Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 14 of 17
Found at i:2598729 original size:27 final size:26
Alignment explanation
Indices: 2598682--2598734 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2598672 AAATATGTTA
2598682 AAATTTAATATAATATAAATATAAAAT
1 AAATTTAATATAATATAAATA-AAAAT
* *
2598709 AAATTTTATATGATA-ATAATAAAAAT
1 AAATTTAATATAATATA-AATAAAAAT
2598735 TTAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATTTAATATAATATAAATAAAAAT
Found at i:2598921 original size:2 final size:2
Alignment explanation
Indices: 2598914--2598939 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2598904 ACATGTTTAG
2598914 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2598940 CTGTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2603439 original size:21 final size:21
Alignment explanation
Indices: 2603396--2603439 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2603386 TTTTAAATTC
* *
2603396 ATTAATAATATATATTTATAT
1 ATTAATAATATATATATACAT
* *
2603417 ATTAATAATATTTATATCCAT
1 ATTAATAATATATATATACAT
2603438 AT
1 AT
2603440 CTATACATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAATAATATATATATACAT
Found at i:2603565 original size:14 final size:15
Alignment explanation
Indices: 2603546--2603580 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2603536 AATATATATA
2603546 TATTTATG-TATTTG
1 TATTTATGTTATTTG
*
2603560 TATTTATGTTATTTT
1 TATTTATGTTATTTG
2603575 TATTTA
1 TATTTA
2603581 AAATATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (15 bp):
TATTTATGTTATTTG
Found at i:2603857 original size:8 final size:9
Alignment explanation
Indices: 2603833--2603878 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 9
2603823 TTATTTGAAG
*
2603833 TATTATAAA
1 TATTATATA
2603842 T-TTATATAA
1 TATTATAT-A
2603851 TATTATATA
1 TATTATATA
2603860 TATATATATA
1 TAT-TATATA
2603870 TATT-TATA
1 TATTATATA
2603878 T
1 T
2603879 GTTTTTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 10 0.30
9 8 0.24
10 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATTATATA
Found at i:2603928 original size:23 final size:23
Alignment explanation
Indices: 2603902--2603958 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2603892 TATCATATTC
*
2603902 ATTTTTTATATTATGTTTTAATT
1 ATTTTTTATATTATATTTTAATT
* *
2603925 ATTTTTTATACTATATTTTTATT
1 ATTTTTTATATTATATTTTAATT
*
2603948 -TTTTGTATATT
1 ATTTTTTATATT
2603959 TAAAGTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
ATTTTTTATATTATATTTTAATT
Found at i:2603931 original size:11 final size:12
Alignment explanation
Indices: 2603896--2603958 Score: 60
Period size: 11 Copynumber: 5.4 Consensus size: 12
2603886 TACTCGTATC
2603896 ATATTCATTTTTT
1 ATATT-ATTTTTT
*
2603909 ATATTATGTTTT
1 ATATTATTTTTT
2603921 A-ATTATTTTTT
1 ATATTATTTTTT
* *
2603932 ATACTATATTTT
1 ATATTATTTTTT
*
2603944 -TATT-TTTTGT
1 ATATTATTTTTT
2603954 ATATT
1 ATATT
2603959 TAAAGTAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 4 0.10
11 17 0.41
12 15 0.37
13 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:2604435 original size:37 final size:39
Alignment explanation
Indices: 2604394--2604471 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 39
2604384 TATTTTTTCG
2604394 TATTAAAAA--TATTATATTTTTATATAAATTTTT-TATA
1 TATTAAAAATTTATTATA-TTTTATATAAATTTTTATATA
* * * *
2604431 TATTAATAATTTATTTTATTTTATGTATATTTTTATATA
1 TATTAAAAATTTATTATATTTTATATAAATTTTTATATA
2604470 TA
1 TA
2604472 CGTATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 8 0.24
38 14 0.41
39 12 0.35
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (39 bp):
TATTAAAAATTTATTATATTTTATATAAATTTTTATATA
Found at i:2604857 original size:19 final size:18
Alignment explanation
Indices: 2604813--2604866 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2604803 TTATTTTATA
2604813 TAATTT-ATCAAAATATTT
1 TAATTTAAT-AAAATATTT
2604831 TAATTTAATAAAA-ATTT
1 TAATTTAATAAAATATTT
*
2604848 TATATGTTAATAATATATT
1 TA-AT-TTAATAAAATATT
2604867 CATATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 10 0.32
20 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTTAATAAAATATTT
Found at i:2604910 original size:16 final size:17
Alignment explanation
Indices: 2604883--2604923 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2604873 ATTTTTAAAT
2604883 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
2604898 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
2604915 AAATTTTAT
1 AAATTTTAT
2604924 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:2605073 original size:7 final size:7
Alignment explanation
Indices: 2605061--2605121 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
2605051 GACAGGCTAA
2605061 AAAAAAG
1 AAAAAAG
2605068 AAAAAAG
1 AAAAAAG
**
2605075 -AATGAG
1 AAAAAAG
2605081 AAAAAAG
1 AAAAAAG
2605088 AAAAAAG
1 AAAAAAG
*
2605095 AAAAAGG
1 AAAAAAG
2605102 AAAGAAA-
1 AAA-AAAG
2605109 AAAATAA-
1 AAAA-AAG
2605116 AAAAAA
1 AAAAAA
2605122 TTATATATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
6 7 0.16
7 36 0.80
8 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:2605094 original size:27 final size:26
Alignment explanation
Indices: 2605061--2605119 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
2605051 GACAGGCTAA
*
2605061 AAAAAAGAAAAAAGAATGAGAAAAAAG
1 AAAAAAGAAAAAAGAAAGA-AAAAAAG
* *
2605088 AAAAAAGAAAAAGGAAAGAAAAAAAT
1 AAAAAAGAAAAAAGAAAGAAAAAAAG
2605114 AAAAAA
1 AAAAAA
2605120 AATTATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (26 bp):
AAAAAAGAAAAAAGAAAGAAAAAAAG
Found at i:2605501 original size:16 final size:18
Alignment explanation
Indices: 2605469--2605507 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2605459 TTTTAATATT
*
2605469 TATAAAATTTTTAATTAA
1 TATAAAATTTATAATTAA
2605487 -ATAAAA-TTATAATTAA
1 TATAAAATTTATAATTAA
2605503 TATAA
1 TATAA
2605508 TTTATTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATTTATAATTAA
Found at i:2606741 original size:202 final size:200
Alignment explanation
Indices: 2606522--2606919 Score: 685
Period size: 202 Copynumber: 2.0 Consensus size: 200
2606512 TTACATTAAC
2606522 TCATAAAATAATTAAAATTTA-TTTTAATAAAAAATTTAAATACATAATAATTATTTAATAAAAT
1 TCATAAAATAATTAAAATTTATTTTTAATAAAAAATTTAAATACATAATAATTATTTAATAAAAT
2606586 TTATTTTATAATTAAATTTTTATTAATAATAACTAAAATTTATAAAATTAAAAAAAGGGGCATAA
66 TTATTTTATAATTAAA-TTTTATTAATAATAACTAAAATTTATAAAATTAAAAAAA--GGCATAA
* *
2606651 CTCTAG-AGTACTTTTAAAATAAGCTACATGAATAGCTCGGTTGACACCTGTCCA-CTTAAATTT
128 CTCTAGTA-TACTTGT-AAATAAGCTACATGAATAGCTAGGTTGACACCTGTCCATCTTAAATTT
2606714 TTTTTTTCAA
191 TTTTTTTCAA
* *
2606724 TCATAAAATAATTAAAATTTATTTTTAATAAAAAATTTAAATACATTATTATTATTTAATAAAAT
1 TCATAAAATAATTAAAATTTATTTTTAATAAAAAATTTAAATACATAATAATTATTTAATAAAAT
2606789 TTATTTTATAATTAAATTTTATTAATAATAACTAAAATTTATAAAATTAAAAAAAGGCATAACTC
66 TTATTTTATAATTAAATTTTATTAATAATAACTAAAATTTATAAAATTAAAAAAAGGCATAACTC
*
2606854 TGGTATACTTGTAAATAAGCTACATGAATAGCTAGGTTGACACCTGTCCATCTTAAATTTTTTTT
131 TAGTATACTTGTAAATAAGCTACATGAATAGCTAGGTTGACACCTGTCCATCTTAAATTTTTTTT
2606919 T
196 T
2606920 AGCCTTAGGT
Statistics
Matches: 188, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
199 37 0.20
200 33 0.18
201 1 0.01
202 60 0.32
203 57 0.30
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (200 bp):
TCATAAAATAATTAAAATTTATTTTTAATAAAAAATTTAAATACATAATAATTATTTAATAAAAT
TTATTTTATAATTAAATTTTATTAATAATAACTAAAATTTATAAAATTAAAAAAAGGCATAACTC
TAGTATACTTGTAAATAAGCTACATGAATAGCTAGGTTGACACCTGTCCATCTTAAATTTTTTTT
TTCAA
Found at i:2606800 original size:17 final size:18
Alignment explanation
Indices: 2606783--2606830 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
2606773 TATTATTTAA
2606783 TAAAATTTATTTTATAAT
1 TAAAATTTATTTTATAAT
* * *
2606801 TAAATTTTATTAATAATAAC
1 TAAAATTTATT--TTATAAT
2606821 TAAAATTTAT
1 TAAAATTTAT
2606831 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAATTTATTTTATAAT
Found at i:2607071 original size:16 final size:16
Alignment explanation
Indices: 2607038--2607070 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2607028 TTATTTATAT
2607038 AATATATAAAAAATAA
1 AATATATAAAAAATAA
2607054 AATATAT-AAAAATAA
1 AATATATAAAAAATAA
2607069 AA
1 AA
2607071 AGTAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATATAAAAAATAA
Found at i:2607345 original size:15 final size:15
Alignment explanation
Indices: 2607322--2607351 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2607312 AATAAATTTT
*
2607322 TAATTTATTTTAAAA
1 TAATATATTTTAAAA
2607337 TAATATATTTTAAAA
1 TAATATATTTTAAAA
2607352 GATTGATCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATTTTAAAA
Found at i:2607580 original size:19 final size:19
Alignment explanation
Indices: 2607551--2607588 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
2607541 ATTTTAGATT
2607551 TTTTATATTTAAGTTTTTAA
1 TTTTATATTTAA-TTTTTAA
2607571 TTTT-TATTTAATTTTTAA
1 TTTTATATTTAATTTTTAA
2607589 ATGATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATATTTAATTTTTAA
Found at i:2608264 original size:21 final size:19
Alignment explanation
Indices: 2608240--2608294 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2608230 ATTATTAAAA
*
2608240 AAATAATTTTTTATAAGATAT
1 AAAT-ATTTTTTA-AAAATAT
*
2608261 AAATAGTTTTTAAAAATAT
1 AAATATTTTTTAAAAATAT
2608280 AAATATTTTTTAAAA
1 AAATATTTTTTAAAA
2608295 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 20 0.65
20 7 0.23
21 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AAATATTTTTTAAAAATAT
Found at i:2608270 original size:19 final size:18
Alignment explanation
Indices: 2608229--2608295 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
2608219 AAGTTTTGTG
* *
2608229 TATTATTAAAAAAAT-AA
1 TATTTTTAAAAATATAAA
*
2608246 T-TTTTTATAAGATATAAA
1 TATTTTTA-AAAATATAAA
2608264 TAGTTTTTAAAAATATAAA
1 TA-TTTTTAAAAATATAAA
*
2608283 TATTTTTTAAAAT
1 TATTTTTAAAAAT
2608296 TTTTTATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
16 5 0.12
17 6 0.15
18 13 0.32
19 11 0.27
20 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTTTTAAAAATATAAA
Found at i:2608495 original size:2 final size:2
Alignment explanation
Indices: 2608488--2608534 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
2608478 TCGTTATTTT
*
2608488 TA TA TA TA -A AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2608529 TA TA TA
1 TA TA TA
2608535 ATGGGGAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2611618 original size:27 final size:26
Alignment explanation
Indices: 2611582--2611663 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 26
2611572 AATAATAATA
2611582 ATAATATTTAAAATATTATATATTTAT
1 ATAAT-TTTAAAATATTATATATTTAT
*
2611609 ATAAATTTTAATATATTA-ATAATTTAT
1 AT-AATTTTAAAATATTATAT-ATTTAT
* * *
2611636 ATTATATAAAAATATT-TGATATTTAT
1 ATAATTTTAAAATATTAT-ATATTTAT
2611662 AT
1 AT
2611664 TATATTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 20 0.43
27 23 0.50
28 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
ATAATTTTAAAATATTATATATTTAT
Found at i:2611642 original size:20 final size:20
Alignment explanation
Indices: 2611594--2611665 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
2611584 AATATTTAAA
2611594 ATATTATATATTTATATAAATTT
1 ATATTATATA-TTA-AT-AATTT
2611617 -TA--ATATATTAATAATTT
1 ATATTATATATTAATAATTT
**
2611634 ATATTATATAAAAAT-ATTT
1 ATATTATATATTAATAATTT
2611653 GATATT-TATATTA
1 -ATATTATATATTA
2611666 TATTTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.12
18 4 0.10
19 12 0.29
20 18 0.44
22 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
ATATTATATATTAATAATTT
Found at i:2612443 original size:33 final size:33
Alignment explanation
Indices: 2612406--2612474 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 33
2612396 ACAAGAATAC
*
2612406 AAAATTAAAAATTAAT-TAAA-ATAT-AATATTAA
1 AAAAATAAAAA-TAATATAAATATATAAATA-TAA
*
2612438 AAAAATAAATATAATATAAATATATAAATATAA
1 AAAAATAAAAATAATATAAATATATAAATATAA
2612471 AAAA
1 AAAA
2612475 TATTTATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 4 0.12
32 13 0.41
33 11 0.34
34 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (33 bp):
AAAAATAAAAATAATATAAATATATAAATATAA
Found at i:2612464 original size:19 final size:19
Alignment explanation
Indices: 2612424--2612502 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
2612414 AAATTAATTA
* *
2612424 AAATATAATATTAAAAAAAT
1 AAATATAATA-TAAATATAT
2612444 AAATATAATATAAATATAT
1 AAATATAATATAAATATAT
2612463 AAATATAA-A-AAATATTTAT
1 AAATATAATATAAATA--TAT
* * *
2612482 AAATATTACATAAATTTAT
1 AAATATAATATAAATATAT
2612501 AA
1 AA
2612503 TATTTTAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.10
18 1 0.02
19 30 0.59
20 11 0.22
21 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATAATATAAATATAT
Found at i:2612469 original size:14 final size:14
Alignment explanation
Indices: 2612424--2612471 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2612414 AAATTAATTA
2612424 AAATAT-AATAT-T
1 AAATATAAATATAT
*
2612436 AAA-A-AAATAAAT
1 AAATATAAATATAT
2612448 ATAATATAAATATAT
1 A-AATATAAATATAT
2612463 AAATATAAA
1 AAATATAAA
2612472 AAATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 2 0.07
14 9 0.31
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:2612473 original size:31 final size:30
Alignment explanation
Indices: 2612414--2612474 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 30
2612404 ACAAAATTAA
2612414 AAATTAATTAAAATATAATATTAAAAAAAT
1 AAATTAATTAAAATATAATATTAAAAAAAT
2612444 AAATATAATATAAATATATAA-ATATAAAAAA
1 AAAT-TAAT-TAAA-ATATAATAT-TAAAAAA
2612475 TATTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 4 0.15
31 4 0.15
32 6 0.22
33 13 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (30 bp):
AAATTAATTAAAATATAATATTAAAAAAAT
Found at i:2612597 original size:33 final size:31
Alignment explanation
Indices: 2612563--2612632 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
2612553 TTCATATATA
*
2612563 AAATAATAAATACATAAAAATATATATAAAAT
1 AAATAATAAATACATAAAAA-ATATACAAAAT
* * *
2612595 AAATTATTAATATATAAAAAATATACAAAA-
1 AAATAATAAATACATAAAAAATATACAAAAT
*
2612625 ATATAATA
1 AAATAATA
2612633 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
30 5 0.16
31 9 0.29
32 17 0.55
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (31 bp):
AAATAATAAATACATAAAAAATATACAAAAT
Found at i:2612659 original size:32 final size:33
Alignment explanation
Indices: 2612558--2612660 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2612548 TTTTTTTCAT
* * *
2612558 ATATAAAATAATAAATACATAAAAATATATATAA
1 ATATAAATTATTAAATACA-AAAAATATATAAAA
* *
2612592 A-ATAAATTATTAATATATAAAAAATATACAAAA
1 ATATAAATTATTAA-ATACAAAAAATATATAAAA
* *
2612625 ATATAATATT-TTAAATA-AAAAAATAAATACAA
1 ATATAA-ATTATTAAATACAAAAAATATATAAAA
2612657 ATAT
1 ATAT
2612661 TTAAATTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
32 16 0.28
33 26 0.45
34 13 0.22
35 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (33 bp):
ATATAAATTATTAAATACAAAAAATATATAAAA
Found at i:2613128 original size:19 final size:20
Alignment explanation
Indices: 2613091--2613128 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2613081 TAATTTTAAA
* *
2613091 AAAGTTTTTTATATTATTTT
1 AAAGTTTTTCATATAATTTT
2613111 AAAGTTTTTCAT-TAATTT
1 AAAGTTTTTCATATAATTT
2613129 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
AAAGTTTTTCATATAATTTT
Found at i:2613527 original size:17 final size:16
Alignment explanation
Indices: 2613495--2613530 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2613485 AACATAATAT
*
2613495 TAATTTAATGATTAAA
1 TAATTTAATAATTAAA
2613511 TAATTTAAATAATTAAA
1 TAATTT-AATAATTAAA
2613528 TAA
1 TAA
2613531 AAGTTGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATTTAATAATTAAA
Found at i:2615071 original size:16 final size:17
Alignment explanation
Indices: 2615043--2615095 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
2615033 AATCTAAACT
2615043 TAAAATATA-TTGAAATC
1 TAAAATA-ACTTGAAATC
2615060 -AAAATAACTTG-AATC
1 TAAAATAACTTGAAATC
2615075 TAAAATAACTTGAAA-C
1 TAAAATAACTTGAAATC
2615091 TAAAA
1 TAAAA
2615096 CGACTTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 5 0.15
16 26 0.79
17 2 0.06
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.28
Consensus pattern (17 bp):
TAAAATAACTTGAAATC
Found at i:2615101 original size:16 final size:16
Alignment explanation
Indices: 2615060--2615111 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2615050 TATTGAAATC
* *
2615060 AAAATAACTTGAATCT
1 AAAACAACTTGAAACT
*
2615076 AAAATAACTTGAAACT
1 AAAACAACTTGAAACT
*
2615092 AAAACGACTT-AAACT
1 AAAACAACTTGAAACT
2615107 CAAAA
1 -AAAA
2615112 TAACCCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 5 0.16
16 27 0.84
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAACAACTTGAAACT
Found at i:2620081 original size:20 final size:21
Alignment explanation
Indices: 2620058--2620099 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2620048 TATATTTTTA
2620058 TTAATTTAAATT-TATTTAAT
1 TTAATTTAAATTATATTTAAT
2620078 TTAATTTAAATTAATATTTAAT
1 TTAATTTAAATT-ATATTTAAT
2620100 AATTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTTAAATTATATTTAAT
Found at i:2620091 original size:10 final size:10
Alignment explanation
Indices: 2620057--2620092 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2620047 ATATATTTTT
2620057 ATTAATTTAA
1 ATTAATTTAA
*
2620067 ATTTATTTAA
1 ATTAATTTAA
*
2620077 TTTAATTTAA
1 ATTAATTTAA
2620087 ATTAAT
1 ATTAAT
2620093 ATTTAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:2620102 original size:20 final size:18
Alignment explanation
Indices: 2620054--2620103 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
2620044 TGAATATATT
*
2620054 TTTATTAATTTAAATTTA
1 TTTAATAATTTAAATTTA
2620072 TTTAATTTAATTTAAATTAATA
1 TTTAA--TAATTTAAATT--TA
2620094 TTTAATAATT
1 TTTAATAATT
2620104 CAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.15
20 16 0.59
22 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATAATTTAAATTTA
Found at i:2620120 original size:48 final size:49
Alignment explanation
Indices: 2620068--2620168 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 49
2620058 TTAATTTAAA
* **
2620068 TTTATTT-AATTTAATT-T-AAATTAATATTTAATAATTCAAAAAATATTT
1 TTTATTTAAATTTAATTATAAAATAAATAAATAATAA-T-AAAAAATATTT
*
2620116 TTTATTTAAATTTAATTATAAAATAAATAAATATTAATAAAAAATATTT
1 TTTATTTAAATTTAATTATAAAATAAATAAATAATAATAAAAAATATTT
2620165 TTTA
1 TTTA
2620169 AAATTTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
48 7 0.15
49 24 0.52
50 2 0.04
51 13 0.28
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (49 bp):
TTTATTTAAATTTAATTATAAAATAAATAAATAATAATAAAAAATATTT
Found at i:2620146 original size:21 final size:21
Alignment explanation
Indices: 2620122--2620161 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2620112 ATTTTTTATT
*
2620122 TAAAT-TTAATTATAAAATAAA
1 TAAATATTAA-TAAAAAATAAA
2620143 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
2620162 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATTAATAAAAAATAAA
Found at i:2620488 original size:15 final size:16
Alignment explanation
Indices: 2620455--2620489 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2620445 AAAAAGTTAA
2620455 ATATACTTATATCGAAT
1 ATATACTTATATC-AAT
2620472 ATATACTTATATC-AT
1 ATATACTTATATCAAT
2620487 ATA
1 ATA
2620490 CTCGTCCCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATACTTATATCAAT
Found at i:2620806 original size:2 final size:2
Alignment explanation
Indices: 2620793--2620826 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2620783 AATTGAATTG
*
2620793 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2620827 TTAACGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2621704 original size:22 final size:20
Alignment explanation
Indices: 2621671--2621713 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
2621661 ATACAGTTTT
2621671 AATATTATTTAAAAATAATAAA
1 AATATTATTT-AAAATAA-AAA
2621693 AATA-TATATTAAAATAAAAA
1 AATATTAT-TTAAAATAAAAA
2621713 A
1 A
2621714 TTAAATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTATTTAAAATAAAAA
Found at i:2622122 original size:17 final size:18
Alignment explanation
Indices: 2622100--2622139 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2622090 TTATTACTTA
* *
2622100 TTTAACT-TTGAAATTTT
1 TTTAACTCTTAAAATTAT
2622117 TTTAACTCTTAAAATTAT
1 TTTAACTCTTAAAATTAT
2622135 TTTAA
1 TTTAA
2622140 TTATATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTAACTCTTAAAATTAT
Found at i:2625357 original size:13 final size:14
Alignment explanation
Indices: 2625333--2625370 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
2625323 AAAGATTATA
2625333 TAAATATTAAAATT
1 TAAATATTAAAATT
2625347 TAAAT-TTAAAATAAT
1 TAAATATTAAAAT--T
2625362 TAAATATTA
1 TAAATATTA
2625371 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 5 0.24
15 6 0.29
16 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:2625380 original size:23 final size:24
Alignment explanation
Indices: 2625351--2625395 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2625341 AAAATTTAAA
2625351 TTTAAAATAATTAAAT-ATTATTT
1 TTTAAAATAATTAAATAATTATTT
*
2625374 TTTAAAATAATTATATAATTAT
1 TTTAAAATAATTAAATAATTAT
2625396 ATAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTAAAATAATTAAATAATTATTT
Found at i:2626043 original size:12 final size:13
Alignment explanation
Indices: 2626010--2626054 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
2626000 TAGTTGGATA
2626010 AAAT-ATAATAAAT
1 AAATAATAAT-AAT
2626023 AAATAAATAATAAT
1 AAAT-AATAATAAT
2626037 -AATAATAATAAT
1 AAATAATAATAAT
2626049 AAATAA
1 AAATAA
2626055 AGGTATGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.31
13 12 0.41
14 3 0.10
15 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:2628189 original size:18 final size:18
Alignment explanation
Indices: 2628166--2628229 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
2628156 ATTGTTGATA
2628166 GATTGCTAAAACTTTTAG
1 GATTGCTAAAACTTTTAG
* *
2628184 GATTGCTAAATCTATCATTGATA
1 GATTGCTAAAACT-T--TT-A-G
2628207 GATTGCTAAAACTTTTAG
1 GATTGCTAAAACTTTTAG
2628225 G-TTGC
1 GATTGC
2628230 CATGTTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.11
18 13 0.35
19 2 0.05
20 2 0.05
21 2 0.05
22 2 0.05
23 12 0.32
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (18 bp):
GATTGCTAAAACTTTTAG
Found at i:2629655 original size:241 final size:240
Alignment explanation
Indices: 2629224--2629877 Score: 927
Period size: 241 Copynumber: 2.7 Consensus size: 240
2629214 TTTCCTGATC
* * *
2629224 TATTCCAAAGTTTAATCACCATAAGTAACTATAAGTTGTCATCATCATCATCAAACAGCAATTCT
1 TATTCCAAAGATTAATCACCATAAGTAACTA-AA--AG---TCATCATCATCAAACAACAATTCT
*
2629289 ATTTTTCCTTCACTTTAATGTTCTCCTGAATCATAAACATCTACATCATGCTCTTC-A-TTGGCA
60 ATTTTTCCTTCACTTTAATGTTCTCCTGAATCAT-ACCATCTACATCATGCTCTTCTAGTTGGCA
* * * * *
2629352 TCTTCCTCTTC-AAAATTGACTGGAAAGTTAAATCCTTTGATCTAGATCTTGCTTGCATTCTAGT
124 TCTTCCTCTTCAAAAATTGATTGGAAAGTTAAACCCTTTGATCTAAACCTCGCTTGCATTCTAGT
** *
2629416 ATAATTCCTTCCAACACCTGCAGTCCTTGCTTTTGGGCCCATGTCATTCTAG
189 ATAATTCCTTCCAACACCTGCAGTCCTTGCTACTGGACCCATGTCATTCTAG
* * *
2629468 TATTCCAAAGATTAATCGCCATAATTAACTAAAAGTCATCATCATCAAACAACAATTCTATGTTT
1 TATTCCAAAGATTAATCACCATAAGTAACTAAAAGTCATCATCATCAAACAACAATTCTATTTTT
*
2629533 CCTTCACTTTAATGTTCTCCTGAATCATACCATGTACATCATGCTCTTCTACGTTGGCATCTTCC
66 CCTTCACTTTAATGTTCTCCTGAATCATACCATCTACATCATGCTCTTCTA-GTTGGCATCTTCC
* **
2629598 TCATCAAAAATTGATTGGAAAGTTAAACCCTTTGATCTAAACCTCGCTTGCATTCTAGTATGCTT
130 TCTTCAAAAATTGATTGGAAAGTTAAACCCTTTGATCTAAACCTCGCTTGCATTCTAGTATAATT
* *
2629663 CCTTCCAACACCTGCAGTTCTTGCTACTGGACCCATGTCCTTCTAG
195 CCTTCCAACACCTGCAGTCCTTGCTACTGGACCCATGTCATTCTAG
* * * *
2629709 TATTCCAAAGATTAATTACCATAAGTAACTAATAGTCATCACCATCAAACAACAATTTTATTTTT
1 TATTCCAAAGATTAATCACCATAAGTAACTAAAAGTCATCATCATCAAACAACAATTCTATTTTT
* * *
2629774 CCTTCACTTTAATGTTCTCCTAAATCATACCATCTACATCATGCTCTTTTTTGTTGGCATCTTCC
66 CCTTCACTTTAATGTTCTCCTGAATCATACCATCTACATCATGCTC-TTCTAGTTGGCATCTTCC
* * *
2629839 TCTTCAAAAGTTGGTTGGAAAGTTAAAGCCTTTGATCTA
130 TCTTCAAAAATTGATTGGAAAGTTAAACCCTTTGATCTA
2629878 CATCATGCTC
Statistics
Matches: 369, Mismatches: 36, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
237 19 0.05
238 57 0.15
240 16 0.04
241 244 0.66
242 3 0.01
243 2 0.01
244 28 0.08
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (240 bp):
TATTCCAAAGATTAATCACCATAAGTAACTAAAAGTCATCATCATCAAACAACAATTCTATTTTT
CCTTCACTTTAATGTTCTCCTGAATCATACCATCTACATCATGCTCTTCTAGTTGGCATCTTCCT
CTTCAAAAATTGATTGGAAAGTTAAACCCTTTGATCTAAACCTCGCTTGCATTCTAGTATAATTC
CTTCCAACACCTGCAGTCCTTGCTACTGGACCCATGTCATTCTAG
Found at i:2629885 original size:68 final size:67
Alignment explanation
Indices: 2629805--2629944 Score: 244
Period size: 68 Copynumber: 2.1 Consensus size: 67
2629795 AAATCATACC
* * *
2629805 ATCTACATCATGCTCTTTTTTGTTGGCATCTTCCTCTTCAAAAGTTGGTTGGAAAGTTAAAGCCT
1 ATCTACATCATGCTCTTCTTTGTTGGCATCTTCCTCTTCAAAA-TTGATTGGAAAGTTAAAGCCC
2629870 TTG
65 TTG
2629873 ATCTACATCATGCTCTTCTTTGTTGGCATCTTCCTCTTCAAAATTGATTGGAAAGTTAAAGCCCT
1 ATCTACATCATGCTCTTCTTTGTTGGCATCTTCCTCTTCAAAATTGATTGGAAAGTTAAAGCCCT
2629938 TG
66 TG
2629940 ATCTA
1 ATCTA
2629945 GATCTCACTT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 27 0.39
68 42 0.61
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (67 bp):
ATCTACATCATGCTCTTCTTTGTTGGCATCTTCCTCTTCAAAATTGATTGGAAAGTTAAAGCCCT
TG
Found at i:2630187 original size:310 final size:308
Alignment explanation
Indices: 2629567--2630168 Score: 863
Period size: 310 Copynumber: 1.9 Consensus size: 308
2629557 TCATACCATG
2629567 TACATCATGCTCTTCTACGTTGGCATCTTCCTCATCAAAAATTGATTGGAAAGTTAAACCCTTTG
1 TACATCATGCTCTTCTACGTTGGCATCTTCCTCATCAAAAATTGATTGGAAAGTTAAACCCTTTG
** *
2629632 ATCTAAACCTCGCTTGCATTCTAGTATGCTTCCTTCCAACACCTGCAGTTCTTGCTACTGGACCC
66 ATCTAAACCTCGCTTGCATTCTAGTATAATTCCTTCCAACACCTGCAGTACTTGCTACTGGACCC
* * *
2629697 ATGTCCTTCTAGTATTCCAAAGATTAATTACCATAAGTAACTAATAGTCATCACCATCAAACAAC
131 ATGTCATTCAAGTATTCCAAAGATTAATCACCATAAGTAACTAATAGTCATCACCATC-AACAAC
* * * *
2629762 AATTTTATTTTTCCTTCACTTTAATGTTCTCCTAAATCATACCATCTACATCATGCTCTTTTTTG
195 AATTCTATGTTTCCTTCACTTTAATGTTCTCCTAAATCATACCATCTACATCATGCTCTTCTTCG
*
2629827 TTGGCATCTTCCTCTTCAAAAGTTGGTTGGAAAGTTAAAGCCTTTGATC
260 TTGGCATCTTCCTCTTCAAAAGTTGATTGGAAAGTTAAAGCCTTTGATC
** *
2629876 TACATCATGCTCTTCTTTGTTGGCATCTTCCTCTTC-AAAATTGATTGGAAAGTTAAAGCCC-TT
1 TACATCATGCTCTTCTACGTTGGCATCTTCCTCATCAAAAATTGATTGGAAAGTTAAA-CCCTTT
* * * * *
2629939 GATCTAGATCTCACTTGCATTTGCATTCTGGTATAATTCCTTCCAACACCTGCCGTACTTGCTAT
65 GATCTA-A--AC-CTCGC--TTGCATTCTAGTATAATTCCTTCCAACACCTGCAGTACTTGCTAC
** *
2630004 TGGACCCATGTCATTCAAGTATTCCAAAGATTAATCACTGTAAGTAACTAA-AGTCATCATCATC
124 TGGACCCATGTCATTCAAGTATTCCAAAGATTAATCACCATAAGTAACTAATAGTCATCACCATC
* **
2630068 -A-AACAATTCTATGTTTCCTTCACTTTAATGTTCTCCTGAATCATACCATCTATGTCATGCTCT
189 AACAACAATTCTATGTTTCCTTCACTTTAATGTTCTCCTAAATCATACCATCTACATCATGCTCT
*
2630131 TCTTCGTTGGCATCTTCCTCTTCAGAAGTTGATTGGAA
254 TCTTCGTTGGCATCTTCCTCTTCAAAAGTTGATTGGAA
2630169 TTGTAAACCG
Statistics
Matches: 260, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
308 29 0.11
309 37 0.14
310 91 0.35
311 2 0.01
312 4 0.02
313 12 0.05
314 85 0.33
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (308 bp):
TACATCATGCTCTTCTACGTTGGCATCTTCCTCATCAAAAATTGATTGGAAAGTTAAACCCTTTG
ATCTAAACCTCGCTTGCATTCTAGTATAATTCCTTCCAACACCTGCAGTACTTGCTACTGGACCC
ATGTCATTCAAGTATTCCAAAGATTAATCACCATAAGTAACTAATAGTCATCACCATCAACAACA
ATTCTATGTTTCCTTCACTTTAATGTTCTCCTAAATCATACCATCTACATCATGCTCTTCTTCGT
TGGCATCTTCCTCTTCAAAAGTTGATTGGAAAGTTAAAGCCTTTGATC
Found at i:2635345 original size:17 final size:16
Alignment explanation
Indices: 2635319--2635353 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2635309 TTAAAGAATG
*
2635319 ATATTTATATTTATAT
1 ATATTTATATTTAAAT
2635335 ATATATTATATTTAAAT
1 ATAT-TTATATTTAAAT
2635352 AT
1 AT
2635354 CAGATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTATATTTAAAT
Found at i:2637592 original size:17 final size:15
Alignment explanation
Indices: 2637533--2637601 Score: 50
Period size: 17 Copynumber: 4.3 Consensus size: 15
2637523 TTAAAAATCC
*
2637533 TTATTGA-AATAAAA
1 TTATTGATAATATAA
*
2637547 TTATTAGCAAAATATAA
1 TTATT-G-ATAATATAA
* *
2637564 TGAATAGATAATAGTAAA
1 T-TATTGATAATA-T-AA
2637582 TTATTGATAATATAA
1 TTATTGATAATATAA
2637597 TTATT
1 TTATT
2637602 AATTTCATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
14 5 0.12
15 8 0.19
16 7 0.16
17 18 0.42
18 5 0.12
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (15 bp):
TTATTGATAATATAA
Found at i:2639027 original size:28 final size:26
Alignment explanation
Indices: 2638982--2639048 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
2638972 TAGATATTTT
* *
2638982 AAAATTATTACATCAAATTAATTAGTCAA
1 AAAATTAATA-ATAAAATTAATT-G-CAA
2639011 AAAATTAATAATAAAATTAATTGCAA
1 AAAATTAATAATAAAATTAATTGCAA
*
2639037 TAAATT-ATAATA
1 AAAATTAATAATA
2639049 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.17
26 8 0.23
27 1 0.03
28 11 0.31
29 9 0.26
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (26 bp):
AAAATTAATAATAAAATTAATTGCAA
Found at i:2643249 original size:20 final size:20
Alignment explanation
Indices: 2643222--2643275 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
2643212 TTAAATTAAT
2643222 ATTTTTTTAAAAAAAAAGATA
1 ATTTTTTTAAAAAAAAA-ATA
* *
2643243 ATTTTTTTAAAATATAAATA
1 ATTTTTTTAAAAAAAAAATA
*
2643263 ATTTTTATAAAAA
1 ATTTTTTTAAAAA
2643276 TATTATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTTTTTAAAAAAAAAATA
Found at i:2643276 original size:21 final size:21
Alignment explanation
Indices: 2643224--2643278 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2643214 AAATTAATAT
*
2643224 TTTTTTAAAAA-AAAAGATAA
1 TTTTTTAAAAATATAAGATAA
*
2643244 TTTTTTTAAAATATAA-ATAA
1 TTTTTTAAAAATATAAGATAA
2643264 TTTTTATAAAAATAT
1 TTTTT-TAAAAATAT
2643279 TATATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTTTAAAAATATAAGATAA
Found at i:2643675 original size:3 final size:3
Alignment explanation
Indices: 2643667--2643703 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2643657 AATCCACCTT
2643667 TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2643704 TCGTTTCGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2643690 original size:20 final size:20
Alignment explanation
Indices: 2643665--2643703 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2643655 CCAATCCACC
2643665 TTTTATTATTATTATTATTA
1 TTTTATTATTATTATTATTA
2643685 TTTTATTATTATTATTATT
1 TTTTATTATTATTATTATT
2643704 TCGTTTCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTATTATTATTATTA
Found at i:2643692 original size:17 final size:17
Alignment explanation
Indices: 2643670--2643704 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2643660 CCACCTTTTA
2643670 TTATTATTATTATTATT
1 TTATTATTATTATTATT
2643687 TTATTATTATTATTATT
1 TTATTATTATTATTATT
2643704 T
1 T
2643705 CGTTTCGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTATTATTATT
Found at i:2644200 original size:15 final size:15
Alignment explanation
Indices: 2644164--2644239 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
2644154 TTTAATATTT
*
2644164 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATT-A
2644181 ATAAAATTATAATTA
1 ATAAAATTATAATTA
2644196 ATAAAATT-T-ATT-
1 ATAAAATTATAATTA
* *
2644208 TTAAAATATTTAATTA
1 ATAAAAT-TATAATTA
* *
2644224 ATAAATTTAAAATTA
1 ATAAAATTATAATTA
2644239 A
1 A
2644240 AATTTAATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
12 6 0.12
13 4 0.08
14 2 0.04
15 19 0.39
16 12 0.24
17 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAAATTATAATTA
Found at i:2644239 original size:28 final size:27
Alignment explanation
Indices: 2644177--2644256 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
2644167 AAATTTTTAA
2644177 TTAAA-TAAAATTATAATTAATAAAAT
1 TTAAATTAAAATTATAATTAATAAAAT
** *
2644203 TTATTTTAAAATATTTAATTAAT-AAAT
1 TTAAATTAAAAT-TATAATTAATAAAAT
*
2644230 TTAAAATTAAAATT-TAATCATATAAAA
1 TT-AAATTAAAATTATAATTA-ATAAAA
2644257 AATTTATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
26 8 0.19
27 15 0.35
28 20 0.47
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
TTAAATTAAAATTATAATTAATAAAAT
Found at i:2644256 original size:43 final size:43
Alignment explanation
Indices: 2644162--2644245 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
2644152 GTTTTAATAT
*
2644162 TTATAAAATTTTTAATTAAATAAAATTATAATTAATAAAATTTA
1 TTATAAAATATTTAATTAAATAAAATTATAA-TAATAAAATTTA
*
2644206 TTTTAAAATATTTAATT-AAT-AAATT-TAA-AATTAAAATTTA
1 TTATAAAATATTTAATTAAATAAAATTATAATAA-TAAAATTTA
2644246 ATCATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
39 2 0.05
40 9 0.24
41 3 0.08
42 5 0.14
43 3 0.08
44 15 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (43 bp):
TTATAAAATATTTAATTAAATAAAATTATAATAATAAAATTTA
Found at i:2644284 original size:22 final size:20
Alignment explanation
Indices: 2644249--2644297 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
2644239 AAATTTAATC
*
2644249 ATATAAAAAATTTATATAAA
1 ATATAAAAAATTTAGATAAA
*
2644269 ATATAAAGTAAATTTAGATATA
1 ATATAAA--AAATTTAGATAAA
2644291 ATATAAA
1 ATATAAA
2644298 TATAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
ATATAAAAAATTTAGATAAA
Found at i:2644572 original size:23 final size:23
Alignment explanation
Indices: 2644528--2644572 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2644518 CATGAATTGC
** *
2644528 GATATGATACTTTAAATTAAATT
1 GATATGATAAATTAAATAAAATT
*
2644551 GATATGATAAATTATATAAAAT
1 GATATGATAAATTAAATAAAAT
2644573 ATGCTATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (23 bp):
GATATGATAAATTAAATAAAATT
Found at i:2644707 original size:23 final size:23
Alignment explanation
Indices: 2644681--2644728 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2644671 AACACGACAT
*
2644681 AAACATAACATAGAAAATAAT-TA
1 AAACACAACATA-AAAATAATATA
*
2644704 AAACACAATATAAAAATAATATA
1 AAACACAACATAAAAATAATATA
2644727 AA
1 AA
2644729 TATGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (23 bp):
AAACACAACATAAAAATAATATA
Found at i:2644726 original size:11 final size:11
Alignment explanation
Indices: 2644679--2644739 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
2644669 GAAACACGAC
* *
2644679 ATAAACATAAC
1 ATAAAAATAAT
2644690 ATAGAAAATAAT
1 ATA-AAAATAAT
*
2644702 -TAAAACACAAT
1 ATAAAA-ATAAT
2644713 ATAAAAATAAT
1 ATAAAAATAAT
* *
2644724 ATAAATATGAT
1 ATAAAAATAAT
2644735 ATAAA
1 ATAAA
2644740 TAAGTAAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 3 0.07
11 27 0.66
12 11 0.27
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.25
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:2645252 original size:11 final size:10
Alignment explanation
Indices: 2645236--2645294 Score: 54
Period size: 9 Copynumber: 6.1 Consensus size: 10
2645226 TATATAAATA
2645236 AAAATATACAT
1 AAAATATA-AT
2645247 AAAATATAAT
1 AAAATATAAT
*
2645257 -AAAT-TATT
1 AAAATATAAT
*
2645265 AATATATAA-
1 AAAATATAAT
2645274 AAAATAT-AT
1 AAAATATAAT
2645283 AAAAATATAAT
1 -AAAATATAAT
2645294 A
1 A
2645295 TTTTAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
8 4 0.10
9 13 0.33
10 12 0.31
11 10 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATATAAT
Found at i:2645288 original size:37 final size:35
Alignment explanation
Indices: 2645227--2645321 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 35
2645217 ACGAATACAT
*
2645227 ATATAAATAAAAATATACATAAAATATAATAAATTATT-A
1 ATATAAA-AAAAATATATA-AAAATATAAT--ATT-TTAA
*
2645266 ATATATAAAAAATATATAAAAATATAATATTTTAA
1 ATATAAAAAAAATATATAAAAATATAATATTTTAA
2645301 ATATAAAAAAAATAATATAAA
1 ATATAAAAAAAAT-ATATAAA
2645322 TACGAGCTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
34 2 0.04
35 16 0.31
36 7 0.14
37 10 0.20
38 10 0.20
39 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
ATATAAAAAAAATATATAAAAATATAATATTTTAA
Found at i:2645321 original size:20 final size:22
Alignment explanation
Indices: 2645279--2645323 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
2645269 TATAAAAAAT
* *
2645279 ATATAAAAATATAATATTTTAA
1 ATATAAAAATATAATAATATAA
2645301 ATATAAAAA-A-AATAATATAA
1 ATATAAAAATATAATAATATAA
2645321 ATA
1 ATA
2645324 CGAGCTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATAAAAATATAATAATATAA
Found at i:2645358 original size:14 final size:14
Alignment explanation
Indices: 2645339--2645365 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2645329 TTATAAGTTA
2645339 TTTCTTTCTTTTTT
1 TTTCTTTCTTTTTT
2645353 TTTCTTTCTTTTT
1 TTTCTTTCTTTTT
2645366 CAGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTCTTTCTTTTTT
Found at i:2645413 original size:12 final size:12
Alignment explanation
Indices: 2645397--2645463 Score: 66
Period size: 12 Copynumber: 5.6 Consensus size: 12
2645387 AGCACAGGGT
2645397 TTTTTTTCTCTT-
1 TTTTTTTCT-TTC
2645409 TTTTTTTCTTTC
1 TTTTTTTCTTTC
*
2645421 TTTCTTTCTTTC
1 TTTTTTTCTTTC
* *
2645433 TTTTTTGCGTTC
1 TTTTTTTCTTTC
*
2645445 -TTCTTTCTTTC
1 TTTTTTTCTTTC
2645456 TTTCTTTT
1 TTT-TTTT
2645464 TCAGCTGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
11 10 0.23
12 31 0.70
13 3 0.07
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:2645414 original size:4 final size:4
Alignment explanation
Indices: 2645405--2645462 Score: 70
Period size: 4 Copynumber: 15.2 Consensus size: 4
2645395 GTTTTTTTTC
*
2645405 TCTT T-TT T-TT TCTT TCTT TCTT TCTT TCTT T-TT TGCGT TC-T TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT
2645450 TCTT TCTT TCTT T
1 TCTT TCTT TCTT T
2645463 TTCAGCTGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
3 12 0.24
4 35 0.71
5 2 0.04
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:2645448 original size:23 final size:23
Alignment explanation
Indices: 2645405--2645458 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2645395 GTTTTTTTTC
*
2645405 TCTTT-TTTTTTCTTTCTTTCTT
1 TCTTTCTTTTTTCGTTCTTTCTT
2645427 TCTTTCTTTTTTGCGTTC-TTCTT
1 TCTTTCTTTTTT-CGTTCTTTCTT
2645450 TCTTTCTTT
1 TCTTTCTTT
2645459 CTTTTTCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 20 0.69
24 4 0.14
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (23 bp):
TCTTTCTTTTTTCGTTCTTTCTT
Found at i:2645492 original size:10 final size:10
Alignment explanation
Indices: 2645477--2645501 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2645467 GCTGAATGCA
2645477 AAAAAAAAAC
1 AAAAAAAAAC
2645487 AAAAAAAAAC
1 AAAAAAAAAC
2645497 AAAAA
1 AAAAA
2645502 TACCACGTGT
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:2649571 original size:22 final size:21
Alignment explanation
Indices: 2649536--2649586 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2649526 ATAAGAGAAT
*
2649536 TTTTTATTTAATTTTATAATA
1 TTTTTATTAAATTTTATAATA
* *
2649557 TTTTTATTAATATTTTTTATTA
1 TTTTTATTAA-ATTTTATAATA
*
2649579 ATTTTATT
1 TTTTTATT
2649587 TTTAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTAAATTTTATAATA
Found at i:2649575 original size:13 final size:13
Alignment explanation
Indices: 2649547--2649597 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
2649537 TTTTATTTAA
2649547 TTTTA-TAATA-T
1 TTTTATTAATATT
2649558 TTTTATTAATATT
1 TTTTATTAATATT
2649571 TTTTATTAAT-TT
1 TTTTATTAATATT
2649583 TATTT-TTAAATATT
1 T-TTTATT-AATATT
2649597 T
1 T
2649598 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.14
12 10 0.29
13 17 0.49
14 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTATTAATATT
Found at i:2649588 original size:16 final size:15
Alignment explanation
Indices: 2649567--2649618 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
2649557 TTTTTATTAA
2649567 TATTTTTTATTAATTT
1 TATTTTTTATT-ATTT
* *
2649583 TATTTTTAAATATTT
1 TATTTTTTATTATTT
*
2649598 GATTTTTTTATTATTT
1 TA-TTTTTTATTATTT
2649614 TATTT
1 TATTT
2649619 GTTAAAATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TATTTTTTATTATTT
Found at i:2649591 original size:12 final size:13
Alignment explanation
Indices: 2649540--2649604 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 13
2649530 GAGAATTTTT
2649540 TATTTAATTTTATAA
1 TATTT-ATTTT-TAA
*
2649555 TATTT-TTATTAA
1 TATTTATTTTTAA
2649567 TATTT-TTTATTAA
1 TATTTATTT-TTAA
2649580 T-TTTATTTTTAAA
1 TATTTATTTTT-AA
2649593 TATTTGATTTTT
1 TATTT-ATTTTT
2649605 TTATTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
12 15 0.35
13 14 0.33
14 3 0.07
15 11 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:2649614 original size:31 final size:34
Alignment explanation
Indices: 2649569--2649633 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
2649559 TTTATTAATA
*
2649569 TTTTTTATTAATTTTATTT-TT-AAATATTTGAT
1 TTTTTTATTAATTTTATTTGTTAAAATACTTGAT
2649601 TTTTTTATT-ATTTTATTTGTTAAAATACTTGAT
1 TTTTTTATTAATTTTATTTGTTAAAATACTTGAT
2649634 ATAAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.30
32 11 0.37
33 10 0.33
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (34 bp):
TTTTTTATTAATTTTATTTGTTAAAATACTTGAT
Found at i:2650197 original size:19 final size:20
Alignment explanation
Indices: 2650175--2650219 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2650165 AAATATTAAA
2650175 ATATTATATAAATTT-TATT
1 ATATTATATAAATTTATATT
**
2650194 ATATT-TATTTATTTATATT
1 ATATTATATAAATTTATATT
2650213 ATATTAT
1 ATATTAT
2650220 TTTTATATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 14 0.64
20 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTATATAAATTTATATT
Found at i:2651141 original size:2 final size:2
Alignment explanation
Indices: 2651134--2651166 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2651124 GAGTGTATGC
2651134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2651167 AACTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2653342 original size:9 final size:8
Alignment explanation
Indices: 2653313--2653404 Score: 58
Period size: 9 Copynumber: 10.0 Consensus size: 8
2653303 CAATTAGACA
2653313 TTATGTTTT
1 TTAT-TTTT
*
2653322 TTATATTAT
1 TTAT-TTTT
2653331 TTATTTTGT
1 TTATTTT-T
2653340 TTATTTTT
1 TTATTTTT
*
2653348 TATTTTTTT
1 T-TATTTTT
2653357 TAATGATTTTT
1 T--T-ATTTTT
2653368 TTAGTTTTT
1 TTA-TTTTT
2653377 TTAATTTTT
1 TT-ATTTTT
2653386 CTTAATTATTT
1 -TT-ATT-TTT
2653397 TTATTTTT
1 TTATTTTT
2653405 AAATTCTTTG
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
8 8 0.11
9 42 0.60
10 11 0.16
11 9 0.13
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.76
Consensus pattern (8 bp):
TTATTTTT
Found at i:2653344 original size:16 final size:16
Alignment explanation
Indices: 2653325--2653358 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2653315 ATGTTTTTTA
2653325 TATTATTTATTTTGTT
1 TATTATTTATTTTGTT
* *
2653341 TATTTTTTATTTTTTT
1 TATTATTTATTTTGTT
2653357 TA
1 TA
2653359 ATGATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TATTATTTATTTTGTT
Found at i:2665880 original size:11 final size:12
Alignment explanation
Indices: 2665863--2665894 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
2665853 AATAATATAA
2665863 ATATAAAAATTT
1 ATATAAAAATTT
2665875 AT-T-AAAATTT
1 ATATAAAAATTT
2665885 ATATAAAAAT
1 ATATAAAAAT
2665895 AATTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.50
11 2 0.11
12 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAAAAATTT
Found at i:2665888 original size:22 final size:21
Alignment explanation
Indices: 2665863--2665949 Score: 71
Period size: 20 Copynumber: 4.3 Consensus size: 21
2665853 AATAATATAA
*
2665863 ATATAAAAATTTATTAAAATTT
1 ATATAAAAA-TAATTAAAATTT
2665885 ATATAAAAATAATTAAAA--T
1 ATATAAAAATAATTAAAATTT
*
2665904 ATACTAAATATAA-TATAAA--T
1 ATA-TAAAAATAATTA-AAATTT
2665924 ATAT--AAATACATTAAAATTT
1 ATATAAAAATA-ATTAAAATTT
2665944 ATATAA
1 ATATAA
2665950 TACATTTAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
17 4 0.07
18 4 0.07
19 9 0.17
20 20 0.37
21 8 0.15
22 9 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAAATAATTAAAATTT
Found at i:2665896 original size:28 final size:28
Alignment explanation
Indices: 2665857--2665949 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
2665847 AATATGAATA
*
2665857 ATATAAATATAAAAATTTATTAAAATTT
1 ATATAAATATAAAAATATATTAAAATTT
* * *
2665885 ATATAAAAATAATTAAAATATACT-AAATATA
1 ATAT--AAAT-ATAAAAATATATTAAAAT-TT
* *
2665916 ATATAAATATATAAATACATTAAAATTT
1 ATATAAATATAAAAATATATTAAAATTT
2665944 ATATAA
1 ATATAA
2665950 TACATTTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 20 0.39
29 8 0.16
30 8 0.16
31 15 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAAATATAAAAATATATTAAAATTT
Found at i:2665948 original size:20 final size:19
Alignment explanation
Indices: 2665875--2665974 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 19
2665865 ATAAAAATTT
2665875 ATTAAAATTTATATAAAAATA-
1 ATTAAAA-TTATAT--AAATAC
*
2665896 ATTAAAA-TATACTAAATAT
1 ATTAAAATTATA-TAAATAC
*
2665915 AATATAAA-TATATAAATAC
1 ATTA-AAATTATATAAATAC
2665934 ATTAAAATT-TATATAATAC
1 ATTAAAATTATATA-AATAC
*
2665953 ATTTAAAAATA-ATAAAATAC
1 A-TTAAAATTATAT-AAATAC
2665973 AT
1 AT
2665975 ATATAAAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
18 12 0.18
19 24 0.36
20 23 0.34
21 8 0.12
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAATTATATAAATAC
Found at i:2665979 original size:59 final size:58
Alignment explanation
Indices: 2665856--2665981 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 58
2665846 AAATATGAAT
** * *
2665856 AATATAAATATAAAAATTTATTAAAATTTATATAAAAATAATTAAAATATACTAAATAT
1 AATATAAATATAAAAATACATTAAAATTTATATAAAAAT-ATTAAAATATAATAAATAC
* *
2665915 AATATAAATATATAAATACATTAAAATTTATATAATACAT-TTAAAA-ATAATAAAATAC
1 AATATAAATATAAAAATACATTAAAATTTATATAA-AAATATTAAAATATAAT-AAATAC
2665973 ATATATAAA
1 A-ATATAAA
2665982 ATTTCAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
57 4 0.07
58 12 0.21
59 39 0.67
60 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (58 bp):
AATATAAATATAAAAATACATTAAAATTTATATAAAAATATTAAAATATAATAAATAC
Found at i:2670894 original size:34 final size:38
Alignment explanation
Indices: 2670814--2670898 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
2670804 ATATAATAAT
* *
2670814 TATTATTTAATTTTGATTAAAAAATATATAAATATTAA
1 TATTAATTAATTTTGATTAAAAAATAAATAAATATTAA
* * *
2670852 TATAAATTAATTTT-TTTAAATAATAAAT-AATA-TAA
1 TATTAATTAATTTTGATTAAAAAATAAATAAATATTAA
2670887 -ATTAATTAATTT
1 TATTAATTAATTT
2670899 AATAAAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 11 0.27
35 3 0.07
36 4 0.10
37 11 0.27
38 12 0.29
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
TATTAATTAATTTTGATTAAAAAATAAATAAATATTAA
Found at i:2670907 original size:14 final size:15
Alignment explanation
Indices: 2670890--2670928 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2670880 AATATAAATT
2670890 AATTAATTTAATAA-
1 AATTAATTTAATAAG
*
2670904 AATTAAGTTAATAAG
1 AATTAATTTAATAAG
*
2670919 ATTTAATTTA
1 AATTAATTTA
2670929 TCAGTGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
AATTAATTTAATAAG
Found at i:2670990 original size:78 final size:79
Alignment explanation
Indices: 2670890--2671061 Score: 256
Period size: 79 Copynumber: 2.2 Consensus size: 79
2670880 AATATAAATT
* ** *
2670890 AATTAATTTAATAAAATTAAGTTAATAAGATTTAATTTATCA-GTGAGTTTATTTTATTTTTATT
1 AATT-ATTAAATAAAAAAAAGTTAATAAAATTTAATTTATCATGTGAGTTTATTTTATTTTTATT
2670954 AAATTAAAAATTTTA
65 AAATTAAAAATTTTA
*
2670969 AATTATTAAATAAAAAAAAGTTAATAAAATTTAATTTATCATGTGAGTTTATTTTGTTTTTATTA
1 AATTATTAAATAAAAAAAAGTTAATAAAATTTAATTTATCATGTGAGTTTATTTTATTTTTATTA
*
2671034 AATTAAAATTTTTA
66 AATTAAAAATTTTA
* *
2671048 AATAAATAAATAAA
1 AATTATTAAATAAA
2671062 TTTTTTTATT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 33 0.39
79 51 0.61
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.47
Consensus pattern (79 bp):
AATTATTAAATAAAAAAAAGTTAATAAAATTTAATTTATCATGTGAGTTTATTTTATTTTTATTA
AATTAAAAATTTTA
Found at i:2679477 original size:45 final size:45
Alignment explanation
Indices: 2679428--2679514 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
2679418 AAAAGAGAAG
*
2679428 TAAAAGAATATAATTAGGTAAAGCAAAAAATGAGAAGGTGAAAAA
1 TAAAAGAATATAATTAGGTAAAGCAAAAAATGAAAAGGTGAAAAA
** *
2679473 TAAAAGAATATGTTTAGGTAAAGCGAAAAATGAAAAGGTGAA
1 TAAAAGAATATAATTAGGTAAAGCAAAAAATGAAAAGGTGAA
2679515 GGGTATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (45 bp):
TAAAAGAATATAATTAGGTAAAGCAAAAAATGAAAAGGTGAAAAA
Found at i:2682723 original size:37 final size:36
Alignment explanation
Indices: 2682675--2682790 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 36
2682665 ATTAAATTTG
2682675 ATAAT-TTTCATATAAAAATAATTAAAATAAAATAT
1 ATAATATTTCATATAAAAATAATTAAAATAAAATAT
*
2682710 ATAATATTATCATAATTAAAAT-A-TATAAATAAATAATAT
1 ATAATATT-TCAT-ATAAAAATAATTA-AAAT-AA-AATAT
* *
2682749 ATTGATATTT-ATATAAATAA-AATTATAATAAAA-AT
1 A-TAATATTTCATATAAA-AATAATTAAAATAAAATAT
*
2682784 TTAATAT
1 ATAATAT
2682791 AAACCCAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
34 5 0.08
35 7 0.11
36 6 0.09
37 15 0.23
38 17 0.26
39 9 0.14
40 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (36 bp):
ATAATATTTCATATAAAAATAATTAAAATAAAATAT
Found at i:2683450 original size:19 final size:18
Alignment explanation
Indices: 2683418--2683458 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 18
2683408 ATTTAAATGT
2683418 TTTATATATATATT-AAA
1 TTTATATATATATTAAAA
2683435 TTTATATATTATTATTAAAA
1 TTTATATA-TA-TATTAAAA
2683455 TTTA
1 TTTA
2683459 AATTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 4 0.19
20 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATATATATTAAAA
Found at i:2683509 original size:73 final size:72
Alignment explanation
Indices: 2683371--2683509 Score: 156
Period size: 73 Copynumber: 1.9 Consensus size: 72
2683361 TTATAATTTT
* * * * * *
2683371 TTATTATTTAAATTTAAATTTATAAAATTATTTTAAAATTTAAATGTTTTATATATATATTAAAT
1 TTATTATTAAAATTTAAATTAATAAAATTATTTTAAAATTTAAATGTTTAAAAAATATAATAAAT
2683436 TTATATA
66 TTATATA
* * *
2683443 TTATTATTAAAATTTAAATTAAATAATATTATTTTTTAAA-TTAAAT-TTATAAAAAATCTAATA
1 TTATTATTAAAATTTAAATT-AATAAAATTA-TTTTAAAATTTAAATGTT-TAAAAAATATAATA
2683506 AATT
63 AATT
2683510 AAGATTTAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
72 21 0.38
73 27 0.49
74 7 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (72 bp):
TTATTATTAAAATTTAAATTAATAAAATTATTTTAAAATTTAAATGTTTAAAAAATATAATAAAT
TTATATA
Found at i:2683998 original size:14 final size:14
Alignment explanation
Indices: 2683944--2684051 Score: 80
Period size: 14 Copynumber: 7.6 Consensus size: 14
2683934 TCAGTTGTTT
**
2683944 TTAATATTTATACC
1 TTAATATTTATATA
*
2683958 TTATTATTTATAT-
1 TTAATATTTATATA
*
2683971 TATATATATATATATA
1 T-TA-ATATTTATATA
2683987 TTAATATTTATATA
1 TTAATATTTATATA
* *
2684001 TT-ATAATTAT-TT
1 TTAATATTTATATA
2684013 TTAATATATTATATA
1 TTAATAT-TTATATA
2684028 TTTAAT-TTTAATATA
1 -TTAATATTT-ATATA
*
2684043 ATAATATTT
1 TTAATATTT
2684052 TTTATTATTT
Statistics
Matches: 75, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
12 3 0.04
13 11 0.15
14 35 0.47
15 20 0.27
16 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATATTTATATA
Found at i:2684000 original size:20 final size:19
Alignment explanation
Indices: 2683975--2684042 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 19
2683965 TTATATTATA
2683975 TATATATATATATTAATATT
1 TATATATATATATTAAT-TT
*
2683995 TATATAT-TATAATTATTTT
1 TATATATATAT-ATTAATTT
2684014 TAATATATTATATATTTAATTT
1 T-ATATA-TATATA-TTAATTT
2684036 TA-ATATA
1 TATATATA
2684043 ATAATATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 8 0.20
20 20 0.49
21 3 0.07
22 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATATATATTAATTT
Found at i:2684062 original size:10 final size:10
Alignment explanation
Indices: 2684047--2684108 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
2684037 AATATAATAA
2684047 TATTTTTTAT
1 TATTTTTTAT
2684057 TA-TTTTTA-
1 TATTTTTTAT
*
2684065 -A-GTTTTAT
1 TATTTTTTAT
2684073 TATTTTTTAT
1 TATTTTTTAT
*
2684083 TATATTTTAAT
1 TAT-TTTTTAT
2684094 TATTTTTATAT
1 TATTTTT-TAT
2684105 TATT
1 TATT
2684109 ATAATTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 6 0.14
9 7 0.16
10 15 0.35
11 15 0.35
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:2684104 original size:17 final size:17
Alignment explanation
Indices: 2683981--2684105 Score: 64
Period size: 17 Copynumber: 7.4 Consensus size: 17
2683971 TATATATATA
* *
2683981 TATATATTAA-TATTTA
1 TATATTTTAATTATTTT
*
2683997 TATATTATAATTATTTT
1 TATATTTTAATTATTTT
* *
2684014 TAATATATT-A-TATATT
1 T-ATATTTTAATTATTTT
**
2684030 TA-ATTTTAA-TATAAT
1 TATATTTTAATTATTTT
* *
2684045 AATATTTTTTATTATTTT
1 TATA-TTTTAATTATTTT
*
2684063 TA-AGTTTTATTATTTTTTAT
1 TATA-TTTTA--ATTATTT-T
2684083 TATATTTTAATTATTTT
1 TATATTTTAATTATTTT
2684100 TATATT
1 TATATT
2684106 ATTATAATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 19
0.69 0.14 0.16
Matches are distributed among these distances:
14 4 0.05
15 8 0.10
16 15 0.18
17 24 0.29
18 16 0.20
19 6 0.07
20 8 0.10
21 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (17 bp):
TATATTTTAATTATTTT
Found at i:2684108 original size:20 final size:21
Alignment explanation
Indices: 2684067--2684107 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2684057 TATTTTTAAG
2684067 TTTT-ATTATTTTTTATTATA
1 TTTTAATTATTTTTTATTATA
2684087 TTTTAATTATTTTTATATTAT
1 TTTTAATTATTTTT-TATTAT
2684108 TATAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTAATTATTTTTTATTATA
Found at i:2684113 original size:20 final size:20
Alignment explanation
Indices: 2683970--2684114 Score: 59
Period size: 20 Copynumber: 6.8 Consensus size: 20
2683960 ATTATTTATA
*
2683970 TTATATATATATATATATTAATAT
1 TTATAT-TAT-TATA-ATT-ATTT
2683994 TTATA-TATTATAATTATTT
1 TTATATTATTATAATTATTT
*
2684013 TTA-ATATATTATATATTTAATT
1 TTATAT-TATTATA-A-TTATTT
*
2684035 TTA-A-TATAATAA-TATTT
1 TTATATTATTATAATTATTT
*
2684052 TT-TATTATTTTTAAGTTTTATTATT
1 TTATATTA-TTATAA---TTA-T-TT
* *
2684077 TTTTATTATATTTTAATTATTT
1 TTATA-T-TATTATAATTATTT
2684099 TTATATTATTATAATT
1 TTATATTATTATAATT
2684115 TAATATTTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 36
0.69 0.06 0.26
Matches are distributed among these distances:
17 7 0.07
18 3 0.03
19 11 0.11
20 25 0.26
21 6 0.06
22 18 0.19
23 3 0.03
24 9 0.09
25 4 0.04
26 2 0.02
27 7 0.07
28 2 0.02
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATATTATTATAATTATTT
Found at i:2684487 original size:20 final size:21
Alignment explanation
Indices: 2684452--2684490 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2684442 GGTTCTGCCC
2684452 TTTTTTTCAAAGTTTTTTTTT
1 TTTTTTTCAAAGTTTTTTTTT
*
2684473 TTTTTTTTAAA-TTTTTTT
1 TTTTTTTCAAAGTTTTTTT
2684491 CATCTGTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTTTTCAAAGTTTTTTTTT
Found at i:2686753 original size:11 final size:12
Alignment explanation
Indices: 2686725--2686755 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2686715 AAGGTTCGAG
2686725 GAGGCTGAAAAA
1 GAGGCTGAAAAA
2686737 GAGGCTGAAAAA
1 GAGGCTGAAAAA
2686749 G-GGCTGA
1 GAGGCTGA
2686756 CTCTGATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.42, C:0.10, G:0.39, T:0.10
Consensus pattern (12 bp):
GAGGCTGAAAAA
Found at i:2687462 original size:2 final size:2
Alignment explanation
Indices: 2687455--2687483 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2687445 ATATTCAATT
2687455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2687484 TGAGACTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2687967 original size:2 final size:2
Alignment explanation
Indices: 2687960--2687989 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2687950 GAAGAAATAC
2687960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2687990 CGACCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2688746 original size:23 final size:23
Alignment explanation
Indices: 2688717--2688774 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
2688707 AATACAAATT
*
2688717 AATAATAAATTAAAAT-TTATATA
1 AATAATAAATTAAAATATAATA-A
*
2688740 AATAATATAATTATAATATAATAA
1 AATAATA-AATTAAAATATAATAA
2688764 AATATATAAAT
1 AATA-ATAAAT
2688775 ATGACACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.23
24 16 0.53
25 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAATAAATTAAAATATAATAA
Found at i:2690048 original size:21 final size:22
Alignment explanation
Indices: 2690002--2690054 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
2689992 CTGGCCTAGT
*
2690002 ATTAATAAATATAAATATTAAG
1 ATTAATAAATATAAATATTAAA
*
2690024 ATTAA-AATTATAAAT-TTAATA
1 ATTAATAAATATAAATATTAA-A
2690045 ATTATATAAA
1 ATTA-ATAAA
2690055 GTGTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 6 0.24
23 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTAATAAATATAAATATTAAA
Found at i:2692129 original size:2 final size:2
Alignment explanation
Indices: 2692122--2692146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2692112 TATCAATCAC
2692122 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2692147 CCTTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2692632 original size:18 final size:19
Alignment explanation
Indices: 2692589--2692634 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2692579 ATAAATTTTG
2692589 ATATTTT-TATTAATTTAT
1 ATATTTTATATTAATTTAT
* *
2692607 ATTTTTTTATATT-TTTTAT
1 A-TATTTTATATTAATTTAT
2692626 ATATTTTAT
1 ATATTTTAT
2692635 TTTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATATTTTATATTAATTTAT
Found at i:2692633 original size:28 final size:26
Alignment explanation
Indices: 2692584--2692647 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
2692574 ATAATATAAA
*
2692584 TTTTGATA-TTTTTATTAATTTATATT
1 TTTTTATATTTTTTATTAATTTAT-TT
*
2692610 TTTTTATATTTTTTATATATTTTATTT
1 TTTTTATATTTTTTAT-TAATTTATTT
*
2692637 TATATTATATT
1 T-TTTTATATT
2692648 AATATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.22
27 10 0.31
28 15 0.47
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTATATTTTTTATTAATTTATTT
Found at i:2692635 original size:26 final size:27
Alignment explanation
Indices: 2692584--2692647 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
2692574 ATAATATAAA
*
2692584 TTTTGATA-TTTTTATTAATTTATATT
1 TTTTTATATTTTTTATTAATTTATATT
2692610 TTTTTATATTTTTTA-TATATTT-TATT
1 TTTTTATATTTTTTATTA-ATTTATATT
2692636 TTATATTATATT
1 TT-T-TTATATT
2692648 AATATTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 15 0.45
27 11 0.33
28 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTTATATTTTTTATTAATTTATATT
Found at i:2692661 original size:26 final size:25
Alignment explanation
Indices: 2692594--2692661 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 25
2692584 TTTTGATATT
* *
2692594 TTTATTAAT-TTATATTTTTTTATA
1 TTTATTAATATTATAATATTTTATA
*
2692618 TTTTTTATATATT-T--TATTTTATA
1 TTTATTA-ATATTATAATATTTTATA
2692641 TTATATTAATATTATAATATT
1 TT-TATTAATATTATAATATT
2692662 ATAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 15 0.43
24 11 0.31
25 3 0.09
26 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTAATATTATAATATTTTATA
Found at i:2699721 original size:21 final size:20
Alignment explanation
Indices: 2699697--2699749 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
2699687 ATATTTGATC
2699697 TAAATTTTATTATAAAAATTA
1 TAAATTTTATTATAAAAA-TA
* * *
2699718 TAAATATTAATATTAAAATA
1 TAAATTTTATTATAAAAATA
*
2699738 -AATTTTTATTAT
1 TAAATTTTATTAT
2699750 TATATAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
21 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATTTTATTATAAAAATA
Found at i:2699747 original size:22 final size:24
Alignment explanation
Indices: 2699722--2699767 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2699712 AAATTATAAA
*
2699722 TATTA-ATATTAA-AATAAATTTT
1 TATTATATATAAACAATAAATTTT
2699744 TATTATTATATAAACAATAAATTT
1 TATTA-TATATAAACAATAAATTT
2699768 AAACTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATATATAAACAATAAATTTT
Found at i:2702040 original size:4 final size:4
Alignment explanation
Indices: 2702033--2702057 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2702023 GTGGCTCCCT
2702033 CCAG CCAG CCAG CCAG CCAG CCAG C
1 CCAG CCAG CCAG CCAG CCAG CCAG C
2702058 ACCTCATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.52, G:0.24, T:0.00
Consensus pattern (4 bp):
CCAG
Found at i:2704436 original size:3 final size:3
Alignment explanation
Indices: 2704428--2704452 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2704418 TTCTTTTTAG
2704428 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2704453 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2705203 original size:13 final size:13
Alignment explanation
Indices: 2705151--2705208 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
2705141 TTAAGTTAAT
*
2705151 AAAATTTATTTAA
1 AAAATTTATATAA
2705164 AAATATTTA-ATAA
1 AAA-ATTTATATAA
2705177 ATAAATTTAATATATAA
1 A-AAA-TT--TATATAA
2705194 AAAATTTATATAA
1 AAAATTTATATAA
2705207 AA
1 AA
2705209 TATAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 17 0.45
14 9 0.24
15 2 0.05
16 5 0.13
17 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTATATAA
Found at i:2705226 original size:17 final size:17
Alignment explanation
Indices: 2705204--2705236 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2705194 AAAATTTATA
2705204 TAAAATATAAAATAAAT
1 TAAAATATAAAATAAAT
*
2705221 TAAAATATAACATAAA
1 TAAAATATAAAATAAA
2705237 CACAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATATAAAATAAAT
Found at i:2706740 original size:2 final size:2
Alignment explanation
Indices: 2706733--2706766 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2706723 AAGCGGGGGA
2706733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2706767 CATAGAGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2707417 original size:20 final size:20
Alignment explanation
Indices: 2707392--2707437 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
2707382 TTTTGAATTG
2707392 ATTTAAAATAATA-ATTTTTA
1 ATTT-AAATAATATATTTTTA
2707412 ATTTAAATAATATA-TTTT-
1 ATTTAAATAATATATTTTTA
2707430 ATTTAAAT
1 ATTTAAAT
2707438 TTAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAATAATATATTTTTA
Found at i:2710344 original size:29 final size:28
Alignment explanation
Indices: 2710300--2710383 Score: 134
Period size: 29 Copynumber: 3.0 Consensus size: 28
2710290 TCTTCACTTT
*
2710300 TTTTTTTTG-TTTTTTTTTTGTTTTTCC
1 TTTTTTTTGTTTTTTTTTTTCTTTTTCC
2710327 TTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTGTTTT-TTTTTTTCTTTTTCC
*
2710356 TTTTTTTTGTTTTTTTTTTCCTTTTTCC
1 TTTTTTTTGTTTTTTTTTTTCTTTTTCC
2710384 AATTGCCATG
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
27 9 0.17
28 17 0.32
29 27 0.51
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (28 bp):
TTTTTTTTGTTTTTTTTTTTCTTTTTCC
Found at i:2710373 original size:21 final size:22
Alignment explanation
Indices: 2710311--2710381 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 22
2710301 TTTTTTTGTT
2710311 TTTTTTTTGTTTTTCCTTTTT--
1 TTTTTTTTGTTTTT-CTTTTTCC
*
2710332 TTTGTTTTGTTTTTTTCTTTTTCC
1 TTT-TTTT-TGTTTTTCTTTTTCC
2710356 TTTTTTTTGTTTTT-TTTTTCC
1 TTTTTTTTGTTTTTCTTTTTCC
2710377 TTTTT
1 TTTTT
2710382 CCAATTGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.34
22 16 0.36
23 10 0.23
24 3 0.07
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.85
Consensus pattern (22 bp):
TTTTTTTTGTTTTTCTTTTTCC
Done.