Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_pilon, whole genome shotgun sequence
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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 21
Found at i:1578051 original size:3 final size:3
Alignment explanation
Indices: 1578043--1578098 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1578033 CGTCACTCCC
1578043 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1578091 ATT ATT AT
1 ATT ATT AT
1578099 ACATCACCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1580578 original size:79 final size:79
Alignment explanation
Indices: 1580447--1580593 Score: 285
Period size: 79 Copynumber: 1.9 Consensus size: 79
1580437 CAGAGAAAAC
*
1580447 TCCTAACAAAAATATGTTATGCATAATCAAAAACATAATAAGTAACTAAAACAAGGAACATGAAG
1 TCCTAACAAAAAAATGTTATGCATAATCAAAAACATAATAAGTAACTAAAACAAGGAACATGAAG
1580512 TTGTCGATGCACTT
66 TTGTCGATGCACTT
1580526 TCCTAACAAAAAAATGTTATGCATAATCAAAAACATAATAAGTAACTAAAACAAGGAACATGAAG
1 TCCTAACAAAAAAATGTTATGCATAATCAAAAACATAATAAGTAACTAAAACAAGGAACATGAAG
1580591 TTG
66 TTG
1580594 CCATGGTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (79 bp):
TCCTAACAAAAAAATGTTATGCATAATCAAAAACATAATAAGTAACTAAAACAAGGAACATGAAG
TTGTCGATGCACTT
Found at i:1582722 original size:15 final size:15
Alignment explanation
Indices: 1582702--1582737 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1582692 TATTATCATT
1582702 ATCATCGACATGATC
1 ATCATCGACATGATC
*
1582717 ATCATCGTCATGATC
1 ATCATCGACATGATC
1582732 ATCATC
1 ATCATC
1582738 ATCCATAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (15 bp):
ATCATCGACATGATC
Found at i:1586305 original size:15 final size:15
Alignment explanation
Indices: 1586285--1586442 Score: 210
Period size: 15 Copynumber: 10.2 Consensus size: 15
1586275 AAGGTTATTA
1586285 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
1586300 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
*
1586315 ATTATAAAATAATTT
1 ATTTTAAAATAATTT
1586330 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
*
1586345 ATTATAAAATAATTT
1 ATTTTAAAATAATTT
*
1586360 ATTATAAAATAATTT
1 ATTTTAAAATAATTT
*
1586375 ATTTTAAAATAAATT
1 ATTTTAAAATAATTT
*
1586390 ATTATAAATATGGATTGATTT
1 ATTTTAAA-AT--A---ATTT
1586411 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
1586426 ATTTT-AAATAATTT
1 ATTTTAAAATAATTT
1586440 ATT
1 ATT
1586443 AGTATGGATT
Statistics
Matches: 129, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
14 12 0.09
15 101 0.78
16 2 0.02
18 2 0.02
20 2 0.02
21 10 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTTAAAATAATTT
Found at i:1586461 original size:22 final size:22
Alignment explanation
Indices: 1586445--1586487 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1586435 AATTTATTAG
1586445 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1586467 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1586488 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1586463 original size:32 final size:32
Alignment explanation
Indices: 1586422--1587119 Score: 279
Period size: 32 Copynumber: 23.4 Consensus size: 32
1586412 TTTTAAAATA
1586422 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1586454 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1586476 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1586508 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1586530 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1586562 ATTTATTTTAAATAATATATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
** **
1586594 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * **
1586623 ATTGTAGTTGTATGGATTGATTTATTTTAAAAT--ATTG
1 ATT-TA-TT-T-T-AAATAATTTA--TTAGTATGGATTG
* * *
1586660 ATTGA-TTT--ATTATTGTAGTT-GTATGAATTG
1 ATTTATTTTAAATAATT-TA-TTAGTATGGATTG
* *
1586690 ATTTATTTTAAATAATTTATTACTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
1586722 ATTTA-TTT---TAA---A--A-TATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1586744 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1586776 ATTTATTTTAAATAATTTATTTGTATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* ** **
1586808 ATTTATTTGAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTG
* * * * * *
1586837 ATTGTAGTTGTATGGATTGATTTATT--T-T-AAATA
1 ATT-TA-TT-T-T-AAATAATTTATTAGTATGGATTG
* * * *
1586870 ATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTG
1 ATTTATT--T-T-AAATAATTTA--TT--AGTATGGATTG
*
1586910 ATTTA--TT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
1586936 ATTTATTTTAAATAATTTATTAGTAT-GAGTTG
1 ATTTATTTTAAATAATTTATTAGTATGGA-TTG
1586968 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
1586990 ACTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
1587022 ATTTATTTT--A-AA---A-TA-CA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1587044 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1587076 ATTTATTTTAAATAATTTATTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1587108 ATTTATTTTAAA
1 ATTTATTTTAAA
1587120 ATATGGATTG
Statistics
Matches: 518, Mismatches: 53, Indels: 190
0.68 0.07 0.25
Matches are distributed among these distances:
22 65 0.13
23 14 0.03
24 5 0.01
25 11 0.02
26 25 0.05
28 15 0.03
29 25 0.05
30 34 0.07
31 31 0.06
32 247 0.48
33 11 0.02
34 13 0.03
35 1 0.00
36 7 0.01
37 3 0.01
38 3 0.01
39 1 0.00
40 7 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:1586486 original size:54 final size:54
Alignment explanation
Indices: 1586422--1586916 Score: 444
Period size: 54 Copynumber: 9.1 Consensus size: 54
1586412 TTTTAAAATA
1586422 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1586476 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1586530 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATAT--ATTTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AATATGGA-TTG
** * ** * * * ***
1586585 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* * * *** *
1586642 ATTTATTTT-AA-AA--TATT-G-ATTGATTTA-TTATTGTAGTTGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
* * *
1586690 ATTTATTTTAAATAATTTATTACTATGAATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1586744 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * ***
1586794 ATTTGTATGGATTAATTTATTTGAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA-TT---AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
1586856 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1586910 ATTTATT
1 ATTTATT
1586917 ATTGTAGTTG
Statistics
Matches: 354, Mismatches: 56, Indels: 62
0.75 0.12 0.13
Matches are distributed among these distances:
48 23 0.06
49 3 0.01
50 20 0.06
51 5 0.01
52 11 0.03
53 7 0.02
54 194 0.55
55 25 0.07
56 21 0.06
57 8 0.02
58 16 0.05
59 2 0.01
61 2 0.01
62 17 0.05
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1586524 original size:22 final size:22
Alignment explanation
Indices: 1586499--1586541 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1586489 AATTTATTAG
1586499 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1586521 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1586542 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1586613 original size:22 final size:22
Alignment explanation
Indices: 1586585--1586670 Score: 100
Period size: 22 Copynumber: 3.7 Consensus size: 22
1586575 AATATATTTG
1586585 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
1586607 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
1586633 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1586655 TATTGATTGATTTATT
1 TATGGATTGATTTATT
1586671 ATTGTAGTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
22 29 0.55
23 3 0.06
24 4 0.08
25 3 0.06
26 14 0.26
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1586636 original size:48 final size:48
Alignment explanation
Indices: 1586582--1586701 Score: 222
Period size: 48 Copynumber: 2.5 Consensus size: 48
1586572 AATAATATAT
1586582 TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAG
1 TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAG
*
1586630 TTGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTGTAG
1 TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAG
*
1586678 TTGTATGAATTGATTTATTTTAAA
1 TTGTATGGATTGATTTATTTTAAA
1586702 TAATTTATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (48 bp):
TTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAG
Found at i:1586722 original size:80 final size:80
Alignment explanation
Indices: 1586632--1586996 Score: 536
Period size: 80 Copynumber: 4.5 Consensus size: 80
1586622 TATTGTAGTT
* *
1586632 GTATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1586697 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* * * *
1586712 CTATGAATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTG
*
1586776 ATTTATTTTAAATAATTTATTT
59 ATTTATTTTAAATAATTTATTA
* *
1586798 GTATGGATTAATTTATTTGAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1586863 TTAAATAATTTATTA
66 TTAAATAATTTATTA
*
1586878 GTATGGATTGATTTATTTTGAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1586943 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* *
1586958 GTAT-GAGTTGATTTATTTTAAAATATAGATTGACTTATT
1 GTATGGA-TTGATTTATTTTAAAATATGGATTGATTTATT
1586997 TTAAATAATT
Statistics
Matches: 256, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
79 2 0.01
80 177 0.69
81 2 0.01
82 4 0.02
84 4 0.02
85 2 0.01
86 65 0.25
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (80 bp):
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
TTAAATAATTTATTA
Found at i:1586765 original size:22 final size:22
Alignment explanation
Indices: 1586713--1586755 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1586703 AATTTATTAC
* *
1586713 TATGAATTGATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
1586735 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
1586756 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:1586804 original size:246 final size:242
Alignment explanation
Indices: 1586521--1587230 Score: 870
Period size: 246 Copynumber: 3.0 Consensus size: 242
1586511 TATTTTAAAA
1586521 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATATATTTGT
1 TATGGATTGATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAATAATATATTTGT
1586586 ATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
65 ATGGATTGATTTATTTT-AAATATGGATTGATTTATTATTGTA-TTGTATGGATTGATTTATTTT
* *
1586651 AAAATATTGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTACTAT
128 AAAATATGGATTGATTTATTATTGTAGTTGTATG-ATTGATTTATTTTAAATAATTTATTAGTAT
*
1586716 GAATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATTAG
192 GAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
1586767 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTAATTTA-TTTGAA-AATATGGA-TT
1 TATGGATTGATTTATTTTAAATAATTTA-TTGTATGGATTGATTTATTTTAAATAATAT--ATTT
** * * *
1586829 G-ATTTATT-ATTGTA-GTT--GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
63 GTATGGATTGATT-TATTTTAAATATGGATTGATTTA--TT--AT--TGTATT-GTATGGATTGA
*
1586889 TTTATTTTGAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
120 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTAT-GATTGATTTATTTTAAATAATTT
* * *
1586954 ATTAGTATGAGTTGATTTATTTTAAAATATAGATTGACTTATTTTAAATAATTTATTAG
184 ATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* * *
1587013 TATGGATTGATTTATTTT-AA-AA--TA---CA--GATTGATTTATTTTAAATAATTTATTAGTA
1 TATGGATTGATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTAAATAATATATTTGTA
1587069 TGGATTGATTTATTTT-AA-AT--A---ATTTA-T-TTGTA---TA--GATTGATTTATTTTAAA
66 TGGATTGATTTATTTTAAATATGGATTGATTTATTATTGTATTGTATGGATTGATTTATTTTAAA
* * *
1587120 ATATGGATTGATTTATTATTGTAGTTGTAAGATTGATTTATTTTAAATAATTTATGAGTATGGAT
131 ATATGGATTGATTTATTATTGTAGTTGTATGATTGATTTATTTTAAATAATTTATTAGTATGAAT
*
1587185 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTGATTA
196 TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1587231 TTGTAGTTGT
Statistics
Matches: 413, Mismatches: 32, Indels: 65
0.81 0.06 0.13
Matches are distributed among these distances:
219 75 0.18
220 45 0.11
222 2 0.00
226 3 0.01
228 1 0.00
231 1 0.00
234 5 0.01
236 10 0.02
237 8 0.02
238 12 0.03
239 7 0.02
240 14 0.03
242 4 0.01
243 5 0.01
244 16 0.04
245 12 0.03
246 190 0.46
247 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (242 bp):
TATGGATTGATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTAAATAATATATTTGTA
TGGATTGATTTATTTTAAATATGGATTGATTTATTATTGTATTGTATGGATTGATTTATTTTAAA
ATATGGATTGATTTATTATTGTAGTTGTATGATTGATTTATTTTAAATAATTTATTAGTATGAAT
TGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1586809 original size:18 final size:18
Alignment explanation
Indices: 1586735--1586816 Score: 72
Period size: 18 Copynumber: 5.0 Consensus size: 18
1586725 TATTTTAAAA
1586735 TATGGATTAATTTATTT-
1 TATGGATTAATTTATTTG
* *
1586752 TA---AATAATTTATTAG
1 TATGGATTAATTTATTTG
*
1586767 TATGGATTGATTTATTT-
1 TATGGATTAATTTATTTG
*
1586784 TA---AATAATTTATTTG
1 TATGGATTAATTTATTTG
1586799 TATGGATTAATTTATTTG
1 TATGGATTAATTTATTTG
1586817 AAAATATGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
14 20 0.41
15 4 0.08
17 4 0.08
18 21 0.43
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TATGGATTAATTTATTTG
Found at i:1586893 original size:18 final size:18
Alignment explanation
Indices: 1586870--1586917 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1586860 ATTTTAAATA
*
1586870 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1586888 ATTTATTTTGAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1586910 ATTTATTA
1 ATTTATTA
1586918 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1586904 original size:22 final size:22
Alignment explanation
Indices: 1586879--1586949 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
1586869 AATTTATTAG
1586879 TATGGATTGATTTATTTTGAAA
1 TATGGATTGATTTATTTTGAAA
**
1586901 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATT-TTG-A--AA
1586927 TATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTGAAA
1586948 TA
1 TA
1586950 ATTTATTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.05
22 16 0.39
23 4 0.10
24 1 0.02
25 2 0.05
26 16 0.39
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTGAAA
Found at i:1586938 original size:214 final size:214
Alignment explanation
Indices: 1586422--1587166 Score: 868
Period size: 214 Copynumber: 3.4 Consensus size: 214
1586412 TTTTAAAATA
1586422 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
1586487 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
62 AT--TGTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATTA
*
1586552 GTATGGATTGATTTATTTTAAATAATATATTTGTATGGATTGATTTATTTTAAAATATGGATTGA
125 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGA
1586617 TTTATTATTGTAGTTGTATGGATTG
190 TTTATTATTGTAGTTGTATGGATTG
* ** * * *
1586642 ATTTATTTTAAA-ATATTGATT-G-ATTTATT-ATTGTAGTTGTATGAAT-T-GATTTATTTTAA
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTGATT-TA-TTTTA-AAATATGGATTGA-TTT--
* * *
1586701 ATAATT-TATTACTATGAATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATT
59 ATTATTGTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATT
* *
1586765 AGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTAATTTATTTGAAAATATGGATTG
124 AGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1586830 ATTTATTATTGTAGTTGTATGGATTG
189 ATTTATTATTGTAGTTGTATGGATTG
*
1586856 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTGAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
** * * * * ** * * *
1586921 TAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAGTATGAGTTGATTTATTTTA-AAATA
66 TA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATTAAT-TTATTTTAAATAATTTATTAGTA
* * * **
1586983 TAGATTGACTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACAGATTGATTT
128 TGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTT
*
1587048 ATTTTAAATAATTTA-TTAGTATGGATTG
193 A--TT--AT--TGTAGTT-GTATGGATTG
* *
1587076 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1587141 TAGTT-GTA-AGATTGATTTATTTTAAA
66 TA-TTAGTATGGATTGATTTATTTTAAA
1587167 TAATTTATGA
Statistics
Matches: 454, Mismatches: 46, Indels: 50
0.83 0.08 0.09
Matches are distributed among these distances:
213 9 0.02
214 252 0.56
215 23 0.05
216 14 0.03
217 8 0.02
218 14 0.03
219 27 0.06
220 106 0.23
221 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (214 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTTTAAATAATTTATTAGTATGG
ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
ATTGTAGTTGTATGGATTG
Found at i:1586990 original size:22 final size:22
Alignment explanation
Indices: 1586965--1587055 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
1586955 TTAGTATGAG
1586965 TTGATTTATTTTAAAATATAGA
1 TTGATTTATTTTAAAATATAGA
*
1586987 TTGACTTATTTTAAATAATTTATTAGTA
1 TTGATTTATTTT-AA-AA--TA-TAG-A
* *
1587015 TGGATTGATTTATTTTAAAATACAGA
1 TTGA-T---TTATTTTAAAATATAGA
1587041 TTGATTTATTTTAAA
1 TTGATTTATTTTAAA
1587056 TAATTTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
22 21 0.39
23 2 0.04
24 2 0.04
25 1 0.02
26 6 0.11
27 5 0.09
28 6 0.11
30 2 0.04
31 2 0.04
32 7 0.13
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (22 bp):
TTGATTTATTTTAAAATATAGA
Found at i:1586996 original size:54 final size:54
Alignment explanation
Indices: 1586931--1587230 Score: 326
Period size: 54 Copynumber: 5.5 Consensus size: 54
1586921 TAGTTGTATG
*
1586931 GATTGATTTATTTTAAATAATTTATTAGTAT-GAGTTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGA-TTGATTTATTTTAAAATACA
*
1586985 GATTGACTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACA
1587039 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAAT--A
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACA
* * * * * * ***
1587090 -ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA-A
1 GATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATACA
* **
1587150 GATTGATTTATTTTAAATAATTTATGAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACA
*
1587204 GATTGATTTATTTTAAATAATTGATTA
1 GATTGATTTATTTTAAATAATTTATTA
1587231 TTGTAGTTGT
Statistics
Matches: 206, Mismatches: 25, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
49 3 0.01
50 14 0.07
51 1 0.00
52 2 0.01
53 6 0.03
54 136 0.66
55 5 0.02
56 3 0.01
57 16 0.08
59 2 0.01
60 1 0.00
61 14 0.07
62 3 0.01
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATACA
Found at i:1587111 original size:18 final size:16
Alignment explanation
Indices: 1587038--1587118 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 16
1587028 TTTAAAATAC
1587038 AGATTGATTTATTTTA
1 AGATTGATTTATTTTA
* *
1587054 A-A-TAATTTATTAGTA
1 AGATTGATTTATT-TTA
*
1587069 TGGATTGATTTATTTTA
1 -AGATTGATTTATTTTA
*
1587086 A-A-TAATTTATTTGTA
1 AGATTGATTTATTT-TA
1587101 TAGATTGATTTATTTTA
1 -AGATTGATTTATTTTA
1587118 A
1 A
1587119 AATATGGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
14 17 0.35
15 6 0.12
16 3 0.06
17 6 0.12
18 17 0.35
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (16 bp):
AGATTGATTTATTTTA
Found at i:1587226 original size:18 final size:20
Alignment explanation
Indices: 1587182--1587229 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
1587172 TATGAGTATG
1587182 GATTGATTTATTTTAAAATA
1 GATTGATTTATTTTAAAATA
1587202 TGGATTGATTTATTTT-AAATA
1 --GATTGATTTATTTTAAAATA
1587223 -ATTGATT
1 GATTGATT
1587230 ATTGTAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.27
21 5 0.19
22 14 0.54
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (20 bp):
GATTGATTTATTTTAAAATA
Found at i:1587229 original size:22 final size:22
Alignment explanation
Indices: 1587178--1587220 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1587168 AATTTATGAG
1587178 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1587200 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1587221 TAATTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1587282 original size:31 final size:31
Alignment explanation
Indices: 1587245--1587303 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1587235 AGTTGTATGG
* * *
1587245 ATTATTTAAATTTTAGTATTGTAAAACTAAA
1 ATTATTTAAATCTAAGTATTGCAAAACTAAA
1587276 ATTATTTAAATCTAAGTATTGCAAAACT
1 ATTATTTAAATCTAAGTATTGCAAAACT
1587304 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTAAGTATTGCAAAACTAAA
Found at i:1594905 original size:20 final size:20
Alignment explanation
Indices: 1594880--1594951 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
1594870 CTGTTGGGTT
1594880 GTATCGATACTCTACCCTTG
1 GTATCGATACTCTACCCTTG
*
1594900 GTATCGATAC-C--CCTGTTGGG
1 GTATCGATACTCTACC-CTT--G
1594920 TTGTATCGATACTCTACCCTTG
1 --GTATCGATACTCTACCCTTG
1594942 GTATCGATAC
1 GTATCGATAC
1594952 CCCATGAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 1 0.02
20 21 0.50
22 11 0.26
23 1 0.02
24 2 0.05
25 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATACTCTACCCTTG
Found at i:1594910 original size:42 final size:42
Alignment explanation
Indices: 1594863--1594954 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
1594853 CTTAAGTGTT
1594863 GATACCCCTGTTGGGTTGTATCGATACTCTACCCTTGGTATC
1 GATACCCCTGTTGGGTTGTATCGATACTCTACCCTTGGTATC
1594905 GATACCCCTGTTGGGTTGTATCGATACTCTACCCTTGGTATC
1 GATACCCCTGTTGGGTTGTATCGATACTCTACCCTTGGTATC
1594947 GATACCCC
1 GATACCCC
1594955 ATGAATATCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (42 bp):
GATACCCCTGTTGGGTTGTATCGATACTCTACCCTTGGTATC
Found at i:1594928 original size:22 final size:22
Alignment explanation
Indices: 1594863--1594931 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
1594853 CTTAAGTGTT
1594863 GATACCCCTGTTGGGTTGTATC
1 GATACCCCTGTTGGGTTGTATC
*
1594885 GATACTCTACC-CTT--G--GTATC
1 GATAC-C--CCTGTTGGGTTGTATC
1594905 GATACCCCTGTTGGGTTGTATC
1 GATACCCCTGTTGGGTTGTATC
1594927 GATAC
1 GATAC
1594932 TCTACCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 1 0.03
20 11 0.30
22 16 0.43
23 1 0.03
24 2 0.05
25 2 0.05
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (22 bp):
GATACCCCTGTTGGGTTGTATC
Found at i:1594965 original size:17 final size:18
Alignment explanation
Indices: 1594943--1594989 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
1594933 CTACCCTTGG
*
1594943 TATCGATACCCC-ATGAA
1 TATCGATACCCCTACGAA
1594960 TATCGATACCACCCTACGAA
1 TATCGATA-C-CCCTACGAA
1594980 TATCGATACC
1 TATCGATACC
1594990 TCACTTACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 4 0.15
20 12 0.46
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23
Consensus pattern (18 bp):
TATCGATACCCCTACGAA
Found at i:1596675 original size:26 final size:26
Alignment explanation
Indices: 1596617--1596681 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
1596607 TCGCTGAGCT
*
1596617 CGACTCAACTCGAAAACTCTGAAATG
1 CGACTCGACTCGAAAACTCTGAAATG
*
1596643 CGACTCGAGTCGAAAACTCTGAAATG
1 CGACTCGACTCGAAAACTCTGAAATG
1596669 C-AGCTCGACTCGA
1 CGA-CTCGACTCGA
1596682 CTTGAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (26 bp):
CGACTCGACTCGAAAACTCTGAAATG
Found at i:1596678 original size:31 final size:29
Alignment explanation
Indices: 1596613--1596692 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 29
1596603 AGTATCGCTG
*
1596613 AGCTCGACTCAACTCGAAAACTCTGAAAT
1 AGCTCGACTCGACTCGAAAACTCTGAAAT
*
1596642 -G--CGACTCGAGTCGAAAACTCTGAAAT
1 AGCTCGACTCGACTCGAAAACTCTGAAAT
*
1596668 GCAGCTCGACTCGACTTGAAAACTC
1 --AGCTCGACTCGACTCGAAAACTC
1596693 GCGAGATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 23 0.55
28 1 0.02
29 1 0.02
31 17 0.40
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.20
Consensus pattern (29 bp):
AGCTCGACTCGACTCGAAAACTCTGAAAT
Found at i:1597310 original size:16 final size:16
Alignment explanation
Indices: 1597286--1597320 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1597276 GACAATTAAA
* *
1597286 TTTATTTTAATTTATT
1 TTTAATTTAATATATT
1597302 TTTAATTTAATATATT
1 TTTAATTTAATATATT
1597318 TTT
1 TTT
1597321 CTCACCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:1597656 original size:23 final size:23
Alignment explanation
Indices: 1597628--1597687 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
1597618 TTACCCTTTA
1597628 TTTTAAATAATTTACCTTTAAAT
1 TTTTAAATAATTTACCTTTAAAT
1597651 TTTTAAATAATTTACCTTTAAAT
1 TTTTAAATAATTTACCTTTAAAT
1597674 TTTTAAATAATTTA
1 TTTTAAATAATTTA
1597688 TAGTTATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAATAATTTACCTTTAAAT
Found at i:1602776 original size:31 final size:31
Alignment explanation
Indices: 1602739--1602801 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1602729 GTTGACGTCG
1602739 GGCACCTAAAAATG-TAACGAAGAAAACGTTA
1 GGCACCT-AAAATGATAACGAAGAAAACGTTA
* *
1602770 GGCACCTAAAATGATAATGGAGAAAACGTTA
1 GGCACCTAAAATGATAACGAAGAAAACGTTA
1602801 G
1 G
1602802 ACATCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.17
Consensus pattern (31 bp):
GGCACCTAAAATGATAACGAAGAAAACGTTA
Found at i:1605364 original size:48 final size:48
Alignment explanation
Indices: 1605293--1605389 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1605283 AAGAGTAAGA
1605293 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1605341 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1605389 A
1 A
1605390 CACCCGACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (48 bp):
AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
Found at i:1606449 original size:48 final size:48
Alignment explanation
Indices: 1606373--1606467 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
1606363 TTAATAAGTC
1606373 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
1 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
* *
1606421 TGATGGCTGTTGCAAACTCCGCGTGAAGAATAGTTTCGCGAGGTTTC
1 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTC
1606468 ATCTCACTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (48 bp):
TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
Found at i:1610743 original size:3 final size:3
Alignment explanation
Indices: 1610725--1610789 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
1610715 AAAGAAAGTT
* * * *
1610725 GAA GAA G-A GAA TAA GAA GAT GAT GAA -AA TAGA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
1610769 GAA GAA GAA GAA GAA TGAA GA
1 GAA GAA GAA GAA GAA -GAA GA
1610790 CTTACCAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (3 bp):
GAA
Found at i:1614063 original size:114 final size:115
Alignment explanation
Indices: 1613786--1614486 Score: 624
Period size: 114 Copynumber: 6.2 Consensus size: 115
1613776 AATATTTTAA
* * * * * * *
1613786 AAATGACATAGAATCTTAACTATTCACGT-CATATTATTTTTAGTGAAATATCCCCTAAAAT-TA
1 AAATGAAAGAGAATCTTAACTATTCACGTCCAT-TTATTTTCAGAGAAATATCACCTTAAATCAA
* * * * * *
1613849 GAACTTCTTTCATATTGAATGAAAAATCTTATCTGATACAATAATTA-TTC
65 AAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
* * *
1613899 AAATGACAA-AGAATGTTAACTATTCAAGTCC-TGTTATTTTCAGTGAAATATCACCTTAAATCA
1 AAATGA-AAGAGAATCTTAACTATTCACGTCCAT-TTATTTTCAGAGAAATATCACCTTAAATCA
* *** * * *
1613962 AAAAC-TATTTCATAGTGAATGAAAAATCAGATCCAATACAATTATGATTTT
64 AAAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
* * *
1614013 AAATGAAAGAGAATCTTAGA-TATTCATGTCCATTTCTTTTCAGAGAAATATCACCTCAAATC-A
1 AAATGAAAGAGAATCTTA-ACTATTCACGTCCATTTATTTTCAGAGAAATATCACCTTAAATCAA
* * * * * *
1614076 GAATTTCTTTCATATTGAATGAAAAATCTTATCTGGTGCAATAATAATTTC
65 AAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
* * * * * ** *
1614127 AAATGAGAGAGAATCTTAACTATTCATGT-CATATTTTTTTACAGTGAGATGCCACCTTAAATGA
1 AAATGAAAGAGAATCTTAACTATTCACGTCCAT-TTATTTT-CAGAGAAATATCACCTTAAATCA
* * * *
1614191 AAAACTTATTTCATAGTGAATGAAAAATCAAATATGGTATAATAAAAATTTC
64 AAAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
* * * * * * *
1614243 AAATGACAGAGAATCTTAATTGTTAACGT-TA-TT-TTTTAAGCA-AAATATCACCTCAAATC-A
1 AAATGAAAGAGAATCTTAACTATTCACGTCCATTTATTTTCAG-AGAAATATCACCTTAAATCAA
* * * **
1614303 AAACTTCTTTCATATTGAATGAAAATTTTTATCTGGTACAATAATAATTTC
65 AAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
* * * *
1614354 AAATGATAGAGAATCTTAACTATTCACATCCTTTTATTTTCA-ATTAAATATCACCTTAAATC-A
1 AAATGAAAGAGAATCTTAACTATTCACGTCCATTTATTTTCAGA-GAAATATCACCTTAAATCAA
* * * * *
1614417 AAACTTATTTTATAGTGAATGAAAAATCAGATTTGGCATAATAATAATTTC
65 AAACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
*
1614468 AAATGATAGAGAATCTTAA
1 AAATGAAAGAGAATCTTAA
1614487 TTTCTTATGT
Statistics
Matches: 475, Mismatches: 95, Indels: 35
0.79 0.16 0.06
Matches are distributed among these distances:
111 67 0.14
112 15 0.03
113 99 0.21
114 209 0.44
115 18 0.04
116 67 0.14
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (115 bp):
AAATGAAAGAGAATCTTAACTATTCACGTCCATTTATTTTCAGAGAAATATCACCTTAAATCAAA
AACTTATTTCATAGTGAATGAAAAATCATATCTGGTACAATAATAATTTC
Found at i:1614291 original size:227 final size:225
Alignment explanation
Indices: 1613786--1614488 Score: 815
Period size: 227 Copynumber: 3.1 Consensus size: 225
1613776 AATATTTTAA
* * * * * * *
1613786 AAATGACATAGAATCTTAACTATTCACGTCATATTATTTTTAGTGAAATATCCCCTAAAATTAGA
1 AAATGACAGAGAATCTTAATTATTCACGTC-TATTATTTTAAG-AAAATATCACCTCAAATCAGA
* * * *
1613851 ACTTCTTTCATATTGAATGAAAAATCTTATCTGATACAATAATTA-TTCAAATGACAAAGAATGT
64 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTCAAATGACAGAGAATCT
*
1613915 TAACTATTCAAGTCCTGTTATTTTCAGTGAAATATCACCTTAAATCAAAAAC-TATTTCATAGTG
129 TAACTATTCAAGTCCT-TTTTTTTCAGTGAAATATCACCTTAAAT-AAAAACTTATTTCATAGTG
**** * * * *
1613979 AATGAAAAATCAGATCCAATACAATTATGATTTT
192 AATGAAAAATCAGATATGGTATAATAATAATTTC
* * * * *
1614013 AAATGAAAGAGAATCTTAGA-TATTCATGTCCATTTCTTTTCAGAGAAATATCACCTCAAATCAG
1 AAATGACAGAGAATCTTA-ATTATTCACGTCTA-TTATTTTAAGA-AAATATCACCTCAAATCAG
* * *
1614077 AATTTCTTTCATATTGAATGAAAAATCTTATCTGGTGCAATAATAATTTCAAATGAGAGAGAATC
63 AACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTCAAATGACAGAGAATC
* * * **
1614142 TTAACTATTCATGTCATATTTTTTTACAGTGAGATGCCACCTTAAATGAAAAACTTATTTCATAG
128 TTAACTATTCAAGTCCT-TTTTTTT-CAGTGAAATATCACCTTAAAT-AAAAACTTATTTCATAG
* *
1614207 TGAATGAAAAATCAAATATGGTATAATAAAAATTTC
190 TGAATGAAAAATCAGATATGGTATAATAATAATTTC
* * *
1614243 AAATGACAGAGAATCTTAATTGTTAACGT-TATT-TTTTAAGCAAAATATCACCTCAAATCAAAA
1 AAATGACAGAGAATCTTAATTATTCACGTCTATTATTTTAAG-AAAATATCACCTCAAATCAGAA
* * *
1614306 CTTCTTTCATATTGAATGAAAATTTTTATCTGGTACAATAATAATTTCAAATGATAGAGAATCTT
65 CTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTCAAATGACAGAGAATCTT
* * * *
1614371 AACTATTCACA-TCCTTTTATTTTCAATTAAATATCACCTTAAATCAAAACTTATTTTATAGTGA
130 AACTATTCA-AGTCCTTTT-TTTTCAGTGAAATATCACCTTAAATAAAAACTTATTTCATAGTGA
* *
1614435 ATGAAAAATCAGATTTGGCATAATAATAATTTC
193 ATGAAAAATCAGATATGGTATAATAATAATTTC
*
1614468 AAATGATAGAGAATCTTAATT
1 AAATGACAGAGAATCTTAATT
1614489 TCTTATGTTC
Statistics
Matches: 405, Mismatches: 61, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
225 67 0.17
226 20 0.05
227 193 0.48
228 40 0.10
229 26 0.06
230 59 0.15
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (225 bp):
AAATGACAGAGAATCTTAATTATTCACGTCTATTATTTTAAGAAAATATCACCTCAAATCAGAAC
TTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTCAAATGACAGAGAATCTTA
ACTATTCAAGTCCTTTTTTTTCAGTGAAATATCACCTTAAATAAAAACTTATTTCATAGTGAATG
AAAAATCAGATATGGTATAATAATAATTTC
Found at i:1616122 original size:29 final size:29
Alignment explanation
Indices: 1616089--1616148 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1616079 CCAAATTTTG
*
1616089 TTTAGTGACTAAAATGTAAGTTTT-GAAAA
1 TTTAGTGACTAAAATG-AAATTTTGGAAAA
1616118 TTTAGTGACTAAAATGAAATTTTGGAAAA
1 TTTAGTGACTAAAATGAAATTTTGGAAAA
1616147 TT
1 TT
1616149 GAAGGGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (29 bp):
TTTAGTGACTAAAATGAAATTTTGGAAAA
Found at i:1618016 original size:36 final size:36
Alignment explanation
Indices: 1617971--1618181 Score: 386
Period size: 36 Copynumber: 5.9 Consensus size: 36
1617961 ATTTATCCAT
1617971 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1618007 TATCAGCTTTGGTACATTTGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1618043 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1618079 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
1618115 TATCAGCTTTGATACATTAGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1618151 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
1618182 CCAGCACCGT
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 168 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1620282 original size:23 final size:23
Alignment explanation
Indices: 1620256--1620313 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
1620246 TTAGCATTTT
*
1620256 AAAAATAAAGAAAGCTTGTAAAG
1 AAAAATAAAGAAAGCTTATAAAG
*
1620279 -AAAATAAAGAAAGTTTATAAAG
1 AAAAATAAAGAAAGCTTATAAAG
1620301 AAAAATAAAGAAA
1 AAAAATAAAGAAA
1620314 AGTGAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.17
Consensus pattern (23 bp):
AAAAATAAAGAAAGCTTATAAAG
Found at i:1633335 original size:13 final size:13
Alignment explanation
Indices: 1633302--1633350 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
1633292 GATACTAATT
*
1633302 TAATAATGATTAC
1 TAATAATGATTAG
1633315 TAAT-ATGATTAG
1 TAATAATGATTAG
1633327 TAATAATGATTAG
1 TAATAATGATTAG
1633340 TAATAATGATT
1 TAATAATGATT
1633351 TACTAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (13 bp):
TAATAATGATTAG
Found at i:1633336 original size:25 final size:26
Alignment explanation
Indices: 1633302--1633350 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1633292 GATACTAATT
1633302 TAATAATGATTACTAAT-ATGATTAG
1 TAATAATGATTACTAATAATGATTAG
*
1633327 TAATAATGATTAGTAATAATGATT
1 TAATAATGATTACTAATAATGATT
1633351 TACTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (26 bp):
TAATAATGATTACTAATAATGATTAG
Found at i:1633365 original size:27 final size:25
Alignment explanation
Indices: 1633302--1633357 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1633292 GATACTAATT
*
1633302 TAATAATGATTACTAATATGATTAG
1 TAATAATGATTACTAATATGATTAC
*
1633327 TAATAATGATTAGTAATAATGATTTAC
1 TAATAATGATTACTAAT-ATGA-TTAC
1633354 TAAT
1 TAAT
1633358 TATTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 16 0.59
26 4 0.15
27 7 0.26
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.41
Consensus pattern (25 bp):
TAATAATGATTACTAATATGATTAC
Found at i:1634830 original size:13 final size:13
Alignment explanation
Indices: 1634812--1634868 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
1634802 AGAACGTCAA
1634812 TATTAGTAATCAT
1 TATTAGTAATCAT
*
1634825 TATTAGTAAATCAC
1 TATTAGT-AATCAT
*
1634839 TATTAGTAATTAT
1 TATTAGTAATCAT
*
1634852 TATTACTAATCA-
1 TATTAGTAATCAT
1634864 TATTA
1 TATTA
1634869 TGCATTAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
12 5 0.13
13 21 0.55
14 12 0.32
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (13 bp):
TATTAGTAATCAT
Found at i:1634842 original size:14 final size:14
Alignment explanation
Indices: 1634812--1634847 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1634802 AGAACGTCAA
*
1634812 TATTAGT-AATCAT
1 TATTAGTAAATCAC
1634825 TATTAGTAAATCAC
1 TATTAGTAAATCAC
1634839 TATTAGTAA
1 TATTAGTAA
1634848 TTATTATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (14 bp):
TATTAGTAAATCAC
Found at i:1634853 original size:27 final size:25
Alignment explanation
Indices: 1634811--1634868 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
1634801 AAGAACGTCA
*
1634811 ATATTAGTAATCATTATTAGTAAATC
1 ATATTAGTAATCATTATTACT-AATC
*
1634837 ACTATTAGTAATTATTATTACTAATC
1 A-TATTAGTAATCATTATTACTAATC
1634863 ATATTA
1 ATATTA
1634869 TGCATTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 6 0.21
27 18 0.62
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (25 bp):
ATATTAGTAATCATTATTACTAATC
Found at i:1635055 original size:24 final size:24
Alignment explanation
Indices: 1635013--1635068 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1635003 TTATGTTATT
*
1635013 TAATAA-TATTAAATCATTATTAG
1 TAATAATTATAAAATCATTATTAG
1635036 TAATAATTATAAAATCATTATTAG
1 TAATAATTATAAAATCATTATTAG
*
1635060 TAATTATTA
1 TAATAATTA
1635069 ATATTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
TAATAATTATAAAATCATTATTAG
Found at i:1635099 original size:31 final size:34
Alignment explanation
Indices: 1635028--1635099 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1635018 ATATTAAATC
* *
1635028 ATTATTAGTAATAATTATAAAATCATTATTAGTA
1 ATTATTAATAATAATAATAAAATCATTATTAGTA
*
1635062 ATTATTAATATTAATAATAAAAT-ATTA-TAGTA
1 ATTATTAATAATAATAATAAAATCATTATTAGTA
1635094 A-TATTA
1 ATTATTA
1635100 CTAAATCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 5 0.14
32 6 0.17
33 4 0.11
34 20 0.57
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (34 bp):
ATTATTAATAATAATAATAAAATCATTATTAGTA
Found at i:1635138 original size:15 final size:15
Alignment explanation
Indices: 1635102--1635144 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1635092 TAATATTACT
* *
1635102 AAATCATATAATTATT
1 AAATCAT-TAAATATC
1635118 AAATCATTAAATATC
1 AAATCATTAAATATC
1635133 AAATCATTAAAT
1 AAATCATTAAAT
1635145 TAATAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:1635177 original size:13 final size:13
Alignment explanation
Indices: 1635151--1635207 Score: 89
Period size: 13 Copynumber: 4.4 Consensus size: 13
1635141 AAATTAATAA
1635151 TATTAGTAAATCAT
1 TATTAGT-AATCAT
1635165 TATTAGTAATCAT
1 TATTAGTAATCAT
*
1635178 TATTACTAATCA-
1 TATTAGTAATCAT
1635190 TATTAGTAATCAT
1 TATTAGTAATCAT
1635203 TATTA
1 TATTA
1635208 AATTATTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.28
13 22 0.55
14 7 0.17
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (13 bp):
TATTAGTAATCAT
Found at i:1635199 original size:25 final size:26
Alignment explanation
Indices: 1635159--1635207 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
1635149 AATATTAGTA
1635159 AATCATTATTAGTAATCATTATTACT
1 AATCATTATTAGTAATCATTATTACT
1635185 AATCA-TATTAGTAATCATTATTA
1 AATCATTATTAGTAATCATTATTA
1635208 AATTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (26 bp):
AATCATTATTAGTAATCATTATTACT
Found at i:1635227 original size:20 final size:21
Alignment explanation
Indices: 1635163--1635228 Score: 53
Period size: 25 Copynumber: 3.0 Consensus size: 21
1635153 TTAGTAAATC
**
1635163 ATTATTAGTAATCATTATTACTA
1 ATTATTAGTAATCAAAATTA--A
**
1635186 ATCATATTAGTAATCATTATTAA
1 AT--TATTAGTAATCAAAATTAA
1635209 ATTATTAGT-ATCAAAATTAA
1 ATTATTAGTAATCAAAATTAA
1635229 GTAATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.23
21 7 0.18
23 5 0.13
25 18 0.46
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTATTAGTAATCAAAATTAA
Found at i:1636244 original size:20 final size:20
Alignment explanation
Indices: 1636219--1636353 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
1636209 AATTGGGAAA
1636219 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1636239 ATCGCAATGCGATACTTAAT
1 ATCGCAATGCGATACTGACT
* *
1636259 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
1636280 ATCACAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
1636300 TTCGCAACGCGATGTTGACT
1 ATCGCAATGCGATACTGACT
* * *
1636320 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1636340 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1636354 TTTCAAAGCG
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.03
20 63 0.69
21 23 0.25
22 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1636281 original size:61 final size:61
Alignment explanation
Indices: 1636216--1636353 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 61
1636206 GCGAATTGGG
* *
1636216 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTT-AATATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGAT-CTTGAATATCGCAACGCGATAATAC
* * * * * * *
1636277 AAAATCACAACGAGATACTGACTTTCGCAACGCGATGTTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATCTTGAATATCGCAACGCGATAATAC
*
1636338 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1636354 TTTCAAAGCG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
60 2 0.03
61 61 0.97
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATCTTGAATATCGCAACGCGATAATAC
Found at i:1636873 original size:20 final size:20
Alignment explanation
Indices: 1636830--1636887 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
1636820 ATTCTCTCTC
** **
1636830 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
*
1636850 GTTGTGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1636870 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1636888 AGAAACTATT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1637078 original size:25 final size:24
Alignment explanation
Indices: 1637024--1637078 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1637014 TGTTTATTAT
* *
1637024 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1637048 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1637074 TGTTT
1 TGTTT
1637079 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1638386 original size:19 final size:20
Alignment explanation
Indices: 1638343--1638387 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1638333 CGCAACACGA
1638343 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGCGG
* * *
1638363 AAATGGCTATCGCAATGC-G
1 AAATGACTATCACAACGCGG
1638382 AAATGA
1 AAATGA
1638388 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:1638393 original size:19 final size:19
Alignment explanation
Indices: 1638371--1638434 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1638361 GGAAATGGCT
1638371 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1638390 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1638404 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1638423 ATCGCAATGCGA
1 ATCGCAATGCGA
1638435 TTTGTGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.57
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1638510 original size:33 final size:33
Alignment explanation
Indices: 1638441--1638552 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
1638431 GCGATTTGTG
* *
1638441 TTTCGCGTTGCGATTTTGTCATTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
1638473 TTTCGCATTACGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1638506 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1638539 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1638553 AGCCATTTCC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 23 0.32
33 50 0.68
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1638532 original size:14 final size:14
Alignment explanation
Indices: 1638446--1638536 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
1638436 TTGTGTTTCG
1638446 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
1638460 CATTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1638476 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
* *
1638492 CGTTGTGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1638509 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1638525 CGTTGCGATTTT
1 CGTTGCGATTTT
1638537 CATTTCGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
14 24 0.41
15 3 0.05
16 11 0.19
17 4 0.07
18 11 0.19
19 5 0.09
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1638571 original size:20 final size:19
Alignment explanation
Indices: 1638537--1638592 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1638527 TTGCGATTTT
*
1638537 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1638556 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1638576 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1638593 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1639074 original size:21 final size:21
Alignment explanation
Indices: 1639007--1639075 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1638997 CTATCCTCCC
*
1639007 TCAAGA-GTCCCCCCCACCGT
1 TCAAGAGGTCCCTCCCACCGT
** *
1639027 TCAAGAGG-CCACTGTCATCGT
1 TCAAGAGGTCC-CTCCCACCGT
* *
1639048 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCACCGT
1639069 TCAAGAG
1 TCAAGAG
1639076 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
20 8 0.22
21 26 0.72
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.20, T:0.19
Consensus pattern (21 bp):
TCAAGAGGTCCCTCCCACCGT
Found at i:1640409 original size:14 final size:14
Alignment explanation
Indices: 1640375--1640413 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1640365 TGATTGTTTT
1640375 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1640389 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1640403 TGTTGATTTGT
1 AATTGATTTGT
1640414 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1640559 original size:14 final size:14
Alignment explanation
Indices: 1640540--1640595 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1640530 GAAACTGACT
1640540 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
1640554 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
*
1640573 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
1640587 ATCGCAATG
1 ATCGCAATG
1640596 CGATTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:1640574 original size:19 final size:17
Alignment explanation
Indices: 1640549--1640598 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
1640539 TATCGCAATG
1640549 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
1640567 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
1640582 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
1640599 TTTTTATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:1640642 original size:20 final size:20
Alignment explanation
Indices: 1640617--1640692 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
1640607 TCGCATTGCG
*
1640617 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
1640637 ATTTTCGCGTTGCGGATTTTC
1 ATTTTCGAGTTGC-GATAGCC
* *
1640658 A-TTTCAAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
1640677 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
1640693 TTCCCCGTTG
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 5 0.12
20 30 0.75
21 5 0.12
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:1640931 original size:20 final size:20
Alignment explanation
Indices: 1640906--1640975 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
1640896 TTGAAGATGA
1640906 TTGCGATTTTTAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*** *
1640926 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*
1640946 TTGCGATTTTTTGTATTATCTCG
1 TTGCGATTTTTAG-A--ATCTCG
1640969 TTGCGAT
1 TTGCGAT
1640976 AGTCAGTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.63
21 1 0.03
23 13 0.34
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTTAGAATCTCG
Found at i:1640984 original size:23 final size:22
Alignment explanation
Indices: 1640920--1640984 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
1640910 GATTTTTAGA
*
1640920 ATCTCGTTGCGAAAGTCAG-A-
1 ATCTCGTTGCGATAGTCAGTAT
** **
1640940 ATCTCGTTGCGATTTTTTGTATT
1 ATCTCGTTGCGATAGTCAGTA-T
1640963 ATCTCGTTGCGATAGTCAGTAT
1 ATCTCGTTGCGATAGTCAGTAT
1640985 CGCATTGCGA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
22 1 0.03
23 17 0.52
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (22 bp):
ATCTCGTTGCGATAGTCAGTAT
Found at i:1641028 original size:20 final size:21
Alignment explanation
Indices: 1640984--1641035 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1640974 ATAGTCAGTA
*
1640984 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1641005 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1641025 TCGCATTGCGA
1 TCGCATTGCGA
1641036 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1641251 original size:12 final size:12
Alignment explanation
Indices: 1641232--1641265 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1641222 CTCTCCGGCG
1641232 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1641244 ATATCCGTTCCT
1 ACATCCGTTCCT
1641256 ACATCC-TTCC
1 ACATCCGTTCC
1641266 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1641849 original size:24 final size:24
Alignment explanation
Indices: 1641822--1641875 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1641812 GTATTCGAAA
*
1641822 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1641846 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1641870 TTTGAT
1 TTTGAT
1641876 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1642067 original size:12 final size:12
Alignment explanation
Indices: 1642050--1642086 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1642040 ATATAATCCT
1642050 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1642062 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1642074 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1642086 G
1 G
1642087 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1644406 original size:33 final size:33
Alignment explanation
Indices: 1644369--1644476 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
1644359 GGAAATTACT
*
1644369 ATCGCAACGAGAGAATCGCAATACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * *
1644402 ATCGCAACGCGA-ATTTCGTAATGCGAAATGAAA
1 ATCGCAACGAGAGA-ATCGCAATGCGAAATGAAA
*
1644435 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1644468 ATCGCAACG
1 ATCGCAACG
1644477 CGAATTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
32 1 0.02
33 63 0.97
34 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:1644414 original size:19 final size:19
Alignment explanation
Indices: 1644382--1644480 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 19
1644372 GCAACGAGAG
*
1644382 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1644401 AATCGCAACGCG-AAT---
1 AATCGCAATGCGAAATGAA
* *
1644416 -TTCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
1644434 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
1644448 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1644467 AATCGCAACGCGAA
1 AATCGCAATGCGAA
1644481 TTTAATTTCG
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
14 17 0.29
15 4 0.07
16 2 0.03
17 2 0.03
18 4 0.07
19 29 0.50
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1644518 original size:19 final size:18
Alignment explanation
Indices: 1644480--1644551 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
1644470 CGCAACGCGA
*
1644480 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
1644498 ATTTTCATTTCGCGTTGCG
1 A-TTTCATTTCGCGTTGCG
*
1644517 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
1644531 ATCTTCATTTCGCATTGCG
1 AT-TTCATTTCGCGTTGCG
1644550 AT
1 AT
1644552 AGTAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
18 1 0.02
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:1644674 original size:15 final size:15
Alignment explanation
Indices: 1644654--1644691 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1644644 CATCAATTAA
*
1644654 ACAAATCAACTTTTT
1 ACAAATCAACCTTTT
1644669 ACAAATC-ACCTTTT
1 ACAAATCAACCTTTT
1644683 ACAAATCAA
1 ACAAATCAA
1644692 TTAAACAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAACCTTTT
Found at i:1646104 original size:21 final size:20
Alignment explanation
Indices: 1646038--1646104 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
1646028 ATGAATCGGG
*
1646038 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
1646058 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAG-GGA
1646080 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAG-GGA
1646101 CTCT
1 CTCT
1646105 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:1646123 original size:42 final size:40
Alignment explanation
Indices: 1646038--1646160 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 40
1646028 ATGAATCGGG
* * * *
1646038 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTC-TCGAGGATGACAGGGGC
*
1646080 CTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAG-GGACTCTCGAGG-ATGACAGGGGC
* * * *
1646122 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACTCTCGA-GGATGACAGG
1646161 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.87
43 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (40 bp):
CTCTTGAACGGTGGGAGGGACTCTCGAGGATGACAGGGGC
Found at i:1646553 original size:91 final size:90
Alignment explanation
Indices: 1646378--1646562 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1646368 ATTTCAAACT
* *
1646378 TTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1646443 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1646471 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
1646535 GTATTGGTAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1646562 T
1 T
1646563 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1648315 original size:14 final size:14
Alignment explanation
Indices: 1648296--1648332 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1648286 GGAAATGACT
1648296 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1648310 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1648324 ATCGCAACG
1 ATCGCAACG
1648333 CGAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1648347 original size:19 final size:19
Alignment explanation
Indices: 1648323--1648406 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
1648313 GCAACGAGAG
1648323 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1648342 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1648361 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1648375 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1648394 AATTGCAATGCGA
1 AATCGCAACGCGA
1648407 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1648376 original size:52 final size:49
Alignment explanation
Indices: 1648272--1648406 Score: 175
Period size: 52 Copynumber: 2.7 Consensus size: 49
1648262 ACGAGATAAT
** *
1648272 GAGAATCGCAACGCGGAAATGACTATCGCAA-CG-AGAGAATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAAGCGAAGAAAATCGCAACGA
1648320 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA-GCG-AA-GAAAATCGCAACGA
*
1648372 GAGAATCGCAACGCGAAATGAAAATTGCAATGCGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA-GCGA
1648407 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
47 14 0.18
48 14 0.18
49 2 0.03
51 2 0.03
52 45 0.58
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (49 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAAGCGAAGAAAATCGCAACGA
Found at i:1648379 original size:33 final size:33
Alignment explanation
Indices: 1648272--1648401 Score: 138
Period size: 33 Copynumber: 3.9 Consensus size: 33
1648262 ACGAGATAAT
**
1648272 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCAACGA
* * ** * *
1648306 GAGAATCGCAACGAGAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGA-AAT-GAAAATCGCAACGA
1648341 -A-AATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
*
1648372 GAGAATCGCAACGCGAAATGAAAATTGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1648402 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
31 9 0.12
32 4 0.05
33 40 0.52
34 17 0.22
35 7 0.09
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1648424 original size:19 final size:18
Alignment explanation
Indices: 1648402--1648468 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
1648392 AAAATTGCAA
*
1648402 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
1648421 TGCGATTTTTTATTCGCGT
1 TGCGATTTTAT-TTCGCGT
*
1648440 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
1648460 TGCGATTTT
1 TGCGATTTT
1648469 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 14 0.34
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:1649019 original size:20 final size:20
Alignment explanation
Indices: 1648994--1649045 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1648984 GCTATGTAAA
1648994 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
1649014 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
1649034 TCGCATTGCGAT
1 TCGCATTGCGAT
1649046 TTTCCTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:1649046 original size:20 final size:20
Alignment explanation
Indices: 1649012--1649268 Score: 175
Period size: 20 Copynumber: 12.7 Consensus size: 20
1649002 CGATAGTAAG
1649012 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTAC-TA
*
1649032 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGA-TTTACTA
1649053 ATTCGCATTGCGATTTACTA
1 ATTCGCATTGCGATTTACTA
*
1649073 ATTCGCGTTGCGATTTACTA
1 ATTCGCATTGCGATTTACTA
* *
1649093 ATTCGCGTTGTGATTTACTA
1 ATTCGCATTGCGATTTACTA
* *
1649113 ATCCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTAC-TA
*
1649133 ATTCGCATTGCGAATTA-TGAA
1 ATTCGCATTGCGATTTACT--A
* ** *
1649154 AATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTAC-TA
* * * **
1649174 AATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTA-CTA
* *
1649195 AATCGCATTGCGA--TAGTCA
1 ATTCGCATTGCGATTTACT-A
* * * *
1649214 GTATCCCATTGCGATTTTCCAA
1 AT-TCGCATTGCGA-TTTACTA
*
1649236 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTA
1649256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1649269 ATTGGGAAAA
Statistics
Matches: 192, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.01
19 3 0.02
20 130 0.68
21 53 0.28
22 3 0.02
23 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTA
Found at i:1649089 original size:61 final size:60
Alignment explanation
Indices: 1649012--1649268 Score: 189
Period size: 61 Copynumber: 4.2 Consensus size: 60
1649002 CGATAGTAAG
1649012 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTCCTAATTCGCATTGCGATTTACTA
* * * * * *
1649073 ATTCGCGTTGCGATTTAC-TAATTCGCGTTGTGATTTACTAATCCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTCCTAATTCGCATTGCGATTTAC-TA
* * * * ** * * * * * * **
1649133 ATTCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTTCCTAATTCGCATTGCGATTTA-CTA
* * * * *
1649195 AATCGCATTGCGATAGT-CAGTA-TCCCATTGCGATTTTCCAAATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGAT-TTAC-GTATTCGCATTGCGA-TTTCCTAATTCGCATTGCGATTTACTA
1649256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1649269 ATTGGGAAAA
Statistics
Matches: 142, Mismatches: 45, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
60 38 0.27
61 72 0.51
62 30 0.21
63 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTCCTAATTCGCATTGCGATTTACTA
Found at i:1649206 original size:21 final size:21
Alignment explanation
Indices: 1649135--1649310 Score: 92
Period size: 21 Copynumber: 8.5 Consensus size: 21
1649125 ATTTACGTAT
*
1649135 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTAGGAAAA
** * *
1649156 TCGCAACGCGAA-TACGTAAA
1 TCGCATTGCGAATTAGGAAAA
*
1649176 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTAGGAAAA
* **
1649197 TCGCATTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTAG-GAAAA
* * *** *
1649217 TCCCATTGCGATTTTCCAAAT
1 TCGCATTGCGAATTAGGAAAA
* *** *
1649238 TCGCATTGCGATTTA-CTTAT
1 TCGCATTGCGAATTAGGAAAA
*
1649258 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTAGGAAAA
**
1649279 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTAGGAAAA
1649300 TCGCATTGCGA
1 TCGCATTGCGA
1649311 TAGTCATAAT
Statistics
Matches: 117, Mismatches: 32, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 46 0.39
21 63 0.54
22 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGAATTAGGAAAA
Found at i:1649265 original size:41 final size:40
Alignment explanation
Indices: 1649012--1649268 Score: 180
Period size: 41 Copynumber: 6.3 Consensus size: 40
1649002 CGATAGTAAG
** *
1649012 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGA-TTTACTA
* *
1649053 ATTCGCATTGCGATTTACTAATTCGCGTTGCGATTTACTA
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACTA
* * * * *
1649093 ATTCGCGTTGTGATTTACTAATCCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTAC-TA
* * * ** *
1649133 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTA-CAAATTCGCATTGCGATTTAC-TA
* * * * * *
1649174 AATCGCAATGCGAATTAGGAAAATCGCATTGCGA--TAGTCA
1 ATTCGCATTGCGATTTA-CAAATTCGCATTGCGATTTACT-A
* * * *
1649214 GTATCCCATTGCGATTTTCCAAATTCGCATTGCGATTTACTT
1 AT-TCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACTA
1649256 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1649269 ATTGGGAAAA
Statistics
Matches: 172, Mismatches: 36, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 63 0.37
41 102 0.59
42 3 0.02
43 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACTA
Found at i:1651452 original size:18 final size:17
Alignment explanation
Indices: 1651398--1651446 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1651388 TTGGACTCCT
* *
1651398 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1651416 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1651434 AGTGCATTCGATG
1 AGTGCA-TCGATG
1651447 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1651512 original size:45 final size:42
Alignment explanation
Indices: 1651415--1651521 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 42
1651405 CGGTGCACTA
* *
1651415 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAAT
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
* *
1651457 AGCCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 AG---AGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT
*
1651504 CAGAGTGCATCAATGCAT
1 -AGAGTGCATCGATGCAT
1651522 GAAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.04
45 45 0.85
47 4 0.08
48 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
Found at i:1651529 original size:19 final size:19
Alignment explanation
Indices: 1651505--1651543 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1651495 TAATTAAATC
1651505 AGAGTGCATCAATGCATGA
1 AGAGTGCATCAATGCATGA
**
1651524 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCAATGCATGA
1651543 A
1 A
1651544 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCAATGCATGA
Found at i:1651593 original size:21 final size:21
Alignment explanation
Indices: 1651569--1651608 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1651559 CAATTTATTC
1651569 ATTGATGCATC-GATGCATGGT
1 ATTGATGCATCAG-TGCATGGT
1651590 ATTGATGCATCAGTGCATG
1 ATTGATGCATCAGTGCATG
1651609 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCAGTGCATGGT
Found at i:1654450 original size:29 final size:30
Alignment explanation
Indices: 1654380--1654439 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1654370 AAATTTAAGG
1654380 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1654411 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1654440 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1654545 original size:21 final size:21
Alignment explanation
Indices: 1654519--1654576 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1654509 AGGGTGTCAA
1654519 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
1654540 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCACCCCTGC
1654561 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1654577 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1654806 original size:20 final size:22
Alignment explanation
Indices: 1654768--1654807 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1654758 TTTTAGTAGA
1654768 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1654790 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1654808 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1655062 original size:34 final size:32
Alignment explanation
Indices: 1655023--1655092 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1655013 TTTTGTAAAG
* *
1655023 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1655057 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1655089 GGGA
1 GGGA
1655093 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1655977 original size:19 final size:20
Alignment explanation
Indices: 1655953--1656000 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1655943 AATGATTTTC
*
1655953 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1655972 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1655992 TTTTGAAAA
1 TTTTGAAAA
1656001 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1657300 original size:29 final size:30
Alignment explanation
Indices: 1657230--1657289 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1657220 AAATTTAAGG
1657230 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1657261 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1657290 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1657395 original size:21 final size:21
Alignment explanation
Indices: 1657369--1657426 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1657359 AGGGTGTCAA
1657369 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
1657390 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCACCCCTGC
1657411 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1657427 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1657656 original size:20 final size:22
Alignment explanation
Indices: 1657618--1657657 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1657608 TTTTAGTAGA
1657618 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1657640 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1657658 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1659478 original size:21 final size:20
Alignment explanation
Indices: 1659430--1659478 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1659420 AATGATTTTC
* * *
1659430 TTTT-AAAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
1659449 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
1659469 TTTTGAAAAA
1 TTTTGAAAAA
1659479 TGATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:1661940 original size:21 final size:22
Alignment explanation
Indices: 1661900--1661940 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1661890 TTAAATATTA
*
1661900 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCAATACTCAT
*
1661922 TAAAGG-AGTTCCAATACTC
1 TAAAGGAAGTACCAATACTC
1661941 CATGTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCAATACTCAT
Found at i:1668303 original size:35 final size:35
Alignment explanation
Indices: 1668259--1668458 Score: 269
Period size: 35 Copynumber: 5.8 Consensus size: 35
1668249 AAGTAGATTT
*
1668259 GAAGAAAGCATCGCACTTTCGATTCAAGTAGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* * *
1668294 GAAAGAAGCATCGTACTTTCGATTCAAGTAGAATG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* * * *
1668329 GAAGGCAGCATCTCACTTTCCATTCAAGTCGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
*
1668364 GAAGGAAGCATCACACTTTCGATTCAAGTAGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* *
1668399 GAAGGAAGCA--GCACTTTCGATTCAAATCGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* *
1668432 GAAAGAAGCATCGCACTTTCAATTCAA
1 GAAGGAAGCATCGCACTTTCGATTCAA
1668459 TTGTTCATCT
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 29 0.20
35 114 0.80
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (35 bp):
GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
Found at i:1671930 original size:16 final size:17
Alignment explanation
Indices: 1671909--1671943 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1671899 TACTATTCAC
1671909 GTGAATAGT-AAATTTT
1 GTGAATAGTGAAATTTT
1671925 GTGAATAGTGAAATTTT
1 GTGAATAGTGAAATTTT
1671942 GT
1 GT
1671944 CGGCGATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
GTGAATAGTGAAATTTT
Found at i:1677555 original size:18 final size:18
Alignment explanation
Indices: 1677518--1677580 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
1677508 TATGGAATTG
* *
1677518 GATTCTAA-TTCCTGACA
1 GATTCTAATTTCTTCACA
1677535 GATTCTAATTTCTTCACA
1 GATTCTAATTTCTTCACA
1677553 GATTCTAATTTCTTCACA
1 GATTCTAATTTCTTCACA
1677571 GATTCTAATT
1 GATTCTAATT
1677581 CTCTCGTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
17 8 0.19
18 35 0.81
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.43
Consensus pattern (18 bp):
GATTCTAATTTCTTCACA
Found at i:1678413 original size:23 final size:21
Alignment explanation
Indices: 1678378--1678421 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1678368 ATAATTATTT
1678378 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
1678400 AAAAATATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
1678422 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:1682210 original size:26 final size:25
Alignment explanation
Indices: 1682149--1682210 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
1682139 ATTTTGTTTC
1682149 TTATTTTTTTTATTATTTAATTGTT
1 TTATTTTTTTTATTATTTAATTGTT
** * *
1682174 CGATTTGTTTTTATTATTTAGTTCTTT
1 TTATTT-TTTTTATTATTTAATT-GTT
1682201 TTATTTTTTT
1 TTATTTTTTT
1682211 AGTTGTATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.14
26 19 0.66
27 6 0.21
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (25 bp):
TTATTTTTTTTATTATTTAATTGTT
Found at i:1685579 original size:18 final size:21
Alignment explanation
Indices: 1685541--1685579 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1685531 TTTTTTTCAA
1685541 ATAATCATATATAAAATAAAT
1 ATAATCATATATAAAATAAAT
1685562 ATAAT-ATA-ATAAAA-AAAT
1 ATAATCATATATAAAATAAAT
1685580 TTATCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 3 0.17
21 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATCATATATAAAATAAAT
Found at i:1686234 original size:18 final size:18
Alignment explanation
Indices: 1686211--1686252 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1686201 GGTTTCCGAA
*
1686211 ATTTTAAAATT-ATTATAT
1 ATTTTAAAATTCA-AATAT
1686229 ATTTTAAAATTCAAATAT
1 ATTTTAAAATTCAAATAT
1686247 ATTTTA
1 ATTTTA
1686253 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAAAATTCAAATAT
Found at i:1689785 original size:17 final size:17
Alignment explanation
Indices: 1689759--1689792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1689749 GAAAAACAAA
1689759 AAATTATGACTTTTTAG
1 AAATTATGACTTTTTAG
*
1689776 AAATTTTGACTTTTTAG
1 AAATTATGACTTTTTAG
1689793 TCAAAGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
AAATTATGACTTTTTAG
Found at i:1689836 original size:29 final size:29
Alignment explanation
Indices: 1689791--1689863 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 29
1689781 TTGACTTTTT
*
1689791 AGTCAAAGTCAATGGTTAACTATCAAACC
1 AGTCAAAGTCAACGGTTAACTATCAAACC
1689820 AGTCAAAGTCAACGGTTAACTATCAAACC
1 AGTCAAAGTCAACGGTTAACTATCAAACC
1689849 -GATCAAAGTCAACGG
1 AG-TCAAAGTCAACGG
1689864 GCAAGTCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 1 0.02
29 41 0.98
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (29 bp):
AGTCAAAGTCAACGGTTAACTATCAAACC
Found at i:1691296 original size:18 final size:18
Alignment explanation
Indices: 1691273--1691328 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
1691263 TGTGACTCTT
1691273 AGCTGGAGTCTGAACAGA
1 AGCTGGAGTCTGAACAGA
*
1691291 AGCTGGAGTCTGAACATA
1 AGCTGGAGTCTGAACAGA
1691309 AGCTGGAGTCTGAACAGA
1 AGCTGGAGTCTGAACAGA
1691327 AG
1 AG
1691329 GTTGATAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (18 bp):
AGCTGGAGTCTGAACAGA
Found at i:1700792 original size:17 final size:18
Alignment explanation
Indices: 1700770--1700804 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1700760 TTTGAAAGGT
*
1700770 TTGGAA-TAAATGATAAG
1 TTGGAATTAAATAATAAG
1700787 TTGGAATTAAATAATAAG
1 TTGGAATTAAATAATAAG
1700805 ACAAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (18 bp):
TTGGAATTAAATAATAAG
Found at i:1702583 original size:80 final size:80
Alignment explanation
Indices: 1702445--1702755 Score: 383
Period size: 80 Copynumber: 3.9 Consensus size: 80
1702435 TATAAGTCCT
* * * * *
1702445 TACGGACCTAAGGATATATTGGGTAGGCCCCAAGGCATATCCTTAGGTCGGTTCCCTTTGGTGTG
1 TACGAACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
*
1702510 TACATAAGGTAACCC
66 TGCATAAGGTAACCC
* *
1702525 TACGAACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTG
1 TACGAACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
*
1702590 TGTATAAGGTAACCC
66 TGCATAAGGTAACCC
* * * *
1702605 TAC-AGACCTAAGGATATCTTGGGTAGGCCCCAAAGTATATCCTTAGATTGGTTCCCTTAGTTGT
1 TACGA-ACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGT
*
1702669 GTGCTTAAGGTAACCC
65 GTGCATAAGGTAACCC
*** ** *
1702685 TACGAGTATAAGGATATCCTTGGGTA-GATCCAAGGTATATCCTTAGGTTGGCTCCCCTTTTTGC
1 TACGAACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGG-TTCCC--TTTGC
1702749 TGTGTGC
62 TGTGTGC
1702756 TGAGGGAAAG
Statistics
Matches: 198, Mismatches: 27, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 174 0.88
81 13 0.07
83 10 0.05
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (80 bp):
TACGAACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:1706102 original size:17 final size:18
Alignment explanation
Indices: 1706080--1706113 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1706070 TTGAAAGGTC
*
1706080 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
1706097 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
1706114 ACTAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:1707908 original size:80 final size:80
Alignment explanation
Indices: 1707759--1708063 Score: 391
Period size: 80 Copynumber: 3.8 Consensus size: 80
1707749 AGTCCTTACG
* * * *
1707759 GACCTAATGATATCTTGGGTAGGCCCCAA-GCATATCCTTAGGTCGGTTCCCTTTGCTGTATGCA
1 GACCTAATGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGTA
1707823 TAAGGTAACCCTACA
66 TAAGGTAACCCTACA
* *
1707838 GACCTAATGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGTA
1 GACCTAATGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGTA
*
1707903 TAAGGTAACACTACA
66 TAAGGTAACCCTACA
* * * *
1707918 GACCTAAAGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGATTGGTTCCCTTAGCTGTGTACT
1 GACCTAATGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGT-GT
*
1707983 -TAAGGTAACCCTACG
65 ATAAGGTAACCCTACA
* * ** *
1707998 GATCTAAGGATATCCTTGGGTA-GATCCAAGGTATATCCTTAGGTTGGCTCCCCTTTTTGCTGTG
1 GACCTAATGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGG-TTCCC--TTTGCTGTG
1708062 TG
62 TG
1708064 CCGAGGGCAA
Statistics
Matches: 197, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
79 28 0.14
80 147 0.75
81 13 0.07
83 9 0.05
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (80 bp):
GACCTAATGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGTA
TAAGGTAACCCTACA
Found at i:1708988 original size:3 final size:3
Alignment explanation
Indices: 1708980--1709043 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
1708970 TCTAATTGTA
1708980 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1709028 ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT AT
1709044 GCTTATTTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1709590 original size:12 final size:12
Alignment explanation
Indices: 1709562--1709611 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1709552 AGGAGATTCA
* *
1709562 GAAAAAAAAAAC
1 GAAAAAAAGAAG
*
1709574 G-AAAATAGAAG
1 GAAAAAAAGAAG
1709585 GAAAAAAAGAAG
1 GAAAAAAAGAAG
*
1709597 AAAAAAAAGAAG
1 GAAAAAAAGAAG
1709609 GAA
1 GAA
1709612 GCTCTCACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (12 bp):
GAAAAAAAGAAG
Found at i:1716236 original size:4 final size:4
Alignment explanation
Indices: 1716227--1716268 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
1716217 AAAAGTATAC
1716227 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1716269 GATACATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Done.