Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 58 of 226
Found at i:23190335 original size:25 final size:25
Alignment explanation
Indices: 23190301--23190353 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
23190291 CAGTCTGGCC
23190301 GATTGACAAAATCAGATTGATATGT
1 GATTGACAAAATCAGATTGATATGT
23190326 GATTGACAAAATCAGATTGATATGT
1 GATTGACAAAATCAGATTGATATGT
23190351 GAT
1 GAT
23190354 GATCTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (25 bp):
GATTGACAAAATCAGATTGATATGT
Found at i:23190600 original size:17 final size:18
Alignment explanation
Indices: 23190568--23190612 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
23190558 TTCATTTTAA
23190568 AATTATTTTTTGTTCAAAT
1 AATTA-TTTTTGTTCAAAT
23190587 AATTATTTTT-TTCAAAT
1 AATTATTTTTGTTCAAAT
23190604 AATT-TTTTT
1 AATTATTTTT
23190613 ATAAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 5 0.19
19 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTATTTTTGTTCAAAT
Found at i:23190626 original size:17 final size:16
Alignment explanation
Indices: 23190562--23190626 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
23190552 AAAAAGTTCA
23190562 TTTTAAAATTATTTTT
1 TTTTAAAATTATTTTT
* * *
23190578 TGTTCAAATAATTATTT
1 TTTTAAAATTATT-TTT
* *
23190595 TTTTCAAATAATTTTT
1 TTTTAAAATTATTTTT
*
23190611 TTATAAAATTATTTTT
1 TTTTAAAATTATTTTT
23190627 CAAAACATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 26 0.63
17 15 0.37
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTAAAATTATTTTT
Found at i:23190636 original size:15 final size:14
Alignment explanation
Indices: 23190580--23190638 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 14
23190570 TTATTTTTTG
23190580 TTCAAATAATTATTTTT
1 TTCAAA-AATTA--TTT
23190597 TTCAAATAATT-TTT
1 TTCAAA-AATTATTT
23190611 TT-ATAAAATTATTT
1 TTCA-AAAATTATTT
23190625 TTCAAAACATTATT
1 TTCAAAA-ATTATT
23190639 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.13
14 15 0.39
15 7 0.18
17 11 0.29
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (14 bp):
TTCAAAAATTATTT
Found at i:23198885 original size:28 final size:27
Alignment explanation
Indices: 23198852--23198931 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
23198842 TAAAAAATTC
23198852 AAATATAAAAATTAGAAAAGAATTAGAA
1 AAATATAAAAATTAGAAAA-AATTAGAA
*
23198880 AAATATAAAAATT-GTAAAAAATTATAA
1 AAATATAAAAATTAG-AAAAAATTAGAA
*
23198907 AATATATAGAAATATA-AAAAAATTA
1 AA-ATATAAAAAT-TAGAAAAAATTA
23198932 TAAATTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
27 10 0.22
28 35 0.76
29 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (27 bp):
AAATATAAAAATTAGAAAAAATTAGAA
Found at i:23198901 original size:10 final size:10
Alignment explanation
Indices: 23198858--23198935 Score: 51
Period size: 10 Copynumber: 8.2 Consensus size: 10
23198848 ATTCAAATAT
*
23198858 AAAAATTAGA
1 AAAAATTATA
*
23198868 AAAGAATTA-G
1 AAA-AATTATA
23198878 AAAAA-TAT-
1 AAAAATTATA
*
23198886 AAAAATTGTA
1 AAAAATTATA
23198896 AAAAATTATA
1 AAAAATTATA
*
23198906 AAATA-TAT-
1 AAAAATTATA
*
23198914 AGAAA-TATAA
1 AAAAATTAT-A
23198924 AAAAATTATA
1 AAAAATTATA
23198934 AA
1 AA
23198936 TTTTATAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
8 13 0.24
9 7 0.13
10 26 0.48
11 8 0.15
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:23198902 original size:38 final size:38
Alignment explanation
Indices: 23198858--23198935 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
23198848 ATTCAAATAT
* *
23198858 AAAAATTAGAAAAGAAT-TAGAAAAATATAAAAATTGTA
1 AAAAATTAGAAAA-AATATAGAAAAATAAAAAAATTATA
* * *
23198896 AAAAATTATAAAATATATAGAAATATAAAAAAATTATA
1 AAAAATTAGAAAAAATATAGAAAAATAAAAAAATTATA
23198934 AA
1 AA
23198936 TTTTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 2 0.06
38 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (38 bp):
AAAAATTAGAAAAAATATAGAAAAATAAAAAAATTATA
Found at i:23199291 original size:23 final size:21
Alignment explanation
Indices: 23199241--23199294 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
23199231 AAATTTAATA
23199241 AATTTTCTAAAATTTATTTTTT
1 AATTTT-TAAAATTTATTTTTT
* *
23199263 ATTTTTTATAAATTTTTTTTTCT
1 AATTTTTA-AAATTTATTTTT-T
23199286 AATTTTTAA
1 AATTTTTAA
23199295 TAAGAGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 8 0.30
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
AATTTTTAAAATTTATTTTTT
Found at i:23199398 original size:90 final size:91
Alignment explanation
Indices: 23199298--23199478 Score: 204
Period size: 90 Copynumber: 2.0 Consensus size: 91
23199288 TTTTTAATAA
* * * * * * *
23199298 GAGCATGGGCTTAATTGCTTTATTGAA-AAATTTTAATGCTCTTTTTTATGTATTTTGAAAGTTT
1 GAGCAAGGGCTTAAATACTTTATTGAATAAATTTGAAGGCT-TTTTTTATGCATTTTGAAAGTTC
*
23199362 AAGTACTCAACTGAGT-GAAAAAAAAG
65 AAGTACTCAACTGAGTACAAAAAAAAG
* * * * *
23199388 GAGCAAGGGCTTAAATACTTTTTTTAATAAGTTTGAGGGCTTTTTTTATGCATTTTGAACGTTCA
1 GAGCAAGGGCTTAAATACTTTATTGAATAAATTTGAAGGCTTTTTTTATGCATTTTGAAAGTTCA
* *
23199453 AGTACTTAATTGAGTACAAAAAAAAG
66 AGTACTCAACTGAGTACAAAAAAAAG
23199479 AAAGGACGTA
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
90 56 0.76
91 18 0.24
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (91 bp):
GAGCAAGGGCTTAAATACTTTATTGAATAAATTTGAAGGCTTTTTTTATGCATTTTGAAAGTTCA
AGTACTCAACTGAGTACAAAAAAAAG
Found at i:23209176 original size:29 final size:28
Alignment explanation
Indices: 23209143--23209229 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
23209133 TCATAAGAAC
23209143 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
23209172 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
23209196 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
23209226 ATTT
1 ATTT
23209230 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:23209396 original size:67 final size:66
Alignment explanation
Indices: 23209321--23209533 Score: 159
Period size: 67 Copynumber: 3.2 Consensus size: 66
23209311 ATTATAATGT
23209321 ATTT-AATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTA
1 ATTTAAATAATAATTATGTTTAAATATGATTAAA-TATTTATTATTGATATTAATAATCTTATTA
23209385 AA
65 AA
* * ** * * * * * * *
23209387 ATTTAAATAACAATAACAAATTT--CTGCTAATTATAAGAATT-TTATT-AAATT-ATATATTTT
1 ATTTAAATAATAAT--TATGTTTAAAT-ATGATTA-AATATTTATTATTGATATTAATA-ATCTT
23209447 AATTAAAA
61 -ATT-AAA
* * *
23209455 TATATTTAATAATAATTATGTTTAAATATGATTAAGATATTTATTACTGATAATAATAATCTTAT
1 -AT-TTAAATAATAATTATGTTTAAATATGATTAA-ATATTTATTATTGATATTAATAATCTTAT
23209520 TAAA
63 TAAA
23209524 ATTTAAATAA
1 ATTTAAATAA
23209534 CATTAACAAT
Statistics
Matches: 105, Mismatches: 26, Indels: 31
0.65 0.16 0.19
Matches are distributed among these distances:
65 3 0.03
66 12 0.11
67 24 0.23
68 18 0.17
69 20 0.19
70 18 0.17
71 7 0.07
72 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (66 bp):
ATTTAAATAATAATTATGTTTAAATATGATTAAATATTTATTATTGATATTAATAATCTTATTAA
A
Found at i:23209424 original size:137 final size:138
Alignment explanation
Indices: 23209277--23209542 Score: 428
Period size: 137 Copynumber: 1.9 Consensus size: 138
23209267 TAAGAATATG
* *
23209277 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* *
23209342 AATATGATTAA-ATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AATATGATTAAGA-TATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
23209406 ATTTCTGCT
130 ATTTCTGCT
****
23209415 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
*
23209479 AATATGATTAAGATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAA
66 AATATGATTAAGATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
23209543 TAATCATTTA
Statistics
Matches: 118, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
137 112 0.95
138 6 0.05
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTAAGATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
TTTCTGCT
Found at i:23209453 original size:18 final size:17
Alignment explanation
Indices: 23209425--23209459 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23209415 AATTATAAGA
*
23209425 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
23209442 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
23209460 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:23209575 original size:137 final size:136
Alignment explanation
Indices: 23209287--23209723 Score: 434
Period size: 156 Copynumber: 3.1 Consensus size: 136
23209277 AATTATTAAG
**** * *
23209287 AATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTAAATATGATTA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTA
* * *
23209352 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAATTTCTGCTAA
66 AATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAATATCT-CTAA
** * *
23209417 TTATAAG
130 CCAAAAC
23209424 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTA
*
23209489 AGA-TATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAAC-AATAATCAT-T
66 A-ATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAAT-ATC-TCT
*
23209551 TACCAAAAC
128 AACCAAAAC
* *
23209560 AATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATA
1 AA--TT-T--T-A-T-T-A-AA--TTA-T--A-TAT-T-TTA--ATTAAAATATATTTAATAATA
*
23209625 ATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAA
46 ATTATGTTTAAATATGATTAAATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAA
*
23209690 CAATAAC-AATAATCAT-TTACCAAAAC
111 CAATAACAAAT-ATC-TCTAACCAAAAC
23209716 AATTTTAT
1 AATTTTAT
23209724 GCTAAGGGTA
Statistics
Matches: 258, Mismatches: 18, Indels: 36
0.83 0.06 0.12
Matches are distributed among these distances:
136 10 0.04
137 108 0.42
138 4 0.02
139 1 0.00
141 1 0.00
142 1 0.00
143 1 0.00
144 1 0.00
145 1 0.00
146 2 0.01
148 3 0.01
149 2 0.01
150 1 0.00
151 2 0.01
152 3 0.01
153 2 0.01
154 4 0.02
155 1 0.00
156 110 0.43
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (136 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTA
AATTATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAATATCTCTAAC
CAAAAC
Found at i:23209580 original size:156 final size:156
Alignment explanation
Indices: 23209401--23209728 Score: 611
Period size: 156 Copynumber: 2.1 Consensus size: 156
23209391 AAATAACAAT
*
23209401 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
*
23209466 ATAATTATGTTTAAATATGATTAAGATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
*
23209531 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
23209557 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
23209622 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
23209687 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
23209713 AACAATTTTATGCTAA
1 AACAATTTTCTGCTAA
23209729 GGGTATTCTA
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 167 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (156 bp):
AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:23209609 original size:18 final size:18
Alignment explanation
Indices: 23209581--23209629 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
23209571 AATTATAAGA
23209581 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
23209598 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
23209614 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
23209630 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:23209615 original size:16 final size:16
Alignment explanation
Indices: 23209581--23209635 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
23209571 AATTATAAGA
23209581 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
23209598 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
23209614 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
23209628 ATGTTTAA
1 AT-TTTAA
23209636 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:23209845 original size:44 final size:45
Alignment explanation
Indices: 23209780--23209870 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
23209770 ACCTCTATTC
* * *
23209780 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
23209824 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
23209869 CA
1 CA
23209871 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:23209885 original size:17 final size:16
Alignment explanation
Indices: 23209851--23209903 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
23209841 GATTAGCTAT
23209851 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
23209867 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
23209884 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
23209900 TACA
1 TACA
23209904 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:23210993 original size:18 final size:17
Alignment explanation
Indices: 23210950--23211005 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
23210940 TAATGGAGAT
*
23210950 ATTAATACAAATGAATACA
1 ATTAATA-AAATAAATA-A
* *
23210969 TTTAATAAAGATAATTAA
1 ATTAATAAA-ATAAATAA
23210987 ATTAATAAAATAAATAA
1 ATTAATAAAATAAATAA
23211004 AT
1 AT
23211006 AAATTATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 9 0.29
18 11 0.35
19 11 0.35
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (17 bp):
ATTAATAAAATAAATAA
Found at i:23214980 original size:77 final size:76
Alignment explanation
Indices: 23214861--23215268 Score: 214
Period size: 77 Copynumber: 5.4 Consensus size: 76
23214851 TGAATTTGAC
* * * * * * **
23214861 TTTTGATAAAATGAAAAATTAAAAGGACATCAACGATGATCTCTAGGCTTGACCCATTTTTAAAA
1 TTTTAATAAAATGAAAACTGAAAAAGACCTCAACAACAATCTCTAGGCTTGACCCATTTTTAAAA
23214926 ACAGATTCGAG
66 ACAGATTCGAG
* * * * *
23214937 TTTTAATAAAATGAAAAACTGAAAAAGACTTCAACAGA-AATCTCGAGG-TTCAACTCATTTTTG
1 TTTTAATAAAATG-AAAACTGAAAAAGACCTCAACA-ACAATCTCTAGGCTT-GACCCATTTTTA
* * *
23215000 AAAATAGATTTGAC
63 AAAACAGATTCGAG
** * * * * *
23215014 TTTTGGTAAAATGAAAAGT-AAAAATACCTCGACAACAATC-CTGAGGTTTGACCCATTTTTTAA
1 TTTTAATAAAATGAAAACTGAAAAAGACCTCAACAACAATCTCT-AGGCTTGACCCATTTTTAAA
*
23215077 AACGGATTCG-G
65 AACAGATTCGAG
** * * **
23215088 CTAGTAATAAAATGAAAAC-GTAAAAAGACCTCAACAA-AAGTCCCAATACTTGACCCATTTTTT
1 -TTTTAATAAAATGAAAACTG-AAAAAGACCTCAACAACAA-TCTCTAGGCTTGACCCA-TTTTT
* * *
23215151 AAAAA-TGAATTCAAC
62 AAAAACAG-ATTCGAG
* * * ** * * *
23215166 CTTTGATGAAAATGAAAACT-AAAAGGACCTTGACAACAATC-CGAGGCTCGAGCCC-TTTTTGA
1 TTTTAAT-AAAATGAAAACTGAAAAAGACCTCAACAACAATCTCTAGGCTTGA-CCCATTTTTAA
*
23215228 AAACAAATTCGA-
64 AAACAGATTCGAG
* * *
23215240 TTTTGATAAAA-GACAA-TTAAAAAGACCTC
1 TTTTAATAAAATGAAAACTGAAAAAGACCTC
23215269 GACAGAGAAT
Statistics
Matches: 250, Mismatches: 62, Indels: 44
0.70 0.17 0.12
Matches are distributed among these distances:
71 1 0.00
72 13 0.05
73 4 0.02
74 8 0.03
75 66 0.26
76 53 0.21
77 91 0.36
78 14 0.06
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (76 bp):
TTTTAATAAAATGAAAACTGAAAAAGACCTCAACAACAATCTCTAGGCTTGACCCATTTTTAAAA
ACAGATTCGAG
Found at i:23215099 original size:152 final size:153
Alignment explanation
Indices: 23214821--23215123 Score: 350
Period size: 152 Copynumber: 2.0 Consensus size: 153
23214811 CCTCCAAGGT
* * *
23214821 AATCTCGAGGCTCAACCATTTTTGTGAACATGAATTTGACTTTTGATAAAATGAAAAATTAAAAG
1 AATCTCGAGGCTCAACCATTTTTGTGAAAATGAATTTGACTTTTGATAAAATGAAAAAGTAAAAA
* ** **
23214886 GACATCAACGATGATCTCTAGGCTTGACCCATTTTTAAAAACAGATTCGAGTTTTAATAAAATGA
66 GACATCAACAACAATCTCTAGGCTTGACCCATTTTTAAAAACAGATTCGAGTAGTAATAAAATG-
*
23214951 AAAAC-TGAAAAAGACTTCAACAGA
130 AAAACGT-AAAAAGACCTCAACAGA
* *
23214975 AATCTCGAGGTTCAACTCA-TTTT-TGAAAAT-AGATTTGACTTTTGGTAAAATG-AAAAGTAAA
1 AATCTCGAGGCTCAAC-CATTTTTGTGAAAATGA-ATTTGACTTTTGATAAAATGAAAAAGTAAA
* * * * * *
23215036 AATACCTCGACAACAATC-CTGAGGTTTGACCCATTTTTTAAAACGGATTCG-GCTAGTAATAAA
64 AAGACATCAACAACAATCTCT-AGGCTTGACCCATTTTTAAAAACAGATTCGAG-TAGTAATAAA
23215099 ATGAAAACGTAAAAAGACCTCAACA
127 ATGAAAACGTAAAAAGACCTCAACA
23215124 AAAGTCCCAA
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
151 22 0.17
152 59 0.46
153 25 0.20
154 19 0.15
155 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (153 bp):
AATCTCGAGGCTCAACCATTTTTGTGAAAATGAATTTGACTTTTGATAAAATGAAAAAGTAAAAA
GACATCAACAACAATCTCTAGGCTTGACCCATTTTTAAAAACAGATTCGAGTAGTAATAAAATGA
AAACGTAAAAAGACCTCAACAGA
Found at i:23215597 original size:94 final size:94
Alignment explanation
Indices: 23215433--23216210 Score: 676
Period size: 94 Copynumber: 8.5 Consensus size: 94
23215423 ACATTTTGGT
* * * *
23215433 GAGATTTAAAAACATCCTTC-AGAGA-GGTTTG-AAA-ATATCTCTAGGGAAAT-TCGAAAGCAT
1 GAGATCTAAAAGCATCC-TCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATAT-GAAAGCAT
*
23215493 CCTCGAGATAGGGTTTGAAAATATCTCAAGA
64 CCTCGAGAGAGGGTTTGAAAATATCTCAAGA
* *
23215524 AAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCATA-GGAGATTTGAAAGCATC
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCATC
* * *
23215588 ATGGAGATAGGGTTTGAAAATATCTCAAGA
65 CTCGAGAGAGGGTTTGAAAATATCTCAAGA
* * * * * *
23215618 GAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATAAATCTCATA-GGAAATCTGAAAGCACC
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATGAAAGCATC
* *
23215682 CTCGAGATAGGATTTGAAAATATCTCAAGA
65 CTCGAGAGAGGGTTTGAAAATATCTCAAGA
* ** * * ** *
23215712 GAGATCTAAAAGCATCCTCGAGAGA-GGACTCAAAA-GTATCTCAAGGGAGAGCT-ACAAGTATC
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGA-AAGCATC
* * *
23215774 CTCAAGAGAGCGTTTGAAGATA--T-----
65 CTCGAGAGAGGGTTTGAAAATATCTCAAGA
* * ** *
23215797 ---A--TGAAAGCTTCCTTGAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATAAAAGCA-CC
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCC
* * * *
23215856 ATTGAGGGAGGATTTGAAAATATCTCAAGG
66 -TCGAGAGAGGGTTTGAAAATATCTCAAGA
* * * * * *
23215886 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATTTCATGAGAGATCTGAAAGCATCT
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCC
* * * *
23215951 TCGAGAG-GGGACTCGAAAGTATCTCAAGG
66 TCGAGAGAGGG-TTTGAAAATATCTCAAGA
* * * * * *
23215980 GAGACCTACAAA-TATCCTCAAGTGAGGGTTTGAAAATATATCTCAAGAGAGATATGAAAGTATT
1 GAGATCTA-AAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATC
* * * *
23216044 CTCGAGGGAAGATTT-AAAAGCATCTCAA-A
65 CTCGAGAGAGGGTTTGAAAA-TATCTCAAGA
* * *
23216073 GGAGATCTAAAAGTATACTTAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATC
1 -GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATC
* *
23216138 CTCGAGAGA-GGATTCAAAAGTATCTCAAGA
65 CTCGAGAGAGGGTTTGAAAA-TATCTCAAGA
**
23216168 GAGATCTAAAAGTGTCCTCAAGAGAGGGTTTGAAAATATATCT
1 GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCT
23216211 ATAAGCATCT
Statistics
Matches: 560, Mismatches: 94, Indels: 63
0.78 0.13 0.09
Matches are distributed among these distances:
80 16 0.03
81 9 0.02
82 35 0.06
83 1 0.00
84 1 0.00
90 3 0.01
91 21 0.04
92 41 0.07
93 22 0.04
94 403 0.72
95 8 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (94 bp):
GAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATGAAAGCATCC
TCGAGAGAGGGTTTGAAAATATCTCAAGA
Found at i:23215637 original size:23 final size:23
Alignment explanation
Indices: 23215611--23215783 Score: 79
Period size: 23 Copynumber: 7.4 Consensus size: 23
23215601 TTGAAAATAT
23215611 CTCAAGAGAGATCTAAAAGCATC
1 CTCAAGAGAGATCTAAAAGCATC
** **
23215634 CTCAAGAGAGGGCTTCAAAATAAAT-
1 CTCAAGAGAGATC-T-AAAA-GCATC
* * *
23215659 CTCATAG-GAAATCTGAAAGCACC
1 CTCA-AGAGAGATCTAAAAGCATC
* * * *
23215682 CTCGAGATAGGATTTGAAAA-TAT-
1 CTCAAGAGA-GATCT-AAAAGCATC
23215705 CTCAAGAGAGATCTAAAAGCATC
1 CTCAAGAGAGATCTAAAAGCATC
* *
23215728 CTCGAGAGAGGA-CTCAAAAGTAT-
1 CTCAAGAGA-GATCT-AAAAGCATC
* * * *
23215751 CTCAAGGGAGAGCTACAAGTATC
1 CTCAAGAGAGATCTAAAAGCATC
23215774 CTCAAGAGAG
1 CTCAAGAGAG
23215784 CGTTTGAAGA
Statistics
Matches: 108, Mismatches: 28, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
21 4 0.04
22 18 0.17
23 53 0.49
24 15 0.14
25 14 0.13
26 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (23 bp):
CTCAAGAGAGATCTAAAAGCATC
Found at i:23215716 original size:140 final size:139
Alignment explanation
Indices: 23215453--23216206 Score: 397
Period size: 140 Copynumber: 5.5 Consensus size: 139
23215443 AACATCCTTC
* * * * * * *
23215453 AGAGAGGTTTGAAAATATCTCTAGGGAAAT-TCGAAAGCATCCTCGAGATAGGGTTTGAAAATAT
1 AGAGAGGTTTGAAAATATCTCAAGGGAGATCT-AAAAGCATCCTCAAGAGAGGGCTTCAAAATAT
* * * *
23215517 CTCAAGAAAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCATAGGAGATTTGAA
65 CTCAAGAAAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATAGGAGATCTAAA
*
23215582 AGCATCATGG
130 AGCATCATCG
* *
23215592 AGATAGGGTTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATAA
1 AGAGA-GGTTTGAAAATATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAAT--
* * * *
23215657 ATCTCATAGGAA-ATCTGAAAGCACCCTCGAGATAGGATTTG-AAA-ATATCTCA-AGAGAGATC
63 ATCTCA-AGAAAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATAG-GAGATC
*
23215718 TAAAAGCATCCTCG
126 TAAAAGCATCATCG
** * * * * * * * *
23215732 AGAGAGGACTCAAAAGTATCTCAAGGGAGAGCTACAAGTATCCTCAAGAGAGCGTTTGAAGATA-
1 AGAGAGGTTTGAAAA-TATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATAT
* * ** * *
23215796 -T-ATGAAAG--CT-------TCCTTGAGAGAGGGTTTGAAAATATATCTCA-AGGGAGATATAA
65 CTCAAGAAAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATA-GGAGATCTAA
* *
23215849 AAGCACCATTG
129 AAGCATCATCG
* * * *
23215860 AGGGAGGATTTGAAAATATCTCAAGGGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATAT
1 AGAGAGG-TTTGAAAATATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTT-CAAA-AT
* * * * * * * * * * * *
23215925 ATTTCATGAGAGATCTGAAAGCATCTTCGAGAGGGGACTCG-AAA-GTATCTCA-AGGGAGACCT
63 ATCTCAAGAAAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATA-GGAGATCT
* * *
23215987 ACAAA-TATCCTCA
127 A-AAAGCATCATCG
* * * * * * * * * * *
23216000 AGTGAGGGTTTGAAAATATATCTCAAGAGAGATATGAAAGTATTCTCGAGGGA-AGATTTAAAAG
1 AGAGA-GGTTTG-AAA-ATATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAA-
* * * ** * *
23216064 CATCTCAA-AGGAGATCTAAAAGTATACTTAAGAGAGGGTTTGAAAATATATCTCA-AGGGAGAT
62 TATCTCAAGA-AAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATA-GGAGAT
* * *
23216127 ATGAAAGCATCCTCG
125 CTAAAAGCATCATCG
* * * ** * *
23216142 AGAGAGGATTCAAAAGTATCTCAAGAGAGATCTAAAAGTGTCCTCAAGAGAGGGTTTGAAAATAT
1 AGAGAGGTTTGAAAA-TATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATAT
23216207 ATCTATAAGC
Statistics
Matches: 471, Mismatches: 107, Indels: 73
0.72 0.16 0.11
Matches are distributed among these distances:
126 14 0.03
127 3 0.01
128 69 0.15
129 8 0.02
130 3 0.01
132 1 0.00
133 8 0.02
134 3 0.01
135 3 0.01
136 1 0.00
138 1 0.00
139 16 0.03
140 205 0.44
141 35 0.07
142 97 0.21
143 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (139 bp):
AGAGAGGTTTGAAAATATCTCAAGGGAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATATC
TCAAGAAAGATCTAAAAGCACCCTCAAGAGAGGATTTGAAAATATATCTCATAGGAGATCTAAAA
GCATCATCG
Found at i:23215752 original size:46 final size:45
Alignment explanation
Indices: 23215433--23216206 Score: 380
Period size: 46 Copynumber: 16.8 Consensus size: 45
23215423 ACATTTTGGT
* * * * *
23215433 GAGATTTAAAAACATCCTTC-AGAGAGGTTTGAAAATATCTCTAGG
1 GAGATCTAAAAGCATCC-TCGAGAGAGGATTGAAAATATCTCAAGA
* * * *
23215478 GAAAT-TCGAAAGCATCCTCGAGATAGGGTTTGAAAATATCTCAAGA
1 GAGATCT-AAAAGCATCCTCGAGAGA-GGATTGAAAATATCTCAAGA
* * *
23215524 AAGATCTAAAAGCATCCTCAAGAGAGGGTTTGAAAATATATCTCATAG-
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTG-AAA-ATATCTCA-AGA
* * * * * *
23215572 GAGATTTGAAAGCATCATGGAGATAGGGTTTGAAAATATCTCAAGA
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTGAAAATATCTCAAGA
* * *
23215618 GAGATCTAAAAGCATCCTCAAGAGAGGGCTTCAAAATAAATCTCATAG-
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTGAAAAT--ATCTCA-AGA
* * * *
23215666 GAAATCTGAAAGCACCCTCGAGATAGGATTTGAAAATATCTCAAGA
1 GAGATCTAAAAGCATCCTCGAGAGAGGA-TTGAAAATATCTCAAGA
* * *
23215712 GAGATCTAAAAGCATCCTCGAGAGAGGACTCAAAAGTATCTCAAGG
1 GAGATCTAAAAGCATCCTCGAGAGAGGATTGAAAA-TATCTCAAGA
* * * * * *
23215758 GAGAGCTACAAGTATCCTCAAGAGAGCGTTTGAAGATA--T-----
1 GAGATCTAAAAGCATCCTCGAGAGAG-GATTGAAAATATCTCAAGA
* * * * *
23215797 ---A--TGAAAGCTTCCTTGAGAGAGGGTTTGAAAATATATCTCAAGG
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTG-AAA-ATATCTCAAGA
* * * *
23215840 GAGATATAAAAGCA-CCATTGAGGGAGGATTTGAAAATATCTCAAGG
1 GAGATCTAAAAGCATCC-TCGAGAGAGGA-TTGAAAATATCTCAAGA
* * * * *
23215886 GAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATATTTCATGA
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTG-AAA-ATATCTCAAGA
* * * * * *
23215934 GAGATCTGAAAGCATCTTCGAGAGGGGACTCGAAAGTATCTCAAGG
1 GAGATCTAAAAGCATCCTCGAGAGAGGA-TTGAAAATATCTCAAGA
* * * * *
23215980 GAGACCTACAAA-TATCCTCAAGTGAGGGTTTGAAAATATATCTCAAGA
1 GAGATCTA-AAAGCATCCTCGAGAGA-GGATTG-AAA-ATATCTCAAGA
* * * * * * * *
23216028 GAGATATGAAAGTATTCTCGAGGGAAGATTTAAAAGCATCTCAA-A
1 GAGATCTAAAAGCATCCTCGAGAGAGGATTGAAAA-TATCTCAAGA
* * ** * *
23216073 GGAGATCTAAAAGTATACTTAAGAGAGGGTTTGAAAATATATCTCAAGG
1 -GAGATCTAAAAGCATCCTCGAGAGA-GGATTG-AAA-ATATCTCAAGA
* * *
23216122 GAGATATGAAAGCATCCTCGAGAGAGGATTCAAAAGTATCTCAAGA
1 GAGATCTAAAAGCATCCTCGAGAGAGGATTGAAAA-TATCTCAAGA
** * *
23216168 GAGATCTAAAAGTGTCCTCAAGAGAGGGTTTGAAAATAT
1 GAGATCTAAAAGCATCCTCGAGAGA-GGATTGAAAATAT
23216207 ATCTATAAGC
Statistics
Matches: 552, Mismatches: 127, Indels: 99
0.71 0.16 0.13
Matches are distributed among these distances:
34 18 0.03
35 3 0.01
36 4 0.01
38 1 0.00
44 4 0.01
45 28 0.05
46 262 0.47
47 62 0.11
48 165 0.30
49 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (45 bp):
GAGATCTAAAAGCATCCTCGAGAGAGGATTGAAAATATCTCAAGA
Found at i:23215886 original size:23 final size:24
Alignment explanation
Indices: 23215860--23216206 Score: 73
Period size: 23 Copynumber: 14.8 Consensus size: 24
23215850 AGCACCATTG
23215860 AGGGAGGATTTGAAAATAT-CTCA
1 AGGGAGGATTTGAAAATATCCTCA
*
23215883 AGGGA-GATCT-AAAAGTATCCTCA
1 AGGGAGGATTTGAAAA-TATCCTCA
* * **
23215906 AGAGAGGGTTTGAAAATATATTTCA
1 AGGGAGGATTTGAAAATAT-CCTCA
* * * ** * *
23215931 TGAGA-GATCTGAAAGCATCTTCG
1 AGGGAGGATTTGAAAATATCCTCA
* * *
23215954 AGAGG-GGACTCGAAAGTAT-CTCA
1 AG-GGAGGATTTGAAAATATCCTCA
**
23215977 AGGGA-GACCT-ACAAATATCCTCA
1 AGGGAGGATTTGA-AAATATCCTCA
* * *
23216000 AGTGAGGGTTTGAAAATATATCTCA
1 AGGGAGGATTTGAAAATAT-CCTCA
* * * * *
23216025 AGAGA-GATATGAAAGTATTCTCG
1 AGGGAGGATTTGAAAATATCCTCA
* *
23216048 AGGGAAGATTT-AAAAGCAT-CTCA
1 AGGGAGGATTTGAAAA-TATCCTCA
* * * *
23216071 AAGGA-GATCT-AAAAGTATACTTA
1 AGGGAGGATTTGAAAA-TATCCTCA
* * *
23216094 AGAGAGGGTTTGAAAATATATCTCA
1 AGGGAGGATTTGAAAATAT-CCTCA
* ** *
23216119 AGGGA-GATATGAAAGCATCCTCG
1 AGGGAGGATTTGAAAATATCCTCA
* *
23216142 AGAGAGGA-TTCAAAAGTAT-CTCA
1 AGGGAGGATTTGAAAA-TATCCTCA
* * *
23216165 AGAGA-GATCT-AAAAGTGTCCTCA
1 AGGGAGGATTTGAAAA-TATCCTCA
* *
23216188 AGAGAGGGTTTGAAAATAT
1 AGGGAGGATTTGAAAATAT
23216207 ATCTATAAGC
Statistics
Matches: 232, Mismatches: 67, Indels: 49
0.67 0.19 0.14
Matches are distributed among these distances:
21 5 0.02
22 37 0.16
23 82 0.35
24 73 0.31
25 35 0.15
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (24 bp):
AGGGAGGATTTGAAAATATCCTCA
Found at i:23215899 original size:128 final size:126
Alignment explanation
Indices: 23215685--23215926 Score: 326
Period size: 128 Copynumber: 1.9 Consensus size: 126
23215675 AAGCACCCTC
* *
23215685 GAGATAGGATTTGAAAATATCTCAAGAGAGATCTAAAAGCATCCTCGAGAGAGGACTCAAAAGTA
1 GAGAGAGGATTTGAAAATATCTCAAGAGAGATATAAAAGCATCCTCGAGAGAGGACTCAAAAGTA
* *
23215750 TCTCAAGGGAGAGCTACAAGTATCCTCAAGAGAGCGTTTGAAGATATATGAAAGCTTCCTT
66 TCTCAAGGGAGAGCTAAAAGTATCCTCAAGAGAGCGTTTGAAAATATATGAAAGCTTCCTT
* * * * * *
23215811 GAGAGAGGGTTTGAAAATATATCTCAAGGGAGATATAAAAGCA-CCATTGAGGGAGGATTTGAAA
1 GAGAGAGGATTTG-AAA-ATATCTCAAGAGAGATATAAAAGCATCC-TCGAGAGAGGA-CTCAAA
* *
23215875 A-TATCTCAAGGGAGATCTAAAAGTATCCTCAAGAGAGGGTTTGAAAATATAT
62 AGTATCTCAAGGGAGAGCTAAAAGTATCCTCAAGAGAGCGTTTGAAAATATAT
23215927 TTCATGAGAG
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
126 11 0.11
127 5 0.05
128 79 0.79
129 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (126 bp):
GAGAGAGGATTTGAAAATATCTCAAGAGAGATATAAAAGCATCCTCGAGAGAGGACTCAAAAGTA
TCTCAAGGGAGAGCTAAAAGTATCCTCAAGAGAGCGTTTGAAAATATATGAAAGCTTCCTT
Found at i:23216168 original size:21 final size:23
Alignment explanation
Indices: 23216021--23216193 Score: 86
Period size: 23 Copynumber: 7.4 Consensus size: 23
23216011 GAAAATATAT
* * *
23216021 CTCAAGAGAGATATGAAAGTATT
1 CTCAAGAGAGATCTAAAAGTATC
* * * *
23216044 CTCGAGGGAAGATTTAAAAGCAT-
1 CTCAAGAG-AGATCTAAAAGTATC
*
23216067 CTCAA-AGGAGATCTAAAAGTATA
1 CTCAAGA-GAGATCTAAAAGTATC
* * * *
23216090 CTTAAGAGAGGGTTTGAAAA-TATAT
1 CTCAAGAGA-GATCT-AAAAGTAT-C
* * * *
23216115 CTCAAGGGAGATATGAAAGCATC
1 CTCAAGAGAGATCTAAAAGTATC
*
23216138 CTCGAGAGAGGAT-TCAAAAGTAT-
1 CTCAAGAGA-GATCT-AAAAGTATC
*
23216161 CTCAAGAGAGATCTAAAAGTGTC
1 CTCAAGAGAGATCTAAAAGTATC
23216184 CTCAAGAGAG
1 CTCAAGAGAG
23216194 GGTTTGAAAA
Statistics
Matches: 112, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
22 22 0.20
23 47 0.42
24 32 0.29
25 11 0.10
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (23 bp):
CTCAAGAGAGATCTAAAAGTATC
Found at i:23226355 original size:24 final size:24
Alignment explanation
Indices: 23226328--23226389 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
23226318 TGCTTTCTGA
*
23226328 TTAAGTGCTCTTTGAAGCTTCTCG
1 TTAAGTGCTCTTTGAAGCTACTCG
* *
23226352 TTAAGTGCTATTTGGAGCTACTCG
1 TTAAGTGCTCTTTGAAGCTACTCG
*
23226376 ATATAG-GCTCTTTG
1 TTA-AGTGCTCTTTG
23226390 TGAGCTTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (24 bp):
TTAAGTGCTCTTTGAAGCTACTCG
Found at i:23229921 original size:13 final size:14
Alignment explanation
Indices: 23229893--23229923 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
23229883 TTTTATAATT
23229893 AATTTAATTTTTTA
1 AATTTAATTTTTTA
23229907 AATTT-ATTTTTTA
1 AATTTAATTTTTTA
23229920 AATT
1 AATT
23229924 AGATTAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTAATTTTTTA
Found at i:23237899 original size:2 final size:2
Alignment explanation
Indices: 23237892--23237919 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23237882 AAAATTTTTA
23237892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23237920 TTTGGGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23243561 original size:43 final size:43
Alignment explanation
Indices: 23243500--23243586 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
23243490 TAAAACAAGG
23243500 TATCGCTCGAAGATGGTAAATACTTGGTGCAAAAAAAAAATCA
1 TATCGCTCGAAGATGGTAAATACTTGGTGCAAAAAAAAAATCA
23243543 TATCGCTCGAAGATGGTAAATACTTGGTGCAAAAAAAAAATCA
1 TATCGCTCGAAGATGGTAAATACTTGGTGCAAAAAAAAAATCA
23243586 T
1 T
23243587 GTAAACTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (43 bp):
TATCGCTCGAAGATGGTAAATACTTGGTGCAAAAAAAAAATCA
Found at i:23253885 original size:23 final size:22
Alignment explanation
Indices: 23253841--23253900 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
23253831 AGGAAGTAAA
*
23253841 ATAAAA-ATA-AAAACATATGT
1 ATAAAATATATAAAACATACGT
23253861 ATAAAATATATATAAACATACGT
1 ATAAAATATATA-AAACATACGT
**
23253884 ATACTATATATAAAACA
1 ATAAAATATATAAAACA
23253901 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 3 0.09
22 6 0.18
23 19 0.56
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAAAATATATAAAACATACGT
Found at i:23253909 original size:23 final size:23
Alignment explanation
Indices: 23253866--23253912 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
23253856 TATGTATAAA
*
23253866 ATATATATAAACATACGTATACT
1 ATATATATAAACATACATATACT
*
23253889 ATATATA-AAACA-ATATATA-T
1 ATATATATAAACATACATATACT
23253909 ATAT
1 ATAT
23253913 TACATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 5 0.23
23 7 0.32
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATATATAAACATACATATACT
Found at i:23254478 original size:21 final size:21
Alignment explanation
Indices: 23254452--23254508 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
23254442 AATCATATCT
*
23254452 TTTAAGATTGCATATATTATA
1 TTTAAGATTGCATATATCATA
23254473 TTTAAGATTGCATATATCATA
1 TTTAAGATTGCATATATCATA
* *
23254494 TCTAAGATTACATAT
1 TTTAAGATTGCATAT
23254509 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TTTAAGATTGCATATATCATA
Found at i:23256253 original size:251 final size:252
Alignment explanation
Indices: 23255803--23256305 Score: 873
Period size: 251 Copynumber: 2.0 Consensus size: 252
23255793 ATTGACATTG
* *
23255803 ATGGGAGTTTTAATCTGGTAATTGCTGATGAAAACTTACTGTATTTTCATTTCTGATGAATGCAA
1 ATGGGAGTTTTAATCTAGTAATTACTGATGAAAACTTACTGTATTTTCATTTCTGATGAATGCAA
* *
23255868 GGTTCTTCCATGCACTACCTATCGTTTTCACGATGAAACTATGAAATTTTAGTATATTTTGCTCG
66 GATTCTTCCATGCACTACCTATCGTTTTCACGATGAAACTATGAAATTTTAGTATATTTTGCTAG
*
23255933 GCATTTTGGTTAGTGGAAGCATTGCCATTAAGTTCATATTTTGAAGTAGATGATTCAGAAACAAT
131 GCATTTTGGTTAGTGGAAGCATTGCCATTAAGTTCATACTTTGAAGTAGATGATTCAGAAACAAT
*
23255998 GTATTATGAATGGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGT
196 GTATTATGAATAGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGT
* *
23256055 ATGGGA-TTTTAATCTAGTAATTACTGATGAAAACTTATTGTATTTTGATTTCTGATGAATGCAA
1 ATGGGAGTTTTAATCTAGTAATTACTGATGAAAACTTACTGTATTTTCATTTCTGATGAATGCAA
* * * * *
23256119 GATTCTTCCGTGCACTAGCTATCTTTTTCATGATGAAACTGTGAAATTTTAGTATATTTTGCTAG
66 GATTCTTCCATGCACTACCTATCGTTTTCACGATGAAACTATGAAATTTTAGTATATTTTGCTAG
23256184 GCATTTTGGTTAGTGGAAGCATTGCCATTAAGTTCATACTTTGAAGTAGATGATTCAGAAACAAT
131 GCATTTTGGTTAGTGGAAGCATTGCCATTAAGTTCATACTTTGAAGTAGATGATTCAGAAACAAT
*
23256249 GTATTATGAATAGATTTAGTGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGT
196 GTATTATGAATAGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGT
23256306 GCTGCTTTCA
Statistics
Matches: 237, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
251 231 0.97
252 6 0.03
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (252 bp):
ATGGGAGTTTTAATCTAGTAATTACTGATGAAAACTTACTGTATTTTCATTTCTGATGAATGCAA
GATTCTTCCATGCACTACCTATCGTTTTCACGATGAAACTATGAAATTTTAGTATATTTTGCTAG
GCATTTTGGTTAGTGGAAGCATTGCCATTAAGTTCATACTTTGAAGTAGATGATTCAGAAACAAT
GTATTATGAATAGATTTAGCGAAAGATTGTATGAACTATGCAATGTTTTGGTAATGT
Found at i:23259080 original size:2 final size:2
Alignment explanation
Indices: 23259073--23259098 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23259063 TGTAAATTAG
23259073 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
23259099 TGGAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23264751 original size:2 final size:2
Alignment explanation
Indices: 23264744--23264770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23264734 CTACCACATG
23264744 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
23264771 TTGGGACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23266735 original size:12 final size:12
Alignment explanation
Indices: 23266718--23266742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23266708 TTGGGAATGA
23266718 GATATGTCAAAT
1 GATATGTCAAAT
23266730 GATATGTCAAAT
1 GATATGTCAAAT
23266742 G
1 G
23266743 CTCTCAAACT
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:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GATATGTCAAAT
Found at i:23269691 original size:25 final size:25
Alignment explanation
Indices: 23269653--23269709 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
23269643 CCGTAATTCC
23269653 TAAAAAACCTTAAC-CTTAACAAAAT
1 TAAAAAACCTTAACTC-TAACAAAAT
*
23269678 TAAAAAA-CTCTAACTCTATCAAAAT
1 TAAAAAACCT-TAACTCTAACAAAAT
23269703 TAAAAAA
1 TAAAAAA
23269710 AAATCCGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 26 0.90
26 1 0.03
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.25
Consensus pattern (25 bp):
TAAAAAACCTTAACTCTAACAAAAT
Found at i:23270358 original size:26 final size:26
Alignment explanation
Indices: 23270329--23270418 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 26
23270319 ACTGTAATGT
23270329 TAAAATTAATTAAATTAATCTCCTTC
1 TAAAATTAATTAAATTAATCTCCTTC
* * * * *
23270355 TAAAATTTAAAATTTTATTTTATGT-TTTC
1 TAAAA-TT--AA-TTAAATTAATCTCCTTC
* *
23270384 -AAAATTAATTAAATTGATTTCCTTC
1 TAAAATTAATTAAATTAATCTCCTTC
23270409 TAAAATTAAT
1 TAAAATTAAT
23270419 CTCCTTTCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
24 8 0.17
25 5 0.10
26 14 0.29
27 4 0.08
28 4 0.08
29 5 0.10
30 8 0.17
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAAATTAATTAAATTAATCTCCTTC
Found at i:23276155 original size:16 final size:16
Alignment explanation
Indices: 23276136--23276174 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
23276126 TGAATTACTG
23276136 ATTACAGCTCTATTAT
1 ATTACAGCTCTATTAT
* *
23276152 ATTACAACTCTATTTT
1 ATTACAGCTCTATTAT
23276168 ATTACAG
1 ATTACAG
23276175 TAAGCCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTACAGCTCTATTAT
Found at i:23283970 original size:2 final size:2
Alignment explanation
Indices: 23283958--23284018 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
23283948 TCTTCTACTC
* *
23283958 TA TA TA AA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23284000 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
23284019 TAATTTCCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23285407 original size:18 final size:18
Alignment explanation
Indices: 23285368--23285432 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 18
23285358 ACATCAACCA
23285368 TAATTATAATTCTAATC-A-
1 TAATTATAA-T-TAATCTAT
23285386 TAATTATAATTAATCTAT
1 TAATTATAATTAATCTAT
*
23285404 TAA-TA-AATAAAT-TAT
1 TAATTATAATTAATCTAT
* *
23285419 TAAATAAAATTAAT
1 TAATTATAATTAAT
23285433 AATTTTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 6 0.15
16 13 0.32
17 10 0.24
18 12 0.29
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATTATAATTAATCTAT
Found at i:23285417 original size:12 final size:13
Alignment explanation
Indices: 23285402--23285434 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23285392 TAATTAATCT
23285402 ATTAATAAAT-AA
1 ATTAATAAATAAA
*
23285414 ATTATTAAATAAA
1 ATTAATAAATAAA
23285427 ATTAATAA
1 ATTAATAA
23285435 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTAATAAATAAA
Found at i:23302309 original size:20 final size:20
Alignment explanation
Indices: 23302281--23302338 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
23302271 AATGAGGAGT
*
23302281 ACGAGTGTGCAATCAGGGGC
1 ACGAATGTGCAATCAGGGGC
** *
23302301 ACGAATGTGCTGTTAGGGGC
1 ACGAATGTGCAATCAGGGGC
* *
23302321 ACGAATGTACAAACAGGG
1 ACGAATGTGCAATCAGGG
23302339 ACACCGAAGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.36, T:0.17
Consensus pattern (20 bp):
ACGAATGTGCAATCAGGGGC
Found at i:23307171 original size:30 final size:30
Alignment explanation
Indices: 23307137--23307220 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
23307127 CTAATATCTC
*
23307137 GATACCCATATATTTGATTTTCCAATATTT
1 GATACCCATATATTTGACTTTCCAATATTT
* * *
23307167 GATACACATATCTTTGACTTTCCATTATTT
1 GATACCCATATATTTGACTTTCCAATATTT
*
23307197 GATAACCATATATTTGACTTTCCA
1 GATACCCATATATTTGACTTTCCA
23307221 TAAATGATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (30 bp):
GATACCCATATATTTGACTTTCCAATATTT
Found at i:23307197 original size:15 final size:16
Alignment explanation
Indices: 23307142--23307222 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 16
23307132 ATCTCGATAC
*
23307142 CCATATATTTGATTTT
1 CCATATATTTGACTTT
*
23307158 CCA-ATATTTGA--TA
1 CCATATATTTGACTTT
*
23307171 CACATATCTTTGACTTT
1 C-CATATATTTGACTTT
**
23307188 CCAT-TATTTGA-TAA
1 CCATATATTTGACTTT
23307202 CCATATATTTGACTTT
1 CCATATATTTGACTTT
23307218 CCATA
1 CCATA
23307223 AATGATTGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
13 2 0.04
14 7 0.14
15 28 0.55
16 12 0.24
17 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (16 bp):
CCATATATTTGACTTT
Found at i:23308237 original size:19 final size:19
Alignment explanation
Indices: 23308208--23308269 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
23308198 ATTTTAGAAT
23308208 ATTTATATTTTTATAATTAA
1 ATTT-TATTTTTATAATTAA
23308228 ATTTTA-TTTTA-AA-T-A
1 ATTTTATTTTTATAATTAA
*
23308243 A--TAATTTTTATAATTAA
1 ATTTTATTTTTATAATTAA
*
23308260 ATTTGATTTT
1 ATTTTATTTT
23308270 AAATAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
13 2 0.06
14 5 0.15
15 4 0.12
16 2 0.06
17 4 0.12
18 5 0.15
19 8 0.24
20 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATTTTTATAATTAA
Found at i:23308252 original size:32 final size:32
Alignment explanation
Indices: 23308214--23308283 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
23308204 GAATATTTAT
*
23308214 ATTTTTATAATTAAATTTTATTTTAAATAATA
1 ATTTTTATAATTAAATTTGATTTTAAATAATA
23308246 ATTTTTATAATTAAATTTGATTTTAAATAATA
1 ATTTTTATAATTAAATTTGATTTTAAATAATA
23308278 ATTTTT
1 ATTTTT
23308284 CATTATCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
ATTTTTATAATTAAATTTGATTTTAAATAATA
Found at i:23311947 original size:25 final size:24
Alignment explanation
Indices: 23311919--23311969 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
23311909 TTTTTAGTAA
*
23311919 TTTAA-TTTTATTTCTTTTATATTTT
1 TTTAACTTTCATTT-TTTT-TATTTT
*
23311944 TTTAACTTTCCTTTTTTTTATTTT
1 TTTAACTTTCATTTTTTTTATTTT
23311968 TT
1 TT
23311970 ATTATTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 9 0.39
26 6 0.26
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTAACTTTCATTTTTTTTATTTT
Found at i:23311977 original size:24 final size:25
Alignment explanation
Indices: 23311933--23311983 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
23311923 ATTTTATTTC
23311933 TTTTATATTTTTTTAACTTTC-CTT
1 TTTTATATTTTTTTAACTTTCTCTT
* *
23311957 TTTTTTATTTTTTATTA-TTTCTCTT
1 TTTTATATTTTTT-TAACTTTCTCTT
23311982 TT
1 TT
23311984 GCTTCTACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTATATTTTTTTAACTTTCTCTT
Found at i:23313363 original size:19 final size:19
Alignment explanation
Indices: 23313339--23313377 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
23313329 TTATCCAATA
23313339 ATATATATTATGATATATAAG
1 ATAT-TATTAT-ATATATAAG
23313360 ATATTATTATATATATAA
1 ATATTATTATATATATAA
23313378 ATAAATAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATTATTATATATATAAG
Found at i:23313721 original size:17 final size:17
Alignment explanation
Indices: 23313699--23313731 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
23313689 ATATTTTTTA
23313699 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
23313716 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
23313732 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:23318514 original size:4 final size:4
Alignment explanation
Indices: 23318505--23318532 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
23318495 GAAGTAATGT
23318505 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
23318533 TTTGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:23320459 original size:36 final size:33
Alignment explanation
Indices: 23320399--23320467 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
23320389 CTGTTTGCTG
* *
23320399 CTATTTTGATGTTATTTTGTTATTATATTACTA
1 CTATTTTGATGTTATTTTGATATTATATAACTA
*
23320432 CTATTTTGTTGTTATTATTCGGATATTATATAACTA
1 CTATTTTGATGTTATT-TT--GATATTATATAACTA
23320468 TTGTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 15 0.50
34 2 0.07
36 13 0.43
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (33 bp):
CTATTTTGATGTTATTTTGATATTATATAACTA
Found at i:23322519 original size:24 final size:23
Alignment explanation
Indices: 23322475--23322538 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
23322465 TCCGAGCTAT
*
23322475 ATAACGGGAAGCTCATGAGAGCCA
1 ATAACGGGAAGCTC-CGAGAGCCA
* *
23322499 ATAACGGGTAGCTCCGAAGAGGCA
1 ATAACGGGAAGCTCCG-AGAGCCA
* *
23322523 TTAACAGGAAGCTCCG
1 ATAACGGGAAGCTCCG
23322539 TATAGCCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.34, C:0.22, G:0.30, T:0.14
Consensus pattern (23 bp):
ATAACGGGAAGCTCCGAGAGCCA
Found at i:23322654 original size:26 final size:26
Alignment explanation
Indices: 23322571--23322671 Score: 84
Period size: 26 Copynumber: 4.0 Consensus size: 26
23322561 CAAGCGAGTC
* *
23322571 ATATCGGGAAGCTC-CGGAGAGCAAT
1 ATATCGGGAAGCTCACGAAGAGCTAT
* * *
23322596 -TAATCAGGAAGCTCACAAAGAGTCTTT
1 AT-ATCGGGAAGCTCACGAAGAG-CTAT
*
23322623 AT-TCGGAAAGCTCACGAAGAGCTAT
1 ATATCGGGAAGCTCACGAAGAGCTAT
* *
23322648 ATATCGGGACGCTCA-TAAGAGCTA
1 ATATCGGGAAGCTCACGAAGAGCTA
23322672 CAATGTGCCT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
24 1 0.02
25 24 0.41
26 31 0.53
27 2 0.03
28 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.21
Consensus pattern (26 bp):
ATATCGGGAAGCTCACGAAGAGCTAT
Found at i:23325477 original size:46 final size:46
Alignment explanation
Indices: 23325425--23325516 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
23325415 ATTGCTATAT
* *
23325425 CTCAGTATGGTTTTCTTCCTTGAAATACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCACAA
23325471 CTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCACAA
23325517 TTTGCCATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (46 bp):
CTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCACAA
Found at i:23327277 original size:18 final size:18
Alignment explanation
Indices: 23327254--23327294 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
23327244 AACCGAAGAT
*
23327254 CTTTCTTCCAAGGTGAAA
1 CTTTCTTCCAAGGTAAAA
23327272 CTTTCTTCCAAGGTAAAA
1 CTTTCTTCCAAGGTAAAA
23327290 CTTTC
1 CTTTC
23327295 AGAAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (18 bp):
CTTTCTTCCAAGGTAAAA
Found at i:23328471 original size:33 final size:33
Alignment explanation
Indices: 23328429--23328496 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
23328419 ATTTGCCTTA
* *
23328429 GAGCATCAGCAACTACATTTGTCTTTCCTGGAT
1 GAGCATCAGCAACTACATTTGCCTTTCCAGGAT
23328462 GAGCATCAGCAACTACATTTGCCTTTCCAGGAT
1 GAGCATCAGCAACTACATTTGCCTTTCCAGGAT
23328495 GA
1 GA
23328497 TAATCAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (33 bp):
GAGCATCAGCAACTACATTTGCCTTTCCAGGAT
Found at i:23333428 original size:26 final size:26
Alignment explanation
Indices: 23333399--23333459 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
23333389 CCATTAATCA
*
23333399 GGAAGCTCACAAAGAGCC-TTTATTTG
1 GGAAGCTCACAAAGAGCCATATA-TTG
**
23333425 GGAAGCTCATGAAGAGCCATATATTG
1 GGAAGCTCACAAAGAGCCATATATTG
*
23333451 GGACGCTCA
1 GGAAGCTCA
23333460 TAAGAGCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.90
27 3 0.10
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATATATTG
Found at i:23336366 original size:2 final size:2
Alignment explanation
Indices: 23336359--23336387 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23336349 AATACTTTGA
23336359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23336388 AAATAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23340660 original size:41 final size:41
Alignment explanation
Indices: 23340603--23340684 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
23340593 CCATAAGCAT
23340603 GAAATGCGCACTTTGTCAAGGTAATAGAGAGGACGAAAATC
1 GAAATGCGCACTTTGTCAAGGTAATAGAGAGGACGAAAATC
23340644 GAAATGCGCACTTTGTCAAGGTAATAGAGAGGACGAAAATC
1 GAAATGCGCACTTTGTCAAGGTAATAGAGAGGACGAAAATC
23340685 ATTTGTTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (41 bp):
GAAATGCGCACTTTGTCAAGGTAATAGAGAGGACGAAAATC
Found at i:23341941 original size:31 final size:29
Alignment explanation
Indices: 23341903--23341972 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 29
23341893 ATCCCAAAAC
23341903 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
* *
23341934 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAACTATGATTTTGTGCAATTG
23341963 TATACATGAA
1 TATACATGAA
23341973 ATTTTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 19 0.51
31 18 0.49
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:23341966 original size:29 final size:30
Alignment explanation
Indices: 23341903--23341982 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
23341893 ATCCCAAAAC
*
23341903 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
*
23341934 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
23341963 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
23341983 GATCCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.38
30 10 0.22
31 18 0.40
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:23341991 original size:30 final size:29
Alignment explanation
Indices: 23341903--23341991 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
23341893 ATCCCAAAAC
* *
23341903 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT--TGTCCAATTG
* *
23341934 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAACTTTGATTTTGTCCAATTG
*
23341963 TATACATGAAATTTTGA-TTTGATCCAATT
1 TATACATG-AACTTTGATTTTG-TCCAATT
23341992 CTTGTAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 21 0.40
30 13 0.25
31 18 0.35
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (29 bp):
TATACATGAACTTTGATTTTGTCCAATTG
Found at i:23342198 original size:29 final size:30
Alignment explanation
Indices: 23342123--23342209 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
23342113 GATTAAATTA
* * *
23342123 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* * *
23342153 ACAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
23342184 AAATTAAAG-TTCATGTATACAATTGC
1 AAATTAAAGTTTCATGTATACAATTGC
23342210 GCATTAAATC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.32
30 8 0.17
31 24 0.51
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:23354505 original size:19 final size:20
Alignment explanation
Indices: 23354474--23354525 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
23354464 TAAAATATGA
23354474 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTG-AATTTTTGA-AAATT
23354494 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
23354514 ATTTT-AATTTTT
1 ATTTTGAATTTTT
23354526 TTTGTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:23364824 original size:73 final size:73
Alignment explanation
Indices: 23364699--23364840 Score: 230
Period size: 73 Copynumber: 1.9 Consensus size: 73
23364689 TCGGGTTTAG
* ** *
23364699 AAAAGGGATCATGCCCAGAAAGTTAGGACACAATCTTTTCTTAATTCTCGAGATCGTTTAAAACT
1 AAAAAGGATCATGCCCAGAAAGTTAGGACACAATCTCCTCTTAATTCCCGAGATCGTTTAAAACT
23364764 TGAGAAAA
66 TGAGAAAA
* *
23364772 AAAAAGGATCATGCCCAGTAAGTTAGGACACGATCTCCTCTTAATTCCCGAGATCGTTTAAAACT
1 AAAAAGGATCATGCCCAGAAAGTTAGGACACAATCTCCTCTTAATTCCCGAGATCGTTTAAAACT
23364837 TGAG
66 TGAG
23364841 TTTGAAATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (73 bp):
AAAAAGGATCATGCCCAGAAAGTTAGGACACAATCTCCTCTTAATTCCCGAGATCGTTTAAAACT
TGAGAAAA
Found at i:23365338 original size:43 final size:41
Alignment explanation
Indices: 23365190--23365340 Score: 109
Period size: 43 Copynumber: 3.7 Consensus size: 41
23365180 AGATGAACAA
* * *
23365190 AATTATAAAA-ATATAAAGTATATA--TATGTGTGTAT-TAA
1 AATTATAAAATATA-AAAATATATATGTATGTATGTATGTAG
* * * *
23365228 AATTATGAAGTATAAAAAATATATGTGGATATATATGTATGT-G
1 AATTATAAAATAT-AAAAATATATAT-G-TATGTATGTATGTAG
* *
23365271 AATTGTAAAATATATGAAA-A-ATATGTATGTATGTATGTACG
1 AATTATAAAATATA-AAAATATATATGTATGTATGTATGTA-G
23365312 AATTATAAAATATAAAAACTATATATGTA
1 AATTATAAAATATAAAAA-TATATATGTA
23365341 AAAGAGGGGT
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
38 8 0.09
39 22 0.26
40 5 0.06
41 17 0.20
42 3 0.04
43 29 0.34
44 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.37
Consensus pattern (41 bp):
AATTATAAAATATAAAAATATATATGTATGTATGTATGTAG
Found at i:23365339 original size:39 final size:38
Alignment explanation
Indices: 23365256--23365340 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
23365246 ATATATGTGG
* *
23365256 ATATATATGTATGTGAATTGTAAAATATATGAAAAATAT
1 ATATGTATGTATGTGAATTATAAAATATA-GAAAAATAT
* *
23365295 GTATGTATGTATGTACGAATTATAAAATATA-AAAACTAT
1 ATATGTATGTATGT--GAATTATAAAATATAGAAAAATAT
23365334 ATATGTA
1 ATATGTA
23365341 AAAGAGGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 25 0.64
41 14 0.36
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (38 bp):
ATATGTATGTATGTGAATTATAAAATATAGAAAAATAT
Found at i:23365545 original size:2 final size:2
Alignment explanation
Indices: 23365532--23365563 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
23365522 ATTAAACATG
*
23365532 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23365564 GCAACATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23365649 original size:41 final size:42
Alignment explanation
Indices: 23365598--23365681 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
23365588 AATAAAAATA
23365598 AAAATCTGATGATAATAACAATAAAATTAATAACAAT-ATTT
1 AAAATCTGATGATAATAACAATAAAATTAATAACAATAATTT
* *
23365639 AAAATTTGATGATAATAACAATAAAATTAATAATAATAATTT
1 AAAATCTGATGATAATAACAATAAAATTAATAACAATAATTT
23365681 A
1 A
23365682 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 35 0.88
42 5 0.12
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (42 bp):
AAAATCTGATGATAATAACAATAAAATTAATAACAATAATTT
Found at i:23365695 original size:41 final size:41
Alignment explanation
Indices: 23365598--23365702 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
23365588 AATAAAAATA
* *
23365598 AAAATCTGATGATAATAACAATAAAATTAATAACAATATTT
1 AAAATTTGATAATAATAACAATAAAATTAATAACAATATTT
* *
23365639 AAAATTTGATGATAATAACAATAAAATTAATAATAATAATTT
1 AAAATTTGATAATAATAACAATAAAATTAATAACAAT-ATTT
** *
23365681 ATTATTT-TTAATAATAA-AATAA
1 AAAATTTGATAATAATAACAATAA
23365703 TCAAAATACA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 5 0.09
41 43 0.75
42 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (41 bp):
AAAATTTGATAATAATAACAATAAAATTAATAACAATATTT
Found at i:23366271 original size:13 final size:13
Alignment explanation
Indices: 23366255--23366302 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
23366245 CAAGTATTCA
23366255 ACCCAACCCAATT
1 ACCCAACCCAATT
23366268 ACCCAACCCAATT
1 ACCCAACCCAATT
23366281 ACCCAACCC-A--
1 ACCCAACCCAATT
23366291 ACCCAACCCAAT
1 ACCCAACCCAAT
23366303 CATAAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
12 1 0.03
13 22 0.67
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:23366455 original size:9 final size:9
Alignment explanation
Indices: 23366405--23366462 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
23366395 GTAGTAATTC
*
23366405 AATTCGGTT
1 AATTCGGGT
*
23366414 AATTCAGGT
1 AATTCGGGT
23366423 AATTCGGGT
1 AATTCGGGT
* * *
23366432 AATCCAGTT
1 AATTCGGGT
23366441 AATTCGGGT
1 AATTCGGGT
*
23366450 AATTCGGTT
1 AATTCGGGT
23366459 AATT
1 AATT
23366463 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (9 bp):
AATTCGGGT
Found at i:23366459 original size:18 final size:18
Alignment explanation
Indices: 23366405--23366462 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
23366395 GTAGTAATTC
*
23366405 AATTCGGTTAATTCAGG-T
1 AATTCGGGTAATTC-GGTT
* *
23366423 AATTCGGGTAATCCAGTT
1 AATTCGGGTAATTCGGTT
23366441 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
23366459 AATT
1 AATT
23366463 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:23367876 original size:31 final size:31
Alignment explanation
Indices: 23367841--23367901 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
23367831 TTAAATAGCA
*
23367841 TATTTAGACAACAAATTCATTATGTTCTTCG
1 TATTTAGACAACAAATACATTATGTTCTTCG
* *
23367872 TATTTAGACAGCAGATACATTATGTTCTTC
1 TATTTAGACAACAAATACATTATGTTCTTC
23367902 AATTGGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (31 bp):
TATTTAGACAACAAATACATTATGTTCTTCG
Found at i:23367924 original size:16 final size:16
Alignment explanation
Indices: 23367903--23367934 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23367893 ATGTTCTTCA
23367903 ATTGGAATCCTTCTTT
1 ATTGGAATCCTTCTTT
*
23367919 ATTGGAATCTTTCTTT
1 ATTGGAATCCTTCTTT
23367935 TGACACCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTGGAATCCTTCTTT
Found at i:23370417 original size:96 final size:96
Alignment explanation
Indices: 23370298--23370494 Score: 322
Period size: 96 Copynumber: 2.1 Consensus size: 96
23370288 ATTTTCCGAG
* * * *
23370298 AATCTCTGTTTAGTTTATTGGAAAACTTTTAAAGCAGCTGAATCATCCTACTCGAATGCTTTATC
1 AATCTCTATTTAGTTTATTGGAAAACTTTTAAAGCAACTGAATCATCCCACTCGAATACTTTATC
*
23370363 AGTCTTAAACAAATTATTCTTCGCATAAACA
66 AGTCTTAAACAAATTATTCTTCACATAAACA
* *
23370394 AATCTCTATTTAGTTTCTTGGAAAACTTTTAAAGCAACTGAATCATCCCACTCGAATACTTTATT
1 AATCTCTATTTAGTTTATTGGAAAACTTTTAAAGCAACTGAATCATCCCACTCGAATACTTTATC
*
23370459 AGTCTTAAACAAATTATTCTTCACATCAACA
66 AGTCTTAAACAAATTATTCTTCACATAAACA
23370490 AATCT
1 AATCT
23370495 TTTCCATTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (96 bp):
AATCTCTATTTAGTTTATTGGAAAACTTTTAAAGCAACTGAATCATCCCACTCGAATACTTTATC
AGTCTTAAACAAATTATTCTTCACATAAACA
Found at i:23370526 original size:12 final size:12
Alignment explanation
Indices: 23370509--23370533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23370499 CATTTATCAG
23370509 TCTTAAACAAAT
1 TCTTAAACAAAT
23370521 TCTTAAACAAAT
1 TCTTAAACAAAT
23370533 T
1 T
23370534 ATTCTTCACA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTTAAACAAAT
Found at i:23374790 original size:30 final size:30
Alignment explanation
Indices: 23374754--23374816 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
23374744 ACTTAACAAG
*
23374754 CAAATGCCTCTAAAATAATAACAAAATTTA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
23374784 CAAATGCCTTTAAAATATTAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
23374814 CAA
1 CAA
23374817 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:23380637 original size:2 final size:2
Alignment explanation
Indices: 23380626--23380663 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
23380616 AAAAGCCGGG
*
23380626 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23380664 ACATATTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23382895 original size:4 final size:4
Alignment explanation
Indices: 23382886--23383102 Score: 398
Period size: 4 Copynumber: 54.2 Consensus size: 4
23382876 AAATGTATAA
23382886 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
23382934 ATGT ATGT ATGT ATGT ATGT ATGT CTGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23382982 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23383030 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
23383078 ATGT ATGC ATGC ATGC ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
23383103 AATACAAGCA
Statistics
Matches: 209, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 209 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:23384451 original size:12 final size:12
Alignment explanation
Indices: 23384434--23384461 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23384424 CTTTCATCAC
23384434 TTAACCAAAAAT
1 TTAACCAAAAAT
23384446 TTAACCAAAAAT
1 TTAACCAAAAAT
23384458 TTAA
1 TTAA
23384462 GAAAGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAACCAAAAAT
Found at i:23388381 original size:61 final size:61
Alignment explanation
Indices: 23388286--23388404 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 61
23388276 TTTGCGCAAT
23388286 AAATATTTAGTTTCTTATTCTCAATTATGTGTATTCAATTCTTAATTTGATGTTTCTAATA
1 AAATATTTAGTTTCTTATTCTCAATTATGTGTATTCAATTCTTAATTTGATGTTTCTAATA
* *
23388347 AAATATTTAGTTTCTTATTCTCAATTATGTGTATTTAATTCTTGATTTGATGTTTCTA
1 AAATATTTAGTTTCTTATTCTCAATTATGTGTATTCAATTCTTAATTTGATGTTTCTA
23388405 GATTATTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (61 bp):
AAATATTTAGTTTCTTATTCTCAATTATGTGTATTCAATTCTTAATTTGATGTTTCTAATA
Found at i:23394767 original size:17 final size:16
Alignment explanation
Indices: 23394738--23394777 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
23394728 TTAAATGTGG
23394738 AAAATAATAAAATAAA
1 AAAATAATAAAATAAA
* *
23394754 AAAATACATTAAATTAA
1 AAAATA-ATAAAATAAA
23394771 AAAATAA
1 AAAATAA
23394778 CTCTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATAAAATAAA
Found at i:23396026 original size:1 final size:1
Alignment explanation
Indices: 23396020--23396047 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
23396010 CTCGTCTTGG
23396020 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
23396048 GTGAGTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23403563 original size:3 final size:3
Alignment explanation
Indices: 23403555--23403637 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
23403545 ATGAGCAAAG
* * * *
23403555 ATA ATA ATA ATG ATA CA-A ATA ACA AT- ATAA AGA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
23403600 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
23403638 TGGAATACAT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.04
3 64 0.93
4 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:23406018 original size:110 final size:105
Alignment explanation
Indices: 23405885--23406078 Score: 282
Period size: 110 Copynumber: 1.8 Consensus size: 105
23405875 ATATAATTAA
*
23405885 AATTTTAAATTTAAAAATAAAATAACTAAATTATTAAAAATAAAAATAG-AGGATCAAAATTCTA
1 AATTTTAAATTTAAAAATAAAATAACTAAATTACTAAAAATAAAAATAGAAGGATC-AAATTCTA
23405949 AATTACGAAAGAGAAATTATTTTATGAGTTAACCCTTGGACTTT
65 AATT---AAAGAGAAATTATTTTATGAGTTAACCCTTGGACTTT
* * *
23405993 AATTTTGAAATTTAAAAAATAAAATAACTAAATTCCTAAAAATAAAAATAGAATGTTCAAATTCT
1 AATTTT-AAATTT-AAAAATAAAATAACTAAATTACTAAAAATAAAAATAGAAGGATCAAATTCT
*
23406058 AAATTAAGGAGAAATTATTTT
64 AAATTAAAGAGAAATTATTTT
23406079 TACGAACCCT
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
107 15 0.19
108 6 0.08
109 6 0.08
110 47 0.60
111 4 0.05
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.34
Consensus pattern (105 bp):
AATTTTAAATTTAAAAATAAAATAACTAAATTACTAAAAATAAAAATAGAAGGATCAAATTCTAA
ATTAAAGAGAAATTATTTTATGAGTTAACCCTTGGACTTT
Found at i:23406370 original size:20 final size:21
Alignment explanation
Indices: 23406331--23406370 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
23406321 ACCTCGAATC
*
23406331 CAAAACCCTAAATCTTGAACT
1 CAAAACCCTAAATATTGAACT
23406352 CAAAACCCT-AATATTGAAC
1 CAAAACCCTAAATATTGAAC
23406371 CCCAAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (21 bp):
CAAAACCCTAAATATTGAACT
Found at i:23406377 original size:20 final size:21
Alignment explanation
Indices: 23406330--23406377 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
23406320 AACCTCGAAT
*
23406330 CCAAAACCCTAAATCTTGAAC
1 CCAAAACCCTAAATATTGAAC
*
23406351 TCAAAACCCT-AATATTGAAC
1 CCAAAACCCTAAATATTGAAC
*
23406371 CCCAAAC
1 CCAAAAC
23406378 TCCAAACCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.44, C:0.33, G:0.04, T:0.19
Consensus pattern (21 bp):
CCAAAACCCTAAATATTGAAC
Found at i:23406488 original size:151 final size:151
Alignment explanation
Indices: 23406196--23406492 Score: 411
Period size: 151 Copynumber: 2.0 Consensus size: 151
23406186 CTTGGACCTC
* *
23406196 GAACCCAAAACCCTAAATCTTAAACCCAAAACTCCAAACCCTAAGTTTTAAACTTGGATCTTAAA
1 GAACCCAAAACCCTAAATATTAAACCCAAAACTCCAAACCCTAAGTTTTAAACTTAGATCTTAAA
*
23406261 CCACAAACCCTAAACTCAATTCTTGAACCTTAAACCTCAAACTCGAACACTAAACCATGAACCTC
66 CCACAAACCCTAAACTCAATTCTTGAACCTTAAACCTCAAACTCGAACACTAAACCATGAAACTC
*
23406326 GAATCCAAAACCCTAAATCTT
131 GAAACCAAAACCCTAAATCTT
* * *
23406347 GAACTCAAAACCCT-AATATTGAACCCCAAACTCCAAACCCTAAGTTTTAAACTTTAGATCTTAA
1 GAACCCAAAACCCTAAATATTAAACCCAAAACTCCAAACCCTAAGTTTTAAAC-TTAGATCTTAA
* * * * ** *
23406411 ACTC-TAAACTCTGAACTCGATTCTTGAACCTTGGACCTCAAACTCGAACCCTAAACCATGAAAC
65 AC-CACAAACCCTAAACTCAATTCTTGAACCTTAAACCTCAAACTCGAACACTAAACCATGAAAC
*
23406475 TC-AAACCTCAAACCCTAA
129 TCGAAACC-AAAACCCTAA
23406493 GGATTTGGGT
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
150 39 0.30
151 88 0.69
152 1 0.01
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (151 bp):
GAACCCAAAACCCTAAATATTAAACCCAAAACTCCAAACCCTAAGTTTTAAACTTAGATCTTAAA
CCACAAACCCTAAACTCAATTCTTGAACCTTAAACCTCAAACTCGAACACTAAACCATGAAACTC
GAAACCAAAACCCTAAATCTT
Found at i:23406526 original size:14 final size:14
Alignment explanation
Indices: 23406500--23406541 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
23406490 TAAGGATTTG
23406500 GGTTT-GGAGTTTAA
1 GGTTTAGGA-TTTAA
23406514 GGTTTAGGATTT-A
1 GGTTTAGGATTTAA
23406527 GAGTTTAGGATTTAA
1 G-GTTTAGGATTTAA
23406542 TATTCATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 19 0.76
15 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (14 bp):
GGTTTAGGATTTAA
Found at i:23406540 original size:21 final size:22
Alignment explanation
Indices: 23406490--23406540 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
23406480 CCTCAAACCC
* *
23406490 TAAGGATTT-GGGTTTGGAGTT
1 TAAGGATTTAGGATTTAGAGTT
23406511 TAAGG-TTTAGGATTTAGAGTT
1 TAAGGATTTAGGATTTAGAGTT
23406532 T-AGGATTTA
1 TAAGGATTTA
23406541 ATATTCATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.43
Consensus pattern (22 bp):
TAAGGATTTAGGATTTAGAGTT
Found at i:23409951 original size:19 final size:20
Alignment explanation
Indices: 23409929--23409967 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23409919 TAATTTGGTC
23409929 ATTTC-CTTTTAATCCCAAA
1 ATTTCTCTTTTAATCCCAAA
*
23409948 ATTTCTGTTTTAATCCCAAA
1 ATTTCTCTTTTAATCCCAAA
23409968 TTAGCCCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTCTCTTTTAATCCCAAA
Found at i:23415653 original size:144 final size:144
Alignment explanation
Indices: 23415270--23415641 Score: 681
Period size: 144 Copynumber: 2.6 Consensus size: 144
23415260 CTAAAGACGA
* * * *
23415270 AGGTATAGAACCAGATAACCCGTTTTCTTGCAATTCAAGGCTGCTCAATCCTTTCAGTACCCCAA
1 AGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAA
23415335 TTCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAA
66 TTCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAA
23415400 GAACTTAACGACTC
131 GAACTTAACGACTC
*
23415414 CGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAA
1 AGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAA
23415479 TTCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAA
66 TTCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAA
23415544 GAACTTAACGACTC
131 GAACTTAACGACTC
*
23415558 AGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCTTTTCAGTTCCCCAA
1 AGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAA
*
23415623 TTCCACCAGGGATTTTCCC
66 TTCCACGAGGGATTTTCCC
23415642 CGAAAACTGA
Statistics
Matches: 220, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 220 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (144 bp):
AGGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAA
TTCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAA
GAACTTAACGACTC
Found at i:23425068 original size:18 final size:18
Alignment explanation
Indices: 23425036--23425074 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
23425026 ATTATTATTA
*
23425036 TTTATTTTTACTATTTTAT
1 TTTATTTTCACTA-TTTAT
23425055 TTTATTTTCA-TATTTAT
1 TTTATTTTCACTATTTAT
23425072 TTT
1 TTT
23425075 TGCAGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTCACTATTTAT
Found at i:23425075 original size:18 final size:19
Alignment explanation
Indices: 23425030--23425075 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
23425020 TTTCCTATTA
*
23425030 TTATTATTTATTTTTACTAT
1 TTATT-TTTATTTTCACTAT
23425050 TT-TATTTTATTTTCA-TAT
1 TTAT-TTTTATTTTCACTAT
23425068 TTATTTTT
1 TTATTTTT
23425076 GCAGGAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTTTATTTTCACTAT
Found at i:23427659 original size:30 final size:29
Alignment explanation
Indices: 23427607--23427669 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
23427597 ATAAACATTA
*
23427607 AAAATTATTTTAAAAATTAAAATAAAAAT
1 AAAAGTATTTTAAAAATTAAAATAAAAAT
23427636 AAAAGTATTTT-AAAATTAAAAAATAAAAAT
1 AAAAGTATTTTAAAAATT--AAAATAAAAAT
23427666 AAAA
1 AAAA
23427670 AATATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 15 0.48
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAGTATTTTAAAAATTAAAATAAAAAT
Found at i:23428849 original size:32 final size:32
Alignment explanation
Indices: 23428795--23428870 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
23428785 CGAATATAAT
*
23428795 AAATAAATTTTTATTTTTATTTTTTA-TCTTA
1 AAATAATTTTTTATTTTTATTTTTTATTCTTA
* *
23428826 AAATACTTTTTTATTTTTTATTTTTTATTTTTA
1 AAATAATTTTTTA-TTTTTATTTTTTATTCTTA
23428859 AAATAATTTTTT
1 AAATAATTTTTT
23428871 GGTGTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 11 0.28
32 13 0.33
33 15 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (32 bp):
AAATAATTTTTTATTTTTATTTTTTATTCTTA
Found at i:23428858 original size:6 final size:7
Alignment explanation
Indices: 23428832--23428857 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23428822 CTTAAAATAC
23428832 TTTTTTA
1 TTTTTTA
23428839 TTTTTTA
1 TTTTTTA
23428846 TTTTTTA
1 TTTTTTA
23428853 TTTTT
1 TTTTT
23428858 AAAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:23428879 original size:33 final size:32
Alignment explanation
Indices: 23428795--23428880 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
23428785 CGAATATAAT
* *
23428795 AAATAAATTTTTA-TTTTTATTTTTTATCTTA
1 AAATAATTTTTTAGTGTTTATTTTTTATCTTA
* * * *
23428826 AAATACTTTTTTATTTTTTATTTTTTATTTTTA
1 AAATAATTTTTTAGTGTTTATTTTTTA-TCTTA
*
23428859 AAATAATTTTTTGGTGTTTATT
1 AAATAATTTTTTAGTGTTTATT
23428881 AAAAAAATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 11 0.24
32 13 0.28
33 22 0.48
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.66
Consensus pattern (32 bp):
AAATAATTTTTTAGTGTTTATTTTTTATCTTA
Found at i:23431255 original size:9 final size:9
Alignment explanation
Indices: 23431243--23431267 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23431233 ATCAAACACC
23431243 AAATAGCCA
1 AAATAGCCA
23431252 AAATAGCCA
1 AAATAGCCA
23431261 AAATAGC
1 AAATAGC
23431268 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (9 bp):
AAATAGCCA
Found at i:23431838 original size:41 final size:41
Alignment explanation
Indices: 23431781--23431861 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
23431771 TGTCATTTCA
23431781 CTATCGCTTTTTATAACTTACTCATTTTTGCCCCCATTATC
1 CTATCGCTTTTTATAACTTACTCATTTTTGCCCCCATTATC
23431822 CTATCGCTTTTTATAACTTACTCATTTTTGCCCCCATTAT
1 CTATCGCTTTTTATAACTTACTCATTTTTGCCCCCATTAT
23431862 TCGACAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (41 bp):
CTATCGCTTTTTATAACTTACTCATTTTTGCCCCCATTATC
Found at i:23439538 original size:16 final size:16
Alignment explanation
Indices: 23439517--23439557 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
23439507 AATAATGGAA
23439517 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
23439533 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
23439549 ATATATAAA
1 ATATATAAA
23439558 TTAAAGAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:23439603 original size:33 final size:31
Alignment explanation
Indices: 23439566--23439635 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
23439556 AATTAAAGAG
*
23439566 TATATAAAAAGTATAGAATTACGTATATATATA
1 TATATAAAAAGTA-AGAA-TACGTATATAAATA
* * *
23439599 TATATGAAAATTAAGAATATGTATATAAATA
1 TATATAAAAAGTAAGAATACGTATATAAATA
23439630 TATATA
1 TATATA
23439636 TATATGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 17 0.53
32 4 0.12
33 11 0.34
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (31 bp):
TATATAAAAAGTAAGAATACGTATATAAATA
Found at i:23443046 original size:60 final size:60
Alignment explanation
Indices: 23442950--23443067 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
23442940 TTCCGATTCT
**
23442950 CGTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAATGAGTCTTAGCA
1 CGTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAGCA
* * * *
23443010 CGTCGATTCTGGGATGATCAAGTATAAGGATTATGCAGCCTCATCGAACAAGTCTTAG
1 CGTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAG
23443068 AATTTTGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (60 bp):
CGTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAGCA
Found at i:23443813 original size:16 final size:16
Alignment explanation
Indices: 23443792--23443829 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
23443782 TTTAGTTCGC
23443792 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
23443808 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
23443824 CGTAAT
1 TGTAAT
23443830 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:23443898 original size:44 final size:46
Alignment explanation
Indices: 23443811--23443903 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
23443801 ATAGAGGTGT
*
23443811 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
23443857 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
23443901 AAT
1 AAT
23443904 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:23443899 original size:39 final size:44
Alignment explanation
Indices: 23443811--23443916 Score: 141
Period size: 39 Copynumber: 2.5 Consensus size: 44
23443801 ATAGAGGTGT
*
23443811 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
23443857 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
23443896 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
23443917 CATAAGGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 19 0.33
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:23444217 original size:10 final size:10
Alignment explanation
Indices: 23444155--23444227 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
23444145 AATACTATAA
23444155 AATATAATTT
1 AATATAATTT
*
23444165 AAAATAA-TT
1 AATATAATTT
*
23444174 -AT-T-ATTA
1 AATATAATTT
23444181 AATATAATTT
1 AATATAATTT
**
23444191 AATA-AAAAT
1 AATATAATTT
23444200 -ATATAATTT
1 AATATAATTT
* *
23444209 AATAAAATTC
1 AATATAATTT
23444219 AATATAATT
1 AATATAATT
23444228 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:23444267 original size:117 final size:118
Alignment explanation
Indices: 23444042--23444278 Score: 406
Period size: 120 Copynumber: 2.0 Consensus size: 118
23444032 TTAATCATAT
* *
23444042 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
23444107 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
23444162 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
* *
23444225 ATTATTCTTATATGAATTTACTAAAATCATATTATATAATACTATAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
23444278 T
1 T
23444279 ATATAATCTA
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
116 5 0.04
117 49 0.43
118 3 0.03
120 56 0.50
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (118 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:23446275 original size:4 final size:4
Alignment explanation
Indices: 23446266--23446292 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23446256 GATGTTCATC
23446266 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
23446293 TTGGTTTATA
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:23448609 original size:153 final size:154
Alignment explanation
Indices: 23448365--23448642 Score: 418
Period size: 153 Copynumber: 1.8 Consensus size: 154
23448355 GAGCTCAAAT
* * *
23448365 GGATAAAATGCTAAAACCCAGGCTTGGCCTAGCCCGTATTAGTTTTTATATAATTTTTAATATAT
1 GGATAAAATGCTAAAACCCAGGCTTGGCCCAACCCGCATTAGTTTTTATATAATTTTTAATATAT
* *
23448430 ATATAATAAATTAAAAATACTAAAAACATTAAAATAAATGTTTTCCAACAAATTAAAAATGAGCC
66 ATATAATAAATCAAAAATACTAAAAACATTAAAACAAATGTTTTCCAACAAATTAAAAATGAGCC
23448495 TAAAATTTTGCCCAAGCCCAGCCA
131 TAAAATTTTGCCCAAGCCCAGCCA
* * * *
23448519 GGATAAAATGCTAGAACCC-GAGCTTGGCCCAACGCGCATTAATTTTT-TATATATTTTTTA-AT
1 GGATAAAATGCTAAAACCCAG-GCTTGGCCCAACCCGCATTAGTTTTTATATA-ATTTTTAATAT
* *
23448581 ATATATAATACATCAAAAATACTAAAAACATTAAAACAAATGTTTTCCAACAAATTGAAAAT
64 ATATATAATAAATCAAAAATACTAAAAACATTAAAACAAATGTTTTCCAACAAATTAAAAAT
23448643 AAATTAAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
153 65 0.59
154 46 0.41
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (154 bp):
GGATAAAATGCTAAAACCCAGGCTTGGCCCAACCCGCATTAGTTTTTATATAATTTTTAATATAT
ATATAATAAATCAAAAATACTAAAAACATTAAAACAAATGTTTTCCAACAAATTAAAAATGAGCC
TAAAATTTTGCCCAAGCCCAGCCA
Found at i:23449349 original size:31 final size:31
Alignment explanation
Indices: 23449307--23449382 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
23449297 AAAATTTGTT
*
23449307 ATTTTAGTCACTC-CAGTTGGATAAGTTGTCA
1 ATTTTAGTCACTCTC-GTTAGATAAGTTGTCA
*
23449338 ATTTTAATCACTCTCGTTAGATAAGTTGTCA
1 ATTTTAGTCACTCTCGTTAGATAAGTTGTCA
23449369 ATTTTAGTCACTCT
1 ATTTTAGTCACTCT
23449383 ACCATTAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (31 bp):
ATTTTAGTCACTCTCGTTAGATAAGTTGTCA
Found at i:23458937 original size:25 final size:25
Alignment explanation
Indices: 23458909--23458964 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
23458899 CTTCTCCTAG
* **
23458909 TTAAACCCTGTTTTTACTTTCTTAC
1 TTAAACCATGTTTTTACTTTCACAC
* *
23458934 TTAAACTATGTTTTTAGTTTCACAC
1 TTAAACCATGTTTTTACTTTCACAC
23458959 TTAAAC
1 TTAAAC
23458965 TTTGATTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (25 bp):
TTAAACCATGTTTTTACTTTCACAC
Found at i:23458965 original size:25 final size:25
Alignment explanation
Indices: 23458917--23458965 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
23458907 AGTTAAACCC
**
23458917 TGTTTTTACTTTCTTACTTAAACTA
1 TGTTTTTACTTTCACACTTAAACTA
*
23458942 TGTTTTTAGTTTCACACTTAAACT
1 TGTTTTTACTTTCACACTTAAACT
23458966 TTGATTAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.53
Consensus pattern (25 bp):
TGTTTTTACTTTCACACTTAAACTA
Done.