATAGCC
*
24359291 GCTATAGGGATGGATAGCC
1 GCTACAGGGATGGATAGCC
24359310 G
1 G
24359311 TTATGCGGGT
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:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (19 bp):
GCTACAGGGATGGATAGCC
Found at i:24360660 original size:14 final size:15
Alignment explanation
Indices: 24360636--24360664 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24360626 TTTTTCTGTG
24360636 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
24360651 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
24360665 AGTTTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:24360902 original size:28 final size:28
Alignment explanation
Indices: 24360856--24360912 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
24360846 TATAGTTTTT
24360856 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
24360884 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
24360912 A
1 A
24360913 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:24361866 original size:43 final size:42
Alignment explanation
Indices: 24361813--24361928 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
24361803 TATGTGTTTT
24361813 CGTGTAAGACCACGTCTGGGACGTCGGCATCGATATCTGATTA
1 CGTGTAAGACCACGTCTGGGACGT-GGCATCGATATCTGATTA
* * *
24361856 CGTGCAAGACC-CTGTCTGGGACAATGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTGGCATCGATATCTGATTA
* *
24361899 CATATAAGACCACGTCTGGGACGATGGCAT
1 CGTGTAAGACCACGTCTGGGACG-TGGCAT
24361929 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
42 1 0.02
43 59 0.95
44 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTGGCATCGATATCTGATTA
Found at i:24364327 original size:32 final size:32
Alignment explanation
Indices: 24364289--24364357 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
24364279 TTTATACAAA
24364289 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
1 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
* * * *
24364321 TCTTAAATGTGGCTAATTGCCTTGTAAGTCCT
1 CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
24364353 CCTTA
1 CCTTA
24364358 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (32 bp):
CCTTAAATGTGACAAATTGCCTTGTAAGCCCT
Found at i:24364457 original size:29 final size:29
Alignment explanation
Indices: 24364402--24364457 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
24364392 TATATTGTGT
**
24364402 TTAAACAAGCCTTTAACCTATTTTTTTAG
1 TTAAACAAGCCTTTAACCTATGGTTTTAG
* * *
24364431 TTAAATAAGCTTTTAACTTATGGTTTT
1 TTAAACAAGCCTTTAACCTATGGTTTT
24364458 TACTCATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (29 bp):
TTAAACAAGCCTTTAACCTATGGTTTTAG
Found at i:24365870 original size:11 final size:11
Alignment explanation
Indices: 24365854--24365878 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24365844 TTGAGTAACA
24365854 AAAAACATAGT
1 AAAAACATAGT
24365865 AAAAACATAGT
1 AAAAACATAGT
24365876 AAA
1 AAA
24365879 TACGTGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAACATAGT
Found at i:24365963 original size:17 final size:17
Alignment explanation
Indices: 24365909--24365966 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
24365899 CAGTAAAAAA
24365909 TACAATAATAATATAAT
1 TACAATAATAATATAAT
* * * *
24365926 TAAAATTAT-GT-TAGTT
1 TACAATAATAATATA-AT
24365942 TACAATAATAATATAAT
1 TACAATAATAATATAAT
24365959 TACAATAA
1 TACAATAA
24365967 ACATAAATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 17 0.57
18 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
TACAATAATAATATAAT
Found at i:24366353 original size:101 final size:103
Alignment explanation
Indices: 24366226--24366607 Score: 450
Period size: 101 Copynumber: 3.6 Consensus size: 103
24366216 TAAAAAACAC
* *
24366226 AAAAAATTACATTTATAAAAAGTCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
1 AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
**
24366291 TCATAAATCCCTAACAAAATAACTTTAAAATAA-TT-A
66 TCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
*
24366327 AAAAAATTGA-ATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAGCCTA
1 AAAAAATT-ACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTA
* *
24366391 ATTATAAAATTACTAACAAAATAACTTTCAAATAATTTAAAAAAAA
65 ATCAT-AAATTACTAACAAAATAACTTTAAAATAATTT------AA
* * *
24366437 ACATAAAATTTTACATTCATAAAAAATCACAATAAATATTAAACTAAACTAAAAACAAACGATTT
1 A-A-AAAA--TTACATTCATAAAAAATCACAAT--A-A--ACACTAAACTAAACACAAACAATTT
* *
24366502 ATAACTTAATCATAAATTACTAACAAAATGACTTTAAAATAATTTTAA
57 ATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TTTAA
*
24366550 AAAAAATTACATTCATAAAAATTCAC-A-AAACACTAAACTAAACACAAACAATTTATAA
1 AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAA
24366608 AACAAAATAA
Statistics
Matches: 241, Mismatches: 19, Indels: 41
0.80 0.06 0.14
Matches are distributed among these distances:
101 63 0.26
102 53 0.22
103 2 0.01
104 1 0.00
105 1 0.00
108 1 0.00
109 19 0.08
110 2 0.01
111 5 0.02
112 5 0.02
113 4 0.02
114 21 0.09
116 1 0.00
117 1 0.00
118 27 0.11
119 35 0.15
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.27
Consensus pattern (103 bp):
AAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAA
TCATAAATTACTAACAAAATAACTTTAAAATAATTTAA
Found at i:24366549 original size:119 final size:114
Alignment explanation
Indices: 24366337--24366607 Score: 305
Period size: 119 Copynumber: 2.4 Consensus size: 114
24366327 AAAAAATTGA
* * * *
24366337 ATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAGCCTAATTATAAAATT
1 ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAACCTAATCATAAAATT
*
24366402 ACTAACAAAATAACTTTCAAATAATTTAAAAAAAAACATAAAATTTTAC
66 ACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
* *
24366451 ATTCATAAAAAATCACAATAAATATTAAACTAAACTAAAAACAAACGATTTATAACTTAATCAT-
1 ATTCATAAAAAATCACAAT--A-A--AAACTAAACTAAAAACAAACAATTTATAACCTAATCATA
* *
24366515 AAATTACTAACAAAATGACTTTAAAATAATTT-----TAAA-A-AAAA--TTAC
61 AAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
* * *
24366560 ATTCATAAAAATTCAC-A-AAACACTAAACTAAACACAAACAATTTATAA
1 ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAA
24366608 AACAAAATAA
Statistics
Matches: 139, Mismatches: 13, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
102 26 0.19
104 1 0.01
105 1 0.01
108 1 0.01
109 19 0.14
111 4 0.03
112 1 0.01
113 3 0.02
114 19 0.14
116 1 0.01
117 1 0.01
118 30 0.22
119 32 0.23
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.27
Consensus pattern (114 bp):
ATTCATAAAAAATCACAATAAAAACTAAACTAAAAACAAACAATTTATAACCTAATCATAAAATT
ACTAACAAAATAACTTTAAAATAATTTAAAAAAAAACATAAAATTTTAC
Found at i:24366709 original size:17 final size:17
Alignment explanation
Indices: 24366687--24366724 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
24366677 AAATACAAAA
*
24366687 AAATAACTAATCTCTTT
1 AAATAACTAATCCCTTT
24366704 AAATAACTAATCCCTTT
1 AAATAACTAATCCCTTT
24366721 AAAT
1 AAAT
24366725 TAAAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAACTAATCCCTTT
Found at i:24366793 original size:20 final size:22
Alignment explanation
Indices: 24366770--24366820 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
24366760 TTTTTTTTTA
*
24366770 TTTCTTTCTTCTTCTT-T-TCC
1 TTTCTTTCTTCTCCTTCTCTCC
*
24366790 TTTCTTTTTTCTCCTTCCTCTCC
1 TTTCTTTCTTCTCCTT-CTCTCC
24366813 TTTCTTTC
1 TTTCTTTC
24366821 CCTCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.56
22 1 0.04
23 10 0.40
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTTTCTTCTCCTTCTCTCC
Found at i:24367511 original size:20 final size:21
Alignment explanation
Indices: 24367474--24367512 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24367464 TTTTAAACAT
* *
24367474 AAATAATTAAAATGTAACTTA
1 AAATAAATAAAATATAACTTA
24367495 AAATAAATAAAA-ATAACT
1 AAATAAATAAAATATAACT
24367513 ATTTTAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATAAATAAAATATAACTTA
Found at i:24371372 original size:25 final size:24
Alignment explanation
Indices: 24371344--24371437 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 24
24371334 AAGCTCTTTC
*
24371344 GAGCCATATAACAGGAAGCTCATGT
1 GAGCCATATAACAGGAAGCTCA-GA
* ** *
24371369 GAGCCATGTAATGGGAAGCTCCAAA
1 GAGCCATATAACAGGAAGCT-CAGA
* *
24371394 GAGCCAT-TAACAGGAAGTTCAAGC
1 GAGCCATATAACAGGAAGCTC-AGA
* *
24371418 GAGCCA-ATATCGGGAAGCTC
1 GAGCCATATAACAGGAAGCTC
24371438 CGGAAAGACA
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
23 1 0.02
24 26 0.49
25 24 0.45
26 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (24 bp):
GAGCCATATAACAGGAAGCTCAGA
Found at i:24371421 original size:24 final size:25
Alignment explanation
Indices: 24371343--24371423 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
24371333 GAAGCTCTTT
* *
24371343 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGTTCAAG
* * ** *
24371368 TGAGCCATGTAATGGGAAGCTCCAA-
1 CGAGCCATATAACAGGAAG-TTCAAG
*
24371393 AGAGCCAT-TAACAGGAAGTTCAAG
1 CGAGCCATATAACAGGAAGTTCAAG
24371417 CGAGCCA
1 CGAGCCA
24371424 ATATCGGGAA
Statistics
Matches: 42, Mismatches: 12, Indels: 5
0.71 0.20 0.08
Matches are distributed among these distances:
23 4 0.10
24 14 0.33
25 22 0.52
26 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGTTCAAG
Found at i:24371451 original size:48 final size:49
Alignment explanation
Indices: 24371347--24371490 Score: 120
Period size: 48 Copynumber: 2.9 Consensus size: 49
24371337 CTCTTTCGAG
* **
24371347 CCATATAACAGGAAGCTCATGTGAGCCATG-TAAT-GGGAAGCTCC-AAAGA
1 CCAT-TAACAGGAAGTTCATAAGAGCCA-GAT-ATCGGGAAGCTCCGAAAGA
*
24371396 GCCATTAACAGGAAGTTCA-AGCGAGCCA-ATATCGGGAAGCTCCGGAAAGA
1 -CCATTAACAGGAAGTTCATA-AGAGCCAGATATCGGGAAGCTCC-GAAAGA
** * *
24371446 -CATTAATGGGAAGTTCATAAGAGCCAGTTATTGGGAAGCTCCGAA
1 CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAA
24371491 GAGCCATATA
Statistics
Matches: 79, Mismatches: 8, Indels: 16
0.77 0.08 0.16
Matches are distributed among these distances:
47 2 0.03
48 35 0.44
49 33 0.42
50 9 0.11
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (49 bp):
CCATTAACAGGAAGTTCATAAGAGCCAGATATCGGGAAGCTCCGAAAGA
Found at i:24371482 original size:25 final size:25
Alignment explanation
Indices: 24371452--24371519 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
24371442 AAGACATTAA
*
24371452 TGGGAAGTTCATAAGAGCCAGT-TAT
1 TGGGAAGCTCATAAGAGCCA-TATAT
**
24371477 TGGGAAGCTCCGAAGAGCCATATAT
1 TGGGAAGCTCATAAGAGCCATATAT
* *
24371502 CGGGACGCTCATAAGAGC
1 TGGGAAGCTCATAAGAGC
24371520 TGCGATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (25 bp):
TGGGAAGCTCATAAGAGCCATATAT
Found at i:24371586 original size:24 final size:24
Alignment explanation
Indices: 24371559--24371665 Score: 81
Period size: 25 Copynumber: 4.4 Consensus size: 24
24371549 ACAACCAATA
*
24371559 GGGATGCTC-CGAAGAGCTATTAAC
1 GGGATGCTCACG-AGAGCTAATAAC
* * * * *
24371583 GGGAAGCTCGCAAGAACCATATAAC
1 GGGATGCTCACGAGAGCTA-ATAAC
* * * *
24371608 GGGAAGCTCATGAGAGCCAAATATC
1 GGGATGCTCACGAGAG-CTAATAAC
*
24371633 GGGATGCTCATGAGAGCTAATAAC
1 GGGATGCTCACGAGAGCTAATAAC
24371657 GGGATGCTC
1 GGGATGCTC
24371666 TTTCGAGCTG
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 28 0.42
25 36 0.55
26 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.18
Consensus pattern (24 bp):
GGGATGCTCACGAGAGCTAATAAC
Found at i:24371674 original size:24 final size:24
Alignment explanation
Indices: 24371603--24371665 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
24371593 CAAGAACCAT
* *
24371603 ATAACGGGAAGCTCATGAGAGCCAA
1 ATAACGGGATGCTCATGAGAG-CTA
*
24371628 ATATCGGGATGCTCATGAGAGCTA
1 ATAACGGGATGCTCATGAGAGCTA
24371652 ATAACGGGATGCTC
1 ATAACGGGATGCTC
24371666 TTTCGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (24 bp):
ATAACGGGATGCTCATGAGAGCTA
Found at i:24373605 original size:28 final size:30
Alignment explanation
Indices: 24373574--24373649 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
24373564 TCCAGAGATT
*
24373574 GCCACAAAGGCTTTCCTTTCA-GAGT-CTC
1 GCCACAAAGGCTTTCCTTTCATAAGTACTC
* *
24373602 GCCACAAAGG-TGTCTTTTCATTAAGTACTC
1 GCCACAAAGGCTTTCCTTTCA-TAAGTACTC
*
24373632 GTCACAAAGGCTTTCCTT
1 GCCACAAAGGCTTTCCTT
24373650 CTTTTGGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 8 0.21
28 10 0.26
29 3 0.08
30 12 0.32
31 5 0.13
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (30 bp):
GCCACAAAGGCTTTCCTTTCATAAGTACTC
Found at i:24381837 original size:46 final size:46
Alignment explanation
Indices: 24381766--24381878 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
24381756 CAACACTAAT
*
24381766 ATGTAGCCGAAGCTACCACTATTATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
24381812 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
*
24381858 ACGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
24381879 ATCAATAACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
Found at i:24381878 original size:23 final size:23
Alignment explanation
Indices: 24381766--24381879 Score: 176
Period size: 23 Copynumber: 5.0 Consensus size: 23
24381756 CAACACTAAT
*
24381766 ATGTAGCCGAAGCTACCACT-ATT
1 ATGTAGCCGAAGCTACCACTGA-A
24381789 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
**
24381812 ATGTAGCCGAAGCTACCACTGTT
1 ATGTAGCCGAAGCTACCACTGAA
24381835 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
24381858 ACGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
24381880 TCAATAACAC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
23 83 0.99
24 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:24386872 original size:141 final size:143
Alignment explanation
Indices: 24386695--24386985 Score: 478
Period size: 141 Copynumber: 2.0 Consensus size: 143
24386685 GTAGGTAGGC
*
24386695 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTGGACGACAAG
1 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
* * * *
24386760 ATCATGCAATTTTGGGCAT-GGGGTTAACTATTTGACCCCGTAAAGAAGGTGATAAAAGATGGAC
66 ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
24386824 ATATCTGCTAAG-
131 ATATCTGCTAAGT
* *
24386836 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCTATGTAGACGGCAAG
1 TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
* *
24386901 ACCATGCAATTTTAGGCATAGGGGTTGACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAG
66 ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
*
24386966 ATGTCTGCTAAGT
131 ATATCTGCTAAGT
24386979 TATTGGA
1 TATTGGA
24386986 CTAAAAAAAC
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 79 0.57
142 52 0.38
143 7 0.05
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (143 bp):
TATTGGAGACATGATTTAAATAAATAAAAGATGGTCATGCACAAATTATCCATGTAGACGACAAG
ACCATGCAATTTTAGGCATAGGGGTTAACTACTTGACCCCGTAAAGAAGGTGATAAAAGATAGAC
ATATCTGCTAAGT
Found at i:24392399 original size:17 final size:17
Alignment explanation
Indices: 24392379--24392429 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
24392369 TATTGTTTAA
24392379 TAAATTAATCTTATTTT
1 TAAATTAATCTTATTTT
*
24392396 TAAAAATAAT-TTATTTTT
1 T-AAATTAATCTTA-TTTT
*
24392414 TAACTTAATCTTATTT
1 TAAATTAATCTTATTT
24392430 ATGTTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAATTAATCTTATTTT
Found at i:24392413 original size:18 final size:20
Alignment explanation
Indices: 24392358--24392416 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
24392348 ATTAAGCACC
*
24392358 AAATGTAATTATATTGTTTAAT
1 AAAT-TAATT-TATTTTTTAAT
24392380 AAATTAATCTTA-TTTTTAA-
1 AAATTAAT-TTATTTTTTAAT
24392399 AAA-TAATTTATTTTTTAA
1 AAATTAATTTATTTTTTAA
24392417 CTTAATCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 3 0.09
18 11 0.32
19 3 0.09
20 6 0.18
21 6 0.18
22 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATTAATTTATTTTTTAAT
Found at i:24392427 original size:18 final size:18
Alignment explanation
Indices: 24392380--24392429 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
24392370 ATTGTTTAAT
24392380 AAATTAATCTTATTTTTA
1 AAATTAATCTTATTTTTA
* *
24392398 AAAATAAT-TTATTTTTT
1 AAATTAATCTTATTTTTA
*
24392415 AACTTAATCTTATTT
1 AAATTAATCTTATTT
24392430 ATGTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTAATCTTATTTTTA
Found at i:24397699 original size:24 final size:24
Alignment explanation
Indices: 24397667--24397716 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
24397657 TAGAGTCCTT
* *
24397667 TACGTCCCACAAATGGCTCTCATA
1 TACGTCCCACAAAGGGCACTCATA
*
24397691 TACGTCCCATAAAGGGCACTCATA
1 TACGTCCCACAAAGGGCACTCATA
24397715 TA
1 TA
24397717 ATGGTGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (24 bp):
TACGTCCCACAAAGGGCACTCATA
Found at i:24398392 original size:31 final size:31
Alignment explanation
Indices: 24398357--24398419 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
24398347 CTAAAGCCCG
24398357 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
1 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
*
24398388 CTTAAATTTGTAAGCTTTTCAAATTAATCTC
1 CTTAAATTTGTAAGCTTTTCAAACTAATCTC
24398419 C
1 C
24398420 AAAATTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (31 bp):
CTTAAATTTGTAAGCTTTTCAAACTAATCTC
Found at i:24399671 original size:25 final size:24
Alignment explanation
Indices: 24399635--24399681 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
24399625 TTTCTATCAT
24399635 ATTACTAAATTTATAATTAAAAATA
1 ATTACTAAATTTA-AATTAAAAATA
*
24399660 ATTA-TAATATTTAATTTAAAAA
1 ATTACTAA-ATTTAAATTAAAAA
24399682 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTACTAAATTTAAATTAAAAATA
Found at i:24406957 original size:20 final size:20
Alignment explanation
Indices: 24406929--24406974 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
24406919 ATATACGTAT
*
24406929 ATATATTATATTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
24406949 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
24406969 ATATAT
1 ATATAT
24406975 ATTTCTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:24419385 original size:44 final size:43
Alignment explanation
Indices: 24419326--24419437 Score: 161
Period size: 44 Copynumber: 2.6 Consensus size: 43
24419316 GAATAGGGCG
*
24419326 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACC-AT
* **
24419370 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAT
*
24419413 AGATCTTATCTCTCTGAAGTTGCAG
1 A-ATCTTATCTCCCTGAAGTTGCAG
24419438 GGAACATATC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 3 0.05
44 58 0.95
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAACCAT
Found at i:24421207 original size:26 final size:24
Alignment explanation
Indices: 24421172--24421220 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
24421162 GCATGTCATT
24421172 TTTATTATTATTTATATTAATTTCG
1 TTTATTATTATTTATATT-ATTTCG
*
24421197 TTTATTTATTATTTATGTTATTTC
1 TTTA-TTATTATTTATATTATTTC
24421221 TATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTATTATTATTTATATTATTTCG
Found at i:24428131 original size:42 final size:41
Alignment explanation
Indices: 24428070--24428371 Score: 388
Period size: 42 Copynumber: 7.2 Consensus size: 41
24428060 TTCTATAAAT
* * *
24428070 GCCGCTATAGGTCATGACCTTTAGCAGCGCTTTTCCAAAAAC
1 GCCGCTATAGATCA-GACCTTTAGCGGCGCTTTTCCACAAAC
* **
24428112 ACCGCTATAGATCAGGACCTTTAGCGGCGCTTCCCCACAAAC
1 GCCGCTATAGATCA-GACCTTTAGCGGCGCTTTTCCACAAAC
*
24428154 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTCCCACAAAC
1 GCCGCTATAGATCA-GACCTTTAGCGGCGCTTTTCCACAAAC
* * *
24428196 GCCGCTATAGCTCAAGATCTTTAGCGGCGCTTTCCCCACAAAC
1 GCCGCTATAGATC-AGACCTTTAGCGGCGCTTT-TCCACAAAC
* * *
24428239 GTCGCTATAGAACAAACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGACCTTTAGCGGCGCTTTT-CCACAAAC
* *
24428281 GTCGCTATAGAGCAGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAGACCTTTAGCGGCGCTTTT-CCACAAAC
*
24428323 GCCGCTATAGAACAGACCTTTAGCGGCGCTTTTCACACAAAC
1 GCCGCTATAGATCAGACCTTTAGCGGCGCTTTTC-CACAAAC
24428365 GCCGCTA
1 GCCGCTA
24428372 AAAACATATC
Statistics
Matches: 235, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.00
42 214 0.91
43 20 0.09
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (41 bp):
GCCGCTATAGATCAGACCTTTAGCGGCGCTTTTCCACAAAC
Found at i:24432233 original size:29 final size:30
Alignment explanation
Indices: 24432167--24432242 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
24432157 ATATTATAAA
**
24432167 AATAAAAGTTTAAAATCTTTTTAAAATTTCT
1 AATAAAA-TTTAAAATCTTTTTAAAATTGAT
*
24432198 AAAAAAATTTAAAATC-TTTTAAAATTGAT
1 AATAAAATTTAAAATCTTTTTAAAATTGAT
** *
24432227 TTTAAAATTTTAAATC
1 AATAAAATTTAAAATC
24432243 ACGAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.61
30 9 0.24
31 6 0.16
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
AATAAAATTTAAAATCTTTTTAAAATTGAT
Found at i:24432240 original size:30 final size:30
Alignment explanation
Indices: 24432168--24432223 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
24432158 TATTATAAAA
*
24432168 ATAAAAGTTTAAAATCTTTTTAAAATTTCT
1 ATAAAAATTTAAAATCTTTTTAAAATTTCT
*
24432198 AAAAAAATTTAAAATC-TTTTAAAATT
1 ATAAAAATTTAAAATCTTTTTAAAATT
24432224 GATTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAAAAATTTAAAATCTTTTTAAAATTTCT
Found at i:24432898 original size:7 final size:7
Alignment explanation
Indices: 24432886--24433041 Score: 59
Period size: 7 Copynumber: 21.7 Consensus size: 7
24432876 ACTAGTTAAT
24432886 CTAAACC
1 CTAAACC
24432893 CTAAACC
1 CTAAACC
* *
24432900 ATAAA-T
1 CTAAACC
*
24432906 TTAAACC
1 CTAAACC
*
24432913 CTAAAACA
1 CT-AAACC
24432921 CTAAAACC
1 CT-AAACC
*
24432929 TTAAACC
1 CTAAACC
24432936 CTAAAACC
1 CT-AAACC
*
24432944 ATAAACC
1 CTAAACC
* *
24432951 CTTAACA
1 CTAAACC
24432958 C-ATAACC
1 CTA-AACC
24432965 TCTAAACC
1 -CTAAACC
*
24432973 TTAAACC
1 CTAAACC
*
24432980 C-CAACC
1 CTAAACC
*
24432986 TTTAAACC
1 -CTAAACC
*
24432994 ATAAACC
1 CTAAACC
*
24433001 AT-AACC
1 CTAAACC
*
24433007 CATAATCC
1 C-TAAACC
24433015 CTAAACC
1 CTAAACC
*
24433022 CATAATCC
1 C-TAAACC
*
24433030 ATAAACC
1 CTAAACC
*
24433037 TTAAA
1 CTAAA
24433042 ATGGCAACAC
Statistics
Matches: 110, Mismatches: 28, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
6 12 0.11
7 61 0.55
8 36 0.33
9 1 0.01
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:24432936 original size:23 final size:23
Alignment explanation
Indices: 24432887--24432955 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
24432877 CTAGTTAATC
*
24432887 TAAACCCT-AAACCAT-AAA-TT
1 TAAACCCTAAAACCATAAAACCT
24432907 TAAACCCTAAAA-CACTAAAACCT
1 TAAACCCTAAAACCA-TAAAACCT
*
24432930 TAAACCCTAAAACCATAAACCCT
1 TAAACCCTAAAACCATAAAACCT
24432953 TAA
1 TAA
24432956 CACATAACCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.24
21 4 0.10
22 3 0.07
23 23 0.55
24 2 0.05
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (23 bp):
TAAACCCTAAAACCATAAAACCT
Found at i:24432979 original size:15 final size:14
Alignment explanation
Indices: 24432887--24433041 Score: 84
Period size: 15 Copynumber: 10.8 Consensus size: 14
24432877 CTAGTTAATC
24432887 TAAACCCTAAACCA
1 TAAACCCTAAACCA
** *
24432901 TAAA-TTTAAACCC
1 TAAACCCTAAACCA
* *
24432914 TAAAACACTAAAACCT
1 T-AAACCCT-AAACCA
24432930 TAAACCCTAAAACCA
1 TAAACCCT-AAACCA
*
24432945 TAAACCCTTAACACA
1 TAAACCCTAAAC-CA
*
24432960 T-AACCTCTAAACCT
1 TAAACC-CTAAACCA
* *
24432974 TAAACCC-CAACCTT
1 TAAACCCTAAACC-A
*
24432988 TAAACCATAAACCA
1 TAAACCCTAAACCA
* *
24433002 T-AACCCATAATCCC
1 TAAACCC-TAAACCA
*
24433016 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
*
24433031 TAAACCTTAAA
1 TAAACCCTAAA
24433042 ATGGCAACAC
Statistics
Matches: 110, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
13 15 0.14
14 34 0.31
15 55 0.50
16 6 0.05
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:24433292 original size:66 final size:66
Alignment explanation
Indices: 24433176--24433309 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
24433166 CCCTAAACTA
*
24433176 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTAATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
24433241 T
66 T
*
24433242 TAGTAATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTTCGATTATATAAGAAATTAT
1 TAGTAATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
24433307 T
66 T
24433308 TA
1 TA
24433310 ATATATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (66 bp):
TAGTAATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
T
Found at i:24433304 original size:33 final size:33
Alignment explanation
Indices: 24433201--24433305 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
24433191 CAATATTTTA
*
24433201 AAATTAATACTATCTCTTTTACGATTATATAAG
1 AAATTAATACTATCTCTTTTTCGATTATATAAG
* * * ** * * *
24433234 AAATTATTTAGTAATAAT-TAATTC-AATATTTTA-
1 AAATTA-ATACT-AT-CTCTTTTTCGATTATATAAG
24433267 AAATTAATACTATCTCTTTTTCGATTATATAAG
1 AAATTAATACTATCTCTTTTTCGATTATATAAG
24433300 AAATTA
1 AAATTA
24433306 TTTAATATAT
Statistics
Matches: 49, Mismatches: 17, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
30 1 0.02
31 6 0.12
32 9 0.18
33 18 0.37
34 9 0.18
35 5 0.10
36 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (33 bp):
AAATTAATACTATCTCTTTTTCGATTATATAAG
Found at i:24433573 original size:42 final size:41
Alignment explanation
Indices: 24433429--24433584 Score: 206
Period size: 41 Copynumber: 3.8 Consensus size: 41
24433419 CCTCAGCATT
* * *
24433429 ATTAGCGGTGCTTTCCCAAAAACGCCGCTAAAGCCCTAGGC
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCTGGGC
* * *
24433470 ATTAGCGGCGCTTTCAC-AAAAATGCCGCTAAAGGCCTGGAC
1 ATTAGCGGTGCTTTC-CTAAAAACGCCGCTAAAGGCCTGGGC
*
24433511 ATTAGCGGTGCTTTCATAAAAACGCCGCTAAAGGCCTGGGGC
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCT-GGGC
* *
24433553 ATTAGCGGTACTTTCCTAAAAATGCCGCTAAA
1 ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAA
24433585 TCCCCGAAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
41 67 0.67
42 33 0.33
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGTGCTTTCCTAAAAACGCCGCTAAAGGCCTGGGC
Found at i:24433738 original size:12 final size:12
Alignment explanation
Indices: 24433723--24433748 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24433713 GTTTTTATCC
24433723 AAACGCCGCTAA
1 AAACGCCGCTAA
24433735 AAACGCCGCTAA
1 AAACGCCGCTAA
24433747 AA
1 AA
24433749 GCCTGTTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:24434033 original size:49 final size:50
Alignment explanation
Indices: 24433913--24434052 Score: 210
Period size: 49 Copynumber: 2.8 Consensus size: 50
24433903 TGTACAGCCA
* * **
24433913 ATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
* * *
24433963 ATGCCATGTGCCAGACATGGTCTTACGTGGGACCTCTCATCTCGGTG-CC
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
24434012 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
24434053 ATCTCAATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 40 0.50
50 40 0.50
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCC
Found at i:24440237 original size:50 final size:50
Alignment explanation
Indices: 24440170--24440313 Score: 200
Period size: 50 Copynumber: 2.9 Consensus size: 50
24440160 TCTTGTACAA
* * **
24440170 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
24440220 CCTATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGGTG
*
24440270 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
24440314 ATCTCAATGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
49 1 0.01
50 79 0.98
51 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:24442572 original size:19 final size:18
Alignment explanation
Indices: 24442524--24442565 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
24442514 CGATAGAATT
24442524 TTTGTCATAAAATAATTAA
1 TTTGT-ATAAAATAATTAA
*
24442543 TTTTTATAAAATAATTAA
1 TTTGTATAAAATAATTAA
*
24442561 ATTGT
1 TTTGT
24442566 GTTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (18 bp):
TTTGTATAAAATAATTAA
Found at i:24444108 original size:14 final size:14
Alignment explanation
Indices: 24444089--24444115 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24444079 AAATGTTTTT
24444089 ACTTAGTTTTTAAC
1 ACTTAGTTTTTAAC
24444103 ACTTAGTTTTTAA
1 ACTTAGTTTTTAA
24444116 TCATCTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (14 bp):
ACTTAGTTTTTAAC
Found at i:24448883 original size:22 final size:21
Alignment explanation
Indices: 24448858--24448901 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
24448848 TGATAAAATT
24448858 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
24448880 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
24448901 T
1 T
24448902 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:24450441 original size:19 final size:18
Alignment explanation
Indices: 24450395--24450442 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
24450385 GATAGAATTT
*
24450395 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
*
24450414 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATTAAA
24450432 TTGTATTAAAA
1 TTGTA-TAAAA
24450443 ATTTTAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:24460334 original size:24 final size:24
Alignment explanation
Indices: 24460259--24460336 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
24460249 ATTGAGCGCC
*
24460259 AGAATAGGGACTGAGAGAGGGGTA
1 AGAATAGAGACTGAGAGAGGGGTA
* *
24460283 AGAATA-AGA-TG-GATTTGAAGCGCT-
1 AGAATAGAGACTGAGA---G-AGGGGTA
24460307 AGAATAGAGACTGAGAGAGGGGTA
1 AGAATAGAGACTGAGAGAGGGGTA
24460331 AGAATA
1 AGAATA
24460337 AGAATAAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 6 0.15
24 20 0.49
25 7 0.17
26 2 0.05
27 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.37, T:0.17
Consensus pattern (24 bp):
AGAATAGAGACTGAGAGAGGGGTA
Found at i:24467652 original size:43 final size:43
Alignment explanation
Indices: 24467562--24467757 Score: 171
Period size: 43 Copynumber: 4.6 Consensus size: 43
24467552 CCATTCCAAT
** * * ** *
24467562 TATACTGGCACGTA-AGTGCATCATTGGATGAAACCGAAGCTAC
1 TATACTGGCACACACAGTGCATCAATGGAT-AAACCAAAGAAAA
*
24467605 TATACTGGCACACACAGTGCATCAATGGATAAATCAAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* * * * * * *
24467648 TATACAGGAAAACACAGTGCATCAACGTAAAAACCGAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* * * *
24467691 TAAACTGGCATACACAGTGCATCATTGGATACACCAAAGAAAA
1 TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
* *
24467734 TATA-TCGGTACACACAATGCATCA
1 TATACT-GGCACACACAGTGCATCA
24467758 TCAGATAAAA
Statistics
Matches: 121, Mismatches: 30, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
42 1 0.01
43 106 0.88
44 14 0.12
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (43 bp):
TATACTGGCACACACAGTGCATCAATGGATAAACCAAAGAAAA
Found at i:24485418 original size:8 final size:8
Alignment explanation
Indices: 24485401--24485435 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
24485391 TTCAAATAGT
24485401 AAATAATA
1 AAATAATA
*
24485409 AAATATTA
1 AAATAATA
*
24485417 AAAAAATA
1 AAATAATA
24485425 AAATAATA
1 AAATAATA
24485433 AAA
1 AAA
24485436 AATTTTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAATAATA
Found at i:24492291 original size:16 final size:16
Alignment explanation
Indices: 24492272--24492306 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
24492262 TAGTAATTTT
24492272 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
24492288 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
24492304 AAT
1 AAT
24492307 TACAAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:24495509 original size:21 final size:21
Alignment explanation
Indices: 24495479--24495535 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
24495469 ATCACAAAGA
* *
24495479 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
24495499 AAAAAGAGAAGTAACTTGGAT
1 AAAAAGAGAAGTAACTTAGAC
*
24495520 AAAAAGAGAACTAACT
1 AAAAAGAGAAGTAACT
24495536 CGAACAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:24497689 original size:42 final size:42
Alignment explanation
Indices: 24497642--24497899 Score: 185
Period size: 43 Copynumber: 6.2 Consensus size: 42
24497632 GAAGCTTTGC
* *
24497642 ACCCAGCGCTGGTCGGTAAAATCGACAAATATGTATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
*
24497684 ACCCAGCACTGGTCGGTAAAATCGAAAAATATTATATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATA-TATATATGTGT
* * * * * *
24497727 GCCCAGCACTAGTCGGTAAAACCAACAAATATATATGTATATAT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATA--TATGTGT
* * * * ** * *
24497771 ATGTCAAGCACTAGTTGGTGGAACCGAAAAATATATATATGTG-
1 A--CCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
* *
24497814 -CCCAACACTGGTCTGTAAAA-CTG-CAAATATATATATG-G-
1 ACCCAGCACTGGTCGGTAAAATC-GACAAATATATATATGTGT
* * *
24497852 --CTAGCACTGGTCGGTAAAACCGGC-AA-ATATATATGTGT
1 ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
*
24497890 GCCCAGCACT
1 ACCCAGCACT
24497900 TCAAGATGCA
Statistics
Matches: 171, Mismatches: 33, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
36 9 0.05
37 20 0.12
38 3 0.02
39 14 0.08
40 20 0.12
42 33 0.19
43 36 0.21
44 9 0.05
46 27 0.16
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (42 bp):
ACCCAGCACTGGTCGGTAAAATCGACAAATATATATATGTGT
Found at i:24497860 original size:37 final size:40
Alignment explanation
Indices: 24497799--24497899 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 40
24497789 TGGAACCGAA
* *
24497799 AAATATATATATGTGCCCAACACTGGTCTGTAAAA-CTGC
1 AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
* *
24497838 AAATATATATATG-G-CTAGCACTGGTCGGTAAAACCGGC
1 AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
* *
24497876 AAATATATATGTGTGCCCAGCACT
1 AAATATATATATGTGCCCAACACT
24497900 TCAAGATGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
37 16 0.30
38 16 0.30
39 14 0.26
40 7 0.13
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (40 bp):
AAATATATATATGTGCCCAACACTGGTCGGTAAAACCGGC
Found at i:24503121 original size:26 final size:25
Alignment explanation
Indices: 24503069--24503130 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
24503059 AAACTCTTCT
*
24503069 AAAAGAAAACTCAAGAGAAATTCTTG
1 AAAA-AAAACTCAAGAGAAATTATTG
*
24503095 AAAAAAAACTCAAAGAGAATTTATTG
1 AAAAAAAACTC-AAGAGAAATTATTG
24503121 ACTAAAAAAA
1 A--AAAAAAA
24503131 TAAGTTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.23
26 17 0.55
28 7 0.23
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (25 bp):
AAAAAAAACTCAAGAGAAATTATTG
Found at i:24505195 original size:25 final size:25
Alignment explanation
Indices: 24505167--24505215 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
24505157 CATGCAGTAG
* *
24505167 CAGTCTGGTCCTGAGCCCTATACAA
1 CAGTCTGGGCCTGAGCCCAATACAA
* *
24505192 CAGTGTGGGCCTTAGCCCAATACA
1 CAGTCTGGGCCTGAGCCCAATACA
24505216 GTAATAGTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (25 bp):
CAGTCTGGGCCTGAGCCCAATACAA
Found at i:24505387 original size:26 final size:26
Alignment explanation
Indices: 24505365--24505426 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
24505355 TGCAGCAAGA
24505365 CTACCAGTAATAGTAATGTAGCAAAG
1 CTACCAGTAATAGTAATGTAGCAAAG
* * *
24505391 CTGCCAGTAACAGTATATGTGGCAAAG
1 CTACCAGTAATAGTA-ATGTAGCAAAG
*
24505418 CCACCAGTA
1 CTACCAGTA
24505427 CAGTATACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (26 bp):
CTACCAGTAATAGTAATGTAGCAAAG
Found at i:24505429 original size:26 final size:27
Alignment explanation
Indices: 24505367--24505433 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
24505357 CAGCAAGACT
* *
24505367 ACCAGTAATAGTA-ATGTAGCAAAGCT
1 ACCAGTAACAGTATATGTAGCAAAGCC
* *
24505393 GCCAGTAACAGTATATGTGGCAAAGCC
1 ACCAGTAACAGTATATGTAGCAAAGCC
24505420 ACCAGT-ACAGTATA
1 ACCAGTAACAGTATA
24505434 CTTACCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (27 bp):
ACCAGTAACAGTATATGTAGCAAAGCC
Found at i:24505598 original size:27 final size:26
Alignment explanation
Indices: 24505580--24505831 Score: 283
Period size: 27 Copynumber: 9.3 Consensus size: 26
24505570 GGGTATAACA
24505580 GTCATTTTACCCTTC-AGGGGTATTTC
1 GTCATTTTACCCTTCGA-GGGTATTTC
*
24505606 GGTCATTTTACCCTGCGAGGGTATTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
* *
24505633 AGTTATTTTACCCTTCGAGGGTTTTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
** *
24505660 GATCATTCCACCCTGCGAGGGTATTTC
1 G-TCATTTTACCCTTCGAGGGTATTTC
* *
24505687 GATCATTTTACCCTTTGAGGGTATTTTG
1 G-TCATTTTACCCTTCGAGGGTA-TTTC
*
24505715 GTCATTTTACCCTTCGGGGGTATTTC
1 GTCATTTTACCCTTCGAGGGTATTTC
24505741 GATCATTTTACCCTTCGAGGGTATTTC
1 G-TCATTTTACCCTTCGAGGGTATTTC
* *
24505768 GGTTACTTTACCCTTC-AGGGGTATTTC
1 -GTCATTTTACCCTTCGA-GGGTATTTC
*
24505795 AGTCATTTTACCCTTCGAGGATATTTC
1 -GTCATTTTACCCTTCGAGGGTATTTC
24505822 AGTCATTTTA
1 -GTCATTTTA
24505832 GGCCCATTAC
Statistics
Matches: 193, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.03
27 180 0.93
28 7 0.04
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (26 bp):
GTCATTTTACCCTTCGAGGGTATTTC
Found at i:24505660 original size:54 final size:54
Alignment explanation
Indices: 24505578--24505831 Score: 318
Period size: 54 Copynumber: 4.7 Consensus size: 54
24505568 AGGGGTATAA
24505578 CAGTCATTTTACCCTTC-AGGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
1 CAGTCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * * **
24505632 CAGTTATTTTACCCTTCGAGGGTTTTTCGATCATTCCACCCTGCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * * *
24505686 C-GATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACCCTTCGGGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
* * *
24505740 C-GATCATTTTACCCTTCGAGGGTATTTCGGTTACTTTACCCTTC-AGGGGTATTT
1 CAG-TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGA-GGGTATTT
* *
24505794 CAGTCATTTTACCCTTCGAGGATATTTCAGTCATTTTA
1 CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA
24505832 GGCCCATTAC
Statistics
Matches: 173, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 170 0.98
55 2 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (54 bp):
CAGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTT
Found at i:24505828 original size:81 final size:81
Alignment explanation
Indices: 24505581--24505831 Score: 328
Period size: 81 Copynumber: 3.1 Consensus size: 81
24505571 GGTATAACAG
* *
24505581 TCATTTTACCCTTC-AGGGGTATTTCGGTCATTTTACCCTGCGAGGGTATTTCAGTTATTTTACC
1 TCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACC
*
24505645 CTTCGAGGGTTTTTCGA
65 CTTCGAGGGTATTTCGA
** * * * **
24505662 TCATTCCACCCTGCGAGGGTATTTCGATCATTTTACCCTTTGAGGGTATTTTGGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
*
24505727 TTCGGGGGTATTTCGA
66 TTCGAGGGTATTTCGA
* *
24505743 TCATTTTACCCTTCGAGGGTATTTCGGTTACTTTACCCTTC-AGGGGTATTTCAGTCATTTTACC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGA-GGGTATTTCAGTCATTTTACC
*
24505807 CTTCGAGGATATTTC-A
65 CTTCGAGGGTATTTCGA
24505823 GTCATTTTA
1 -TCATTTTA
24505832 GGCCCATTAC
Statistics
Matches: 145, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.01
81 142 0.98
82 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCC
TTCGAGGGTATTTCGA
Found at i:24511405 original size:12 final size:12
Alignment explanation
Indices: 24511388--24511412 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24511378 CTTGTAAACC
24511388 TTTCAAAACACT
1 TTTCAAAACACT
24511400 TTTCAAAACACT
1 TTTCAAAACACT
24511412 T
1 T
24511413 ACGGATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTCAAAACACT
Found at i:24513118 original size:9 final size:9
Alignment explanation
Indices: 24513104--24513171 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
24513094 GTAGTGATTC
24513104 AATTCGGTT
1 AATTCGGTT
24513113 AATTCGGTT
1 AATTCGGTT
* *
24513122 AATTCAGAT
1 AATTCGGTT
*
24513131 AATTCGGGT
1 AATTCGGTT
*
24513140 AATTCAGTT
1 AATTCGGTT
*
24513149 AATTCGGGT
1 AATTCGGTT
24513158 AATTCGGTT
1 AATTCGGTT
24513167 AATTC
1 AATTC
24513172 AATTAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:24513136 original size:27 final size:27
Alignment explanation
Indices: 24513104--24513179 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
24513094 GTAGTGATTC
*
24513104 AATTCGGTTAATTCGGTTAATTCAGAT
1 AATTCGGTTAATTCAGTTAATTCAGAT
* * *
24513131 AATTCGGGTAATTCAGTTAATTCGGGT
1 AATTCGGTTAATTCAGTTAATTCAGAT
*
24513158 AATTCGGTTAATTCAATTAATT
1 AATTCGGTTAATTCAGTTAATT
24513180 TGATTAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (27 bp):
AATTCGGTTAATTCAGTTAATTCAGAT
Found at i:24513187 original size:27 final size:27
Alignment explanation
Indices: 24513098--24513188 Score: 94
Period size: 27 Copynumber: 3.3 Consensus size: 27
24513088 AATTATGTAG
*
24513098 TGATTCAATTCGGTTAATTCGGTTAATT
1 TGATT-AATTCGGTTAATTCAGTTAATT
* *
24513126 CAGA-TAATTCGGGTAATTCAGTTAATT
1 -TGATTAATTCGGTTAATTCAGTTAATT
* ** *
24513153 CGGGTAATTCGGTTAATTCAATTAATT
1 TGATTAATTCGGTTAATTCAGTTAATT
24513180 TGATTAATT
1 TGATTAATT
24513189 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.92
28 1 0.02
29 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (27 bp):
TGATTAATTCGGTTAATTCAGTTAATT
Found at i:24528755 original size:14 final size:14
Alignment explanation
Indices: 24528736--24528766 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24528726 TTGCAAGGAG
24528736 AATGCAATTTATTC
1 AATGCAATTTATTC
24528750 AATGCAATTTATTC
1 AATGCAATTTATTC
24528764 AAT
1 AAT
24528767 CTGTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
AATGCAATTTATTC
Found at i:24540019 original size:42 final size:43
Alignment explanation
Indices: 24539911--24540068 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
24539901 AGCTCGTACA
** * * *
24539911 ATGCCAACATCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCAGACATGGTCTTACACGAAATCATATATCG
*
24539954 ATGCC-ACTATCCCAGACAAGGTCTTACACGAAATCATATA-CG
1 ATGCCAAC-ATCCCAGACATGGTCTTACACGAAATCATATATCG
* * *
24539996 AAGCCAATATCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAACATCCCAGACATGGTCTTACACG-AAATCAT-ATATCG
* *
24540040 ATGCCAACATCCTAGACGTGGTCTTACAC
1 ATGCCAACATCCCAGACATGGTCTTACAC
24540069 AAGATCACAT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 30 0.31
43 39 0.41
44 27 0.28
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
ATGCCAACATCCCAGACATGGTCTTACACGAAATCATATATCG
Found at i:24541852 original size:24 final size:24
Alignment explanation
Indices: 24541820--24541870 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
24541810 TTATGGGGAG
24541820 AAGTGTCATATGTTTTCTGATCAT
1 AAGTGTCATATGTTTTCTGATCAT
24541844 AAGTGTCATATGTTTTCTGATCAT
1 AAGTGTCATATGTTTTCTGATCAT
24541868 AAG
1 AAG
24541871 AGTTTGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (24 bp):
AAGTGTCATATGTTTTCTGATCAT
Found at i:24550350 original size:22 final size:21
Alignment explanation
Indices: 24550296--24550350 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
24550286 GCAAATCTGT
24550296 CTAAAA-TAATA-AAAATTAA
1 CTAAAATTAATATAAAATTAA
*
24550315 -TGAAAATTTGATATAAAATTAA
1 CT-AAAA-TTAATATAAAATTAA
24550337 CTAAAATTCAATAT
1 CTAAAATT-AATAT
24550351 GTTCATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
21 6 0.21
22 16 0.57
23 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (21 bp):
CTAAAATTAATATAAAATTAA
Found at i:24553203 original size:24 final size:23
Alignment explanation
Indices: 24553171--24553220 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
24553161 AGTGTAAAAT
*
24553171 ATTAATAATTTAAT-AAATTGAAA
1 ATTAATAATTAAATAAAATT-AAA
24553194 ATTAATTAATTAAATAAAATTAAA
1 ATTAA-TAATTAAATAAAATTAAA
24553218 ATT
1 ATT
24553221 TAGGAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 14 0.58
25 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTAATAATTAAATAAAATTAAA
Found at i:24559570 original size:32 final size:32
Alignment explanation
Indices: 24559534--24559598 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
24559524 GCCTAGGGAC
*
24559534 TGATTTGCAAAACTGTTAAAGGATTAGGGTTT
1 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
24559566 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
1 TGATTTGCAAAACTATTAAAGGATTAGGGTTT
24559598 T
1 T
24559599 TCATAAACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (32 bp):
TGATTTGCAAAACTATTAAAGGATTAGGGTTT
Found at i:24560191 original size:41 final size:41
Alignment explanation
Indices: 24560145--24560333 Score: 236
Period size: 41 Copynumber: 4.6 Consensus size: 41
24560135 TAGTTAATTA
** *
24560145 ACCCCTGAATTGCACATATGTATCCCTATTTGTACTT-TAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* * *
24560185 TACCCCTGAATTACACATATGTGCCCCTATTTGGACTTCGAT
1 -ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* *
24560227 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* * * *
24560268 ACCCCTAAATTACACATATATGCCCCTATTTGTTCTTCGAG
1 ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
* *
24560309 ACCCTTGAATTGCACATACGTGCCC
1 ACCCCTGAATTGCACATATGTGCCC
24560334 TTGTTTACAC
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
41 124 0.99
42 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (41 bp):
ACCCCTGAATTGCACATATGTGCCCCTATTTGTACTTCGAG
Found at i:24560254 original size:21 final size:21
Alignment explanation
Indices: 24560187--24560254 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
24560177 TACTTTAGTA
* *
24560187 CCCCTGAATTACACATATGTG
1 CCCCTGAATTGCACATACGTG
* * * *
24560208 CCCCT-ATTTGGAC-TTCGATA
1 CCCCTGAATTGCACATACG-TG
24560228 CCCCTGAATTGCACATACGTG
1 CCCCTGAATTGCACATACGTG
24560249 CCCCTG
1 CCCCTG
24560255 TTTGTACTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 11 0.32
21 18 0.53
22 3 0.09
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (21 bp):
CCCCTGAATTGCACATACGTG
Found at i:24560282 original size:82 final size:82
Alignment explanation
Indices: 24560145--24560339 Score: 266
Period size: 82 Copynumber: 2.4 Consensus size: 82
24560135 TAGTTAATTA
* ** * * * *
24560145 ACCCCTGAATTGCACATATGTATCCCTATTTGTACTTTAGTACCCCTGAATTACACATATGTGCC
1 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTGAGTACCCCTAAATTACACATATATGCC
*
24560210 CCTATTTGGACTTCGAT
66 CCTATTTGGACTTCGAG
24560227 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCGAG-ACCCCTAAATTACACATATATGC
1 ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTT-GAGTACCCCTAAATTACACATATATGC
**
24560291 CCCTATTTGTTCTTCGAG
65 CCCTATTTGGACTTCGAG
* *
24560309 ACCCTTGAATTGCACATACGTGCCCTTGTTT
1 ACCCCTGAATTGCACATACGTGCCCCTGTTT
24560340 ACACTCCAGT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
82 98 0.98
83 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (82 bp):
ACCCCTGAATTGCACATACGTGCCCCTGTTTGTACTTGAGTACCCCTAAATTACACATATATGCC
CCTATTTGGACTTCGAG
Found at i:24561667 original size:74 final size:74
Alignment explanation
Indices: 24561544--24561688 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 74
24561534 AAGTTTTGAG
*
24561544 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGGAT
1 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
24561609 TGATTATTA
66 TGATTATTA
* *
24561618 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATTATGTGGTTATGTGAATAATTGTGAAT
1 TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
24561683 TGATTA
66 TGATTA
24561689 CTGTGATGCG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (74 bp):
TGTAAGCTTTCTATTTCCTTTGTTTTATTTTGGCAAATCATGTGATTATGTGAATAATTGTGAAT
TGATTATTA
Found at i:24564191 original size:17 final size:17
Alignment explanation
Indices: 24564171--24564210 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
24564161 TATACCAAAA
24564171 AAATAAAACAAATAAAT
1 AAATAAAACAAATAAAT
* **
24564188 AAATAAAATAAATTCAT
1 AAATAAAACAAATAAAT
24564205 AAATAA
1 AAATAA
24564211 TGAGAGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACAAATAAAT
Found at i:24564328 original size:27 final size:26
Alignment explanation
Indices: 24564294--24564345 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
24564284 AATTTGGCAT
*
24564294 AAAATATATAAATAAATAA-AATAATG
1 AAAATATAAAAAT-AATAATAATAATG
24564320 AAAACTATAAAAATAATAATAATAAT
1 AAAA-TATAAAAATAATAATAATAAT
24564346 AATAGTAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAATATAAAAATAATAATAATAATG
Found at i:24566260 original size:217 final size:216
Alignment explanation
Indices: 24565965--24566465 Score: 693
Period size: 217 Copynumber: 2.3 Consensus size: 216
24565955 TCTGTTTGCA
* * *
24565965 CCACTGCAACTTCAGGGGTATAAGATCTGCTTGCTTAGTCTGCTCCGCTACAAGTTCAGGGAGAT
1 CCACTGCAACTTCAGGGGGATAAGAT-TGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGAT
*
24566030 AAGACTAGATGCGATCTGCTCTCTTCAACTTCAGAGAGATAAGATCTGTCATTTTAATACGCTCC
65 AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTCATTTTAATACGCTCC
* *
24566095 GCTACAACTTCAGGGAGATAGGATTATTGAATTTAATCTACTCCACTGCAACTTCAGGGAGATAA
130 ACTACAACTTCAAGGAGATAGGATTATTGAATTTAATCTACTCCACTGCAACTTCAGGGAGATAA
* *
24566160 GATTCGTC-ATCTTCAATCTGC-
195 GATT-ATCTATCTTCAATCCGCT
* * * *
24566181 CCTACTGCAACTTTAGGGGGATAAGAGTTGGTTGCTTAGTCTGCTCCGCTGCAACTTTACGGAGA
1 CC-ACTGCAACTTCAGGGGGATAAGA-TTGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGA
* **
24566246 TAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTTATTTTAATTTGCTC
64 TAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTCATTTTAATACGCTC
* ** * * *
24566311 CACTGCAACTTCAAGGAGATAGGATTATTGGTTTTAATTTGCTCCACTGTAACTTCAGGGAGATA
129 CACTACAACTTCAAGGAGATAGGATTATTGAATTTAATCTACTCCACTGCAACTTCAGGGAGATA
24566376 AGATTATCTATCTTCAATCCGCT
194 AGATTATCTATCTTCAATCCGCT
* * * *
24566399 CCACTGCAACTTCAGGGAGATAGGATTTGCTAT-CTTCAGTCCGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGGGGATAAGA-TTGCT-TGCTT-AGTCTGCTCCGCTGCAACTTCAGGGAG
24566463 ATA
63 ATA
24566466 GGATTTGTAT
Statistics
Matches: 249, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
216 4 0.02
217 215 0.86
218 30 0.12
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (216 bp):
CCACTGCAACTTCAGGGGGATAAGATTGCTTGCTTAGTCTGCTCCGCTGCAACTTCAGGGAGATA
AGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTCATTTTAATACGCTCCA
CTACAACTTCAAGGAGATAGGATTATTGAATTTAATCTACTCCACTGCAACTTCAGGGAGATAAG
ATTATCTATCTTCAATCCGCT
Found at i:24566321 original size:44 final size:43
Alignment explanation
Indices: 24565965--24566543 Score: 353
Period size: 44 Copynumber: 13.3 Consensus size: 43
24565955 TCTGTTTGCA
** *
24565965 CCACTGCAACTTCAGGG-GTATAAGATCTGCTTGCTT-AGTCTGCT
1 CCACTGCAACTTCAGGGAG-ATAAGAT-TG-TTATTTCAATCTGCT
* * * * * *
24566009 CCGCTACAAGTTCAGGGAGATAAGACTAG--A-TGCGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTGTTATTTCAATCTGCT
* * * * *
24566050 -CTCTTCAACTTCAGAGAGATAAGATCTGTCATTTTAATAC-GCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TGTTATTTCAAT-CTGCT
* * * * *
24566093 CCGCTACAACTTCAGGGAGATAGGATTATTGAATTT-AATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTGTT--ATTTCAATCTGCT
*
24566137 CCACTGCAACTTCAGGGAGATAAGATTCGTCATCTTCAATCTGC-
1 CCACTGCAACTTCAGGGAGATAAGATT-GTTAT-TTCAATCTGCT
* * ** *
24566181 CCTACTGCAACTTTAGGGGGATAAGAGTTGGTTGCTT-AGTCTGCT
1 CC-ACTGCAACTTCAGGGAGATAAGA-TT-GTTATTTCAATCTGCT
* * * * * *
24566226 CCGCTGCAACTTTACGGAGATAAGACTAG--A-TGCGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTGTTATTTCAATCTGCT
* * * *
24566267 -CTCTGCAACTTCAGAGAGATAAGATCTGTTATTTTAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TGTTATTTCAATCTGCT
* * * * * *
24566310 CCACTGCAACTTCAAGGAGATAGGATTATTGGTTTTAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGTT-ATTTCAATCTGCT
* * *
24566354 CCACTGTAACTTCAGGGAGATAAGATTATCTATCTTCAATCCGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGT-TAT-TTCAATCTGCT
* * * *
24566399 CCACTGCAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCCGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTGTTAT-TTCAATCTGCT
* *
24566444 CCACTGCAACTTCAGGGAGATAGGATT-TGTATCTTCAATCCGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGT-TAT-TTCAATCTGCT
* * *
24566488 CCACTGCAACTTTAGGGAGATAGGATT-TGTATCTTCAATCCGCT
1 CCACTGCAACTTCAGGGAGATAAGATTGT-TAT-TTCAATCTGCT
24566532 CCACTGCAACTT
1 CCACTGCAACTT
24566544 TAAGAAGATA
Statistics
Matches: 431, Mismatches: 75, Indels: 58
0.76 0.13 0.10
Matches are distributed among these distances:
39 2 0.00
40 44 0.10
41 12 0.03
42 2 0.00
43 22 0.05
44 234 0.54
45 109 0.25
46 6 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
CCACTGCAACTTCAGGGAGATAAGATTGTTATTTCAATCTGCT
Found at i:24566423 original size:89 final size:89
Alignment explanation
Indices: 24566269--24566543 Score: 339
Period size: 89 Copynumber: 3.1 Consensus size: 89
24566259 GATCTGCTCT
* * ** *
24566269 CTGCAACTTCAGAGAGATAAGATCTGTTAT-TTTAATTTGCTCCACTGCAACTTCAAGGAGATAG
1 CTGCAACTTCAGGGAGATAAGAT-T-TTATCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAG
* **
24566333 GATTATTGGT-T-TT-AATTTGCTCCA
64 GATT-TTGCTATCTTCAATCCGCTCCA
*
24566357 CTGTAACTTCAGGGAGATAAGATTATCTATCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAG
1 CTGCAACTTCAGGGAGATAAGATT-T-TATCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAG
*
24566422 GA-TTTGCTATCTTCAGTCCGCTCCA
64 GATTTTGCTATCTTCAATCCGCTCCA
* *
24566447 CTGCAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTGCAACTTTAGGGAGATAGG
1 CTGCAACTTCAGGGAGATAAGATTT-TATCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAGG
24566512 A-TTTG-TATCTTCAATCCGCTCCA
65 ATTTTGCTATCTTCAATCCGCTCCA
24566535 CTGCAACTT
1 CTGCAACTT
24566544 TAAGAAGATA
Statistics
Matches: 166, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
87 6 0.04
88 52 0.31
89 78 0.47
90 30 0.18
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (89 bp):
CTGCAACTTCAGGGAGATAAGATTTTATCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
TTTTGCTATCTTCAATCCGCTCCA
Found at i:24566544 original size:44 final size:44
Alignment explanation
Indices: 24566055--24566561 Score: 396
Period size: 44 Copynumber: 11.5 Consensus size: 44
24566045 CTGCTCTCTT
* * * * * *
24566055 CAACTTCAGAGAGATAAGATCTGTCAT-TTTAATAC-GCTCCGCTA
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAAT-CTGCTCCACTG
* *
24566099 CAACTTCAGGGAGATAGGATTATTGAAT-TT-AATCTACTCCACTG
1 CAACTTCAGGGAGATAGGA-T-TTGTATCTTCAATCTGCTCCACTG
* *
24566143 CAACTTCAGGGAGATAAGATTCGTCATCTTCAATCTGC-CCTACTG
1 CAACTTCAGGGAGATAGGATTTGT-ATCTTCAATCTGCTCC-ACTG
* * * * * *
24566188 CAACTTTAGGGGGATAAGAGTTGGT-TGCTT-AGTCTGCTCCGCTG
1 CAACTTCAGGGAGATAGGA-TTTGTAT-CTTCAATCTGCTCCACTG
* * * * * * * *
24566232 CAACTTTACGGAGATAAGACTAG-A--TGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
* * * * *
24566272 CAACTTCAGAGAGATAAGATCTGTTAT-TTTAATTTGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTG-TATCTTCAATCTGCTCCACTG
* *
24566316 CAACTTCAAGGAGATAGGATTATTGGT-T-TT-AATTTGCTCCACTG
1 CAACTTCAGGGAGATAGGA-T-TT-GTATCTTCAATCTGCTCCACTG
* * * *
24566360 TAACTTCAGGGAGATAAGATTATCTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATT-TGTATCTTCAATCTGCTCCACTG
* *
24566405 CAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTG-TATCTTCAATCTGCTCCACTG
*
24566450 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
* *
24566494 CAACTTTAGGGAGATAGGATTTGTATCTTCAATCCGCTCCACTG
1 CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
* * *
24566538 CAACTTTAAGAAGATAGGATTTGT
1 CAACTTCAGGGAGATAGGATTTGT
24566562 GGTTTCACCG
Statistics
Matches: 386, Mismatches: 53, Indels: 48
0.79 0.11 0.10
Matches are distributed among these distances:
40 22 0.06
41 6 0.02
42 5 0.01
43 16 0.04
44 213 0.55
45 115 0.30
46 8 0.02
47 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATTTGTATCTTCAATCTGCTCCACTG
Found at i:24567471 original size:26 final size:26
Alignment explanation
Indices: 24567442--24567492 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
24567432 CAAGTATCTT
24567442 GAAAAGAACAAAGTATTCCAAGAACG
1 GAAAAGAACAAAGTATTCCAAGAACG
* *
24567468 GAAAATAATAAAGTATTCCAAGAAC
1 GAAAAGAACAAAGTATTCCAAGAAC
24567493 AACAAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (26 bp):
GAAAAGAACAAAGTATTCCAAGAACG
Found at i:24568792 original size:23 final size:23
Alignment explanation
Indices: 24568762--24568806 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24568752 AATTCTGGGC
*
24568762 TTTGGTTTTTTATATTT-TTTGTA
1 TTTGGTTTATTAT-TTTCTTTGTA
24568785 TTTGGTTTATTATTTTCTTTGT
1 TTTGGTTTATTATTTTCTTTGT
24568807 GTATGCGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.73
Consensus pattern (23 bp):
TTTGGTTTATTATTTTCTTTGTA
Found at i:24569940 original size:16 final size:16
Alignment explanation
Indices: 24569889--24569931 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
24569879 TATCTTAAAA
24569889 TATGAATATGTGTTTAT
1 TATG-ATATGTGTTTAT
*
24569906 TGTGATATGTGTTTA-
1 TATGATATGTGTTTAT
24569921 TATGATATGTG
1 TATGATATGTG
24569932 ACTATTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 11 0.46
17 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (16 bp):
TATGATATGTGTTTAT
Found at i:24584200 original size:21 final size:20
Alignment explanation
Indices: 24584176--24584217 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
24584166 TGAAATGCAA
24584176 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
24584197 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
24584217 T
1 T
24584218 GACCATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:24596530 original size:24 final size:24
Alignment explanation
Indices: 24596498--24596554 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
24596488 ATGGTGAAGT
*
24596498 CACTCAATAACGTTGTGGCCAAGC
1 CACTCAATAACATTGTGGCCAAGC
* *
24596522 CACTCAATAGCATTGTGGTCAAGC
1 CACTCAATAACATTGTGGCCAAGC
24596546 CACTCAATA
1 CACTCAATA
24596555 TCGCAGACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (24 bp):
CACTCAATAACATTGTGGCCAAGC
Found at i:24596593 original size:87 final size:87
Alignment explanation
Indices: 24596447--24596617 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
24596437 ACACTCCACG
* * *
24596447 TTGTGGCCAAGCCACTCAATATCGTAGACAAGCTGCACATTATGGTGAAGTCACTCAATAACGTT
1 TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
*
24596512 GTGGCCAAGCCACTCAATAGCA
66 GTGACCAAGCCACTCAATAGCA
* *
24596534 TTGTGGTCAAGCCACTCAATATCGCAGACAAGCTGCACGTTATGGTCAAGCCACTCAATAACGTT
1 TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
24596599 GTGACCAAGCCACTCAATA
66 GTGACCAAGCCACTCAATA
24596618 TTGCAGTAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (87 bp):
TTGTGGCCAAGCCACTCAATATCGCAGACAAGCTGCACATTATGGTCAAGCCACTCAATAACGTT
GTGACCAAGCCACTCAATAGCA
Found at i:24597663 original size:11 final size:11
Alignment explanation
Indices: 24597649--24597695 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
24597639 GGTCCGGCAA
24597649 TGGTGAAGTGG
1 TGGTGAAGTGG
*
24597660 TGGTGCAGTGG
1 TGGTGAAGTGG
*
24597671 TGGTGAGGTGG
1 TGGTGAAGTGG
24597682 TGGTGAAGTGG
1 TGGTGAAGTGG
24597693 TGG
1 TGG
24597696 AGAATGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.13, C:0.02, G:0.57, T:0.28
Consensus pattern (11 bp):
TGGTGAAGTGG
Found at i:24608097 original size:15 final size:16
Alignment explanation
Indices: 24608069--24608098 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24608059 CACGTTCTCT
24608069 AAAGAACATGAAAAAG
1 AAAGAACATGAAAAAG
24608085 AAAGAAC-TGAAAAA
1 AAAGAACATGAAAAA
24608099 TAAACCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (16 bp):
AAAGAACATGAAAAAG
Found at i:24608767 original size:27 final size:27
Alignment explanation
Indices: 24608737--24609057 Score: 376
Period size: 27 Copynumber: 11.9 Consensus size: 27
24608727 GTTATAACCA
* *
24608737 AAATACCTCCATAGGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
24608764 AAATACACCCATAGGGTAGAATAACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
24608791 AAATACCTCCAT-GAGGT-AGATGATCG
1 AAATACCCCCATAG-GGTAAAATGACCG
*
24608817 AAATACCCCCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
24608844 AAATACCCCCATAGGGTAAAATGATTG
1 AAATACCCCCATAGGGTAAAATGACCG
* ** *
24608871 AAATACCCTCATAGAATAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* ***
24608898 AAATATCCCCATAGGGTAAAATGAATA
1 AAATACCCCCATAGGGTAAAATGACCG
*
24608925 AAATACCCCCATAGGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
24608952 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
24608979 AAATACCCCCATAAGGTAGAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
24609006 ACATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
*
24609033 ACATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
24609058 TGTTATACCC
Statistics
Matches: 248, Mismatches: 43, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
26 20 0.08
27 228 0.92
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:24623710 original size:23 final size:24
Alignment explanation
Indices: 24623684--24623752 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 24
24623674 TATCGAGTTA
*
24623684 AAACGGTAAGCTCCGT-AGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
*
24623707 AAACAGTAAGCT-CATAAGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
*
24623730 AAACGGTAAGCT-CATACGAGCTG
1 AAACGGTAAGCTCCATAAGAGCTG
24623753 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.05
23 39 0.95
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.17
Consensus pattern (24 bp):
AAACGGTAAGCTCCATAAGAGCTG
Done.