Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 8 of 240
Found at i:3040570 original size:16 final size:16
Alignment explanation
Indices: 3040549--3040580 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3040539 GCAATAAATG
3040549 AATTTGAAACTACTTA
1 AATTTGAAACTACTTA
3040565 AATTTGAAACTACTTA
1 AATTTGAAACTACTTA
3040581 GGACCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTTGAAACTACTTA
Found at i:3043589 original size:28 final size:28
Alignment explanation
Indices: 3043534--3043602 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
3043524 TTTTAGAAAT
* *** *
3043534 ATAATAATATATGATCTTACTTTCAAAA
1 ATAATAATATATGATATTAAAATAAAAA
3043562 ATAATAATATATGATATTAAAATAAAAA
1 ATAATAATATATGATATTAAAATAAAAA
*
3043590 TTAATATATATAT
1 ATAATA-ATATAT
3043603 TAAGTTTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (28 bp):
ATAATAATATATGATATTAAAATAAAAA
Found at i:3043820 original size:14 final size:14
Alignment explanation
Indices: 3043798--3043831 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3043788 AGCTGTGTTT
*
3043798 GTTTATTTGTAAAA
1 GTTTTTTTGTAAAA
3043812 GTTTTTTTGTAAAA
1 GTTTTTTTGTAAAA
3043826 GTTTTT
1 GTTTTT
3043832 CAACATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTTTTTTGTAAAA
Found at i:3044044 original size:18 final size:19
Alignment explanation
Indices: 3044023--3044060 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3044013 TTATAAATGA
3044023 TTTAATCA-AAATAATTTT
1 TTTAATCATAAATAATTTT
*
3044041 TTTAATTATTAAATAATTTT
1 TTTAATCA-TAAATAATTTT
3044061 ATCATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATCATAAATAATTTT
Found at i:3045150 original size:30 final size:30
Alignment explanation
Indices: 3045086--3045151 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
3045076 TTTTTCTGAT
*
3045086 TTAT-TTTGATTTAAATTTCATAATATATA
1 TTATATTTGATTTAAACTTCATAATATATA
* *
3045115 -AATATTTGATTTTAACTTCA-AATATATTA
1 TTATATTTGATTTAAACTTCATAATATA-TA
3045144 TTATATTT
1 TTATATTT
3045152 ATTCTGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 8 0.27
29 16 0.53
30 6 0.20
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATATTTGATTTAAACTTCATAATATATA
Found at i:3048179 original size:19 final size:18
Alignment explanation
Indices: 3048141--3048175 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3048131 TAAATTTTAA
3048141 ATTTTAAATAATATAAAT
1 ATTTTAAATAATATAAAT
3048159 ATTTATAAA-AATATAAA
1 ATTT-TAAATAATATAAA
3048176 ATATAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTTAAATAATATAAAT
Found at i:3049440 original size:20 final size:20
Alignment explanation
Indices: 3049414--3049459 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3049404 AATTTTTTCT
*
3049414 TATAAAAAATAAT-TAAAAA
1 TATAAAAAATAATCAAAAAA
*
3049433 TATAAAAAATCATCAAAAAA
1 TATAAAAAATAATCAAAAAA
3049453 TATAAAA
1 TATAAAA
3049460 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
TATAAAAAATAATCAAAAAA
Found at i:3049441 original size:10 final size:9
Alignment explanation
Indices: 3049414--3049478 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
3049404 AATTTTTTCT
3049414 TATAAAAAA
1 TATAAAAAA
*
3049423 TAATTAAAAA
1 T-ATAAAAAA
3049433 TATAAAAAA
1 TATAAAAAA
3049442 TCATCAAAAAA
1 T-AT-AAAAAA
**
3049453 TATAAAATT
1 TATAAAAAA
3049462 TATTAAAAAA
1 TA-TAAAAAA
*
3049472 GATAAAA
1 TATAAAA
3049479 TTTAATAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
9 20 0.44
10 18 0.40
11 7 0.16
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (9 bp):
TATAAAAAA
Found at i:3049469 original size:19 final size:19
Alignment explanation
Indices: 3049428--3049488 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
3049418 AAAAATAATT
* * *
3049428 AAAAATATAAAAAATCATCA
1 AAAAATAT-AAAATTTATTA
3049448 AAAAATATAAAATTTATTA
1 AAAAATATAAAATTTATTA
* *
3049467 AAAAAGATAAAATTTAATA
1 AAAAATATAAAATTTATTA
3049486 AAA
1 AAA
3049489 CTTATTTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 28 0.78
20 8 0.22
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATATAAAATTTATTA
Found at i:3049541 original size:21 final size:21
Alignment explanation
Indices: 3049503--3049542 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3049493 TTTACATTTT
*
3049503 TATAAAAACATATTAAAATTC
1 TATAAAAACATATAAAAATTC
3049524 TATAAAAATCATA-AAAAAT
1 TATAAAAA-CATATAAAAAT
3049543 ATTAAAAGTG
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:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAACATATAAAAATTC
Found at i:3050014 original size:20 final size:18
Alignment explanation
Indices: 3049989--3050041 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
3049979 TTAATTCAAG
3049989 TTTTATAGTCTTTTAATAGT
1 TTTTATA-TCTTTTAATA-T
3050009 TTTTATAAAT-TTTTAATAT
1 TTTTAT--ATCTTTTAATAT
3050028 TTTTAATATCTTTT
1 TTTT-ATATCTTTT
3050042 TTACAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.07
19 9 0.31
20 16 0.55
21 1 0.03
22 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTATATCTTTTAATAT
Found at i:3050041 original size:10 final size:9
Alignment explanation
Indices: 3049999--3050041 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
3049989 TTTTATAGTC
3049999 TTTTAATAGT
1 TTTTAATA-T
*
3050009 TTTTATAAAT
1 TTTTA-ATAT
3050019 TTTTAATAT
1 TTTTAATAT
3050028 TTTTAATAT
1 TTTTAATAT
3050037 CTTTT
1 -TTTT
3050042 TTACAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 12 0.41
10 15 0.52
11 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTAATAT
Found at i:3050062 original size:21 final size:20
Alignment explanation
Indices: 3050038--3050084 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
3050028 TTTTAATATC
3050038 TTTTTTACAATTTCTTATTA-T
1 TTTTTTACAA-TT-TTATTACT
* *
3050059 TTTTTAAGAATTTTATTACT
1 TTTTTTACAATTTTATTACT
3050079 TTTTTT
1 TTTTTT
3050085 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 8 0.36
21 8 0.36
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTTACAATTTTATTACT
Found at i:3053388 original size:18 final size:18
Alignment explanation
Indices: 3053365--3053469 Score: 92
Period size: 18 Copynumber: 5.7 Consensus size: 18
3053355 GTTGTATATA
*
3053365 TTAATAACGTATTTTATT
1 TTAATAATGTATTTTATT
3053383 TTAATAATGTATATTTCATATGCT
1 TTAATAATG--TATTT--TAT--T
3053407 ATTAATAATGTATTTTA-T
1 -TTAATAATGTATTTTATT
* *
3053425 TTCATAATGTA---TATA
1 TTAATAATGTATTTTATT
3053440 TTAATAATGTATTTTATT
1 TTAATAATGTATTTTATT
3053458 TTAATAATGTAT
1 TTAATAATGTAT
3053470 ATTTCATATG
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
14 2 0.03
15 10 0.14
17 10 0.14
18 24 0.34
20 5 0.07
21 2 0.03
22 3 0.04
23 5 0.07
24 1 0.01
25 9 0.13
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (18 bp):
TTAATAATGTATTTTATT
Found at i:3053410 original size:43 final size:43
Alignment explanation
Indices: 3053363--3053490 Score: 152
Period size: 43 Copynumber: 3.2 Consensus size: 43
3053353 CAGTTGTATA
*
3053363 TATTAATAACGTATTTTATTTTAATAATGTATATTTCATATGC
1 TATTAATAATGTATTTTATTTTAATAATGTATATTTCATATGC
*
3053406 TATTAATAATGTATTTTA-TTTCATAATG------T-ATA---
1 TATTAATAATGTATTTTATTTTAATAATGTATATTTCATATGC
3053438 TATTAATAATGTATTTTATTTTAATAATGTATATTTCATATGC
1 TATTAATAATGTATTTTATTTTAATAATGTATATTTCATATGC
*
3053481 TATTATTAAT
1 TATTAATAAT
3053491 TAATTTCAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
32 18 0.26
33 9 0.13
35 3 0.04
36 1 0.01
39 1 0.01
40 3 0.04
42 9 0.13
43 26 0.37
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (43 bp):
TATTAATAATGTATTTTATTTTAATAATGTATATTTCATATGC
Found at i:3053426 original size:28 final size:30
Alignment explanation
Indices: 3053383--3053472 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 30
3053373 GTATTTTATT
*
3053383 TTAATAATGTA---TATTTCAT-ATG-CTA
1 TTAATAATGTATTTTATTTCATAATGTATA
3053408 TTAATAATGTATTTTATTTCATAATGTATATA
1 TTAATAATGTATTTTATTTCATAATG--TATA
*
3053440 TTAATAATGTATTTTATTTTAATAATGTATA
1 TTAATAATGTATTTTA-TTTCATAATGTATA
3053471 TT
1 TT
3053473 TCATATGCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
25 11 0.20
28 8 0.15
29 3 0.05
31 6 0.11
32 18 0.33
33 9 0.16
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (30 bp):
TTAATAATGTATTTTATTTCATAATGTATA
Found at i:3053446 original size:32 final size:33
Alignment explanation
Indices: 3053406--3053471 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
3053396 TTTCATATGC
*
3053406 TATTAATAATGTATTTTA-TTTCATAATGTATA
1 TATTAATAATGTATTTTATTTTAATAATGTATA
3053438 TATTAATAATGTATTTTATTTTAATAATGTATA
1 TATTAATAATGTATTTTATTTTAATAATGTATA
3053471 T
1 T
3053472 TTCATATGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (33 bp):
TATTAATAATGTATTTTATTTTAATAATGTATA
Found at i:3060432 original size:15 final size:14
Alignment explanation
Indices: 3060406--3060437 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
3060396 TCAATTTAAT
3060406 TAAAATTTTAATAA
1 TAAAATTTTAATAA
3060420 TAAAA-TTT-ATAA
1 TAAAATTTTAATAA
3060432 TAAAAT
1 TAAAAT
3060438 ATGATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.53
13 3 0.18
14 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATTTTAATAA
Found at i:3062996 original size:123 final size:123
Alignment explanation
Indices: 3062854--3063105 Score: 504
Period size: 123 Copynumber: 2.0 Consensus size: 123
3062844 TTTGAAATCA
3062854 TATATAATCAATTTTCAAAGCAAAAGAAGAAGATATTTTAGTATAATAAACATGAATAATTAATA
1 TATATAATCAATTTTCAAAGCAAAAGAAGAAGATATTTTAGTATAATAAACATGAATAATTAATA
3062919 AACTTATTTAGGTTTTAAAAATTGTTATTTTAGAAACTTTTAAAAATTTTAAGTTTTT
66 AACTTATTTAGGTTTTAAAAATTGTTATTTTAGAAACTTTTAAAAATTTTAAGTTTTT
3062977 TATATAATCAATTTTCAAAGCAAAAGAAGAAGATATTTTAGTATAATAAACATGAATAATTAATA
1 TATATAATCAATTTTCAAAGCAAAAGAAGAAGATATTTTAGTATAATAAACATGAATAATTAATA
3063042 AACTTATTTAGGTTTTAAAAATTGTTATTTTAGAAACTTTTAAAAATTTTAAGTTTTT
66 AACTTATTTAGGTTTTAAAAATTGTTATTTTAGAAACTTTTAAAAATTTTAAGTTTTT
3063100 TATATA
1 TATATA
3063106 TTTTTTTATA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 129 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (123 bp):
TATATAATCAATTTTCAAAGCAAAAGAAGAAGATATTTTAGTATAATAAACATGAATAATTAATA
AACTTATTTAGGTTTTAAAAATTGTTATTTTAGAAACTTTTAAAAATTTTAAGTTTTT
Found at i:3077078 original size:14 final size:14
Alignment explanation
Indices: 3077059--3077086 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3077049 TCCTTCTTTT
3077059 ATACTATTCATTTG
1 ATACTATTCATTTG
3077073 ATACTATTCATTTG
1 ATACTATTCATTTG
3077087 TCACTTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
ATACTATTCATTTG
Found at i:3077460 original size:4 final size:4
Alignment explanation
Indices: 3077451--3077481 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3077441 GCTCAAAGTT
3077451 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
3077482 TGTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:3083637 original size:8 final size:8
Alignment explanation
Indices: 3083626--3083657 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3083616 TAAGTTATTA
3083626 TATTATAT
1 TATTATAT
*
3083634 TATTATAA
1 TATTATAT
3083642 TATTATAT
1 TATTATAT
3083650 TATTATAT
1 TATTATAT
3083658 AGATAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:3083644 original size:16 final size:16
Alignment explanation
Indices: 3083620--3083656 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3083610 AATAAGTAAG
*
3083620 TTATTATATTATATTA
1 TTATAATATTATATTA
3083636 TTATAATATTATATTA
1 TTATAATATTATATTA
3083652 TTATA
1 TTATA
3083657 TAGATAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAATATTATATTA
Found at i:3084740 original size:25 final size:25
Alignment explanation
Indices: 3084712--3084870 Score: 174
Period size: 25 Copynumber: 6.6 Consensus size: 25
3084702 ACTTTAGCGC
3084712 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
3084737 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * *
3084762 GCTCTCTGACTACTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
3084787 GCTCTCTGATT-TTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTAGT
**
3084811 GCTCTCTG--T-TTAGCACACCT-GT
1 GCTCTCTGATTATTAGCAC-GTTAGT
*
3084833 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
3084855 GCTCTCTG-TTCATTAG
1 GCTCTCTGATT-ATTAG
3084871 TGCATACAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.01
22 35 0.30
23 1 0.01
24 19 0.16
25 60 0.52
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:3086898 original size:56 final size:56
Alignment explanation
Indices: 3086824--3086995 Score: 344
Period size: 56 Copynumber: 3.1 Consensus size: 56
3086814 CGATTAATTG
3086824 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
1 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
3086880 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
1 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
3086936 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
1 GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
3086992 GATA
1 GATA
3086996 TCATATCTTA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 116 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (56 bp):
GATACAAGTTAAAATTATAAAATGTTAGAAACTATCATATATTAATTAATTCCATT
Found at i:3093501 original size:74 final size:74
Alignment explanation
Indices: 3093380--3093527 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
3093370 TGGACACATG
* *
3093380 TATATTTACTTCTTTGAAGAGTTTTCATGCGTTTTATGAGTCATTGGAAGATCGTATTTCAATGC
1 TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
3093445 CCTTGTATA
66 CCTTGTATA
*
3093454 TATATTTGCTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
1 TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
3093519 CCTTGTATA
66 CCTTGTATA
3093528 GGGTTAAATG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (74 bp):
TATATTTACTTCTTTGAAGAGTTTTCATGCATTTTATGAGTCATTGGAAGATCATATTTCAATGC
CCTTGTATA
Found at i:3099940 original size:19 final size:18
Alignment explanation
Indices: 3099916--3099951 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3099906 CAACCACTTC
3099916 TTCTTTTTTCTTTTTTTTT
1 TTCTTTTTT-TTTTTTTTT
3099935 TTCTTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTTT
3099952 GCAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTTTT
Found at i:3099949 original size:13 final size:12
Alignment explanation
Indices: 3099919--3099948 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3099909 CCACTTCTTC
3099919 TTTTTTCTTTTT
1 TTTTTTCTTTTT
3099931 TTTTTTCTTTTT
1 TTTTTTCTTTTT
3099943 TTTTTT
1 TTTTTT
3099949 TTTGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:3102639 original size:26 final size:26
Alignment explanation
Indices: 3102597--3102652 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3102587 CTATAAATTG
3102597 ATTAAAATATTTAAAAAATCATAA-AA
1 ATTAAAATATTT-AAAAATCATAATAA
* *
3102623 ATTAAAA-ATTCTTAAAATTATAATAA
1 ATTAAAATATT-TAAAAATCATAATAA
3102649 ATTA
1 ATTA
3102653 TACAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
ATTAAAATATTTAAAAATCATAATAA
Found at i:3103845 original size:21 final size:21
Alignment explanation
Indices: 3103801--3103880 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
3103791 TCATTTCTGT
* * *
3103801 CATAGCCCCCACCACCACCTC
1 CATAGCCACCACCGCCACCAC
* *
3103822 CATAGCCACCACTGCCCCCAC
1 CATAGCCACCACCGCCACCAC
**
3103843 CATAGCTGCCACCGCCACCAC
1 CATAGCCACCACCGCCACCAC
*
3103864 CATATCCACCACCGCCA
1 CATAGCCACCACCGCCA
3103881 TAACCGCTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.25, C:0.56, G:0.09, T:0.10
Consensus pattern (21 bp):
CATAGCCACCACCGCCACCAC
Found at i:3108652 original size:26 final size:26
Alignment explanation
Indices: 3108601--3108653 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3108591 ATTAATCAAA
*
3108601 AAGCCCACAAAGAACATTTAATCGGG
1 AAGCCCACAAAGAACATATAATCGGG
* *
3108627 AAGCTCACAAAGAGCAATATAA-CGGG
1 AAGCCCACAAAGAAC-ATATAATCGGG
3108653 A
1 A
3108654 CGTTTATAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (26 bp):
AAGCCCACAAAGAACATATAATCGGG
Found at i:3109693 original size:13 final size:13
Alignment explanation
Indices: 3109675--3109702 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3109665 CTTTATTTTG
3109675 TTATTTTTCATCT
1 TTATTTTTCATCT
3109688 TTATTTTTCATCT
1 TTATTTTTCATCT
3109701 TT
1 TT
3109703 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTTTCATCT
Found at i:3110567 original size:20 final size:18
Alignment explanation
Indices: 3110537--3110579 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3110527 CCAGAGTTTA
3110537 CTGAACA-TTTTCAATAATT
1 CTGAACATTTTTC-AT-ATT
3110556 CTGAATCATTTTTCATATT
1 CTGAA-CATTTTTCATATT
3110575 CTGAA
1 CTGAA
3110580 AATAATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.59
20 4 0.18
21 5 0.23
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (18 bp):
CTGAACATTTTTCATATT
Found at i:3111535 original size:67 final size:67
Alignment explanation
Indices: 3111427--3111558 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
3111417 TTTTCAATTC
* *
3111427 AGAGAGCACATTATCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTACCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
3111492 CA
66 CA
* *
3111494 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACTAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTACCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
3111559 TAATATAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (67 bp):
AGAGAGCACACTACCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:3118268 original size:61 final size:61
Alignment explanation
Indices: 3118193--3118318 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
3118183 GAAAGACAAA
3118193 AAGTACCCTTATAATGATATAATTTATTTGAAATATGGTTATTTTAGTAATTTCTTTGACT
1 AAGTACCCTTATAATGATATAATTTATTTGAAATATGGTTATTTTAGTAATTTCTTTGACT
3118254 AAGTACCCTTATAATGATATAATTTATTTGAAATATGGTTATTTTAGTAATTTCTTTGACT
1 AAGTACCCTTATAATGATATAATTTATTTGAAATATGGTTATTTTAGTAATTTCTTTGACT
3118315 AAGT
1 AAGT
3118319 TGGTGTCGAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (61 bp):
AAGTACCCTTATAATGATATAATTTATTTGAAATATGGTTATTTTAGTAATTTCTTTGACT
Found at i:3118284 original size:33 final size:31
Alignment explanation
Indices: 3118192--3118286 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 31
3118182 TGAAAGACAA
3118192 AAAGTACCCTTATAATGATATAATTTATTTG
1 AAAGTACCCTTATAATGATATAATTTATTTG
*** * *
3118223 AAA-TATGGTTAT--T-TTAGTAATTTCTTTG
1 AAAGTACCCTTATAATGATA-TAATTTATTTG
3118251 ACTAAGTACCCTTATAATGATATAATTTATTTG
1 A--AAGTACCCTTATAATGATATAATTTATTTG
3118284 AAA
1 AAA
3118287 TATGGTTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
27 2 0.04
28 12 0.26
30 8 0.17
31 11 0.23
33 12 0.26
34 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (31 bp):
AAAGTACCCTTATAATGATATAATTTATTTG
Found at i:3123535 original size:16 final size:16
Alignment explanation
Indices: 3123466--3123533 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
3123456 TTTGGTTCGC
3123466 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3123482 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3123498 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * * *
3123514 TATAATGGAATAGATG
1 TGTATTGGATTAGAGG
3123530 TGTA
1 TGTA
3123534 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3123567 original size:45 final size:44
Alignment explanation
Indices: 3123516--3123608 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 44
3123506 ATTAGAGGTA
* * *
3123516 TAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAATG
1 TAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAATG
* **
3123561 TAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAATG
1 TAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAATG
3123605 TAAT
1 TAAT
3123609 AGAGGTGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.43
45 24 0.57
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (44 bp):
TAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAATG
Found at i:3123791 original size:18 final size:17
Alignment explanation
Indices: 3123770--3123804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3123760 TTATTATTTA
*
3123770 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3123788 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3123805 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3123798 original size:28 final size:27
Alignment explanation
Indices: 3123728--3123800 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
3123718 TTTATTACCA
*
3123728 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
3123756 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
3123783 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
3123801 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:3123938 original size:18 final size:17
Alignment explanation
Indices: 3123917--3123951 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3123907 TTATTATTAA
*
3123917 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3123935 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3123952 TCTTAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3123963 original size:147 final size:149
Alignment explanation
Indices: 3123689--3123963 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
3123679 ATGATTATTG
*
3123689 TTATTGTTATTTAAATTTTAATAAGATTATTTATTACCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATACCAAAAATAAATAATTTAATCATATTTAA
*
3123754 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
3123819 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
3123838 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATACCAAAAATAAATAATTTAATCATATTTAA
3123901 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
3123964 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATACCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:3124028 original size:15 final size:15
Alignment explanation
Indices: 3124010--3124065 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3124000 GATACTGTAA
3124010 AATATAAATTAAAAT
1 AATATAAATTAAAAT
3124025 AATA-ATAATTAAATAT
1 AATATA-AATTAAA-AT
*
3124041 ATTAT-AATTAAAAT
1 AATATAAATTAAAAT
*
3124055 -ATATAATTTAA
1 AATATAAATTAA
3124066 TAAAATTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
15 18 0.53
16 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAATTAAAAT
Found at i:3124032 original size:147 final size:147
Alignment explanation
Indices: 3123730--3124043 Score: 345
Period size: 147 Copynumber: 2.1 Consensus size: 147
3123720 TATTACCAAA
*
3123730 AATAAATAATTTAATCATATTTAAACATAATTATTATTTAATATATTTTAATTAAAATATATAAT
1 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
* * * * ** * ** * * *
3123795 TTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAATTTTAATA
66 TTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATCATAATATTGAAACTGTAATA
* *
3123860 AGATTATTAATATCAAT
131 AGATTATAAATATAAAT
3123877 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
1 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
* ** *
3123942 TTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTG
66 TTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-AAATCATAATAT-TGAAACTG
3124007 T-A-AA-A-TATAAAT-TAAAAT
126 TAATAAGATTATAAATAT-AAAT
*
3124025 AAT-AATAATTAAAT-ATATT
1 AATAAATAATTTAATCATATT
3124044 ATAATTAAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
146 5 0.04
147 98 0.70
148 12 0.09
149 5 0.04
150 6 0.04
151 10 0.07
152 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (147 bp):
AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
TTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATCATAATATTGAAACTGTAATA
AGATTATAAATATAAAT
Found at i:3124056 original size:16 final size:16
Alignment explanation
Indices: 3124016--3124061 Score: 69
Period size: 15 Copynumber: 3.0 Consensus size: 16
3124006 GTAAAATATA
3124016 AATTAAAATA-ATAAT
1 AATTAAAATATATAAT
*
3124031 AATT-AAATATATTAT
1 AATTAAAATATATAAT
3124046 AATTAAAATATATAAT
1 AATTAAAATATATAAT
3124062 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 5 0.19
15 12 0.44
16 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAATATATAAT
Found at i:3124130 original size:61 final size:61
Alignment explanation
Indices: 3123945--3124131 Score: 174
Period size: 61 Copynumber: 3.1 Consensus size: 61
3123935 ATATAATTTA
*
3123945 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATAATCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * *
3124006 GTAAAATATAAATTAA-AA-TAATAATAATTAAAT--ATATTA-T--AATTAAAATATATAAT-T
1 ATAAAAT-T--CTTAATAATTAATAAT-CTTATATGAAT-TTACTCAAATCATAATATATGATAC
3124063 T
61 T
*
3124064 AATAAAATTCTTAATAATTAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATAATCTTATATGAATTTACTCAAATCATAATATATGATACT
3124126 ATAAAA
1 ATAAAA
3124132 GAAAATTTGA
Statistics
Matches: 94, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
56 4 0.04
57 7 0.07
58 11 0.12
59 22 0.23
61 28 0.30
62 11 0.12
63 7 0.07
64 4 0.04
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATAATCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:3124203 original size:120 final size:120
Alignment explanation
Indices: 3123897--3124192 Score: 488
Period size: 120 Copynumber: 2.5 Consensus size: 120
3123887 TTAATCATAT
*
3123897 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
3123962 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 TAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAA
*
3124018 TTAAAATAA-TAATAATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAAATAATTAAT-ATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
3124082 TAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAA
65 TAATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAA
* *
3124137 TTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -TTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
3124193 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
119 6 0.04
120 149 0.91
121 9 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (120 bp):
TTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
AATAGTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAA
Found at i:3124930 original size:16 final size:16
Alignment explanation
Indices: 3124909--3124944 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3124899 TAAGAAATCA
3124909 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
3124925 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
3124941 CAGC
1 CAGC
3124945 TCCTGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (16 bp):
CAGCCATGTACTCCTG
Found at i:3127186 original size:23 final size:24
Alignment explanation
Indices: 3127141--3127186 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3127131 GAAATCTAAA
*
3127141 ATTTATATTTAATTTTACTTTTTGT
1 ATTTATATTT-ATTATACTTTTTGT
3127166 ATTTATATTT-TTATACTTTTT
1 ATTTATATTTATTATACTTTTT
3127187 TAGTTTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTATATTTATTATACTTTTTGT
Found at i:3140331 original size:4 final size:4
Alignment explanation
Indices: 3140324--3140376 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
3140314 TATGCATGCG
* **
3140324 TGTA TGTA TGTA TG-A TGTA TGCA TGCG TGTA TGTA TGTA TGTAA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT-A TGTA
3140372 TGTA T
1 TGTA T
3140377 CGAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.84
5 4 0.09
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:3140340 original size:27 final size:27
Alignment explanation
Indices: 3140310--3140373 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
3140300 AAATTTCTTG
3140310 GATGTATGCATGCGTGTATGTATGTAT
1 GATGTATGCATGCGTGTATGTATGTAT
3140337 GATGTATGCATGCGTGTATGTATGTAT
1 GATGTATGCATGCGTGTATGTATGTAT
3140364 GTAATGTATG
1 G--ATGTATG
3140374 TATCGAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 28 0.80
29 7 0.20
ACGTcount: A:0.23, C:0.06, G:0.30, T:0.41
Consensus pattern (27 bp):
GATGTATGCATGCGTGTATGTATGTAT
Found at i:3144446 original size:46 final size:46
Alignment explanation
Indices: 3144379--3144562 Score: 278
Period size: 46 Copynumber: 4.0 Consensus size: 46
3144369 GGGGATATAG
3144379 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
1 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
3144425 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
1 ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
* * * * *
3144471 GTCTATTTATTTTTCCAGATTACTTAGCATGATGGAGAGATTATTAG
1 ATCTATTTA-TTTACCATATTACTTAGCATGATTGAGAGATTATTAC
* * *
3144518 ATCTATTCATTTACCATATTACTTGGTATGATTTGAGAGATTATT
1 ATCTATTTATTTACCATATTACTTAGCATGA-TTGAGAGATTATT
3144563 TCCTTCGTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
46 72 0.58
47 52 0.42
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (46 bp):
ATCTATTTATTTACCATATTACTTAGCATGATTGAGAGATTATTAC
Found at i:3145316 original size:15 final size:15
Alignment explanation
Indices: 3145298--3145334 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3145288 TTTATTTATT
3145298 TATTTTTTATAATTA
1 TATTTTTTATAATTA
*
3145313 TATTTATTATAATTA
1 TATTTTTTATAATTA
3145328 TATTTTT
1 TATTTTT
3145335 ACTCACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATAATTA
Found at i:3146498 original size:18 final size:18
Alignment explanation
Indices: 3146475--3146510 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3146465 GTTTATTTTG
3146475 TTTAATAAAGAAAAGGAA
1 TTTAATAAAGAAAAGGAA
3146493 TTTAATAAAGAAAAGGAA
1 TTTAATAAAGAAAAGGAA
3146511 AGTGAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (18 bp):
TTTAATAAAGAAAAGGAA
Found at i:3148899 original size:15 final size:14
Alignment explanation
Indices: 3148881--3148927 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
3148871 CTGAAATTTT
3148881 TAAAATTTAAAAATA
1 TAAAA-TTAAAAATA
3148896 TAAAAATTAAAAATGA
1 T-AAAATTAAAAAT-A
*
3148912 TCAAATT-AAAATA
1 TAAAATTAAAAATA
3148925 TAA
1 TAA
3148928 GTACTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 14 0.50
16 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
TAAAATTAAAAATA
Found at i:3151688 original size:96 final size:96
Alignment explanation
Indices: 3151524--3151716 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
3151514 CAATGCTCTC
*
3151524 AGTGACCCTTAGCTCCACTGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
1 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
3151589 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
66 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
*
3151620 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCATCTTGGTGTTTC
1 AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
3151685 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
66 CGTCCTTGTAATCTGTAATCCGAAATGAGGT
3151716 A
1 A
3151717 TTGCTGCTTG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (96 bp):
AGTGACCCTTAGCTCCAATGATGAAGTAAATGACCTTGATTTTTCAAGCTTCACCTTGGTGTTTC
CGTCCTTGTAATCTGTAATCCGAAATGAGGT
Found at i:3156296 original size:2 final size:2
Alignment explanation
Indices: 3156289--3156313 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3156279 AAGTATCATT
3156289 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
3156314 TTTAGTTCAT
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:3160567 original size:3 final size:3
Alignment explanation
Indices: 3160559--3160583 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3160549 ATAAGCTTTC
3160559 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3160584 ACAGAATACA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3184588 original size:60 final size:59
Alignment explanation
Indices: 3184524--3184670 Score: 172
Period size: 61 Copynumber: 2.5 Consensus size: 59
3184514 AAAAGAGTAG
** * * *
3184524 GTACCAAATTAAGAAAATTTGTCAAGTTTAGGTACCAAATTGGATCCCCAAAAAT-TTTAA
1 GTACCAAATTAAGAAAAAATGTCAAATTTAGGTACCAAATTGAAT--CAAAAAATATTTAA
*
3184584 GTACCAACTTAAGAAAAAAATGTCAAATTTAGGTACCAAATTGAATCAAAAAATATTTAA
1 GTACCAAATTAAG-AAAAAATGTCAAATTTAGGTACCAAATTGAATCAAAAAATATTTAA
* * *
3184644 ATATCAAATT-AGAAAAAATATCAAATT
1 GTACCAAATTAAGAAAAAATGTCAAATT
3184671 CGAATACCAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 14 0.19
59 9 0.12
60 24 0.32
61 28 0.37
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (59 bp):
GTACCAAATTAAGAAAAAATGTCAAATTTAGGTACCAAATTGAATCAAAAAATATTTAA
Found at i:3212915 original size:19 final size:19
Alignment explanation
Indices: 3212877--3212912 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3212867 TATTATAAAA
3212877 AATATATATATTTTTTTTC
1 AATATATATATTTTTTTTC
3212896 AATATATA-ATTTTTTTT
1 AATATATATATTTTTTTT
3212913 TCACTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
AATATATATATTTTTTTTC
Found at i:3212924 original size:20 final size:19
Alignment explanation
Indices: 3212887--3212925 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3212877 AATATATATA
*
3212887 TTTTTTTTCAATATATAAT
1 TTTTTTTTCAATAAATAAT
*
3212906 TTTTTTTTCACTAGAATAAT
1 TTTTTTTTCAATA-AATAAT
3212926 GAGTGTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTTTTCAATAAATAAT
Found at i:3216912 original size:20 final size:22
Alignment explanation
Indices: 3216887--3216929 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
3216877 TGTTATCAAT
*
3216887 TTAATTA-TATATTT-TAATTA
1 TTAATTATTAAATTTATAATTA
3216907 TTAATTATTAAATTTATAATTA
1 TTAATTATTAAATTTATAATTA
3216929 T
1 T
3216930 AACTGTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATTAAATTTATAATTA
Found at i:3217212 original size:21 final size:21
Alignment explanation
Indices: 3217174--3217214 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3217164 ACAACCAAAG
*
3217174 TTAAACTATAATTATTAAAAT
1 TTAAAATATAATTATTAAAAT
3217195 TTAAAATA-AATTATTTAAAA
1 TTAAAATATAATTA-TTAAAA
3217215 GAAGAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATATAATTATTAAAAT
Found at i:3221680 original size:31 final size:30
Alignment explanation
Indices: 3221642--3221700 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
3221632 ATATATTTAC
*
3221642 TATAATAAAACAAAAAAATAATATAATAATG
1 TATAATAAAACAAAAAAAGAATA-AATAATG
*
3221673 TATAATAAAACAAATAAAGAATAAATAA
1 TATAATAAAACAAAAAAAGAATAAATAA
3221701 AAAGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (30 bp):
TATAATAAAACAAAAAAAGAATAAATAATG
Found at i:3222453 original size:24 final size:24
Alignment explanation
Indices: 3222421--3222480 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
3222411 GTGTTTTGCA
3222421 ATTGAAATTGATTG-ATTTAGTATGTG
1 ATTG-AATTGATTGAATTTA-TAT-TG
*
3222447 A-TGAATTTATTGAATTTATATTG
1 ATTGAATTGATTGAATTTATATTG
*
3222470 ATTGGATTGAT
1 ATTGAATTGAT
3222481 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.10
24 18 0.62
25 7 0.24
26 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (24 bp):
ATTGAATTGATTGAATTTATATTG
Found at i:3222770 original size:40 final size:40
Alignment explanation
Indices: 3222637--3222751 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 40
3222627 ACTTCGAGTC
*
3222637 GATGAGACACTGGGTGTCAATTTACTACTTC-AGATTAATTT
1 GATGAGACACTGGGTGTCAATTTATTACTTCGA-ATTAA-TT
* * * *
3222678 GATGAGGCACTCGGTGCCAA---ATTACTTCGATTTAATT
1 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTAATT
3222715 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTA
1 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTA
3222752 TCCAATGAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
37 19 0.31
38 11 0.18
39 1 0.02
40 13 0.21
41 17 0.28
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGAATTAATT
Found at i:3225360 original size:16 final size:16
Alignment explanation
Indices: 3225323--3225364 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3225313 AAATTAAAAG
*
3225323 TTATTTTTTAATTTAA
1 TTATTATTTAATTTAA
3225339 TGTATTATTT-ATTTATA
1 T-TATTATTTAATTTA-A
3225356 TTATTATTT
1 TTATTATTT
3225365 TTCACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTATTTAATTTAA
Found at i:3240293 original size:21 final size:22
Alignment explanation
Indices: 3240264--3240310 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3240254 CAGAAGGAGT
*
3240264 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3240286 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3240307 GAGT
1 GAGT
3240311 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3247261 original size:14 final size:15
Alignment explanation
Indices: 3247242--3247278 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3247232 GATTTGATAC
3247242 AAACAATCAA-CTAT
1 AAACAATCAACCTAT
*
3247256 AAACAA-AAACCTAT
1 AAACAATCAACCTAT
3247270 AAACAATCA
1 AAACAATCA
3247279 CAATCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 2 0.11
14 16 0.84
15 1 0.05
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACAATCAACCTAT
Found at i:3248008 original size:11 final size:11
Alignment explanation
Indices: 3247992--3248026 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
3247982 AAGCAATCAC
3247992 AAAAAAGAAAA
1 AAAAAAGAAAA
3248003 AAAAAAGAAAA
1 AAAAAAGAAAA
3248014 AAGAAGAAGAAAA
1 AA-AA-AAGAAAA
3248027 TCTAATCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
12 2 0.09
13 7 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:3249275 original size:18 final size:20
Alignment explanation
Indices: 3249250--3249293 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3249240 TCAAAATTTT
3249250 ACTTTAA-TTTATT-TATAC
1 ACTTTAATTTTATTATATAC
*
3249268 ATTTTAATTTTATTATATAC
1 ACTTTAATTTTATTATATAC
3249288 ACTTTA
1 ACTTTA
3249294 TTACCTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
ACTTTAATTTTATTATATAC
Found at i:3252027 original size:13 final size:12
Alignment explanation
Indices: 3252005--3252035 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
3251995 TAAATTTATC
3252005 CAAAAAAAAAAA
1 CAAAAAAAAAAA
3252017 CAAAAACAAAAAA
1 CAAAAA-AAAAAA
3252030 CAAAAA
1 CAAAAA
3252036 GATTAGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:3260413 original size:9 final size:9
Alignment explanation
Indices: 3260399--3260431 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3260389 TTTGGTTAAA
3260399 AATTAACCG
1 AATTAACCG
3260408 AATTAACCG
1 AATTAACCG
*
3260417 AATTACCCG
1 AATTAACCG
3260426 AATTAA
1 AATTAA
3260432 ATCACTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:3260459 original size:17 final size:17
Alignment explanation
Indices: 3260437--3260499 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
3260427 ATTAAATCAC
3260437 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
3260454 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
3260474 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
3260491 TACATAATT
1 TACATAATT
3260500 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 17 0.50
18 4 0.12
19 5 0.15
20 8 0.24
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:3260478 original size:37 final size:37
Alignment explanation
Indices: 3260431--3260502 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
3260421 ACCCGAATTA
*
3260431 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
3260468 AATCACTACATAATTAAAAACATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
3260503 GAAATTAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:3260728 original size:39 final size:39
Alignment explanation
Indices: 3260632--3260746 Score: 180
Period size: 39 Copynumber: 3.0 Consensus size: 39
3260622 ACTTAAGAGT
* *
3260632 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGA
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
*
3260670 T-GACTTTAGTTTTAATTTTATTGTGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
*
3260708 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
3260747 CTGGGTTGGA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
37 24 0.34
38 11 0.16
39 35 0.50
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAATTTTATTGGGTTGGGTAATTGGG
Found at i:3261594 original size:44 final size:44
Alignment explanation
Indices: 3261536--3261630 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
3261526 TGAAACAATT
*
3261536 ATAAAG-A-AAAATTCATTATTTAATTAATATAAAGTATAATGA
1 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
3261578 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
1 ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
3261622 ATAAAGAAC
1 ATAAAGAAC
3261631 CGGAAAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 6 0.12
43 1 0.02
44 43 0.86
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (44 bp):
ATAAAGAACAAAATTCATTATTTAACTAATATAAAGTATAATGA
Found at i:3276892 original size:16 final size:16
Alignment explanation
Indices: 3276864--3276904 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3276854 GCTTTGATCT
3276864 TTTTCGTTC-TTTCTC-
1 TTTTC-TTCTTTTCTCA
3276879 TCTTTCTTCTTTTCTCA
1 T-TTTCTTCTTTTCTCA
3276896 TTTTCTTCT
1 TTTTCTTCT
3276905 GCTGAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTCTTCTTTTCTCA
Found at i:3277607 original size:6 final size:6
Alignment explanation
Indices: 3277593--3277622 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3277583 TATTTGTTAA
*
3277593 ATATAT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT
3277623 CTTCTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:3292639 original size:46 final size:44
Alignment explanation
Indices: 3292614--3292773 Score: 178
Period size: 46 Copynumber: 3.5 Consensus size: 44
3292604 GATCAAGTGA
* * *
3292614 CAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
* * * *
3292659 CAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
*
3292705 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGAT
*
3292751 CAAGTGACAAGTGAAAAGTGATA
1 CAAGTGACAAGTGATAAGTGATA
3292774 AGTGATAGCT
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
44 2 0.02
45 19 0.18
46 86 0.80
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (44 bp):
CAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGAT
Found at i:3292815 original size:144 final size:144
Alignment explanation
Indices: 3292555--3292822 Score: 455
Period size: 144 Copynumber: 1.9 Consensus size: 144
3292545 TTTGAGTACT
* * *
3292555 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * *
3292620 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGC
66 AAAAGTGATAAGTAATAGCTACGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTTATAGC
3292685 TTCGGCTATACTTA
131 TTCGGCTATACTTA
*
3292699 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
3292764 AAAAGTGATAAGTGATAGCTACGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
66 AAAAGTGATAAGTAATAGCTACGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
3292823 GGCTACACTT
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 115 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (144 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTACGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTTATAGC
TTCGGCTATACTTA
Found at i:3292823 original size:98 final size:97
Alignment explanation
Indices: 3292561--3292823 Score: 338
Period size: 98 Copynumber: 2.7 Consensus size: 97
3292551 TACTTCTGAT
* ** *
3292561 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC------AAAGT
* *
3292626 GATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG
59 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTG
*
3292665 --A-T--AAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
3292725 GATAGCTTCGGCTACACTTATCTGATCAAGTG
66 GATAGCTTCGGCTACACTTATCTGATCAAGTG
* *
3292757 ACAAGTGAAAAGTGATAAGTGATAGCTACGGCTATACTTATCTGATCAAGAGACAAAGTGATAAG
1 -CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAG
3292822 TG
65 TG
3292824 GCTACACTTA
Statistics
Matches: 143, Mismatches: 10, Indels: 18
0.84 0.06 0.11
Matches are distributed among these distances:
92 42 0.29
95 1 0.01
96 1 0.01
98 97 0.68
101 1 0.01
102 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
GATAGCTTCGGCTACACTTATCTGATCAAGTG
Found at i:3292833 original size:37 final size:37
Alignment explanation
Indices: 3292786--3292896 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
3292776 TGATAGCTAC
*
3292786 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
3292823 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
3292860 GGCTACACTTATCTGATCAAGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
3292896 G
1 G
3292897 ATCATACGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:3294201 original size:19 final size:16
Alignment explanation
Indices: 3294160--3294216 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
3294150 ACATGTCAAC
3294160 ATTTAATTATTTTTAT
1 ATTTAATTATTTTTAT
3294176 ATTTAATTATTTTTGAT
1 ATTTAATTATTTTT-AT
*
3294193 AATTTTAATGATTTTTAT
1 -A-TTTAATTATTTTTAT
*
3294211 TTTTAA
1 ATTTAA
3294217 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 19 0.53
17 2 0.06
18 3 0.08
19 12 0.33
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
ATTTAATTATTTTTAT
Found at i:3296156 original size:23 final size:26
Alignment explanation
Indices: 3296125--3296174 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
3296115 CATTTAATAT
3296125 TTATATTTTT-A-TTAAA-TTGATTA
1 TTATATTTTTGAGTTAAATTTGATTA
*
3296148 TTATTTTTTTGAGTTAAATTTGATTA
1 TTATATTTTTGAGTTAAATTTGATTA
3296174 T
1 T
3296175 CAACTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 1 0.04
25 5 0.22
26 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATATTTTTGAGTTAAATTTGATTA
Found at i:3302623 original size:345 final size:345
Alignment explanation
Indices: 3301992--3302682 Score: 1382
Period size: 345 Copynumber: 2.0 Consensus size: 345
3301982 TGACTTCGTC
3301992 GGTGACAGCAGGTAAAGATAAATGGACATCTACAATAACATTAGGGATTAACTCCTGTACTTCGT
1 GGTGACAGCAGGTAAAGATAAATGGACATCTACAATAACATTAGGGATTAACTCCTGTACTTCGT
3302057 GCCAAACATATTTTAGCAGTATTGATATATTACCCCGAGTACATAAATTGTCAAGGGTGTGACTC
66 GCCAAACATATTTTAGCAGTATTGATATATTACCCCGAGTACATAAATTGTCAAGGGTGTGACTC
3302122 TATGATGCATATATAAAAGATCATGTTATTATTTAGGTTGAAAGACTCACATAGATACACAGACC
131 TATGATGCATATATAAAAGATCATGTTATTATTTAGGTTGAAAGACTCACATAGATACACAGACC
3302187 CCAAGTGCATAAATAATCAAGGGCGAGTCATCATTTTCTTTGGTTTTAATTTCTGGGTTCGAGTT
196 CCAAGTGCATAAATAATCAAGGGCGAGTCATCATTTTCTTTGGTTTTAATTTCTGGGTTCGAGTT
3302252 AGTTTAATGGTGTAGGTGGTCTGATAAATACAAGTTAAACTAAAGTGATAATATGTGTGCTCGGT
261 AGTTTAATGGTGTAGGTGGTCTGATAAATACAAGTTAAACTAAAGTGATAATATGTGTGCTCGGT
3302317 TATCCAGGTCGAGTATCTTT
326 TATCCAGGTCGAGTATCTTT
3302337 GGTGACAGCAGGTAAAGATAAATGGACATCTACAATAACATTAGGGATTAACTCCTGTACTTCGT
1 GGTGACAGCAGGTAAAGATAAATGGACATCTACAATAACATTAGGGATTAACTCCTGTACTTCGT
3302402 GCCAAACATATTTTAGCAGTATTGATATATTACCCCGAGTACATAAATTGTCAAGGGTGTGACTC
66 GCCAAACATATTTTAGCAGTATTGATATATTACCCCGAGTACATAAATTGTCAAGGGTGTGACTC
3302467 TATGATGCATATATAAAAGATCATGTTATTATTTAGGTTGAAAGACTCACATAGATACACAGACC
131 TATGATGCATATATAAAAGATCATGTTATTATTTAGGTTGAAAGACTCACATAGATACACAGACC
3302532 CCAAGTGCATAAATAATCAAGGGCGAGTCATCATTTTCTTTGGTTTTAATTTCTGGGTTCGAGTT
196 CCAAGTGCATAAATAATCAAGGGCGAGTCATCATTTTCTTTGGTTTTAATTTCTGGGTTCGAGTT
3302597 AGTTTAATGGTGTAGGTGGTCTGATAAATACAAGTTAAACTAAAGTGATAATATGTGTGCTCGGT
261 AGTTTAATGGTGTAGGTGGTCTGATAAATACAAGTTAAACTAAAGTGATAATATGTGTGCTCGGT
3302662 TATCCAGGTCGAGTATCTTT
326 TATCCAGGTCGAGTATCTTT
3302682 G
1 G
3302683 ATGCAAAAGC
Statistics
Matches: 346, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
345 346 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (345 bp):
GGTGACAGCAGGTAAAGATAAATGGACATCTACAATAACATTAGGGATTAACTCCTGTACTTCGT
GCCAAACATATTTTAGCAGTATTGATATATTACCCCGAGTACATAAATTGTCAAGGGTGTGACTC
TATGATGCATATATAAAAGATCATGTTATTATTTAGGTTGAAAGACTCACATAGATACACAGACC
CCAAGTGCATAAATAATCAAGGGCGAGTCATCATTTTCTTTGGTTTTAATTTCTGGGTTCGAGTT
AGTTTAATGGTGTAGGTGGTCTGATAAATACAAGTTAAACTAAAGTGATAATATGTGTGCTCGGT
TATCCAGGTCGAGTATCTTT
Found at i:3311474 original size:16 final size:16
Alignment explanation
Indices: 3311453--3311484 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3311443 GTCAAATGTT
*
3311453 TATATATGTATGTATG
1 TATATATGCATGTATG
3311469 TATATATGCATGTATG
1 TATATATGCATGTATG
3311485 CATGTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (16 bp):
TATATATGCATGTATG
Found at i:3313521 original size:33 final size:33
Alignment explanation
Indices: 3313482--3313547 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3313472 TTCATCACAG
* *
3313482 ACCTTCAAATTTTTCTCTTAGATTATGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
*
3313515 ACCTTCATATTGTACTCTTAGATTATGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
3313548 TTGTCGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (33 bp):
ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
Found at i:3318437 original size:3 final size:3
Alignment explanation
Indices: 3318429--3318453 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3318419 CACTCTTGGC
3318429 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
3318454 TGTATTTTCA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3322394 original size:8 final size:8
Alignment explanation
Indices: 3322381--3322405 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3322371 TATTTAATTC
3322381 TTTTAAAT
1 TTTTAAAT
3322389 TTTTAAAT
1 TTTTAAAT
3322397 TTTTAAAT
1 TTTTAAAT
3322405 T
1 T
3322406 AATAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAAAT
Found at i:3329412 original size:23 final size:24
Alignment explanation
Indices: 3329386--3329436 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3329376 ATAGTAATAA
3329386 ATTTAGTT-TTTAATATTT-ATTTT
1 ATTTAGTTATTTAAT-TTTAATTTT
3329409 ATTT-GTTATTTAATTTTAATTTT
1 ATTTAGTTATTTAATTTTAATTTT
*
3329432 GTTTA
1 ATTTA
3329437 AGGATTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (24 bp):
ATTTAGTTATTTAATTTTAATTTT
Found at i:3332890 original size:40 final size:39
Alignment explanation
Indices: 3332835--3332970 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 39
3332825 ACCAGTTTGG
* *
3332835 CACCCAGTGGCTCATCGAATAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATAATCCGAAGT-ATAAATTGA
** * *
3332875 CACCCAGTGTCTCATCGTCTAAACCGAAGT-T-AATTGG
1 CACCCAGTGTCTCATCGAATAATCCGAAGTATAAATTGA
* * *
3332912 TACCCAGTGCCTCATCGAATTAATCCGAAGCAGTAAATTGA
1 CACCCAGTGTCTCATCGAA-TAATCCGAAGTA-TAAATTGA
*
3332953 CACCTAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
3332971 CTCGAAGTCG
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 20 0.26
38 10 0.13
40 26 0.34
41 20 0.26
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGAATAATCCGAAGTATAAATTGA
Found at i:3332967 original size:41 final size:40
Alignment explanation
Indices: 3332835--3332970 Score: 129
Period size: 41 Copynumber: 3.5 Consensus size: 40
3332825 ACCAGTTTGG
* * *
3332835 CACCCAGTGGCTCATCGAA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAATCCGAAG-AGTAAATTGA
* * *
3332875 CACCCAGTGTCTCATCG--TCTAAACCG-A-AGTTAATTGG
1 CACCCAGTGTCTCATCGAAT-TAATCCGAAGAGTAAATTGA
* *
3332912 TACCCAGTGCCTCATCGAATTAATCCGAAGCAGTAAATTGA
1 CACCCAGTGTCTCATCGAATTAATCCGAAG-AGTAAATTGA
*
3332953 CACCTAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
3332971 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
37 22 0.29
38 6 0.08
39 3 0.04
40 21 0.28
41 23 0.31
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCCAGTGTCTCATCGAATTAATCCGAAGAGTAAATTGA
Found at i:3333928 original size:5 final size:5
Alignment explanation
Indices: 3333920--3333973 Score: 92
Period size: 5 Copynumber: 10.8 Consensus size: 5
3333910 ATTTTATCAT
3333920 TATAA TATAA TATAA TGA-AA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA TATAA TATAA TATAA
3333970 TATA
1 TATA
3333974 TACTTAATAC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 1 0.02
5 45 0.96
6 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3357505 original size:27 final size:27
Alignment explanation
Indices: 3357467--3357521 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3357457 ATTGCAGGTA
3357467 TAGGTCTTAATTCCACCTGAATTTAAT
1 TAGGTCTTAATTCCACCTGAATTTAAT
3357494 TAGGTCTTAATTCCACCTGAATTTAAT
1 TAGGTCTTAATTCCACCTGAATTTAAT
3357521 T
1 T
3357522 TAAGTGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (27 bp):
TAGGTCTTAATTCCACCTGAATTTAAT
Found at i:3376754 original size:9 final size:9
Alignment explanation
Indices: 3376740--3376767 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3376730 TTCGAGTTCG
3376740 TTTATCTTC
1 TTTATCTTC
3376749 TTTATCTTC
1 TTTATCTTC
3376758 TTTATCTTC
1 TTTATCTTC
3376767 T
1 T
3376768 GAACTTAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATCTTC
Found at i:3382165 original size:28 final size:28
Alignment explanation
Indices: 3382125--3382180 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3382115 TGTAAAAGAT
3382125 AGGGTGGAAACGAGACATCATGGAAAAA
1 AGGGTGGAAACGAGACATCATGGAAAAA
3382153 AGGGTGGAAACGAGACATCATGGAAAAA
1 AGGGTGGAAACGAGACATCATGGAAAAA
3382181 CTCTATAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.32, T:0.11
Consensus pattern (28 bp):
AGGGTGGAAACGAGACATCATGGAAAAA
Found at i:3382998 original size:35 final size:35
Alignment explanation
Indices: 3382952--3383021 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3382942 AGTCATGAGT
3382952 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
1 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
3382987 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
1 AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
3383022 CTACTGCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (35 bp):
AAGTTCACTTAATTCTAACCTGTAAAATTGTGTTC
Found at i:3384644 original size:13 final size:12
Alignment explanation
Indices: 3384625--3384663 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3384615 TGAGTATGTA
3384625 TTTTTTATATAT
1 TTTTTTATATAT
3384637 TATTTTTATA-AT
1 T-TTTTTATATAT
*
3384649 TTTTTCATATAT
1 TTTTTTATATAT
3384661 TTT
1 TTT
3384664 AATGATCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 7 0.29
12 9 0.38
13 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTATATAT
Found at i:3385588 original size:30 final size:31
Alignment explanation
Indices: 3385549--3385608 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3385539 GGAGGTGGAA
3385549 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
* *
3385580 TGGG-AGGGAGTAAAAGTTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAGTTTTAGGGGAAAA
3385609 TAAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
Found at i:3397070 original size:31 final size:31
Alignment explanation
Indices: 3397032--3397091 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3397022 AGAAAACAAA
3397032 TATTTCATCTTATTTAAGATATTTAATATGG
1 TATTTCATCTTATTTAAGATATTTAATATGG
*
3397063 TATTTCATTTTATTTAAGATATTTAATAT
1 TATTTCATCTTATTTAAGATATTTAATAT
3397092 AAAAGAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (31 bp):
TATTTCATCTTATTTAAGATATTTAATATGG
Found at i:3398389 original size:19 final size:18
Alignment explanation
Indices: 3398365--3398403 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3398355 AACAAGATGC
3398365 AATTTTAAAAGTTATTTAA
1 AATTTTAAAAGTT-TTTAA
* *
3398384 AATTTTTATAGTTTTTAA
1 AATTTTAAAAGTTTTTAA
3398402 AA
1 AA
3398404 GAACCATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
AATTTTAAAAGTTTTTAA
Found at i:3399539 original size:32 final size:30
Alignment explanation
Indices: 3399493--3399561 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
3399483 AAGAAGCATT
* * *
3399493 AATTTGACTATTTTTGAAAAGGTTGATGGTCA
1 AATTTAACTATTTTT-AAAA-ATTGAGGGTCA
*
3399525 AATTTAACTTTTTTTAAAAATTGAGGGTCA
1 AATTTAACTATTTTTAAAAATTGAGGGTCA
3399555 AATTTAA
1 AATTTAA
3399562 TTAAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 16 0.48
31 4 0.12
32 13 0.39
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACTATTTTTAAAAATTGAGGGTCA
Found at i:3399996 original size:31 final size:30
Alignment explanation
Indices: 3399935--3399997 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
3399925 AGATAATTGG
* *
3399935 GTGATCAAAAAGACAAAATTAAATAATTAA
1 GTGACCAAAAAGACAAAATAAAATAATTAA
*
3399965 GTGACCAAAAA-ATAAAATAAAATATAGTTAA
1 GTGACCAAAAAGACAAAATAAAATA-A-TTAA
3399996 GT
1 GT
3399998 TACTACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (30 bp):
GTGACCAAAAAGACAAAATAAAATAATTAA
Found at i:3400643 original size:16 final size:16
Alignment explanation
Indices: 3400622--3400655 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3400612 TCGGTCACTA
3400622 TTCATTTCATCCTATT
1 TTCATTTCATCCTATT
3400638 TTCATTTCATCCTATT
1 TTCATTTCATCCTATT
3400654 TT
1 TT
3400656 AGAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCATTTCATCCTATT
Found at i:3402050 original size:23 final size:23
Alignment explanation
Indices: 3402024--3402093 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
3402014 ACGCGATTTC
3402024 CTGACGCGTACCCTGACATCGTG
1 CTGACGCGTACCCTGACATCGTG
* * * * *
3402047 CTGACGTGGA-CGTG--AT-TTC
1 CTGACGCGTACCCTGACATCGTG
*
3402066 CTGACGCGTACCCTGACATCGCG
1 CTGACGCGTACCCTGACATCGTG
3402089 CTGAC
1 CTGAC
3402094 ATGGACGCGA
Statistics
Matches: 32, Mismatches: 11, Indels: 8
0.63 0.22 0.16
Matches are distributed among these distances:
19 9 0.28
20 5 0.16
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (23 bp):
CTGACGCGTACCCTGACATCGTG
Found at i:3402077 original size:42 final size:42
Alignment explanation
Indices: 3402000--3402108 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
3401990 CGTCAGCATC
* *
3402000 TCGCGCTAACGTAGACGCGATTTCCTGACGCGTACCCTGACA
1 TCGCGCTGACGTGGACGCGATTTCCTGACGCGTACCCTGACA
* *
3402042 TCGTGCTGACGTGGACGTGATTTCCTGACGCGTACCCTGACA
1 TCGCGCTGACGTGGACGCGATTTCCTGACGCGTACCCTGACA
*
3402084 TCGCGCTGACATGGACGCGATTTCC
1 TCGCGCTGACGTGGACGCGATTTCC
3402109 CGGAAAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (42 bp):
TCGCGCTGACGTGGACGCGATTTCCTGACGCGTACCCTGACA
Found at i:3419547 original size:30 final size:30
Alignment explanation
Indices: 3419470--3419556 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
3419460 TTACGAGGAC
* *
3419470 GTTCAGGAACTTGAGAAGACTCGATATCTT
1 GTTCAGGATCTTGGGAAGACTCGATATCTT
* * *
3419500 GTTCGGGAGT-TTAGGAAGACTGGATATCTT
1 GTTCAGGA-TCTTGGGAAGACTCGATATCTT
3419530 GTTCAGGATCTTGGGAAGA-TCCGATAT
1 GTTCAGGATCTTGGGAAGACT-CGATAT
3419557 TTGATTTTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 2 0.04
30 44 0.96
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (30 bp):
GTTCAGGATCTTGGGAAGACTCGATATCTT
Found at i:3421247 original size:127 final size:125
Alignment explanation
Indices: 3421010--3421503 Score: 712
Period size: 127 Copynumber: 3.9 Consensus size: 125
3421000 AACTCGCACA
* * * *
3421010 ATGCC-ATATCCCAGATATGGTCTTACATGCT-ATCAT-ATATCGATGCTAATGTCCCAGACATG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-TAATC-TCATATCGATGCCAATGTCCCAGACATG
* *
3421072 GTCTTACACATAATC-TCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACG
64 GTCTTACA-AGAATCAT-ATA-CGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
* *
3421136 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCGGACATGAT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
*
3421201 CTTACAAGTAATC-TCATATCAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
66 CTTACAAG-AATCAT-ATA-CGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
3421263 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
* *
3421328 CTTACACGAATCATATACGATGCCAATGTCCCAGACATGGTCTTACACATAATC-TCATATCG
66 CTTACAAGAATCATATACGATGCCAATGTCCCAGACATGGTCTTACAC-GAATCAT-ATA-CG
* *
3421390 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCTAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
* *
3421455 CTTACACGAATCATATACGATGCCAATGTCTCAGACATGGTCTTACACG
66 CTTACAAGAATCATATACGATGCCAATGTCCCAGACATGGTCTTACACG
3421504 TTCGAAATTC
Statistics
Matches: 342, Mismatches: 18, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
125 31 0.09
126 22 0.06
127 289 0.85
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (125 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
CTTACAAGAATCATATACGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACG
Found at i:3421425 original size:211 final size:211
Alignment explanation
Indices: 3421008--3421504 Score: 834
Period size: 211 Copynumber: 2.4 Consensus size: 211
3420998 ATAACTCGCA
* * * * *
3421008 CAATGCC-ATATCCCAGATATGGTCTTACATGCTATCATATATCGATGCTAATGTCCCAGACATG
1 CAATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATA-CGATGCCAATGTCCCAGACATG
*
3421072 GTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGA
64 GTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGA
* *
3421137 TGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCGGACATGATC
129 TGCCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATC
3421202 TTACAAGTAATCTCATAT
194 TTACAAGTAATCTCATAT
3421220 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
*
3421285 CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATG
66 CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGATG
* *
3421350 CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCTAGACATGGTCTT
131 CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATCTT
*
3421415 ACACGTAATCTCATAT
196 ACAAGTAATCTCATAT
* * *
3421431 CGATGCCAATGTCCTAGACATGGTCTTACACGAATCATATACGATGCCAATGTCTCAGACATGGT
1 CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
3421496 CTTACACGT
66 CTTACACGT
3421505 TCGAAATTCT
Statistics
Matches: 269, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
211 233 0.87
212 15 0.06
213 21 0.08
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (211 bp):
CAATGCCAATGTCCCAGACATGGTCTTACACGAATCATATACGATGCCAATGTCCCAGACATGGT
CTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGATCTTACACGAATCATATACGATG
CCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCCAGACATGATCTT
ACAAGTAATCTCATAT
Found at i:3421503 original size:84 final size:86
Alignment explanation
Indices: 3421010--3421504 Score: 705
Period size: 84 Copynumber: 5.9 Consensus size: 86
3421000 AACTCGCACA
* * * *
3421010 ATGCC-ATATCCCAGATATGGTCTTACATGCT-ATCAT-ATATCGATGCTAATGTCCCAGACATG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-TAATC-TCATATCGATGCCAATGTCCCAGACATG
*
3421072 GTCTTACACATAATCTCATATCG
64 GTCTTACACGTAATCTCATATCG
*
3421095 ATGCCAATGTCCCAGACATGATCTTACACG-AA--TCATATACGATGCCAATGTCCCAGACATGG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATAT-CGATGCCAATGTCCCAGACATGG
3421157 TCTTACACGTAATCTCATATCG
65 TCTTACACGTAATCTCATATCG
* * * *
3421179 ATGCCAATGTCCCGGACATGATCTTACAAGTAATCTCATATCAATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
3421244 CTTACACG-AA--TCATATACG
66 CTTACACGTAATCTCATAT-CG
3421263 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
3421328 CTTACACG-AA--TCATATACG
66 CTTACACGTAATCTCATAT-CG
* *
3421347 ATGCCAATGTCCCAGACATGGTCTTACACATAATCTCATATCGATGCCAATGTCCTAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
3421412 CTTACACGTAATCTCATATCG
66 CTTACACGTAATCTCATATCG
* *
3421433 ATGCCAATGTCCTAGACATGGTCTTACACG-AA--TCATATACGATGCCAATGTCTCAGACATGG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATAT-CGATGCCAATGTCCCAGACATGG
3421495 TCTTACACGT
65 TCTTACACGT
3421505 TCGAAATTCT
Statistics
Matches: 379, Mismatches: 19, Indels: 25
0.90 0.04 0.06
Matches are distributed among these distances:
82 1 0.00
83 16 0.04
84 255 0.67
85 14 0.04
86 81 0.21
87 12 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (86 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGACATGGT
CTTACACGTAATCTCATATCG
Found at i:3421676 original size:31 final size:30
Alignment explanation
Indices: 3421635--3421755 Score: 161
Period size: 31 Copynumber: 4.0 Consensus size: 30
3421625 CAACAATATA
*
3421635 TATATTCATATACGAATCAAATTCGGCAACG
1 TATAATCATATACGAATC-AATTCGGCAACG
* * *
3421666 TATAATCATATACAAATCAATTTGGCAATG
1 TATAATCATATACGAATCAATTCGGCAACG
* * *
3421696 TATAACCATATATGAATCAAATTCGGCAATG
1 TATAATCATATACGAATC-AATTCGGCAACG
3421727 TATAATCATATACGAATCAATTCGGCAAC
1 TATAATCATATACGAATCAATTCGGCAAC
3421756 CTATTTTCTT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
30 35 0.45
31 43 0.55
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (30 bp):
TATAATCATATACGAATCAATTCGGCAACG
Found at i:3421775 original size:61 final size:61
Alignment explanation
Indices: 3421649--3421809 Score: 178
Period size: 61 Copynumber: 2.6 Consensus size: 61
3421639 TTCATATACG
* * ** *
3421649 AATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATGTATAACCATATATG
1 AATCAAATTCGGCAATGTATAATCATATACAAATCAATTCGGCAACCTATAACCATATATA
* *** * *
3421710 AATCAAATTCGGCAATGTATAATCATATACGAATCAATTCGGCAACCTATTTTCTTTTATA
1 AATCAAATTCGGCAATGTATAATCATATACAAATCAATTCGGCAACCTATAACCATATATA
* ** * *
3421771 AATCAACTTCGATAATGTATAACCATATACAAATAAATT
1 AATCAAATTCGGCAATGTATAATCATATACAAATCAATT
3421810 TTAGCAATGT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 83 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (61 bp):
AATCAAATTCGGCAATGTATAATCATATACAAATCAATTCGGCAACCTATAACCATATATA
Found at i:3421797 original size:92 final size:91
Alignment explanation
Indices: 3421635--3421870 Score: 242
Period size: 92 Copynumber: 2.6 Consensus size: 91
3421625 CAACAATATA
* * * *
3421635 TATATTCATATACGAATCAAATTCGGCAACGTATAATCATATACAAATCAATTTGGCAATGTATA
1 TATAATCATATACGAATC-AATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATA
** *
3421700 ACCATATATGAATCAAA-TTCGGCAATG
65 ACCATATACAAAT-AAATTTCAGCAATG
** * * * *
3421727 TATAATCATATACGAATCAATTCGGCAACCTATTTTCTTTTATAAATCAACTTCGATAATGTATA
1 TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAA-TTCGACAATGTATA
*
3421792 ACCATATACAAATAAATTTTAGCAATG
65 ACCATATACAAATAAATTTCAGCAATG
* * * * * *
3421819 TATAATTATATACGAATTAATTCAGCAACTTAT-ATCCACATACAATTCAATT
1 TATAATCATATACGAATCAATTCGGCAACCTATAAT-CATATACAAATCAATT
3421871 TGAACAACTT
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
91 32 0.27
92 85 0.73
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (91 bp):
TATAATCATATACGAATCAATTCGGCAACCTATAATCATATACAAATCAATTCGACAATGTATAA
CCATATACAAATAAATTTCAGCAATG
Found at i:3432014 original size:22 final size:22
Alignment explanation
Indices: 3431974--3432029 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3431964 AATAAAATTG
*
3431974 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
3431994 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* *
3432016 TATTAATAAATTAT
1 AAATAATAAATTAT
3432030 TATATGACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 9 0.29
21 2 0.06
22 20 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:3435198 original size:17 final size:17
Alignment explanation
Indices: 3435172--3435206 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3435162 GCATCCTCTG
*
3435172 TTCCAATTATATATATA
1 TTCCAATTATACATATA
*
3435189 TTCCAGTTATACATATA
1 TTCCAATTATACATATA
3435206 T
1 T
3435207 GGGTTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (17 bp):
TTCCAATTATACATATA
Found at i:3442641 original size:3 final size:3
Alignment explanation
Indices: 3442633--3442661 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3442623 AAAATCATTC
3442633 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3442662 GATTATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3446990 original size:22 final size:22
Alignment explanation
Indices: 3446964--3447041 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
3446954 ATAAAGAGAG
3446964 TTAAAATTTTAATTTTTTTAAA
1 TTAAAATTTTAATTTTTTTAAA
3446986 TTAAAATTTTAATTTTTTTAAA
1 TTAAAATTTTAATTTTTTTAAA
3447008 TTAAAATTTTAATTTTTTTTAAA
1 TTAAAATTTTAA-TTTTTTTAAA
*
3447031 ATAATAATTTT
1 TTAA-AATTTT
3447042 GGGGTCAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
22 34 0.64
23 13 0.25
24 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAAATTTTAATTTTTTTAAA
Found at i:3448538 original size:40 final size:40
Alignment explanation
Indices: 3448484--3448587 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
3448474 GCGTTTAGAT
* *
3448484 AAAAAACGTCGCTAAAAATCAAGCAATAGCGGCGTTTTAG
1 AAAAAACGCCGCTAAAAATCAAGCAATAGCGGCGTTTTAC
* * * * *
3448524 AAAAAATGCCGCTAAAGATCCAA-TATTAGCGGCGTTTTTC
1 AAAAAACGCCGCTAAAAAT-CAAGCAATAGCGGCGTTTTAC
* *
3448564 ATAAAACGCCGCAAAAAAT-AAGCA
1 AAAAAACGCCGCTAAAAATCAAGCA
3448588 TTAGAGAAGC
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 44 0.88
41 3 0.06
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.20
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCAATAGCGGCGTTTTAC
Found at i:3448729 original size:41 final size:41
Alignment explanation
Indices: 3448655--3448899 Score: 233
Period size: 41 Copynumber: 5.7 Consensus size: 41
3448645 GTTTTTGGGC
* * * * *
3448655 CTTTAGCGGCGTTTTTTTAAAAAGTGCCACTAATGCTCGGGG
1 CTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCGGGT
*
3448697 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
3448738 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGGCTTGCTCT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC--GG---G---T
**
3448787 GGGCTTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAATGCTC-TAT
1 ---CTTTAGCGGCGTTTTT-GAAGAAGCGCCGCTAATGCTCGGGT
* * * **
3448830 TTTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTTTGGT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
*
3448871 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGC
3448900 AAAAAATATT
Statistics
Matches: 170, Mismatches: 19, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
39 2 0.01
40 30 0.18
41 87 0.51
42 11 0.06
43 2 0.01
46 1 0.01
49 1 0.01
52 33 0.19
53 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCGGGT
Done.