Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 179 of 226
Found at i:54633301 original size:130 final size:130
Alignment explanation
Indices: 54633153--54633570 Score: 644
Period size: 130 Copynumber: 3.3 Consensus size: 130
54633143 ATTTAAAGTA
*
54633153 TTAATATATATATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAA
1 TTAACATATA-ATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAA
*
54633218 TGTATTAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATAT
65 CGTATTAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATAT
54633283 T
130 T
* *
54633284 TTAACATATAATTTTAATATATAAGCTATCTAATATATTAGTCTTAATTTCGATAGTTACTTAAC
1 TTAACATATAATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAAC
*
54633349 GTATAAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTA-T--TA-ATA--
66 GTATTAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATT
*
54633408 -T---ATAT--TTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTTGGTAGTTACTTAAC
1 TTAACATATAATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAAC
54633467 GTATTAATATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATA
66 GTATT-A-ATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATT-A-ATATA
54633532 TATTT
127 TA-TT
54633537 TTAACATATAATTTTAATATATAAGCTATTTAAT
1 TTAACATATAATTTTAATATATAAGCTATTTAAT
54633571 CTGTGCCATA
Statistics
Matches: 261, Mismatches: 9, Indels: 30
0.87 0.03 0.10
Matches are distributed among these distances:
118 55 0.21
119 1 0.00
120 51 0.20
121 1 0.00
123 1 0.00
125 2 0.01
126 6 0.02
127 2 0.01
129 1 0.00
130 105 0.40
131 9 0.03
133 4 0.02
135 23 0.09
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (130 bp):
TTAACATATAATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAAC
GTATTAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATT
Found at i:54633372 original size:22 final size:23
Alignment explanation
Indices: 54633344--54633392 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
54633334 CGATAGTTAC
*
54633344 TTAACGTATAAATATA-TATAAT
1 TTAACGTATAAATATATTAAAAT
*
54633366 TTAACGTATTAATATATTAAAAT
1 TTAACGTATAAATATATTAAAAT
54633389 TTAA
1 TTAA
54633393 TTTAACGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAACGTATAAATATATTAAAAT
Found at i:54633379 original size:249 final size:253
Alignment explanation
Indices: 54633038--54633570 Score: 959
Period size: 249 Copynumber: 2.1 Consensus size: 253
54633028 TAATGTAGTA
*
54633038 ATATATATATTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAACGTA
1 ATATA-AT-TTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGATAGTTACTTAACGTA
54633103 TAAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAAAGTATTAATATATATATTT
64 TAAATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAAAGTATTAATATATAT-TTT
*
54633168 TAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAATGTATT-A-ATATAT
128 TAATATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAACGTATTAATATATAT
54633231 ATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATT-A-ATATATA-TTTTAAC
193 ATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATATTTTTAAC
*
54633289 ATATAATTTTAATATATAAGCTATCTAATATATTAGTCTTAATTTCGATAGTTACTTAACGTATA
1 ATATAATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGATAGTTACTTAACGTATA
*
54633354 AATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATTTTTAA
66 AATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAAAGTATTAATATATATTTTTAA
*
54633419 TATATAAGCTATTTAATATATTAGTCTTAATTTTGGTAGTTACTTAACGTATTAATATATATATA
131 TATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAACGTATTAATATATATATA
54633484 ATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATATTTTTAAC
196 ATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATATTTTTAAC
54633542 ATATAATTTTAATATATAAGCTATTTAAT
1 ATATAATTTTAATATATAAGCTATTTAAT
54633571 CTGTGCCATA
Statistics
Matches: 271, Mismatches: 6, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
248 57 0.21
249 115 0.42
250 51 0.19
251 6 0.02
252 7 0.03
253 35 0.13
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (253 bp):
ATATAATTTTAATATATAAGCTATTTAATATATTAGTCTTAATTTCGATAGTTACTTAACGTATA
AATATATATAATTTAACGTATTAATATATTAAAATTTAATTTAAAGTATTAATATATATTTTTAA
TATATAAGCTATTTAATATATTAGTCTTAATTTCGGTAGTTACTTAACGTATTAATATATATATA
ATTTAACGTATTAATATATTAAAATTTAATTTAACGTATTAATATATATATTTTTAAC
Found at i:54633394 original size:28 final size:28
Alignment explanation
Indices: 54633362--54633530 Score: 116
Period size: 28 Copynumber: 5.8 Consensus size: 28
54633352 TAAATATATA
54633362 TAATTTAACGTATTAATATATTAAAATT
1 TAATTTAACGTATTAATATATTAAAATT
**
54633390 TAATTTAACGTATTAATATA-T-ATTTT
1 TAATTTAACGTATTAATATATTAAAATT
*
54633416 TAATATATAA-GCTATTTAATATATT--AGTCT
1 TAAT-T-TAACG-TA-TTAATATATTAAAAT-T
* **
54633446 TAATTTTGGTA-GTTACTTAACGTATTAATATATAT
1 TAA-TTT--AACG-TA-TTAATATATTAA-A-AT-T
54633481 ATAATTTAACGTATTAATATATTAAAATT
1 -TAATTTAACGTATTAATATATTAAAATT
54633510 TAATTTAACGTATTAATATAT
1 TAATTTAACGTATTAATATAT
54633531 ATATTTTTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
26 7 0.06
27 3 0.03
28 46 0.41
29 11 0.10
30 8 0.07
31 14 0.12
32 10 0.09
33 3 0.03
34 2 0.02
35 5 0.04
36 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (28 bp):
TAATTTAACGTATTAATATATTAAAATT
Found at i:54634415 original size:14 final size:15
Alignment explanation
Indices: 54634385--54634418 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54634375 CTGTTTAGGG
*
54634385 TTTCATTTCTATCCA
1 TTTCATTACTATCCA
54634400 TTTCATTACT-TCCA
1 TTTCATTACTATCCA
54634414 TTTCA
1 TTTCA
54634419 CTTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCATTACTATCCA
Found at i:54634910 original size:31 final size:31
Alignment explanation
Indices: 54634872--54634934 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54634862 TATATAAGTG
54634872 ATGAAATGAGATAAGATCAAAGTGATACATT
1 ATGAAATGAGATAAGATCAAAGTGATACATT
*
54634903 ATGAAATGAGATATGATCAAAGTGATACATT
1 ATGAAATGAGATAAGATCAAAGTGATACATT
54634934 A
1 A
54634935 GTAAAGAAAC
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:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (31 bp):
ATGAAATGAGATAAGATCAAAGTGATACATT
Found at i:54636175 original size:17 final size:17
Alignment explanation
Indices: 54636155--54636247 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 17
54636145 TTATTTTCTA
54636155 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
54636172 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
54636186 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * *
54636202 TATTAGTATT-AAAATT
1 TATAAGTTTTCTAAATT
* *
54636218 TATTAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
*
54636233 TGTAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
54636248 AAAGTGTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 10 0.17
14 2 0.03
15 10 0.17
16 15 0.25
17 22 0.37
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:54636183 original size:30 final size:30
Alignment explanation
Indices: 54636148--54636204 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54636138 TATTGTTTTA
*
54636148 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
*
54636178 TTTTCTAAATAATTTTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
54636205 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:54636198 original size:13 final size:13
Alignment explanation
Indices: 54636148--54636200 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
54636138 TATTGTTTTA
*
54636148 TTTTCTATATAAG
1 TTTTCTAAATAAG
54636161 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
54636178 TTTTCTAAATAAT
1 TTTTCTAAATAAG
54636191 TTTTCTAAAT
1 TTTTCTAAAT
54636201 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:54636218 original size:16 final size:16
Alignment explanation
Indices: 54636197--54636230 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54636187 TAATTTTTCT
54636197 AAATTTATTAGTATTA
1 AAATTTATTAGTATTA
54636213 AAATTTATTAGTATTA
1 AAATTTATTAGTATTA
54636229 AA
1 AA
54636231 TTTGTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AAATTTATTAGTATTA
Found at i:54636231 original size:15 final size:15
Alignment explanation
Indices: 54636196--54636233 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
54636186 ATAATTTTTC
54636196 TAAATTTATTAGTAT
1 TAAATTTATTAGTAT
54636211 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
54636227 TAAATTT
1 TAAATTT
54636234 GTAAGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:54636294 original size:15 final size:15
Alignment explanation
Indices: 54636274--54636396 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 15
54636264 TTATTTGCTT
54636274 ACATAATACATAATA
1 ACATAATACATAATA
54636289 ACATAATACATAACTTA
1 ACATAATACATAA--TA
* * *
54636306 TATATAAGCTTGCATAACTT
1 -ACATAA---TACATAA-TA
* *
54636326 ACATAATAACTTCCATA
1 ACATAAT-ACAT-AATA
* *
54636343 ACCT-ATATATAATA
1 ACATAATACATAATA
*
54636357 ACATAAT--A-AATT
1 ACATAATACATAATA
54636369 ACATAATACATAATA
1 ACATAATACATAATA
54636384 ACATAATACATAA
1 ACATAATACATAA
54636397 CTTATATATA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
12 10 0.12
13 1 0.01
14 7 0.09
15 33 0.41
16 3 0.04
17 8 0.10
18 6 0.08
19 5 0.06
20 1 0.01
21 6 0.08
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (15 bp):
ACATAATACATAATA
Found at i:54636323 original size:21 final size:20
Alignment explanation
Indices: 54636297--54636354 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
54636287 TAACATAATA
*
54636297 CATAACTTATATATAAGCTTG
1 CATAACTTATATATAA-CTTC
*
54636318 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTC
*
54636339 CATAACCTATATATAA
1 CATAACTTATATATAA
54636355 TAACATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (20 bp):
CATAACTTATATATAACTTC
Found at i:54636364 original size:8 final size:7
Alignment explanation
Indices: 54636351--54636396 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
54636341 TAACCTATAT
54636351 ATAATAAC
1 ATAAT-AC
54636359 ATAATA-
1 ATAATAC
*
54636365 A-ATTAC
1 ATAATAC
54636371 ATAATAC
1 ATAATAC
54636378 ATAATAAC
1 ATAAT-AC
54636386 ATAATAC
1 ATAATAC
54636393 ATAA
1 ATAA
54636397 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:54636418 original size:21 final size:21
Alignment explanation
Indices: 54636392--54636468 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
54636382 TAACATAATA
* *
54636392 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
54636413 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
** *
54636434 CATAACTTA-ATACACCACTTA
1 CATAACTTACATA-ATAACTTC
*
54636455 AATAACTTACATAA
1 CATAACTTACATAA
54636469 CTTACATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 37 0.79
22 7 0.15
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:54636468 original size:9 final size:9
Alignment explanation
Indices: 54636450--54636950 Score: 180
Period size: 9 Copynumber: 58.3 Consensus size: 9
54636440 TTAATACACC
*
54636450 ACTTAAATA
1 ACTTACATA
54636459 ACTTACATA
1 ACTTACATA
54636468 ACTTACATA
1 ACTTACATA
*
54636477 GCTTACATA
1 ACTTACATA
* *
54636486 A-AT-CATT
1 ACTTACATA
54636493 ACTTACATA
1 ACTTACATA
*
54636502 ACATACATA
1 ACTTACATA
54636511 A--TACATA
1 ACTTACATA
54636518 ACTTACATA
1 ACTTACATA
* * *
54636527 A--AATAGA
1 ACTTACATA
54636534 ACTTACATA
1 ACTTACATA
*
54636543 TCTTACATA
1 ACTTACATA
54636552 A--TACATA
1 ACTTACATA
*
54636559 ACTTATATA
1 ACTTACATA
54636568 A--TACA-A
1 ACTTACATA
*
54636574 CACTTACAGA
1 -ACTTACATA
* *
54636584 AATTAAATA
1 ACTTACATA
*
54636593 ACTTGCATA
1 ACTTACATA
*
54636602 A--AACATA
1 ACTTACATA
* *
54636609 GCCTACATA
1 ACTTACATA
*
54636618 ACTTATATA
1 ACTTACATA
*
54636627 ACTTTCATA
1 ACTTACATA
**
54636636 AAATAC--A
1 ACTTACATA
54636643 ACTTACATA
1 ACTTACATA
**
54636652 TTTTACATAAA
1 ACTTACAT--A
54636663 ACTTACATA
1 ACTTACATA
54636672 A--TACATA
1 ACTTACATA
*
54636679 ACTTAC-TT
1 ACTTACATA
54636687 ACATAATACA-A
1 AC-T--TACATA
*
54636698 CACTTACACA
1 -ACTTACATA
*
54636708 ACTTAAATA
1 ACTTACATA
*
54636717 ACTTGCATA
1 ACTTACATA
54636726 A--TACATA
1 ACTTACATA
54636733 GAC-TACATA
1 -ACTTACATA
*
54636742 ACTTA-ATTTG
1 ACTTACA--TA
*
54636752 TCTTACATA
1 ACTTACATA
54636761 A--TACA-A
1 ACTTACATA
*
54636767 CACTTACACA
1 -ACTTACATA
*
54636777 ACTTAAATA
1 ACTTACATA
*
54636786 ACTTGCATA
1 ACTTACATA
54636795 A--TACATA
1 ACTTACATA
* *
54636802 GCCTACATA
1 ACTTACATA
*
54636811 ACTTA-ATTTT
1 ACTTACA--TA
*
54636821 CCTTACATA
1 ACTTACATA
54636830 A--TACA-A
1 ACTTACATA
54636836 CACTTACATA
1 -ACTTACATA
54636846 ACTTACATA
1 ACTTACATA
**
54636855 GGTTACATA
1 ACTTACATA
54636864 A--TACATA
1 ACTTACATA
*
54636871 ACTTAAATA
1 ACTTACATA
*
54636880 ACTTATATA
1 ACTTACATA
54636889 A--TACATA
1 ACTTACATA
54636896 ACTTACATA
1 ACTTACATA
* *
54636905 ATTTACTTA
1 ACTTACATA
54636914 A--TACATA
1 ACTTACATA
* *
54636921 A-ATATATA
1 ACTTACATA
* *
54636929 TCATATCATA
1 ACTTA-CATA
54636939 ACTTACATA
1 ACTTACATA
54636948 ACT
1 ACT
54636951 CATTTAATTT
Statistics
Matches: 361, Mismatches: 79, Indels: 104
0.66 0.15 0.19
Matches are distributed among these distances:
6 3 0.01
7 81 0.22
8 15 0.04
9 227 0.63
10 20 0.06
11 13 0.04
12 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (9 bp):
ACTTACATA
Found at i:54636501 original size:25 final size:25
Alignment explanation
Indices: 54636462--54636527 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
54636452 TTAAATAACT
* *
54636462 TACATAACTTACATAGCTTACATAA
1 TACATAACTTACATAACATACATAA
*
54636487 -ATCATTACTTACATAACATACATAA
1 TA-CATAACTTACATAACATACATAA
54636512 TACATAACTTACATAA
1 TACATAACTTACATAA
54636528 AATAGAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAACATACATAA
Found at i:54636528 original size:41 final size:40
Alignment explanation
Indices: 54636450--54636568 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 40
54636440 TTAATACACC
* * **
54636450 ACTTAAATAACTTACATAACTTACATAGCTTACATAAATCATT
1 ACTTACATAACTTACATAA--TACATAACTTACATAAAT-AGA
*
54636493 ACTTACATAACATACATAATACATAACTTACATAAAATAGA
1 ACTTACATAACTTACATAATACATAACTTACAT-AAATAGA
* *
54636534 ACTTACATATCTTACATAATACATAACTTATATAA
1 ACTTACATAACTTACATAATACATAACTTACATAA
54636569 TACAACACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.03
41 44 0.66
42 4 0.06
43 17 0.25
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.33
Consensus pattern (40 bp):
ACTTACATAACTTACATAATACATAACTTACATAAATAGA
Found at i:54636551 original size:34 final size:34
Alignment explanation
Indices: 54636505--54636672 Score: 88
Period size: 34 Copynumber: 4.7 Consensus size: 34
54636495 TTACATAACA
*
54636505 TACATAA--TACATAACTTACATAAAATAGAACT
1 TACATAACTTACATAACTTACATAAAATAAAACT
* * *
54636537 TACATATCTTACATAATACATAACTTATATAATACAACACT
1 TACATAACTTACAT-A-AC-TTAC--ATAAAATA-AA-ACT
* * * * * * * *
54636578 TACAGAAATTAAATAACTTGCATAAAACATAGCC
1 TACATAACTTACATAACTTACATAAAATAAAACT
* * *
54636612 TACATAACTTATATAACTTTCATAAAATACAACT
1 TACATAACTTACATAACTTACATAAAATAAAACT
**
54636646 TACATATTTTACATAAAACTTACATAA
1 TACATAACTTACAT--AACTTACATAA
54636673 TACATAACTT
Statistics
Matches: 98, Mismatches: 27, Indels: 18
0.69 0.19 0.13
Matches are distributed among these distances:
32 6 0.06
34 43 0.44
35 2 0.02
36 18 0.18
37 3 0.03
38 2 0.02
39 9 0.09
40 2 0.02
41 13 0.13
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (34 bp):
TACATAACTTACATAACTTACATAAAATAAAACT
Found at i:54636556 original size:16 final size:16
Alignment explanation
Indices: 54636496--54636948 Score: 121
Period size: 16 Copynumber: 27.0 Consensus size: 16
54636486 AATCATTACT
*
54636496 TACATAACATACATAA
1 TACATAACTTACATAA
54636512 TACATAACTTACATAA
1 TACATAACTTACATAA
54636528 -A-ATAGA---AC-T--
1 TACATA-ACTTACATAA
*
54636537 TACATATCTTACATAA
1 TACATAACTTACATAA
*
54636553 TACATAACTTATATAA
1 TACATAACTTACATAA
*
54636569 TACA-ACACTTACAGAAA
1 TACATA-ACTTACA-TAA
* *
54636586 TTAAATAACTTGCATAA
1 -TACATAACTTACATAA
* * *
54636603 AACATAGCCTACATAA
1 TACATAACTTACATAA
* *
54636619 CTTATATAACTTTCATAA
1 --TACATAACTTACATAA
* * * *
54636637 AATACAACTTACATATTT
1 TACATAACTTACATA--A
54636655 TACATAAAACTTACATAA
1 TACAT--AACTTACATAA
54636673 TACATAACTTACTTACATAA
1 TACAT-A---ACTTACATAA
*
54636693 TACA-ACACTTACACAA
1 TACATA-ACTTACATAA
* *
54636709 CTTAAATAACTTGCATAA
1 --TACATAACTTACATAA
54636727 TACATAGAC-TACATAA
1 TACATA-ACTTACATAA
**
54636743 CTTA-ATTTGTCTTACATAA
1 --TACA--TAACTTACATAA
*
54636762 TACA-ACACTTACACAA
1 TACATA-ACTTACATAA
* *
54636778 CTTAAATAACTTGCATAA
1 --TACATAACTTACATAA
* *
54636796 TACATAGCCTACATAA
1 TACATAACTTACATAA
**
54636812 CTTA-ATTTTCCTTACATAA
1 --TACA--TAACTTACATAA
54636831 TACA-ACACTTACATAA
1 TACATA-ACTTACATAA
**
54636847 CTTACATAGGTTACATAA
1 --TACATAACTTACATAA
*
54636865 TACATAACTTAAATAA
1 TACATAACTTACATAA
*
54636881 CTTATATAA--TACATAA
1 --TACATAACTTACATAA
* *
54636897 CTTACATAATTTACTTAA
1 --TACATAACTTACATAA
* * *
54636915 TACATAAATATATATCA
1 TACATAACT-TACATAA
54636932 TATCATAACTTACATAA
1 TA-CATAACTTACATAA
54636949 CTCATTTAAT
Statistics
Matches: 319, Mismatches: 67, Indels: 101
0.66 0.14 0.21
Matches are distributed among these distances:
10 1 0.00
11 4 0.01
12 2 0.01
13 2 0.01
14 4 0.01
15 3 0.01
16 146 0.46
17 25 0.08
18 87 0.27
19 21 0.07
20 24 0.08
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:54636728 original size:34 final size:34
Alignment explanation
Indices: 54636683--54636896 Score: 188
Period size: 34 Copynumber: 6.3 Consensus size: 34
54636673 TACATAACTT
*
54636683 ACTTACATAATACAACACTTACACAACTTAAATA
1 ACTTACATAATACAACACTTACATAACTTAAATA
* * * *
54636717 ACTTGCATAATACATAGAC-TACATAACTTAATTTG
1 ACTTACATAATACA-ACACTTACATAACTTAA-ATA
* *
54636752 TCTTACATAATACAACACTTACACAACTTAAATA
1 ACTTACATAATACAACACTTACATAACTTAAATA
* * *
54636786 ACTTGCATAATACATAGC-C-TACATAACTTAATTTT
1 ACTTACATAATACA-A-CACTTACATAACTTAA-ATA
* *
54636821 CCTTACATAATACAACACTTACATAACTTACATA
1 ACTTACATAATACAACACTTACATAACTTAAATA
** * *
54636855 GGTTACATAATACATA-ACTTAAATAACTTATATA
1 ACTTACATAATACA-ACACTTACATAACTTAAATA
54636889 A--TACATAA
1 ACTTACATAA
54636897 CTTACATAAT
Statistics
Matches: 145, Mismatches: 26, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
32 7 0.05
33 1 0.01
34 82 0.57
35 54 0.37
36 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (34 bp):
ACTTACATAATACAACACTTACATAACTTAAATA
Found at i:54636765 original size:69 final size:69
Alignment explanation
Indices: 54636684--54636884 Score: 307
Period size: 69 Copynumber: 2.9 Consensus size: 69
54636674 ACATAACTTA
54636684 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
54636749 TTGT-
66 TT-TC
*
54636753 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATAACTTAAT
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
54636818 TTTC
66 TTTC
* * ** * *
54636822 CTTACATAATACAACACTTACATAACTTACATAGGTTACATAATACATA-ACTTAAATAACTTA
1 CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGAC-TACATAACTTA
54636885 TATAATACAT
Statistics
Matches: 122, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
68 2 0.02
69 120 0.98
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (69 bp):
CTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGACTACATAACTTAAT
TTTC
Found at i:54636868 original size:25 final size:25
Alignment explanation
Indices: 54636840--54636921 Score: 110
Period size: 25 Copynumber: 3.3 Consensus size: 25
54636830 ATACAACACT
**
54636840 TACATAACTTACATAGGTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
54636865 TACATAACTTAAATAACTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
54636890 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
54636915 TACATAA
1 TACATAA
54636922 ATATATATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:54640839 original size:66 final size:66
Alignment explanation
Indices: 54640675--54640824 Score: 212
Period size: 66 Copynumber: 2.3 Consensus size: 66
54640665 AGTAAATTAC
* * * *
54640675 ACAACTTAAAACGGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
54640740 T
66 T
* *
54640741 ACAATTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAGGAAAG-TATGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
54640805 CT
65 CT
* *
54640807 GCAGCTTAAAGCAGATGC
1 ACAACTTAAAGCAGATGC
54640825 GACAGCAGGA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 70 0.95
67 4 0.05
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:54640851 original size:21 final size:21
Alignment explanation
Indices: 54640827--54640885 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
54640817 GCAGATGCGA
54640827 CAGC-AGGAGAAGCAGAGGCTG
1 CAGCGAGG-GAAGCAGAGGCTG
*
54640848 CAGCGAGGGAAGTAGAGGCTG
1 CAGCGAGGGAAGCAGAGGCTG
*
54640869 CAACGAGGGAAGCAGAG
1 CAGCGAGGGAAGCAGAG
54640886 CAGCGTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.34, C:0.17, G:0.44, T:0.05
Consensus pattern (21 bp):
CAGCGAGGGAAGCAGAGGCTG
Found at i:54641303 original size:43 final size:42
Alignment explanation
Indices: 54641233--54641518 Score: 313
Period size: 43 Copynumber: 6.7 Consensus size: 42
54641223 AAAAACTCCA
* * *
54641233 CTAAAGGTCATGGTCATTT-GCGACGTTTGTGGGAAAGGCGCCA
1 CTAAAGGTCATGGTC-TTTAGCGGCGTTTGTCGGAAA-GCGCCG
* ** *
54641276 CTAAAGATCGGGGTCTTTAGCGGCGTTTGTTTGGAAAGCGCCG
1 CTAAAGGTCATGGTCTTTAGCGGCGTTTG-TCGGAAAGCGCCG
*
54641319 CTAAAGGTCATTGTCTTTAGCGGCGTTTGTCGGATAAGCGCCG
1 CTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGA-AAGCGCCG
* *
54641362 CTAAAGGTCATGGTCTTTAGCGGCATTTGTCGGATATGCGCCG
1 CTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGA-AAGCGCCG
* *
54641405 CTATAGGTCATGGTCTTTAGTGGCGTTTGTCGGAAAAGCGCCG
1 CTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG-AAAGCGCCG
** ** *
54641448 CTAAAGACCATGACCTTTAGCGGCGTTTGTGGTGAAAGCGCCG
1 CTAAAGGTCATGGTCTTTAGCGGCGTTTGTCG-GAAAGCGCCG
* * * *
54641491 CTTAATGTCTTGGTCTTAAGCGGCGTTT
1 CTAAAGGTCATGGTCTTTAGCGGCGTTT
54641519 ATTTCTAAAA
Statistics
Matches: 205, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
42 7 0.03
43 190 0.93
44 8 0.04
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (42 bp):
CTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAAAGCGCCG
Found at i:54644593 original size:19 final size:19
Alignment explanation
Indices: 54644569--54644607 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54644559 TTTTAACATA
54644569 GTGAGTACAAACAAATATT
1 GTGAGTACAAACAAATATT
54644588 GTGAGTACAAACAAATATT
1 GTGAGTACAAACAAATATT
54644607 G
1 G
54644608 AGATCTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (19 bp):
GTGAGTACAAACAAATATT
Found at i:54647152 original size:21 final size:21
Alignment explanation
Indices: 54647126--54647172 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54647116 AACTAAAAGT
*
54647126 AGAGGCGGCAGTGAGAGAAGA
1 AGAGGCGGCAGCGAGAGAAGA
* *
54647147 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCGGCAGCGAGAGAAGA
54647168 AGAGG
1 AGAGG
54647173 TTCAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.47, T:0.04
Consensus pattern (21 bp):
AGAGGCGGCAGCGAGAGAAGA
Found at i:54648450 original size:30 final size:30
Alignment explanation
Indices: 54648414--54648472 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
54648404 TTTTGGTAAC
*
54648414 ATCTCTTATCCGTACTAATCGACAGGATGG
1 ATCTCTTATCCGTACCAATCGACAGGATGG
*
54648444 ATCTCTTATCCGTACCAATCGATAGGATG
1 ATCTCTTATCCGTACCAATCGACAGGATG
54648473 AATAAGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (30 bp):
ATCTCTTATCCGTACCAATCGACAGGATGG
Found at i:54649277 original size:183 final size:182
Alignment explanation
Indices: 54648928--54649281 Score: 430
Period size: 182 Copynumber: 1.9 Consensus size: 182
54648918 AGCGCCGCAA
* * * * *
54648928 AAATCTTAACGAAAACGCATCGTTTTGGTATCGATGTATATTAGAATTAGTGGCGCTTACAAAAA
1 AAATCTTAACCAAAACGCAGCGGTTTGGTATCGATGTATAATACAATTAGTGGCGCTTACAAAAA
**
54648993 AAGCCAGTAAAAGAAGTATTAGCGGCGTTTACTAAAAACGCCGCAAAATATGATAACCAAAACGC
66 AAGCCAGTAAAAGAAAAATTAGCGGCGTTTACTAAAAACGCCGCAAAATATGATAACCAAAACGC
*
54649058 AGAGTTTTGATCTTGATGTATATTAGAATTAGTGGCGCTTAATAGAAGTGCC
131 AGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTAATAGAAGTGCC
* * **
54649110 AAATGTTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTAGTTAAA
1 AAATCTTAACCAAAACGCAGCGGTTTGGTATCGATGTATAATACAATTAGTGGCGCTTA-CAAAA
* ** * * * *
54649174 AACGCC-GCT-AAAGTATAAAATTAGCGGCGATTTTTTAGAATCGCCGCAAGATATGCA-CACCA
65 AAAGCCAG-TAAAAG-A-AAAATTAGCGGCG-TTTACTAAAAACGCCGCAAAATATG-ATAACCA
* *
54649236 AAACGCAGAG-TTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTA
125 AAACGCAGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTA
54649282 CGGAAAAACG
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
181 8 0.06
182 58 0.40
183 44 0.30
184 34 0.23
185 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (182 bp):
AAATCTTAACCAAAACGCAGCGGTTTGGTATCGATGTATAATACAATTAGTGGCGCTTACAAAAA
AAGCCAGTAAAAGAAAAATTAGCGGCGTTTACTAAAAACGCCGCAAAATATGATAACCAAAACGC
AGAGTTTTGATCTTGAGGTATATTAGAATTAGTGGCGCTTAATAGAAGTGCC
Found at i:54649291 original size:114 final size:114
Alignment explanation
Indices: 54649118--54649680 Score: 422
Period size: 114 Copynumber: 4.9 Consensus size: 114
54649108 CCAAATGTTA
* * * * *
54649118 ACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTA-GTTAAAAACGCCG
1 ACCAAAACGCAG-AGTTTGGTCTTGAGGTATAATAGAATTAGTGGCGCTTACG-GAAAAACGCCG
** * *
54649181 CTAAAGTATAAAATTAGCGGCGATTTTTTAGAATCGCCGCAAGATATGCAC
64 CTAAAGTATACTATTAGCGGCGATTTTTTAGAAGCGCCGCAAGATATACAC
* *
54649232 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACGGAAAAACGCCGCT
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATAATAGAATTAGTGGCGCTTACGGAAAAACGCCGCT
** ** * * *
54649297 AAAG-AGTACTATTAGCGGCGCGTTTGGAGAAGCGCCGCTATAT-TTCTTA-
66 AAAGTA-TACTATTAGCGGCGATTTTTTAGAAGCGCCGCAAGATATAC--AC
* * * *
54649346 ACCAAAACTCA-ACGTTTTGGTCTTGATGTATAATATAATTAGTGGCGCTTAC-AATAAAACGCC
1 ACCAAAACGCAGA-G-TTTGGTCTTGAGGTATAATAGAATTAGTGGCGCTTACGGA-AAAACGCC
* * * *
54649409 GCTAAA-TATCAGTATTAGCGGCG--CTTTCAGTTAAGCGCCGCAAGGTATACAC
63 GCTAAAGTAT-ACTATTAGCGGCGATTTTTTAG--AAGCGCCGCAAGATATACAC
* * * * *
54649461 ACCAAAACGCAAAGTTTAGTATTGAGGTATATTAGAATTAGTGGCGCTTATTGG-AAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATAATAGAATTAGTGGCGCTTA-CGGAAAAACGCCGC
* * *
54649525 TAAAGTATACTATTAACGGC-ACTTTCTTAGAAGCGCCGCAAGATATATTA-
65 TAAAGTATACTATTAGCGGCGA-TTTTTTAGAAGCGCCGCAAGATATA-CAC
** * * ** * * * *
54649575 ACCGGAACGCTGCGTTTAAATCTTGATGTATACTGGAATTAGTGGCG-TTCAC-GAGAAATCGCC
1 ACCAAAACGCAGAGTTT-GGTCTTGAGGTATAATAGAATTAGTGGCGCTT-ACGGA-AAAACGCC
* *
54649638 GCTAAA-TCATATTATTAGCGGC-ACTTTTTTATAAGCGCCGCAA
63 GCTAAAGT-ATACTATTAGCGGCGA-TTTTTTAGAAGCGCCGCAA
54649681 AAGACCTTTA
Statistics
Matches: 360, Mismatches: 62, Indels: 53
0.76 0.13 0.11
Matches are distributed among these distances:
113 37 0.10
114 159 0.44
115 157 0.44
116 7 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (114 bp):
ACCAAAACGCAGAGTTTGGTCTTGAGGTATAATAGAATTAGTGGCGCTTACGGAAAAACGCCGCT
AAAGTATACTATTAGCGGCGATTTTTTAGAAGCGCCGCAAGATATACAC
Found at i:54649601 original size:229 final size:226
Alignment explanation
Indices: 54649115--54649680 Score: 577
Period size: 229 Copynumber: 2.5 Consensus size: 226
54649105 GTGCCAAATG
* ** * *
54649115 TTAACCAAAACGCAGCGGTTT-GGTCTCGATGTATAATACAATTAGTGGCGTTA-GTTAAAAACG
1 TTAACCAAAACGCAAC-GTTTAAATCTTGATGTATAATACAATTAGTGGCGTTACGAT-AAAACG
* * * * *
54649178 CCGCTAAAGTATAAAATTAGCGGCGATTTTTTAGAATCGCCGCAAGATATGCACACCAAAACGCA
64 CCGCTAAA-TATAATATTAGCGGCGCTTTGTTA-AAGCGCCGCAAGATATACACACCAAAACGCA
* * * *
54649243 GAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACGGAAAAACGCCGCTAAAGAGTACTA
127 AAGTTTAGTATTGAGGTATATTAGAATTAGTGGCGCTTACGGAAAAACGCCGCTAAAGAGTACTA
* * * * * *
54649308 TTAGCGGCGCGTTTGGAGAAGCGCCGCTATATTTC
192 TTAACGGCACGTTTGGAGAAGCGCCGCAAGATATA
* *** * *
54649343 TTAACCAAAACTCAACGTTTTGGTCTTGATGTATAATATAATTAGTGGCGCTTACAATAAAACGC
1 TTAACCAAAACGCAACGTTTAAATCTTGATGTATAATACAATTAGTGGCG-TTACGATAAAACGC
* *
54649408 CGCTAAATATCAGTATTAGCGGCGCTTTCAGTT-AAGCGCCGCAAGGTATACACACCAAAACGCA
65 CGCTAAATAT-AATATTAGCGGCGCTTT--GTTAAAGCGCCGCAAGATATACACACCAAAACGCA
*
54649472 AAGTTTAGTATTGAGGTATATTAGAATTAGTGGCGCTTATTGG-AAAACGCCGCTAAAGTA-TAC
127 AAGTTTAGTATTGAGGTATATTAGAATTAGTGGCGCTTA-CGGAAAAACGCCGCTAAAG-AGTAC
**
54649535 TATTAACGGCAC-TTTCTTAGAAGCGCCGCAAGATATA
190 TATTAACGGCACGTTT-GGAGAAGCGCCGCAAGATATA
** ** * ** * *
54649572 TTAACCGGAACGCTGCGTTTAAATCTTGATGTATACTGGAATTAGTGGCGTTCACGAGAAATCGC
1 TTAACCAAAACGCAACGTTTAAATCTTGATGTATAATACAATTAGTGGCGTT-ACGATAAAACGC
* * *
54649637 CGCTAAATCATATTATTAGCGGCACTTTTTTATAAGCGCCGCAA
65 CGCTAAAT-ATAATATTAGCGGCGCTTTGTTA-AAGCGCCGCAA
54649681 AAGACCTTTA
Statistics
Matches: 282, Mismatches: 43, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
227 6 0.02
228 49 0.17
229 219 0.78
230 6 0.02
231 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (226 bp):
TTAACCAAAACGCAACGTTTAAATCTTGATGTATAATACAATTAGTGGCGTTACGATAAAACGCC
GCTAAATATAATATTAGCGGCGCTTTGTTAAAGCGCCGCAAGATATACACACCAAAACGCAAAGT
TTAGTATTGAGGTATATTAGAATTAGTGGCGCTTACGGAAAAACGCCGCTAAAGAGTACTATTAA
CGGCACGTTTGGAGAAGCGCCGCAAGATATA
Found at i:54650030 original size:22 final size:21
Alignment explanation
Indices: 54650005--54650070 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
54649995 TTTATGATGT
* *
54650005 GGGTTATGGTGTTTTGGGTTTA
1 GGGTT-TGGAGTTTGGGGTTTA
54650027 GGGTTTAGGAGTTTGGGGTTTA
1 GGGTTT-GGAGTTTGGGGTTTA
* * *
54650049 AGATTTGGGGTTTGGGGTTTA
1 GGGTTTGGAGTTTGGGGTTTA
54650070 G
1 G
54650071 ACTGCTTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.41
22 22 0.59
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (21 bp):
GGGTTTGGAGTTTGGGGTTTA
Found at i:54650057 original size:14 final size:15
Alignment explanation
Indices: 54650022--54650061 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54650012 GGTGTTTTGG
* *
54650022 GTTTAGGGTTTAGGA
1 GTTTGGGGTTTAAGA
54650037 GTTTGGGGTTTAAGA
1 GTTTGGGGTTTAAGA
54650052 -TTTGGGGTTT
1 GTTTGGGGTTT
54650062 GGGGTTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (15 bp):
GTTTGGGGTTTAAGA
Found at i:54651651 original size:13 final size:14
Alignment explanation
Indices: 54651626--54651654 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54651616 TGACAAAATC
54651626 AAAATGTATTTAAA
1 AAAATGTATTTAAA
54651640 AAAATGTA-TTAAA
1 AAAATGTATTTAAA
54651653 AA
1 AA
54651655 TGTCAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAATGTATTTAAA
Found at i:54651943 original size:22 final size:24
Alignment explanation
Indices: 54651917--54651961 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
54651907 ATAAAAATGT
*
54651917 ATGAACATATAAAT-TT-TAAAAC
1 ATGAAAATATAAATATTATAAAAC
54651939 ATGAAAATATAAATATTATAAAA
1 ATGAAAATATAAATATTATAAAA
54651962 ATATGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
ATGAAAATATAAATATTATAAAAC
Found at i:54651964 original size:17 final size:18
Alignment explanation
Indices: 54651942--54651985 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
54651932 TTAAAACATG
54651942 AAAATATAAATAT-TATA
1 AAAATATAAATATATATA
* *
54651959 AAAATATGAATGTATATA
1 AAAATATAAATATATATA
54651977 AAATATATA
1 AAA-ATATA
54651986 TAAACTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 7 0.32
19 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAATATAAATATATATA
Found at i:54652715 original size:15 final size:15
Alignment explanation
Indices: 54652695--54652730 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
54652685 AATCTATTTA
54652695 TTCTTTTCTT-GTATT
1 TTCTTTT-TTCGTATT
54652710 TTCTTTTTTCGTATT
1 TTCTTTTTTCGTATT
54652725 TTCTTT
1 TTCTTT
54652731 AACTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCGTATT
Found at i:54653307 original size:44 final size:44
Alignment explanation
Indices: 54653224--54653308 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 44
54653214 TTTTCTTCAA
* *
54653224 AGAGCTTCATTCCATCCTACTGCAACGTCAGAGGTATAGGAACT
1 AGAGCTTCATTCCATCCTACTACAACATCAGAGGTATAGGAACT
54653268 AGAGCTTCGA-TCCACTCC-ACTACAACATCA-AGGTGATAGGA
1 AGAGCTTC-ATTCCA-TCCTACTACAACATCAGAGGT-ATAGGA
54653309 TTTGGGTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
43 4 0.11
44 28 0.78
45 4 0.11
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (44 bp):
AGAGCTTCATTCCATCCTACTACAACATCAGAGGTATAGGAACT
Found at i:54653842 original size:45 final size:45
Alignment explanation
Indices: 54653784--54654055 Score: 186
Period size: 45 Copynumber: 6.1 Consensus size: 45
54653774 CCCAGGGAGA
*
54653784 CAAGG-CTGGTATCTTC-GATCTGCTTCGCTGTCAATACAGGAAGG
1 CAAGGTCTGCTATCTTCAG-TCTGCTTCGCTGTCAATACAGGAAGG
* * *
54653828 CAAGGTCCGCTATCTTCAGTCTGC-TCTGCTGTAAACT-CAGGGAGG
1 CAAGGTCTGCTATCTTCAGTCTGCTTC-GCTGTCAA-TACAGGAAGG
* * * * * *
54653873 CAAGG-CTGGTGTCTT-TGATCTGCTTCGTTGTCAGTACAAGAAGG
1 CAAGGTCTGCTATCTTCAG-TCTGCTTCGCTGTCAATACAGGAAGG
* * * ** *
54653917 CAAGATCTGCTATCTTCAGTCTGCTCCGCTGTAAACCCAGGGAGG
1 CAAGGTCTGCTATCTTCAGTCTGCTTCGCTGTCAATACAGGAAGG
* * * * * *
54653962 CAAGG-CTGGTGTCTT-TGATCTGCTTCGTTGTCAGTACAAGAAGG
1 CAAGGTCTGCTATCTTCAG-TCTGCTTCGCTGTCAATACAGGAAGG
* * *
54654006 CAAGATCTGCTATATTCAGTCTGCTCCGCTG-CAA-ACTCAGGAAGG
1 CAAGGTCTGCTATCTTCAGTCTGCTTCGCTGTCAATA--CAGGAAGG
54654051 CAAGG
1 CAAGG
54654056 CTGAAGTTAC
Statistics
Matches: 167, Mismatches: 47, Indels: 27
0.69 0.20 0.11
Matches are distributed among these distances:
43 4 0.02
44 66 0.40
45 93 0.56
46 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (45 bp):
CAAGGTCTGCTATCTTCAGTCTGCTTCGCTGTCAATACAGGAAGG
Found at i:54653905 original size:89 final size:89
Alignment explanation
Indices: 54653776--54654058 Score: 449
Period size: 89 Copynumber: 3.2 Consensus size: 89
54653766 AGCTGCTGCC
* * * * * * * *
54653776 CAGGGAGACAAGGCTGGTATCTTCGATCTGCTTCGCTGTCAATACAGGAAGGCAAGGTCCGCTAT
1 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
*
54653841 CTTCAGTCTGCTCTGCTGTAAACT
66 CTTCAGTCTGCTCCGCTGTAAACT
54653865 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
*
54653930 CTTCAGTCTGCTCCGCTGTAAACC
66 CTTCAGTCTGCTCCGCTGTAAACT
54653954 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
* *
54654019 ATTCAGTCTGCTCCGCTGCAAACT
66 CTTCAGTCTGCTCCGCTGTAAACT
*
54654043 CAGGAAGGCAAGGCTG
1 CAGGGAGGCAAGGCTG
54654059 AAGTTACACC
Statistics
Matches: 180, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 180 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (89 bp):
CAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGAAGGCAAGATCTGCTAT
CTTCAGTCTGCTCCGCTGTAAACT
Found at i:54653918 original size:44 final size:44
Alignment explanation
Indices: 54653870--54654009 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 44
54653860 AAACTCAGGG
54653870 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGA
1 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGA
* * * * * * * *** * *
54653914 AGGCAAGATCTGCTATC-TTCAGTCTGCTCCGCTGTAAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTTGA-TCTGCTTCGTTGTCAGTACAAGA
54653959 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGA
1 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGA
54654003 AGGCAAG
1 AGGCAAG
54654010 ATCTGCTATA
Statistics
Matches: 69, Mismatches: 24, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
44 38 0.55
45 31 0.45
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGTCAGTACAAGA
Found at i:54655819 original size:10 final size:10
Alignment explanation
Indices: 54655806--54655842 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
54655796 TTTCTTTTTA
54655806 TTTTTTGTTC
1 TTTTTTGTTC
54655816 TTTTTTGTTC
1 TTTTTTGTTC
*
54655826 TCTTTTTTTTC
1 T-TTTTTGTTC
54655837 TTTTTT
1 TTTTTT
54655843 CTATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTC
Found at i:54655821 original size:17 final size:17
Alignment explanation
Indices: 54655789--54655820 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54655779 CGGTAGAGGT
54655789 TTTTTTGTTTCTTTTTA
1 TTTTTTGTTTCTTTTTA
54655806 TTTTTTG-TTCTTTTT
1 TTTTTTGTTTCTTTTT
54655821 TGTTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (17 bp):
TTTTTTGTTTCTTTTTA
Found at i:54658148 original size:19 final size:19
Alignment explanation
Indices: 54658124--54658160 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54658114 GCATGACCTC
54658124 TATATGCACCTGAACGATG
1 TATATGCACCTGAACGATG
*
54658143 TATATGTACCTGAACGAT
1 TATATGCACCTGAACGAT
54658161 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TATATGCACCTGAACGATG
Found at i:54660204 original size:18 final size:17
Alignment explanation
Indices: 54660178--54660212 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54660168 AATATTAAGA
*
54660178 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54660195 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54660213 TTAATAGTAA
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:54660224 original size:120 final size:120
Alignment explanation
Indices: 54660071--54660354 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
54660061 TAATTGAAAA
* * *
54660071 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAGTATTATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
* *
54660135 TTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
* * *
54660190 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
*
54660255 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
54660310 TATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
54660355 ATGATTAAAT
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 131 0.87
121 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:54660326 original size:18 final size:17
Alignment explanation
Indices: 54660298--54660332 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54660288 ATTATTAAGA
*
54660298 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54660315 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54660333 TTAATAAAAA
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:54660332 original size:16 final size:16
Alignment explanation
Indices: 54660298--54660352 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
54660288 ATTATTAAGA
54660298 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
54660315 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
54660331 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
54660345 ATGTTTAA
1 AT-TTTAA
54660353 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:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:54660589 original size:16 final size:16
Alignment explanation
Indices: 54660568--54660635 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
54660558 GATTTGCTAT
54660568 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
54660584 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
54660600 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54660616 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54660632 TACA
1 TACA
54660636 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54660899 original size:15 final size:15
Alignment explanation
Indices: 54660881--54660916 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
54660871 AATTTGTTTA
54660881 TTCTTTTCTT-GTATT
1 TTCTTTT-TTCGTATT
54660896 TTCTTTTTTCGTATT
1 TTCTTTTTTCGTATT
54660911 TTCTTT
1 TTCTTT
54660917 AACTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCGTATT
Found at i:54661616 original size:44 final size:44
Alignment explanation
Indices: 54661553--54661643 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
54661543 TCTTGCGTCC
* *
54661553 TTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAATCGCCTCA
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCA
* *
54661597 TTCTTGCCGAATTTCTTGAAATCCGAAATCCCTAAATCGCCTCA
1 TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCA
54661641 TTC
1 TTC
54661644 CTCCTTCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (44 bp):
TTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCCTCA
Found at i:54663322 original size:35 final size:35
Alignment explanation
Indices: 54663278--54663358 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
54663268 TAAAGTTATA
* *
54663278 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
54663313 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
54663348 TTTTAAATATT
1 TTTTAAATATT
54663359 AAAATTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTGAATCACGAATAT
Found at i:54663407 original size:18 final size:17
Alignment explanation
Indices: 54663376--54663431 Score: 78
Period size: 16 Copynumber: 3.3 Consensus size: 17
54663366 TTTAAGTTCA
54663376 AATTTCATAACTTACGT
1 AATTTCATAACTTACGT
* *
54663393 AATTTACATATCTTACAT
1 AATTT-CATAACTTACGT
54663411 AA-TTCATAACTTACGT
1 AATTTCATAACTTACGT
54663427 AATTT
1 AATTT
54663432 AAATTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.36
17 9 0.27
18 12 0.36
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (17 bp):
AATTTCATAACTTACGT
Found at i:54663451 original size:29 final size:33
Alignment explanation
Indices: 54663381--54663453 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 33
54663371 GTTCAAATTT
*
54663381 CATAACTTACGTAATTTACATATCTTACATAATT
1 CATAACTTACGTAATTTACATATCTTA-ATAATA
54663415 CATAACTTACGTAATTTA-A-AT-TT-ATAATA
1 CATAACTTACGTAATTTACATATCTTAATAATA
54663444 CATAACTTAC
1 CATAACTTAC
54663454 ATAACTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
29 15 0.39
31 2 0.05
32 2 0.05
33 1 0.03
34 18 0.47
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (33 bp):
CATAACTTACGTAATTTACATATCTTAATAATA
Found at i:54663573 original size:23 final size:22
Alignment explanation
Indices: 54663523--54663723 Score: 65
Period size: 22 Copynumber: 9.3 Consensus size: 22
54663513 AAAAAAATTG
54663523 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
54663546 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
54663566 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
* * * *
54663587 TTAAATTTAGCA-ATCATATCATAAC
1 ATACA--TA-CATAACTTA-CATAAC
* *
54663612 TTACATACATAA-TTA-GT-A-
1 ATACATACATAACTTACATAAC
*
54663630 AT-CATATCACAACTTACATAACC
1 ATACATA-CATAACTTACATAA-C
*
54663653 A-ACATA-ATGACTTACATAATAAC
1 ATACATACATAACTTAC---ATAAC
* * *
54663676 CTACATA-ATAACTTATATAATA
1 ATACATACATAACTTACATAA-C
54663698 ATACATA-ATAA--TACATAAC
1 ATACATACATAACTTACATAAC
54663717 ATACATA
1 ATACATA
54663724 AATTAAATAA
Statistics
Matches: 133, Mismatches: 23, Indels: 48
0.65 0.11 0.24
Matches are distributed among these distances:
17 4 0.03
18 11 0.08
19 19 0.14
20 10 0.08
21 14 0.11
22 22 0.17
23 20 0.15
24 22 0.17
25 11 0.08
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:54663671 original size:12 final size:12
Alignment explanation
Indices: 54663654--54663708 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
54663644 TACATAACCA
*
54663654 ACATAATGACTT
1 ACATAATAACTT
*
54663666 ACATAATAACCT
1 ACATAATAACTT
54663678 ACATAATAACTT
1 ACATAATAACTT
*
54663690 ATATAATAA--T
1 ACATAATAACTT
54663700 ACATAATAA
1 ACATAATAA
54663709 TACATAACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
10 9 0.24
12 29 0.76
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.31
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:54663681 original size:24 final size:24
Alignment explanation
Indices: 54663647--54663715 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
54663637 CACAACTTAC
* *
54663647 ATAACCAACATAATGACTTACATA
1 ATAACCTACATAATAACTTACATA
*
54663671 ATAACCTACATAATAACTTATATA
1 ATAACCTACATAATAACTTACATA
54663695 ATAA--TACATAATAA--TACATA
1 ATAACCTACATAATAACTTACATA
54663715 A
1 A
54663716 CATACATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.15
22 10 0.24
24 25 0.61
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:54663809 original size:95 final size:95
Alignment explanation
Indices: 54663699--54664120 Score: 684
Period size: 95 Copynumber: 4.5 Consensus size: 95
54663689 TATATAATAA
* *
54663699 TACATAATAATACATAACATACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
54663764 ATAACTTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
54663794 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
54663859 ATAACTTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
54663889 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
54663954 ATAACTTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
*
54663984 TACATAATAATACATACCGTAC---------ATAAGTTACATAATAAACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
* * **
54664040 ATAACTTACATAATAACTTACAT-AATAACT
66 ATAACTTACATAATATCCTACATCCCT-ACT
* *
54664070 TACATAATAATGCATACCCTACATAAATTAAATAAGTTACATAATACACAA
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAA
54664121 TAAGGTTAAA
Statistics
Matches: 307, Mismatches: 10, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
85 1 0.00
86 77 0.25
95 229 0.75
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (95 bp):
TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
ATAACTTACATAATATCCTACATCCCTACT
Found at i:54664080 original size:15 final size:12
Alignment explanation
Indices: 54664040--54664079 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
54664030 AAAAACTTAC
54664040 ATAACTTACATA
1 ATAACTTACATA
54664052 ATAACTTACATA
1 ATAACTTACATA
54664064 ATAACTTACATA
1 ATAACTTACATA
54664076 ATAA
1 ATAA
54664080 TGCATACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:54664169 original size:19 final size:19
Alignment explanation
Indices: 54664140--54664205 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
54664130 AAACATAGTG
54664140 TAACTTACATAATAATACA
1 TAACTTACATAATAATACA
54664159 T-ACTCTACATAATAATACA
1 TAACT-TACATAATAATACA
*
54664178 TAACTTAC---ATAAGACA
1 TAACTTACATAATAATACA
54664194 TAACTTACATAA
1 TAACTTACATAA
54664206 GTTTCATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
16 15 0.37
18 3 0.07
19 20 0.49
20 3 0.07
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (19 bp):
TAACTTACATAATAATACA
Found at i:54664180 original size:190 final size:186
Alignment explanation
Indices: 54663671--54664205 Score: 601
Period size: 181 Copynumber: 2.9 Consensus size: 186
54663661 GACTTACATA
* * *
54663671 ATAACCTACATAATAACTTATATAATAA--TACATAATAATACATAACATACATAAATTAAATAA
1 ATAACTTACATAATAACTTACATAATAACTTACATAATAATACATACCATACATAAATTAAATAA
* *
54663734 GTTACATAATACACAAAAACAAAAACTTACATAACTTACATAATATCCTACATCCCTACTTACAT
66 GTTACATAATACACAAAAACAAAAACTTACATAACTTACATAATA--ATACAT-ACT-C-TACAT
** * *
54663799 AATAATACAT-ACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
126 AATAATACATAACAATACATAAAGTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
* * ** *
54663859 ATAACTTACATAATATCCTACATCCCT-ACTTACATAATAATACATACCGTACATAAATTAAATA
1 ATAACTTACATAATAACTTACAT-AATAACTTACATAATAATACATACCATACATAAATTAAATA
* * *
54663923 AGTTACATAATACACAAAAACAAAAACTTACATAACTTACATAAT-AT-CCTACATC--CCTACT
65 AGTTACATAATACACAAAAACAAAAACTTACATAACTTACATAATAATACATAC-TCTACATAAT
* ** *
54663984 --TACATAATAATACATACCGTACATAAGTTACATAATAAACAAAAACAAAAACTTAC
129 AATACATAACAATACATAAAGTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
* *
54664040 ATAACTTACATAATAACTTACATAATAACTTACATAATAATGCATACCCTACATAAATTAAATAA
1 ATAACTTACATAATAACTTACATAATAACTTACATAATAATACATACCATACATAAATTAAATAA
** * **
54664105 GTTACATAATACACAATAAGGTTAAAAACATAGTGTAACTTACATAATAATACATACTCTACATA
66 GTTACATAATACACAA-AA--ACAAAAACTTA-CATAACTTACATAATAATACATACTCTACATA
* * *
54664170 ATAATACATAAC-TTACAT-AAG-ACATAACTTACATAA
127 ATAATACATAACAATACATAAAGTAAATAAGTTACATAA
54664206 GTTTCATAAT
Statistics
Matches: 291, Mismatches: 40, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
180 6 0.02
181 115 0.40
182 6 0.02
184 8 0.03
185 15 0.05
186 7 0.02
187 19 0.07
188 25 0.09
189 6 0.02
190 84 0.29
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.28
Consensus pattern (186 bp):
ATAACTTACATAATAACTTACATAATAACTTACATAATAATACATACCATACATAAATTAAATAA
GTTACATAATACACAAAAACAAAAACTTACATAACTTACATAATAATACATACTCTACATAATAA
TACATAACAATACATAAAGTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
Found at i:54664186 original size:9 final size:9
Alignment explanation
Indices: 54664140--54664277 Score: 114
Period size: 9 Copynumber: 15.8 Consensus size: 9
54664130 AAACATAGTG
54664140 TAACTTACA
1 TAACTTACA
54664149 TAA-TAATACA
1 TAACT--TACA
54664159 T-ACTCTACA
1 TAACT-TACA
54664168 TAA-TAATACA
1 TAACT--TACA
54664178 TAACTTACA
1 TAACTTACA
*
54664187 TAA--GACA
1 TAACTTACA
54664194 TAACTTACA
1 TAACTTACA
* *
54664203 TAAGTTTCA
1 TAACTTACA
54664212 TAA--TACA
1 TAACTTACA
*
54664219 CAACTTACA
1 TAACTTACA
*
54664228 CAACTTACA
1 TAACTTACA
*
54664237 CAACTTACA
1 TAACTTACA
54664246 TAACTTACA
1 TAACTTACA
54664255 TAACTTACA
1 TAACTTACA
54664264 TAA--TACA
1 TAACTTACA
54664271 TAACTTA
1 TAACTTA
54664278 TTCCTAAATC
Statistics
Matches: 108, Mismatches: 9, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
7 18 0.17
8 1 0.01
9 74 0.69
10 14 0.13
11 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.30
Consensus pattern (9 bp):
TAACTTACA
Found at i:54664189 original size:16 final size:16
Alignment explanation
Indices: 54664170--54664277 Score: 86
Period size: 16 Copynumber: 6.9 Consensus size: 16
54664160 ACTCTACATA
54664170 ATAATACATAACTTAC
1 ATAATACATAACTTAC
*
54664186 ATAAGACATAACTTAC
1 ATAATACATAACTTAC
*
54664202 AT-A-A-GT---TT-C
1 ATAATACATAACTTAC
*
54664211 ATAATACACAACTTAC
1 ATAATACATAACTTAC
* *
54664227 ACAACTTACACAACTTAC
1 ATAA--TACATAACTTAC
54664245 ATAACTTACATAACTTAC
1 ATAA--TACATAACTTAC
54664263 ATAATACATAACTTA
1 ATAATACATAACTTA
54664278 TTCCTAAATC
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 1 0.01
13 1 0.01
14 1 0.01
15 3 0.04
16 32 0.42
18 32 0.42
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAATACATAACTTAC
Found at i:54664213 original size:25 final size:25
Alignment explanation
Indices: 54664174--54664277 Score: 136
Period size: 25 Copynumber: 4.1 Consensus size: 25
54664164 TACATAATAA
*
54664174 TACATAACTTACATAAGACATAACT
1 TACATAACTTACATAATACATAACT
* * *
54664199 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACATAACT
* *
54664224 TACACAACTTACACAACTTACATAACT
1 TACATAACTTACATAA--TACATAACT
54664251 TACATAACTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
54664276 TA
1 TA
54664278 TTCCTAAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 44 0.67
27 22 0.33
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:54666512 original size:41 final size:41
Alignment explanation
Indices: 54666455--54666571 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
54666445 AGTTTTTGGG
* *
54666455 GCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCGA
1 GCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATACTAGA
*
54666496 GCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATACTAGG
1 GCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATACTAGA
* *
54666537 GGCTTTAGCGGCGTTTTTGGGAA-AAGCGCCGCTAA
1 GCCTTTAGCGGCGTTTTT--AAAGAAGCGCCGCTAA
54666572 AAACATTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 55 0.80
42 12 0.17
43 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (41 bp):
GCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATACTAGA
Found at i:54666956 original size:15 final size:15
Alignment explanation
Indices: 54666918--54666952 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54666908 ACTATTTTAA
54666918 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
54666933 GGTTTAGGGATTAT-
1 GGTTTAGGGAGTATG
54666947 GGTTTA
1 GGTTTA
54666953 AGGGTTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:54666994 original size:23 final size:23
Alignment explanation
Indices: 54666963--54667026 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
54666953 AGGGTTGAGA
*
54666963 TTTAAGGTTTAGAGGTTAGAGGG
1 TTTAGGGTTTAGAGGTTAGAGGG
* *
54666986 TTTAGGGTTTAGGGGTAAGAGGG
1 TTTAGGGTTTAGAGGTTAGAGGG
54667009 -TTAGCGGTTTAGAGGTTA
1 TTTAG-GGTTTAGAGGTTA
54667027 AACGTTAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.11
23 31 0.89
ACGTcount: A:0.23, C:0.02, G:0.41, T:0.34
Consensus pattern (23 bp):
TTTAGGGTTTAGAGGTTAGAGGG
Found at i:54667025 original size:8 final size:8
Alignment explanation
Indices: 54666963--54667025 Score: 53
Period size: 7 Copynumber: 8.2 Consensus size: 8
54666953 AGGGTTGAGA
54666963 TTTA-AGG
1 TTTAGAGG
54666970 TTTAGAGG
1 TTTAGAGG
54666978 -TTAGAGGG
1 TTTAGA-GG
54666986 TTTAG-GG
1 TTTAGAGG
54666993 TTTAG-GG
1 TTTAGAGG
* *
54667000 GTAAGAGG
1 TTTAGAGG
* *
54667008 GTTAGCGG
1 TTTAGAGG
54667016 TTTAGAGG
1 TTTAGAGG
54667024 TT
1 TT
54667026 AAACGTTAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
7 21 0.46
8 21 0.46
9 4 0.09
ACGTcount: A:0.22, C:0.02, G:0.41, T:0.35
Consensus pattern (8 bp):
TTTAGAGG
Found at i:54667277 original size:14 final size:15
Alignment explanation
Indices: 54667251--54667288 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
54667241 GTTTAGAGAG
54667251 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
54667266 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
54667280 TAT-GATTTA
1 TATGGATTTA
54667289 AGGGTTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 14 0.64
15 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:54667418 original size:298 final size:299
Alignment explanation
Indices: 54667031--54667768 Score: 988
Period size: 298 Copynumber: 2.4 Consensus size: 299
54667021 AGGTTAAACG
* * * ** *
54667031 TTAGGGGTTAAGAAAGTTAGGGATTTAAGGTTTAGGGATTCAAAGGTCGAGTTAGGATTTTGGGC
1 TTAGGGGTT-A-ACAGTTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGGTTTT-GG-
*
54667096 GTTTAGATTAA-T-TTTTTAAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAA
62 GTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAA
** * ***
54667159 TAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAGGTCAATTTA
127 TAATAAATTTGTTTAGGGTTTTAAGTTTAGGGTATATGATTAATTTAAGATTTAAAACCAATTTA
* * *
54667224 AGAGTTCATATTTTAAGGTTTAGAGAGTATGGATTTAGGGATTATGGATTAGGGATTATGATTTA
192 AGAGCTCATATTTTAAGGATTAGAGAGTATGGATCTAGGGATTATGGATTAGGGATTATGATTTA
** *
54667289 AGGGTTGAGATTTAAGGTTTAAG-GGTT-AGATGGTTAGGGG-T-
257 AGGGTTGAGATTTAAACTTT-AGCGGTTAAG-GGGTTAGGGGTTA
*
54667330 TTAGGGGTTAGACATGTTATGGG-TTAAAAG-TTAGGGATTCAGGGGTCGGGTTAGGGTTTTGGG
1 TTAGGGGTTA-ACA-GTTA-GGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGG
*
54667393 TTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATGATTGTAAAAGAGATAAT
63 TTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAAT
** *
54667458 AATAAATTTGTTTAGGGTTTTAAGTTTAGGGTATATGATTAATTTAAGATTTAAAACCGGTTTAG
128 AATAAATTTGTTTAGGGTTTTAAGTTTAGGGTATATGATTAATTTAAGATTTAAAACCAATTTAA
* *
54667523 GAGCTCATATTTTAAGGATTAGGGAGTATGGATCTAGGGATTATGGATTAGGGATTATGGTTTAA
193 GAGCTCATATTTTAAGGATTAGAGAGTATGGATCTAGGGATTATGGATTAGGGATTATGATTTAA
*
54667588 GGGTTGGGATTTAAACTTTAGCGGTTAAGGGGTTAGGGGTTAGA
258 GGGTTGAGATTTAAACTTTAGCGGTTAAGGGGTTAGGGGTT--A
* * * * * *
54667632 CGTTAGGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGATTCAGGGGCCGAGTTAAGGTTTTGAGT
1 --TTAGGGGTTAACAGTTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGT
*
54667697 TTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAATAGATAAT
64 TTAGATTAATTA-TTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAAT
54667762 AATAAAT
128 AATAAAT
54667769 CAAATATATT
Statistics
Matches: 388, Mismatches: 36, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
296 11 0.03
297 5 0.01
298 225 0.58
299 21 0.05
300 3 0.01
301 3 0.01
302 9 0.02
303 44 0.11
304 67 0.17
ACGTcount: A:0.30, C:0.03, G:0.26, T:0.41
Consensus pattern (299 bp):
TTAGGGGTTAACAGTTAGGGATTAAAAGTTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTT
AGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAATAAT
AAATTTGTTTAGGGTTTTAAGTTTAGGGTATATGATTAATTTAAGATTTAAAACCAATTTAAGAG
CTCATATTTTAAGGATTAGAGAGTATGGATCTAGGGATTATGGATTAGGGATTATGATTTAAGGG
TTGAGATTTAAACTTTAGCGGTTAAGGGGTTAGGGGTTA
Found at i:54667574 original size:14 final size:14
Alignment explanation
Indices: 54667538--54667582 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
54667528 CATATTTTAA
*
54667538 GGATTAGGGAGTAT
1 GGATTAGGGATTAT
54667552 GGATCTAGGGATTAT
1 GGAT-TAGGGATTAT
54667567 GGATTAGGGATTAT
1 GGATTAGGGATTAT
54667581 GG
1 GG
54667583 TTTAAGGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.27, C:0.02, G:0.40, T:0.31
Consensus pattern (14 bp):
GGATTAGGGATTAT
Found at i:54667638 original size:14 final size:14
Alignment explanation
Indices: 54667605--54667653 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
54667595 GATTTAAACT
* *
54667605 TTAGCGGTTAAGGGG
1 TTAGGGGTTAA-GAG
54667620 TTAGGGGTT-AGACG
1 TTAGGGGTTAAGA-G
54667634 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
54667648 TTAGGG
1 TTAGGG
54667654 ATTTAAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.22, C:0.04, G:0.45, T:0.29
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:54671168 original size:2 final size:2
Alignment explanation
Indices: 54671161--54671201 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54671151 TATTTTTCCC
54671161 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
54671202 AAGTTGTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:54672576 original size:43 final size:43
Alignment explanation
Indices: 54672529--54672865 Score: 388
Period size: 43 Copynumber: 7.8 Consensus size: 43
54672519 TTTCTACGAG
* * *
54672529 AAGCGTCGCTAAAGGTCTCGAGCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * * *
54672572 AAGCGTCGCTAAAGGCCTCGAGCTATAGCGGCATTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * * *
54672615 AATCTCCGCTAAAGGCCTTGAGCTATAGCGGCGTTTTTGGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GGGAA
**
54672659 AA-CGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGCAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * * *
54672701 AAGCACTGCTAAAGCTCTTGATCTATAGCGGCGTTTTTGGGAG
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* **
54672744 AAGCGCCGCTAAAGGTCTTGATCTCTAGCGGCGTTTGTGCAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * **
54672787 AAGCGCCGTTAAAGCTCTTGATTTATAGCGATGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* *
54672830 AAGCGCCACTAAAGGTCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
54672866 ATTCCTAAAA
Statistics
Matches: 248, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
42 5 0.02
43 236 0.95
44 7 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
Found at i:54676476 original size:21 final size:21
Alignment explanation
Indices: 54676452--54676505 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
54676442 GCAAAGGCGG
* * *
54676452 CAGCGAGGGAAGCAGATGCTA
1 CAGCGAGAGAAGCAGAGGCCA
54676473 CAGCGAGAGAAGCAGAGGCCA
1 CAGCGAGAGAAGCAGAGGCCA
54676494 CAGCGAGAGAAG
1 CAGCGAGAGAAG
54676506 TAGTGAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.39, T:0.04
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCCA
Found at i:54676528 original size:12 final size:12
Alignment explanation
Indices: 54676494--54676532 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54676484 GCAGAGGCCA
54676494 CAGCGAGAGAAG
1 CAGCGAGAGAAG
* *
54676506 TAGTGAGAGAAG
1 CAGCGAGAGAAG
*
54676518 CAGCGATAGAAG
1 CAGCGAGAGAAG
54676530 CAG
1 CAG
54676533 AGGTTCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.38, T:0.08
Consensus pattern (12 bp):
CAGCGAGAGAAG
Found at i:54677072 original size:43 final size:42
Alignment explanation
Indices: 54677024--54677122 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
54677014 GAACATTACT
*
54677024 TTTAGCGGCGTTTTGGGAGAAAACGCCACTAAAGAACATGATA
1 TTTAGCGGCGTTTT-GGACAAAACGCCACTAAAGAACATGATA
*** * * * *
54677067 TTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAACATGATC
1 TTTAGCGGCGTTTTGGACAAAACGCCACTAAAGAACATGATA
54677109 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
54677123 TTTCTGTAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 34 0.71
43 14 0.29
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTGGACAAAACGCCACTAAAGAACATGATA
Found at i:54680243 original size:19 final size:19
Alignment explanation
Indices: 54680192--54680246 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
54680182 CAAAATCTTG
54680192 AAAAATTAAAAATTCTTTTTA
1 AAAAATT-AAAATT-TTTTTA
** *
54680213 AAACTTTTAAATTTTTTTA
1 AAAAATTAAAATTTTTTTA
54680232 AAAAATTAAAATTTT
1 AAAAATTAAAATTTT
54680247 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 18 0.64
20 5 0.18
21 5 0.18
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATTAAAATTTTTTTA
Found at i:54681904 original size:17 final size:17
Alignment explanation
Indices: 54681869--54681905 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
54681859 CTTGATTCTT
*
54681869 AAAAATTTAAAATTAAA
1 AAAAATTTAAAAATAAA
54681886 AAAAATTTAAACAATAAA
1 AAAAATTTAAA-AATAAA
54681904 AA
1 AA
54681906 TTATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATTTAAAAATAAA
Found at i:54690472 original size:26 final size:27
Alignment explanation
Indices: 54690420--54690482 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
54690410 ATAAAAAATA
54690420 ACCAAAATATTATAATTTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
54690447 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTTATTT
54690473 ACCAAAATAT
1 ACCAAAATAT
54690483 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAATTTTTTTTATTT
Found at i:54690634 original size:27 final size:27
Alignment explanation
Indices: 54690542--54690641 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
54690532 CCCTGGTCAG
* *
54690542 GCCAAGGTGATTGGCGGCACCAAAGGT
1 GCCAAGCTGATTGGCGGCACCAATGGT
*
54690569 GCCAAAGC-CATTGGCGGCACCAATGGT
1 GCC-AAGCTGATTGGCGGCACCAATGGT
** *
54690596 GCCAAGGAGATTGGCTGCACCAATGGT
1 GCCAAGCTGATTGGCGGCACCAATGGT
54690623 GCCATA-CTGATTGGCGGCA
1 GCCA-AGCTGATTGGCGGCA
54690642 TTACTCGTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.05
27 54 0.89
28 4 0.07
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (27 bp):
GCCAAGCTGATTGGCGGCACCAATGGT
Found at i:54690741 original size:11 final size:11
Alignment explanation
Indices: 54690725--54690764 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
54690715 GGTGCTACGG
54690725 AAAAGAAGAGA
1 AAAAGAAGAGA
54690736 AAAAG-AGAGA
1 AAAAGAAGAGA
* *
54690746 AAGAGAAGACA
1 AAAAGAAGAGA
54690757 AAAAGAAG
1 AAAAGAAG
54690765 GTATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:54690754 original size:21 final size:20
Alignment explanation
Indices: 54690724--54690762 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
54690714 AGGTGCTACG
*
54690724 GAAAAGAAGAGAAAAAGAGA
1 GAAAAGAAGACAAAAAGAGA
54690744 GAAAGAGAAGACAAAAAGA
1 GAAA-AGAAGACAAAAAGA
54690763 AGGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (20 bp):
GAAAAGAAGACAAAAAGAGA
Found at i:54690899 original size:3 final size:3
Alignment explanation
Indices: 54690893--54690933 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54690883 ATTATTATTA
54690893 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
54690934 AGTATTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:54696762 original size:27 final size:27
Alignment explanation
Indices: 54696724--54696779 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
54696714 TTAGCCACAT
*
54696724 ATTGGTGCCGCCTTTTTATTCCTCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
54696751 ATTGGTGCCGCCTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
54696778 AT
1 AT
54696780 CACCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.09, C:0.34, G:0.14, T:0.43
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTTATTCCCCTCC
Found at i:54697555 original size:42 final size:40
Alignment explanation
Indices: 54697490--54697652 Score: 126
Period size: 40 Copynumber: 4.1 Consensus size: 40
54697480 TAAAAATTAC
*
54697490 CTTTTTTTCTTTTTTTTCC-TTCCTTCCCTCTTCTTCTTCTT
1 CTTTTTTT-TTCTTTTTCCTTTCCTT-CCTCTTCTTCTTCTT
*
54697531 CTTTTTTTTTCTTTTCTCCTTTCC-T--T-TTCTT-TCCTT
1 CTTTTTTTTTCTTTT-TCCTTTCCTTCCTCTTCTTCTTCTT
* *
54697567 CTTTTTCTTTCTTTTTCCTCTCCTTTCCTCTTCTTCTTCTT
1 CTTTTTTTTTCTTTTTCCTTTCC-TTCCTCTTCTTCTTCTT
* * * * *
54697608 -TTTTTCTCTTCTCCTTTCCTTTTCTTTC-CTTCTTTTTCTTT
1 CTTTTT-TTTTCT-TTTTCCTTTCCTTCCTCTTCTTCTTC-TT
54697649 CTTT
1 CTTT
54697653 CCTCTCATTC
Statistics
Matches: 98, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
35 7 0.07
36 18 0.18
37 6 0.06
38 1 0.01
39 1 0.01
40 25 0.26
41 25 0.26
42 15 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (40 bp):
CTTTTTTTTTCTTTTTCCTTTCCTTCCTCTTCTTCTTCTT
Found at i:54697600 original size:32 final size:32
Alignment explanation
Indices: 54697527--54697688 Score: 111
Period size: 32 Copynumber: 4.9 Consensus size: 32
54697517 CTCTTCTTCT
* * *
54697527 TCTTCTTTTTTTTTCTTTTCTCCTTTCCTTTTCTT
1 TCTTCTTTTTCTTTCTTTT-TCCTCTCC-TTTC-C
54697562 TCCTTCTTTTTCTTTCTTTTTCCTCTCCTTTCC
1 T-CTTCTTTTTCTTTCTTTTTCCTCTCCTTTCC
* *
54697595 TCTTCTTCTTCTTT-TTTTCTCTTCTCCTTTCC
1 TCTTCTTTTTCTTTCTTTT-TCCTCTCCTTTCC
* *
54697627 TTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT-CATTCC
1 TCTTCTTT--TTC--TTTC-TT-TTTCCTCTCCTTTCC
*
54697664 T-TTC--TTTCTTTC-TTTCCCTCTCCTT
1 TCTTCTTTTTCTTTCTTTTTCCTCTCCTT
54697689 CTCCCCCCCA
Statistics
Matches: 106, Mismatches: 11, Indels: 27
0.74 0.08 0.19
Matches are distributed among these distances:
27 7 0.07
28 3 0.03
30 4 0.04
31 4 0.04
32 33 0.31
33 1 0.01
34 8 0.08
35 8 0.08
36 23 0.22
37 6 0.06
38 7 0.07
39 2 0.02
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.67
Consensus pattern (32 bp):
TCTTCTTTTTCTTTCTTTTTCCTCTCCTTTCC
Found at i:54697626 original size:72 final size:73
Alignment explanation
Indices: 54697489--54697652 Score: 246
Period size: 72 Copynumber: 2.2 Consensus size: 73
54697479 ATAAAAATTA
* *
54697489 CCTT-TTTTTCTTT-TTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTTTCTTTTCTCCTT
1 CCTTCTTTTTCTTTCTTTTTCCTTCCTT--CTCCTCTTCTTCTTC-TTTTTTTTCTCTTCTCCTT
54697552 TCCTTTTCTTT
63 TCCTTTTCTTT
54697563 CCTTCTTTTTCTTTCTTTTTCCTCTCCTT-TCCTCTTCTTCTTC-TTTTTTTCTCTTCTCCTTTC
1 CCTTCTTTTTCTTTCTTTTTCCT-TCCTTCTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTC
54697626 CTTTTCTTT
65 CTTTTCTTT
54697635 CCTTCTTTTTCTTTCTTT
1 CCTTCTTTTTCTTTCTTT
54697653 CCTCTCATTC
Statistics
Matches: 85, Mismatches: 2, Indels: 8
0.89 0.02 0.08
Matches are distributed among these distances:
72 46 0.54
74 17 0.20
75 9 0.11
76 8 0.09
77 5 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (73 bp):
CCTTCTTTTTCTTTCTTTTTCCTTCCTTCTCCTCTTCTTCTTCTTTTTTTTCTCTTCTCCTTTCC
TTTTCTTT
Found at i:54697634 original size:10 final size:10
Alignment explanation
Indices: 54697549--54697680 Score: 68
Period size: 10 Copynumber: 13.6 Consensus size: 10
54697539 TTCTTTTCTC
54697549 CTTTCCTTTT
1 CTTTCCTTTT
54697559 CTTTCCTTCTT
1 CTTTCCTT-TT
54697570 -TTT-CTTTCT
1 CTTTCCTTT-T
* * *
54697579 TTTTCCTCTC
1 CTTTCCTTTT
*
54697589 CTTTCCTCTT
1 CTTTCCTTTT
*
54697599 CTTCTTCTTTT
1 CTT-TCCTTTT
*
54697610 -TTTCTCTTCTC
1 CTTTC-CTT-TT
54697621 CTTTCCTTTT
1 CTTTCCTTTT
54697631 CTTTCCTTCTT
1 CTTTCCTT-TT
54697642 -TTT-C-TTT
1 CTTTCCTTTT
*
54697649 CTTTCC-TCT
1 CTTTCCTTTT
*
54697658 CATTCC-TTT
1 CTTTCCTTTT
54697667 CTTT-C-TTT
1 CTTTCCTTTT
54697675 CTTTCC
1 CTTTCC
54697681 CTCTCCTTCT
Statistics
Matches: 97, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
7 2 0.02
8 13 0.13
9 20 0.21
10 42 0.43
11 16 0.16
12 4 0.04
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:54697663 original size:27 final size:27
Alignment explanation
Indices: 54697633--54697685 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
54697623 TTCCTTTTCT
*
54697633 TTCCTTCTTTTTCTTTCTTT-CCTCTCA
1 TTCCTT-TCTTTCTTTCTTTCCCTCTCA
54697660 TTCCTTTCTTTCTTTCTTTCCCTCTC
1 TTCCTTTCTTTCTTTCTTTCCCTCTC
54697686 CTTCTCCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (27 bp):
TTCCTTTCTTTCTTTCTTTCCCTCTCA
Found at i:54697800 original size:27 final size:27
Alignment explanation
Indices: 54697724--54697791 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
54697714 TATTATAAGC
*
54697724 TTGGTGCTGCCAATGAGTTTGGCACCA
1 TTGGTGCCGCCAATGAGTTTGGCACCA
54697751 TTGGTGCCGCCAATGAGTTTGGCACCA
1 TTGGTGCCGCCAATGAGTTTGGCACCA
54697778 TTGGTGCCGCCAAT
1 TTGGTGCCGCCAAT
54697792 CACCTTGGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (27 bp):
TTGGTGCCGCCAATGAGTTTGGCACCA
Found at i:54697891 original size:25 final size:27
Alignment explanation
Indices: 54697861--54697923 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
54697851 TTTTTTTGGT
54697861 ATATTTTGGTAAAT-AAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
54697886 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
54697914 ATATTTTGGT
1 ATATTTTGGT
54697924 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.40
27 6 0.17
28 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:54706257 original size:24 final size:24
Alignment explanation
Indices: 54706229--54706280 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54706219 TTAGTAGGTC
* *
54706229 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
54706253 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
54706277 AAAT
1 AAAT
54706281 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:54711234 original size:26 final size:24
Alignment explanation
Indices: 54711205--54711256 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
54711195 TCTTTACAAA
*
54711205 ATCAATGTAATTAAATCAATGATATT
1 ATCAATGT-ATTAAAT-AATAATATT
54711231 ATCAATGTATTAAATAATAATATT
1 ATCAATGTATTAAATAATAATATT
54711255 AT
1 AT
54711257 TTTCAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.40
25 7 0.28
26 8 0.32
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
ATCAATGTATTAAATAATAATATT
Found at i:54712483 original size:103 final size:101
Alignment explanation
Indices: 54712300--54712560 Score: 242
Period size: 103 Copynumber: 2.6 Consensus size: 101
54712290 GTTCTTTTTG
* * * * * * ** * *
54712300 TGCCATAGTCCAACTATGGTCTTACATGTG--CATTGCCATGGCCCTGCCATGGTCTTACATT-T
1 TGCCATAGCCCAAATATGGTCTTACATTTGAACACTACCATGGTCCAACCATGGTCTTACGTTCA
* * * *
54712362 GTAGTGCCATAACTCAGTTATGGTCTTATCATCAGAA
66 AT-GTGTCATAACCCAGTTATGGTCTTATCATCAAAA
* ** *
54712399 TGGCATAGCCCAGCTATGGTCTTACATATAT-ATATACTACCATGGTCCAACCATGGTCTTACGT
1 TGCCATAGCCCAAATATGGTCTTACAT-T-TGA-ACACTACCATGGTCCAACCATGGTCTTACGT
* * *
54712463 TCAATGTGTCATAACCCAGTTATGGTTTTTTCATTAAAA
63 TCAATGTGTCATAACCCAGTTATGGTCTTATCATCAAAA
* * *
54712502 TGCCATAGCCTAAATATGGTCTTACATTTGAACATTGCCATGGTCCAACCATGGTCTTA
1 TGCCATAGCCCAAATATGGTCTTACATTTGAACACTACCATGGTCCAACCATGGTCTTA
54712561 TCTGTCAATT
Statistics
Matches: 129, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
99 24 0.19
101 27 0.21
102 2 0.02
103 75 0.58
104 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (101 bp):
TGCCATAGCCCAAATATGGTCTTACATTTGAACACTACCATGGTCCAACCATGGTCTTACGTTCA
ATGTGTCATAACCCAGTTATGGTCTTATCATCAAAA
Found at i:54713678 original size:10 final size:10
Alignment explanation
Indices: 54713663--54713696 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
54713653 TGACACTCTG
54713663 TAAATATTTA
1 TAAATATTTA
54713673 TAAATATTTA
1 TAAATATTTA
**
54713683 TAGCTATTTA
1 TAAATATTTA
54713693 TAAA
1 TAAA
54713697 AATTGTCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
TAAATATTTA
Found at i:54714255 original size:21 final size:21
Alignment explanation
Indices: 54714217--54714256 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54714207 ATTTTTACCG
*
54714217 ATTTTTAATTTTGAAAATCGA
1 ATTTTTAATTTGGAAAATCGA
* *
54714238 ATTTTTAGTTTGGTAAATC
1 ATTTTTAATTTGGAAAATC
54714257 ATACTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
ATTTTTAATTTGGAAAATCGA
Found at i:54719309 original size:23 final size:24
Alignment explanation
Indices: 54719268--54719312 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54719258 AGTAAGATAC
54719268 TTTTTACTTTAGTTCCTTTAGTTA
1 TTTTTACTTTAGTTCCTTTAGTTA
*
54719292 TTTTTACTTTAG-TGCTTTAGT
1 TTTTTACTTTAGTTCCTTTAGT
54719313 AAAATTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTTTACTTTAGTTCCTTTAGTTA
Found at i:54723743 original size:24 final size:26
Alignment explanation
Indices: 54723707--54723754 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54723697 TGTTTATGCC
54723707 AATGCAG-TATTTTTC-AGAAAACGT
1 AATGCAGTTATTTTTCTAGAAAACGT
54723731 AATGCAGGTT-TTTTTCTAGAAAAC
1 AATGCA-GTTATTTTTCTAGAAAAC
54723755 ATCCTATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
25 7 0.33
26 8 0.38
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (26 bp):
AATGCAGTTATTTTTCTAGAAAACGT
Found at i:54723752 original size:26 final size:24
Alignment explanation
Indices: 54723707--54723754 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
54723697 TGTTTATGCC
54723707 AATGCAGTATTTTTCAGAAAACGT
1 AATGCAGTATTTTTCAGAAAACGT
*
54723731 AATGCAGGTTTTTTTCTAGAAAAC
1 AATGCA-GTATTTTTC-AGAAAAC
54723755 ATCCTATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 8 0.38
26 7 0.33
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (24 bp):
AATGCAGTATTTTTCAGAAAACGT
Found at i:54733660 original size:163 final size:157
Alignment explanation
Indices: 54733384--54733684 Score: 345
Period size: 163 Copynumber: 1.9 Consensus size: 157
54733374 GGACATCATA
54733384 ACCTAAACTATATTATTTTTCTCATCTCGGTACTTAAACTGTTTTTCGTCACAAGTGATACATAA
1 ACCTAAACTATATTATTTTTCTCATCTCGGTACTTAAACTGTTTTTCGTCACAAGTGATACATAA
** * * ** ** * *
54733449 ATTACTTTTTTTCTCAAGTTGATACCTCCGTTTGTCTAACTGTTAGTCAAATTGTTAAGTTTATT
66 ACAACTTTTTTCCCCAAGTTGATACCT-C-TTTGTCTAACCATTAGTCAAATTGAGAAGTCTATA
54733514 TTTAAAAAAGGCTTAACCTACGAATTGGT
129 TTTAAAAAAGGCTTAACCTACGAATTGGT
* * * * * *
54733543 ACCTAAATTATATTATTTATTTCTCATTTTGGTACTTAAACATTTATTTTGGTCACAAGTGGTAC
1 ACCTAAACTATATTA-TT-TTTCTCATCTCGGTACTTAAAC-TGT-TTTTCGTCACAAGTGATAC
*
54733608 ATAAACAACTTTTATTCCCCAAGTTGGTACCT-TTATAG-CTTAACCATTAGTCAAATTGAGAAG
62 ATAAACAACTTTT-TTCCCCAAGTTGATACCTCTT-T-GTC-TAACCATTAGTCAAATTGAGAAG
54733671 TCTATATTTAAAAA
123 TCTATATTTAAAAA
54733685 GATATTACTT
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
159 14 0.12
160 2 0.02
161 22 0.19
162 4 0.03
163 60 0.51
164 15 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (157 bp):
ACCTAAACTATATTATTTTTCTCATCTCGGTACTTAAACTGTTTTTCGTCACAAGTGATACATAA
ACAACTTTTTTCCCCAAGTTGATACCTCTTTGTCTAACCATTAGTCAAATTGAGAAGTCTATATT
TAAAAAAGGCTTAACCTACGAATTGGT
Found at i:54746815 original size:18 final size:18
Alignment explanation
Indices: 54746781--54746815 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54746771 ACATTTGTAA
* *
54746781 TATATATTATTTTATTTT
1 TATATATTATGTAATTTT
54746799 TATATATTATGTAATTT
1 TATATATTATGTAATTT
54746816 ACTTTACTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:54747295 original size:24 final size:24
Alignment explanation
Indices: 54747268--54747317 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
54747258 AGTTAAAGTC
* *
54747268 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
54747292 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
54747316 AA
1 AA
54747318 TTCTTCTAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54752316 original size:24 final size:24
Alignment explanation
Indices: 54752289--54752345 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
54752279 AAACCTAATT
54752289 CTAATCAAA-GTCAAATATATTATG
1 CTAAT-AAATGTCAAATATATTATG
* *
54752313 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATG
*
54752337 CTCATAAAT
1 CTAATAAAT
54752346 ACTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:54752351 original size:24 final size:24
Alignment explanation
Indices: 54752301--54752352 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54752291 AATCAAAGTC
* **
54752301 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
54752325 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
54752349 AAAT
1 AAAT
54752353 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:54760837 original size:10 final size:11
Alignment explanation
Indices: 54760775--54760836 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 11
54760765 CAAAAAAATT
54760775 AAGAAAAAAAA
1 AAGAAAAAAAA
54760786 AAGGAAACAGGAAAA
1 AA-GAAA-A--AAAA
54760801 ACA-AAACAACAAA
1 A-AGAAA-AA-AAA
54760814 AAGAAAAAAAA
1 AAGAAAAAAAA
54760825 AAGAAAAAAAA
1 AAGAAAAAAAA
54760836 A
1 A
54760837 GGAACATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
11 17 0.39
12 8 0.18
13 8 0.18
14 5 0.11
15 5 0.11
16 1 0.02
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:54765183 original size:25 final size:25
Alignment explanation
Indices: 54765124--54765211 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 25
54765114 TAAGAGTTGA
*
54765124 AATCGGGAAG-TTC-AAGCGAGCCAAT
1 AATCGGGAAGCTTCGAA--GAGCCATT
*
54765149 -ATCAGGAAGCTTCGAAGAGCCATT
1 AATCGGGAAGCTTCGAAGAGCCATT
* *
54765173 AATCGGGAAGCTTATGAAAGAGCCTTT
1 AATCGGGAAGCTT-CG-AAGAGCCATT
54765200 AATCGGGAAGCT
1 AATCGGGAAGCT
54765212 CTAAAGAGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 15 0.28
25 14 0.26
26 3 0.06
27 21 0.40
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
AATCGGGAAGCTTCGAAGAGCCATT
Found at i:54765223 original size:25 final size:27
Alignment explanation
Indices: 54765163--54765223 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
54765153 GGAAGCTTCG
*
54765163 AAGAGCCATTAATCGGGAAGCTTATGA
1 AAGAGCCTTTAATCGGGAAGCTTATGA
*
54765190 AAGAGCCTTTAATCGGGAAGC-TCT-A
1 AAGAGCCTTTAATCGGGAAGCTTATGA
54765215 AAGAGCCTT
1 AAGAGCCTT
54765224 ATATCGGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 10 0.31
26 2 0.06
27 20 0.62
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (27 bp):
AAGAGCCTTTAATCGGGAAGCTTATGA
Found at i:54765229 original size:25 final size:27
Alignment explanation
Indices: 54765147--54765230 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 27
54765137 AAGCGAGCCA
* *
54765147 ATATCAGGAAGCTT-CG-AAGAGCCATT
1 ATATCGGGAAGCTTATGAAAGAGCC-TT
54765173 A-ATCGGGAAGCTTATGAAAGAGCCTT
1 ATATCGGGAAGCTTATGAAAGAGCCTT
*
54765199 -TAATCGGGAAGC-TCT-AAAGAGCCTT
1 AT-ATCGGGAAGCTTATGAAAGAGCCTT
54765224 ATATCGG
1 ATATCGG
54765231 CACACTCATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
25 26 0.52
26 7 0.14
27 17 0.34
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (27 bp):
ATATCGGGAAGCTTATGAAAGAGCCTT
Found at i:54788230 original size:23 final size:22
Alignment explanation
Indices: 54788198--54788245 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
54788188 TTAGGATTTG
*
54788198 TTTTTATTATTTTATTTTTATCT
1 TTTTTATTATTTTATTATT-TCT
*
54788221 TTTTTGTTATTTTATTATTTCT
1 TTTTTATTATTTTATTATTTCT
54788243 TTT
1 TTT
54788246 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTATTTTATTATTTCT
Found at i:54788328 original size:21 final size:22
Alignment explanation
Indices: 54788295--54788337 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
54788285 TCCCCTTTTA
*
54788295 CACGTTCATTTTTGTTTTTCCC
1 CACGTTCATTTTTCTTTTTCCC
54788317 CACGTT-ATTTTTCTTTTTCCC
1 CACGTTCATTTTTCTTTTTCCC
54788338 ATAATATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.09, C:0.28, G:0.07, T:0.56
Consensus pattern (22 bp):
CACGTTCATTTTTCTTTTTCCC
Found at i:54790144 original size:11 final size:10
Alignment explanation
Indices: 54790120--54790144 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54790110 CTTAATATCT
54790120 AAAAATTATG
1 AAAAATTATG
54790130 AAAAATTATG
1 AAAAATTATG
54790140 AAAAA
1 AAAAA
54790145 GACATTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAAATTATG
Found at i:54794593 original size:42 final size:42
Alignment explanation
Indices: 54794528--54794644 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
54794518 AGTTCATACA
** *
54794528 ATGCCACCATCCCAGAC-GTGGTCTTACATATAATCAAATATC
1 ATGCCACTGTCCCAGACAG-GGTCTTACACATAATCAAATATC
* * *
54794570 ATGCCACTGTCCCAGACAGGGTCTTACACGA-AGTCATATATG
1 ATGCCACTGTCCCAGACAGGGTCTTACAC-ATAATCAAATATC
* * *
54794612 ATGCCAATGTCCTAGACATGGTCTTACACATAA
1 ATGCCACTGTCCCAGACAGGGTCTTACACATAA
54794645 ATCTCAAGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.02
42 59 0.95
43 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACATAATCAAATATC
Found at i:54794678 original size:44 final size:43
Alignment explanation
Indices: 54794528--54794734 Score: 192
Period size: 44 Copynumber: 4.8 Consensus size: 43
54794518 AGTTCATACA
* * * * *
54794528 ATGCCACCATCCCAGACGTGGTCTTACATATAATC-AAATATC-
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCTCAA-ATCG
* * *
54794570 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAGTCAT-ATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAAATC-TCAAATCG
* * * *
54794612 ATGCCAATGTCCTAGACATGGTCTTACACATAAATCTCAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACA-AAATCTCAAATCG
*
54794656 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAATCTCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACA-CAAAATCTCAAATCG
*
54794700 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATC
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATC
54794735 ACATACTGGA
Statistics
Matches: 133, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 51 0.38
43 14 0.11
44 66 0.50
45 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCTCAAATCG
Found at i:54800254 original size:21 final size:23
Alignment explanation
Indices: 54800228--54800274 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
54800218 TCTTGGATGT
*
54800228 GGGAAA-TTAGGGATTTTAG-GG
1 GGGAAAGTTAGGGATTTCAGAGG
*
54800249 GGGAAAGTTGGGGATTTCAGAGG
1 GGGAAAGTTAGGGATTTCAGAGG
54800272 GGG
1 GGG
54800275 GGGGAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.26, C:0.02, G:0.49, T:0.23
Consensus pattern (23 bp):
GGGAAAGTTAGGGATTTCAGAGG
Found at i:54800856 original size:107 final size:106
Alignment explanation
Indices: 54800603--54800916 Score: 517
Period size: 106 Copynumber: 3.0 Consensus size: 106
54800593 ATATATTTTT
*
54800603 ATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAAGTTTTTA--TT-TTTTTTATAAATTGA
1 ATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
* *
54800665 TTTATTTTTTGCGACGTTTTTACAAAAAAACGCCGCTATTTC
66 TTTATTTTTTGCGGCGTTTTTA-TAAAAAACGCCGCTATTTC
*
54800707 ATTTTGAACAAAAGGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
1 ATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
*
54800772 TTTATTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTTC
66 TTTATTTTTTGCGGCGTTTTTATAAAAAACGCCGCTATTTC
* * *
54800813 ATTTTGAACAAAATGACACCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
1 ATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
*
54800878 TTTATTTTTTGCTGCGTTTTTATAAAAAACGCCGCTATT
66 TTTATTTTTTGCGGCGTTTTTATAAAAAACGCCGCTATT
54800917 GCTTACCTTT
Statistics
Matches: 197, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
104 43 0.22
106 119 0.60
107 35 0.18
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (106 bp):
ATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAATTGA
TTTATTTTTTGCGGCGTTTTTATAAAAAACGCCGCTATTTC
Found at i:54800982 original size:250 final size:249
Alignment explanation
Indices: 54800703--54801380 Score: 895
Period size: 251 Copynumber: 2.7 Consensus size: 249
54800693 AACGCCGCTA
*
54800703 TTTCATTTTGAACAAAAGGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTATTTTTTATAAA
1 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCT-AAAATTTTTTATTTTATTTTTTATAAA
54800768 TTGATTTATTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTTCATTTTGAACAAAATGACACC
65 TTGATTTATTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTTCATTTTGAACAAAATGACACC
*
54800833 GTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCTGCGTTTT
130 GTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCAGCGTTTT
54800898 TATAAAAAACGCCGCTATTGCTTACCTTTAGCGGCGTTTTTTAT-TGCAAAATTTT
195 TATAAAAAACGCCGCTATTGCTTACCTTTAGCGGC-TTTTTTATATGCAAAATTTT
*
54800953 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAATTTTTTTATTTTGTTTTTTATAAA
1 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAA-TTTTTTATTTTATTTTTTATAAA
* *
54801018 TTGATTTATTTTTTGCAGCGTTTTTATAAAAAAACG-CGACTATTTCATTTTGAACAAAATGACA
65 TTGATTTATTTTTTGCGGCATTTTTAT-AAAAAACGCCG-CTATTTCATTTTGAACAAAATGACA
*
54801082 CCATTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCAGCGTT
128 CCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCAGCGTT
*
54801147 TTTATAAAAACCGCCGCTATTGCTTACCTTTAGCGGCTTTTTTATAAAAAACGCTGCAAAATTTT
193 TTTATAAAAAACGCCGCTATTGCTTACCTTTAGCGGCTTTTTTAT-----A---TGCAAAATTTT
* **
54801212 TTTCATTTTGAACAAAACGACGCCGTTATGCTA---T----TTTGGT-TTTTA-----T-T-AAT
1 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAATTTTTTATTTTATTTTTTATAAAT
* * * *
54801262 TGATTTATTATTTGCGGCATTTTTATGAAAAATGCCGCAAAATATTATTTCATTTTGAACAAAGT
66 TGATTTATTTTTTGCGGCATTTTTATAAAAAACGCCGC-------TATTTCATTTTGAACAAAAT
* * * *
54801327 GACGCCGTTTTGCTATGCTAAAATTTTTTTATTTTGTTTTTTATAATTTGATTT
124 GACACCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTT
54801381 TTTATAAAAT
Statistics
Matches: 386, Mismatches: 22, Indels: 41
0.86 0.05 0.09
Matches are distributed among these distances:
242 7 0.02
243 28 0.07
244 1 0.00
245 1 0.00
249 72 0.19
250 97 0.25
251 136 0.35
256 1 0.00
259 43 0.11
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (249 bp):
TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAATTTTTTATTTTATTTTTTATAAAT
TGATTTATTTTTTGCGGCATTTTTATAAAAAACGCCGCTATTTCATTTTGAACAAAATGACACCG
TTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAATTGATTTATTTTTTGCAGCGTTTTT
ATAAAAAACGCCGCTATTGCTTACCTTTAGCGGCTTTTTTATATGCAAAATTTT
Found at i:54801074 original size:107 final size:107
Alignment explanation
Indices: 54800953--54801156 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 107
54800943 GCAAAATTTT
* * * * *
54800953 TTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAAATTTTTTTATTTTGTTTTTTATAAA
1 TTTCATTTTGAACAAAACGACACCATTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
54801018 TTGATTTATTTTTTGCAGCGTTTTTATAAAAAAACGCGACTA
66 TTGATTTATTTTTTGCAGCGTTTTTATAAAAAAACGCGACTA
*
54801060 TTTCATTTTGAACAAAATGACACCATTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
1 TTTCATTTTGAACAAAACGACACCATTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
54801125 TTGATTTATTTTTTGCAGCGTTTTTATAAAAA
66 TTGATTTATTTTTTGCAGCGTTTTTATAAAAA
54801157 CCGCCGCTAT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 91 1.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (107 bp):
TTTCATTTTGAACAAAACGACACCATTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
TTGATTTATTTTTTGCAGCGTTTTTATAAAAAAACGCGACTA
Found at i:54801376 original size:14 final size:15
Alignment explanation
Indices: 54801349--54801387 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
54801339 CTATGCTAAA
*
54801349 ATTTTTT-TATTTTG
1 ATTTTTTATAATTTG
54801363 -TTTTTTATAATTTG
1 ATTTTTTATAATTTG
54801377 ATTTTTTATAA
1 ATTTTTTATAA
54801388 AATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
15 10 0.45
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
ATTTTTTATAATTTG
Done.