Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 20 of 31
Found at i:4415571 original size:15 final size:15
Alignment explanation
Indices: 4415537--4415573 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
4415527 TTGATCTTAA
*
4415537 ATAATTTTAAATTTT
1 ATAATTTTAAAATTT
4415552 A-AATTTTAAAATTT
1 ATAATTTTAAAATTT
4415566 ATAATTTT
1 ATAATTTT
4415574 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATTTTAAAATTT
Found at i:4416570 original size:16 final size:17
Alignment explanation
Indices: 4416537--4416588 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
4416527 CTAATTTACT
4416537 TATTTAATTTTTAAATA
1 TATTTAATTTTTAAATA
* *
4416554 TATTTATTTTTTTATATTCA
1 TATTTA-ATTTTTA-AAT-A
*
4416574 TATTTATTTTTTAAA
1 TATTTAATTTTTAAA
4416589 ATTTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.21
18 7 0.24
19 9 0.31
20 7 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTAATTTTTAAATA
Found at i:4417283 original size:2 final size:2
Alignment explanation
Indices: 4417276--4417304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4417266 AAATTGTTTT
4417276 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4417305 GTCAAGTTGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4418499 original size:28 final size:28
Alignment explanation
Indices: 4418434--4418543 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 28
4418424 TAGTTAATTC
*
4418434 AATTGAAATAATT--TTAAATATTAAA-AA
1 AATT-AAATAATTAATTAAATA-TAAATAT
4418461 AATT-AAT-ATTAATTAAATCATAAATAT
1 AATTAAATAATTAATTAAAT-ATAAATAT
*
4418488 AA-TAAATAATTAATATAAATATAAATTT
1 AATTAAATAATTAAT-TAAATATAAATAT
*
4418516 AATTTAATAATATAATTTATAATATAAA
1 AATTAAATAAT-TAA-TTA-AATATAAA
4418544 ATTTAAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
24 3 0.04
25 3 0.04
26 11 0.16
27 11 0.16
28 15 0.22
29 12 0.17
30 5 0.07
31 9 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
AATTAAATAATTAATTAAATATAAATAT
Found at i:4418501 original size:34 final size:34
Alignment explanation
Indices: 4418448--4418513 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
4418438 GAAATAATTT
*
4418448 TAAATATTAAAAAAATTAATATTAAT-TAAATCA
1 TAAATATTAAAAAAATTAATATAAATATAAATCA
4418481 TAAATA-TAATAAATAATTAATATAAATATAAAT
1 TAAATATTAA-AAA-AATTAATATAAATATAAAT
4418514 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.10
33 9 0.31
34 12 0.41
35 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAATATTAAAAAAATTAATATAAATATAAATCA
Found at i:4418522 original size:22 final size:23
Alignment explanation
Indices: 4418460--4418524 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
4418450 AATATTAAAA
*
4418460 AAAT-TAAT-ATTAATTAAATCAT
1 AAATATAATAATTAATTTAAT-AT
*
4418482 AAATATAATAAATAA-TTAATAT
1 AAATATAATAATTAATTTAATAT
*
4418504 AAATATAA-ATTTAATTTAATA
1 AAATATAATAATTAATTTAATA
4418525 ATATAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.11
22 20 0.56
23 8 0.22
24 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATAATAATTAATTTAATAT
Found at i:4418531 original size:34 final size:32
Alignment explanation
Indices: 4418461--4418549 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 32
4418451 ATATTAAAAA
*
4418461 AATTAATATTAAT-TAAATCATAAATATAATAAAT
1 AATTAATA-TAATATAAAT--TTAATATAATAAAT
*
4418495 AATTAATATAAATATAAATTTAATTTAATAATAT
1 AATTAATAT-AATATAAATTTAATATAATAA-AT
4418529 AATT--TATAATATAAAATTTAA
1 AATTAATATAATAT-AAATTTAA
4418550 AAAAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
31 5 0.10
32 11 0.22
33 11 0.22
34 17 0.35
35 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
AATTAATATAATATAAATTTAATATAATAAAT
Found at i:4418546 original size:32 final size:29
Alignment explanation
Indices: 4418463--4418549 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
4418453 ATTAAAAAAA
*
4418463 TTAAT-ATTAAT-TAAATCATAAATATAA-
1 TTAATAATTAATATAAAT-ATAAATTTAAT
*
4418490 TAAATAATTAATATAAATATAAATTTAAT
1 TTAATAATTAATATAAATATAAATTTAAT
*
4418519 TTAATAATATAATTTATAATATAAAATTTAA
1 TTAATAAT-TAATATA-AATAT-AAATTTAA
4418550 AAAAAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.08
28 15 0.30
29 12 0.24
30 6 0.12
31 5 0.10
32 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TTAATAATTAATATAAATATAAATTTAAT
Found at i:4419101 original size:17 final size:19
Alignment explanation
Indices: 4419068--4419103 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
4419058 AAAAAATTTA
4419068 TATATTTAATAATTTATAT
1 TATATTTAATAATTTATAT
4419087 TATATTT-AT-ATTTATAT
1 TATATTTAATAATTTATAT
4419104 GATTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTTAATAATTTATAT
Found at i:4424120 original size:16 final size:16
Alignment explanation
Indices: 4424099--4424130 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4424089 ATTTAGATTC
4424099 CTTCACAAAATAATCA
1 CTTCACAAAATAATCA
*
4424115 CTTCACAAAATCATCA
1 CTTCACAAAATAATCA
4424131 TTATTTTTTT
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:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (16 bp):
CTTCACAAAATAATCA
Found at i:4429829 original size:4 final size:4
Alignment explanation
Indices: 4429820--4429848 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4429810 TAGTAACAGC
4429820 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
4429849 GTTTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:4430178 original size:20 final size:21
Alignment explanation
Indices: 4430137--4430181 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
4430127 TTACGAAAAA
4430137 ATAATATAAATAAAAATTTAAC
1 ATAATATAAATAAAAA-TTAAC
4430159 ATAATAATAAA-AAAAA-TAAC
1 ATAAT-ATAAATAAAAATTAAC
4430179 ATA
1 ATA
4430182 CAATTAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
22 10 0.45
23 5 0.23
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAATATAAATAAAAATTAAC
Found at i:4430584 original size:34 final size:36
Alignment explanation
Indices: 4430523--4430602 Score: 114
Period size: 34 Copynumber: 2.3 Consensus size: 36
4430513 ATAAAAATTT
*
4430523 AAAATAATA-ATAAATTTATTATCAAAATAAT-ATA
1 AAAATAATATTTAAATTTATTATCAAAATAATGATA
4430557 AAAATAATATTTAAATTTATTAT-AAAATAATGATA
1 AAAATAATATTTAAATTTATTATCAAAATAATGATA
*
4430592 TAAA-AATATTT
1 AAAATAATATTT
4430603 TTTATTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 24 0.57
35 18 0.43
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (36 bp):
AAAATAATATTTAAATTTATTATCAAAATAATGATA
Found at i:4430601 original size:24 final size:24
Alignment explanation
Indices: 4430546--4430601 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
4430536 ATTTATTATC
* *
4430546 AAAATAATATAAAAATAATATTTA
1 AAAATATTATAAAAATAATATATA
**
4430570 AATTTATTAT-AAAATAATGATATA
1 AAAATATTATAAAAATAAT-ATATA
4430594 AAAATATT
1 AAAATATT
4430602 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATATTATAAAAATAATATATA
Found at i:4430634 original size:24 final size:25
Alignment explanation
Indices: 4430582--4430641 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
4430572 TTTATTATAA
*
4430582 AATAATGATATAAAAATATTTTTTATT
1 AATAAT-AT-TAAAAATATTTTGTATT
4430609 AA-AATATTAAAAATATTTATGT-TT
1 AATAATATTAAAAATATTT-TGTATT
4430633 AATAATATT
1 AATAATATT
4430642 TTAAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 15 0.50
25 10 0.33
26 3 0.10
27 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
AATAATATTAAAAATATTTTGTATT
Found at i:4432090 original size:27 final size:27
Alignment explanation
Indices: 4432041--4432093 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
4432031 CTTTGTAAAT
* *
4432041 GGGAGATATGAAGGGGATTGGGTGGAA
1 GGGAGATACGAAGGGGATGGGGTGGAA
* *
4432068 GGGAGATACGATGGGTATGGGGTGGA
1 GGGAGATACGAAGGGGATGGGGTGGA
4432094 GAGCTGGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.53, T:0.19
Consensus pattern (27 bp):
GGGAGATACGAAGGGGATGGGGTGGAA
Found at i:4435370 original size:3 final size:3
Alignment explanation
Indices: 4435364--4435392 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4435354 CATCATCATC
4435364 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4435393 AAAATTCAAT
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):
ATT
Found at i:4435809 original size:33 final size:31
Alignment explanation
Indices: 4435772--4435839 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 31
4435762 AATATTAATG
4435772 TAATAAAAA-TATATAAATATTTAAAATTTTATA
1 TAATAAAAATTAT-TAAAT-TTTAAAA-TTTATA
** *
4435805 TAATATGAATTATTAAATTTTATAATTTATA
1 TAATAAAAATTATTAAATTTTAAAATTTATA
4435836 TAAT
1 TAAT
4435840 TATAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 10 0.32
32 6 0.19
33 12 0.39
34 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAATAAAAATTATTAAATTTTAAAATTTATA
Found at i:4435810 original size:25 final size:24
Alignment explanation
Indices: 4435782--4435828 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
4435772 TAATAAAAAT
4435782 ATATAAA-TATTTAAAATTTTATATA
1 ATATAAATTA-TT-AAATTTTATATA
*
4435807 ATATGAATTATTAAATTTTATA
1 ATATAAATTATTAAATTTTATA
4435829 ATTTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 8 0.40
26 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATAAATTATTAAATTTTATATA
Found at i:4435840 original size:25 final size:23
Alignment explanation
Indices: 4435781--4435862 Score: 64
Period size: 25 Copynumber: 3.5 Consensus size: 23
4435771 GTAATAAAAA
*
4435781 TATATAAATATTTAAAATTTTATAT
1 TATATAATTA-TT-AAATTTTATAT
*
4435806 AATATGAATTATTAAATTTTATAATT
1 TATAT-AATTATTAAATTTTAT-A-T
4435832 TATATAATTA-TAATATTTTA-A-
1 TATATAATTATTAA-ATTTTATAT
4435853 -ATATAATTAT
1 TATATAATTAT
4435863 AACATAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
20 9 0.18
23 1 0.02
24 12 0.24
25 18 0.37
26 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TATATAATTATTAAATTTTATAT
Found at i:4440090 original size:2 final size:2
Alignment explanation
Indices: 4440083--4440116 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4440073 TTTTGACTTT
4440083 TA TA TA TA TA TA TA TA TA TA -A T- 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
4440117 GCATTAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4440122 original size:16 final size:16
Alignment explanation
Indices: 4440089--4440122 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4440079 CTTTTATATA
*
4440089 TATATATATATATAAT
1 TATATATATATAGAAT
*
4440105 TATATATATATAGCAT
1 TATATATATATAGAAT
4440121 TA
1 TA
4440123 GGTTAGGGAT
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:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATATATATAGAAT
Found at i:4440157 original size:22 final size:22
Alignment explanation
Indices: 4440131--4440189 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
4440121 TAGGTTAGGG
4440131 ATTATGATATAATATATAAAAA
1 ATTATGATATAATATATAAAAA
* * *
4440153 ATTATGTTATATTATATTAAAA
1 ATTATGATATAATATATAAAAA
* *
4440175 ATTATAATATGATAT
1 ATTATGATATAATAT
4440190 TTTTATTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTATGATATAATATATAAAAA
Found at i:4441047 original size:22 final size:22
Alignment explanation
Indices: 4441022--4441065 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4441012 AATAAATATT
*
4441022 TTATTTAAAT-TTAATTATAAAA
1 TTATATAAATATTAA-TATAAAA
4441044 TTATATAAATATTAATATAAAA
1 TTATATAAATATTAATATAAAA
4441066 ATAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATAAATATTAATATAAAA
Found at i:4442254 original size:43 final size:40
Alignment explanation
Indices: 4442207--4442285 Score: 104
Period size: 43 Copynumber: 1.9 Consensus size: 40
4442197 ATAATATTTT
*
4442207 TTATTTAATATATTAAAAATAATAAATAAAATTATTAATTATA
1 TTATTTAATATAAT-AAAATAATAAA-AAAA-TATTAATTATA
* *
4442250 TTATTTAATATAATAATATTATAAAAAAATATTAAT
1 TTATTTAATATAATAAAATAATAAAAAAATATTAAT
4442286 AAATCTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 7 0.21
41 4 0.12
42 9 0.27
43 13 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
TTATTTAATATAATAAAATAATAAAAAAATATTAATTATA
Found at i:4442287 original size:22 final size:21
Alignment explanation
Indices: 4442256--4442300 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4442246 TATATTATTT
4442256 AATATAATAATAT-TATAAAAA
1 AATATAATAA-ATCTATAAAAA
*
4442277 AATATTAATAAATCTTTAAAAA
1 AATA-TAATAAATCTATAAAAA
4442299 AA
1 AA
4442301 ATTTACGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAATAAATCTATAAAAA
Found at i:4443386 original size:12 final size:13
Alignment explanation
Indices: 4443366--4443390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4443356 AGAAAATTAT
4443366 AATTAAAAAAAAG
1 AATTAAAAAAAAG
4443379 AATTAAAAAAAA
1 AATTAAAAAAAA
4443391 TTTATAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATTAAAAAAAAG
Found at i:4447828 original size:70 final size:69
Alignment explanation
Indices: 4447712--4447843 Score: 219
Period size: 70 Copynumber: 1.9 Consensus size: 69
4447702 AAACAGAAGC
* *
4447712 AACAACATAAAAGATTGAATTACAATCTTGCTATCATATATATGACAATCATTAGTTGAAAAAAA
1 AACAACATAAAACAGTGAATTACAATCTTGCTATCATATATATGACAATCATTAG-TGAAAAAAA
4447777 AGGGT
65 AGGGT
* *
4447782 AACAACATAGAACAGTGAATTACAATCTTGCTATCATATATCTGACAATCATTAGTGAAAAA
1 AACAACATAAAACAGTGAATTACAATCTTGCTATCATATATATGACAATCATTAGTGAAAAA
4447844 CTTACTTAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 7 0.12
70 51 0.88
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (69 bp):
AACAACATAAAACAGTGAATTACAATCTTGCTATCATATATATGACAATCATTAGTGAAAAAAAA
GGGT
Found at i:4449767 original size:20 final size:21
Alignment explanation
Indices: 4449731--4449773 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4449721 TTATTTTTAT
4449731 TTAAAATTAATTATAAAAATA
1 TTAAAATTAATTATAAAAATA
*
4449752 TTAATATTAA-TATAAAAATA
1 TTAAAATTAATTATAAAAATA
4449772 TT
1 TT
4449774 TTTTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATTAATTATAAAAATA
Found at i:4449781 original size:18 final size:19
Alignment explanation
Indices: 4449736--4449783 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
4449726 TTTATTTAAA
4449736 ATTAATTATAAAAATATTAAT
1 ATTAA-TATAAAAATATT-AT
4449757 ATTAATATAAAAATATT-T
1 ATTAATATAAAAATATTAT
*
4449775 TTTAATATA
1 ATTAATATA
4449784 TTTAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.35
20 12 0.46
21 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATATAAAAATATTAT
Found at i:4452337 original size:2 final size:2
Alignment explanation
Indices: 4452330--4452368 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4452320 TGTGATTTAA
4452330 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4452369 AACATAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4452434 original size:2 final size:2
Alignment explanation
Indices: 4452427--4452456 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4452417 TTTAATGATT
4452427 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4452457 GGCTGTGATT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4454665 original size:2 final size:2
Alignment explanation
Indices: 4454660--4454688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4454650 GAATCCCCCC
4454660 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4454689 AGAAAGACAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4456132 original size:3 final size:3
Alignment explanation
Indices: 4456124--4456159 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4456114 CATGGGCTCA
4456124 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4456160 TGGATAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4457258 original size:20 final size:21
Alignment explanation
Indices: 4457212--4457259 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4457202 ATATATATAA
* *
4457212 TAATTTTTTATCTAGTCAATT
1 TAATTTTTAATCTAGTCAAAT
* *
4457233 TTATTTTTAATCTA-TTAAAT
1 TAATTTTTAATCTAGTCAAAT
4457253 TAATTTT
1 TAATTTT
4457260 ACCCAACTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTTTAATCTAGTCAAAT
Found at i:4457853 original size:18 final size:18
Alignment explanation
Indices: 4457832--4457876 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
4457822 ATTTTTTTTG
4457832 TTAATGATATAT-TTTATT
1 TTAAT-ATATATATTTATT
4457850 TTAATATATATATTTATAT
1 TTAATATATATATTTAT-T
4457869 ATTAATAT
1 -TTAATAT
4457877 GATGTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 1 0.04
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTAATATATATATTTATT
Found at i:4458758 original size:19 final size:19
Alignment explanation
Indices: 4458731--4458769 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4458721 ATTTTAAAAC
4458731 AATAAAATTATTTAA-ATA
1 AATAAAATTATTTAATATA
4458749 AATAATAATTATTTAATATA
1 AATAA-AATTATTTAATATA
4458769 A
1 A
4458770 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 10 0.53
20 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAATTATTTAATATA
Found at i:4464257 original size:2 final size:2
Alignment explanation
Indices: 4464250--4464278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4464240 CTATAAGTGG
4464250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4464279 AAATATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4467317 original size:30 final size:30
Alignment explanation
Indices: 4467281--4467340 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4467271 AGCCTAAAAG
4467281 AAAGATGATGAAAATGAATTGAATATTACT
1 AAAGATGATGAAAATGAATTGAATATTACT
4467311 AAAGATGATGAAAATGAATTGAATATTACT
1 AAAGATGATGAAAATGAATTGAATATTACT
4467341 TCAAAGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (30 bp):
AAAGATGATGAAAATGAATTGAATATTACT
Found at i:4470707 original size:23 final size:24
Alignment explanation
Indices: 4470664--4470712 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
4470654 CTTTTTATGT
*
4470664 TATTTAAATTTTTTATATATT-TA
1 TATTTAAATTTTATATATATTATA
4470687 TATTTAAATTTTATACT-TATTATA
1 TATTTAAATTTTATA-TATATTATA
4470711 TA
1 TA
4470713 GTAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTAAATTTTATATATATTATA
Found at i:4472718 original size:19 final size:19
Alignment explanation
Indices: 4472694--4472731 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4472684 TTAAAGTGTG
*
4472694 AATGTCTGATGCCTGTATC
1 AATGTCTAATGCCTGTATC
*
4472713 AATGTCTAATGCCTTTATC
1 AATGTCTAATGCCTGTATC
4472732 TTATACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (19 bp):
AATGTCTAATGCCTGTATC
Found at i:4474063 original size:15 final size:15
Alignment explanation
Indices: 4474045--4474075 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4474035 TTAATTTTTT
*
4474045 TTTATTTTTAAAATA
1 TTTATATTTAAAATA
4474060 TTTATATTTAAAATA
1 TTTATATTTAAAATA
4474075 T
1 T
4474076 ATTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTTAAAATA
Found at i:4476357 original size:20 final size:20
Alignment explanation
Indices: 4476324--4476363 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4476314 AATTTATATT
4476324 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
4476344 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
4476364 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:4479439 original size:15 final size:14
Alignment explanation
Indices: 4479414--4479448 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4479404 ACCAATCAAG
4479414 TAATATATTTAAAAT
1 TAAT-TATTTAAAAT
4479429 ATAATTATTTAAAAT
1 -TAATTATTTAAAAT
4479444 TAATT
1 TAATT
4479449 TGATAAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 10 0.53
16 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTATTTAAAAT
Found at i:4481218 original size:34 final size:34
Alignment explanation
Indices: 4481175--4481244 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
4481165 TTCACAGAGA
*
4481175 TCCACATAAACATAGTTCTTTTATTTCTTTTATT
1 TCCACATAAACATACTTCTTTTATTTCTTTTATT
4481209 TCCACATAAACATACTTCTTTTATTTCTTTTATT
1 TCCACATAAACATACTTCTTTTATTTCTTTTATT
4481243 TC
1 TC
4481245 TAGTTGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.01, T:0.53
Consensus pattern (34 bp):
TCCACATAAACATACTTCTTTTATTTCTTTTATT
Found at i:4481639 original size:3 final size:3
Alignment explanation
Indices: 4481633--4481657 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4481623 TTTTTTTTTT
4481633 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4481658 ATTATTATTA
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:4481664 original size:3 final size:3
Alignment explanation
Indices: 4481658--4481699 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4481648 ATAATAATAA
4481658 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4481700 TTAGCATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4482261 original size:2 final size:2
Alignment explanation
Indices: 4482254--4482297 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4482244 AATGTGCTTC
*
4482254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4482296 TA
1 TA
4482298 AGTGCATTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4486373 original size:14 final size:14
Alignment explanation
Indices: 4486356--4486397 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
4486346 AAAATTATAT
*
4486356 TTAGTGTATTATTA
1 TTAGTATATTATTA
*
4486370 TTAGTATATAATT-
1 TTAGTATATTATTA
4486383 TTA-TATATTATTA
1 TTAGTATATTATTA
4486396 TT
1 TT
4486398 GTTAATGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 8 0.33
13 5 0.21
14 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTAGTATATTATTA
Found at i:4489969 original size:18 final size:19
Alignment explanation
Indices: 4489941--4489976 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4489931 TTTACATCGA
*
4489941 ATATATTTATTTTTATTAC
1 ATATATTTATTATTATTAC
4489960 ATAT-TTTATTATTATTA
1 ATATATTTATTATTATTA
4489977 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATATTTATTATTATTAC
Found at i:4490005 original size:20 final size:21
Alignment explanation
Indices: 4489967--4490008 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
4489957 TACATATTTT
4489967 ATTATTATTATAAAAATATAA
1 ATTATTATTATAAAAATATAA
* *
4489988 ATTATT-TTTTAAATATATAA
1 ATTATTATTATAAAAATATAA
4490008 A
1 A
4490009 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTATTATTATAAAAATATAA
Found at i:4491003 original size:2 final size:2
Alignment explanation
Indices: 4490996--4491043 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4490986 ATATAGGATA
4490996 AT AT AT AT 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 AT AT AT AT
4491038 AT AT AT
1 AT AT AT
4491044 TTAAAAGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4493028 original size:18 final size:18
Alignment explanation
Indices: 4493011--4493045 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4493001 TAATTTTAAT
*
4493011 TTAATTGAT-TTATATAA
1 TTAATTAATATTATATAA
4493028 TTAATTAATATTATATAA
1 TTAATTAATATTATATAA
4493046 ATTTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAATTAATATTATATAA
Found at i:4493860 original size:20 final size:20
Alignment explanation
Indices: 4493831--4493870 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4493821 TTCTATTTTC
*
4493831 AAGTTTATTAGTTAAGGTTT
1 AAGTTGATTAGTTAAGGTTT
*
4493851 AAGTTGATTAGTTATGGTTT
1 AAGTTGATTAGTTAAGGTTT
4493871 CTATCATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (20 bp):
AAGTTGATTAGTTAAGGTTT
Found at i:4494028 original size:2 final size:2
Alignment explanation
Indices: 4494023--4494077 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
4494013 AAAAAATTAA
* *
4494023 AT AT AT TT AT AT A- AA 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 AT AT AT AT
*
4494064 AT GT AT AT CAT AT A
1 AT AT AT AT -AT AT A
4494078 ATTATCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4494030 original size:19 final size:21
Alignment explanation
Indices: 4494006--4494054 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4493996 TATACAAAAC
4494006 ATATTT-TAAAAAAT-TAAAT
1 ATATTTATAAAAAATATAAAT
* *
4494025 ATATTTATATAAAATATATAT
1 ATATTTATAAAAAATATAAAT
*
4494046 ATATATATA
1 ATATTTATA
4494055 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.24
20 7 0.28
21 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTTATAAAAAATATAAAT
Found at i:4494162 original size:2 final size:2
Alignment explanation
Indices: 4494157--4494194 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4494147 TATATATATA
4494157 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4494195 CATGAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4496189 original size:22 final size:21
Alignment explanation
Indices: 4496138--4496204 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
4496128 GTATTAACCT
4496138 AAAT-TATT-ATTTAATTATTA
1 AAATATATTAATTTAATTA-TA
*
4496158 AAA-ATTTTAAATTTAATTATA
1 AAATATATT-AATTTAATTATA
4496179 AAATATATTAATATTAA-TATA
1 AAATATATTAAT-TTAATTATA
4496200 AAATA
1 AAATA
4496205 ATTTTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 6 0.15
21 17 0.43
22 17 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATATTAATTTAATTATA
Found at i:4496497 original size:2 final size:2
Alignment explanation
Indices: 4496457--4496488 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4496447 TGCATTAATC
4496457 TA 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
4496489 CAAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4497556 original size:32 final size:31
Alignment explanation
Indices: 4497520--4497587 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 31
4497510 ATAGTTTTGG
4497520 ATAATTCAAT-ATAAAATTTTAAGAAA-TTAAAA
1 ATAATT-AATAAT-AAATTTTAA-AAATTTAAAA
*
4497552 ATAATTAATAATTAATTTTAAAAATTTTAAAA
1 ATAATTAATAATAAATTTTAAAAA-TTTAAAA
4497584 ATAA
1 ATAA
4497588 AAAATTATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 3 0.09
31 11 0.34
32 18 0.56
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (31 bp):
ATAATTAATAATAAATTTTAAAAATTTAAAA
Found at i:4497617 original size:41 final size:40
Alignment explanation
Indices: 4497531--4497618 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 40
4497521 TAATTCAATA
*
4497531 TAAAATTTTAAGAAATTAAAAATAATTAATAATTAATTTT
1 TAAAATTTTAAGAAATAAAAAATAATTAATAATTAATTTT
* * *
4497571 AAAAATTTTAA-AAATAAAAAATTATCTTAATAATTATTTTT
1 TAAAATTTTAAGAAATAAAAAA-TA-ATTAATAATTAATTTT
4497612 TAAAATT
1 TAAAATT
4497619 ATATCTCTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 9 0.22
40 12 0.29
41 20 0.49
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (40 bp):
TAAAATTTTAAGAAATAAAAAATAATTAATAATTAATTTT
Found at i:4498366 original size:19 final size:18
Alignment explanation
Indices: 4498325--4498366 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
4498315 AATTTAATTA
4498325 ATAATTTTATAAAAAAAT
1 ATAATTTTATAAAAAAAT
4498343 A-AATTTT-TAATATAAAAT
1 ATAATTTTATAA-A-AAAAT
4498361 ATAATT
1 ATAATT
4498367 AAAAATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 7 0.33
19 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTTTATAAAAAAAT
Found at i:4499595 original size:12 final size:12
Alignment explanation
Indices: 4499569--4499601 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4499559 AAACAGTTCT
4499569 TTTTTATT-TTA
1 TTTTTATTATTA
4499580 -TTTTATTATTA
1 TTTTTATTATTA
4499591 TTTTTATTATT
1 TTTTTATTATT
4499602 TTCAAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 3 0.15
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:4502296 original size:2 final size:2
Alignment explanation
Indices: 4502291--4502320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4502281 ACATACGTGC
4502291 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
4502321 GAATTAGGTT
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:4504084 original size:18 final size:18
Alignment explanation
Indices: 4504058--4504105 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
4504048 TATTTAATAT
*
4504058 AAATATATTTAATATTTTA
1 AAAT-TATTTAATATTTAA
*
4504077 AAATTATTAAATATTTAA
1 AAATTATTTAATATTTAA
*
4504095 AAAATATTTAA
1 AAATTATTTAA
4504106 AAAATTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTTAATATTTAA
Found at i:4504099 original size:11 final size:11
Alignment explanation
Indices: 4504085--4504110 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4504075 TAAAATTATT
4504085 AAATATTTAAA
1 AAATATTTAAA
4504096 AAATATTTAAA
1 AAATATTTAAA
4504107 AAAT
1 AAAT
4504111 TTATCCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATTTAAA
Found at i:4507290 original size:22 final size:22
Alignment explanation
Indices: 4507265--4507318 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
4507255 CGAAAAAGTT
* *
4507265 AAAAGCAAAAGCACAAAAAATG-
1 AAAAG-AAAAACAAAAAAAATGC
*
4507287 AAAAGAAAAATAAAAAAAATGC
1 AAAAGAAAAACAAAAAAAATGC
*
4507309 AAAAGTAAAA
1 AAAAGAAAAA
4507319 TAAGGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.07
Consensus pattern (22 bp):
AAAAGAAAAACAAAAAAAATGC
Found at i:4507327 original size:22 final size:21
Alignment explanation
Indices: 4507279--4507321 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
4507269 GCAAAAGCAC
4507279 AAAAAATGAAAAGAAAAATAA
1 AAAAAATGAAAAGAAAAATAA
*
4507300 AAAAAATGCAAAAGTAAAATAA
1 AAAAAATG-AAAAGAAAAATAA
4507322 GGAAAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (21 bp):
AAAAAATGAAAAGAAAAATAA
Found at i:4508645 original size:28 final size:28
Alignment explanation
Indices: 4508603--4508828 Score: 230
Period size: 28 Copynumber: 8.2 Consensus size: 28
4508593 ATATATAGTA
*
4508603 TTTTAAAGTCCACAACTCTGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCATCC
* **
4508631 TTTTAAAGTCTACAACTCCGTTGTAAT-C
1 TTTTAAAGTCCACAACTCCG-TGGCATCC
*
4508659 TTTTAAAGTCCACAATTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCATCC
*
4508687 TTTTAAAGTCCACAA-----TGGCATCT
1 TTTTAAAGTCCACAACTCCGTGGCATCC
* * * *
4508710 TTTTAAAGTTCACAATTTCGTGGCATCT
1 TTTTAAAGTCCACAACTCCGTGGCATCC
* * * * *
4508738 TTTTAAAGTCTATAATTCCGTGACAACC
1 TTTTAAAGTCCACAACTCCGTGGCATCC
* *
4508766 TTTTAAAGTCCACAACTCCGTGACATCT
1 TTTTAAAGTCCACAACTCCGTGGCATCC
* *
4508794 TTTTAGAGTCCACAACTCCGTGACATCC
1 TTTTAAAGTCCACAACTCCGTGGCATCC
4508822 TTTTAAA
1 TTTTAAA
4508829 ATTTAAATAT
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
23 21 0.13
27 4 0.02
28 137 0.83
29 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCATCC
Found at i:4508713 original size:23 final size:23
Alignment explanation
Indices: 4508679--4508725 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4508669 CACAATTCCG
4508679 TGGCATCCTTTTAAAGTCCACAA
1 TGGCATCCTTTTAAAGTCCACAA
* *
4508702 TGGCATCTTTTTAAAGTTCACAA
1 TGGCATCCTTTTAAAGTCCACAA
4508725 T
1 T
4508726 TTCGTGGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (23 bp):
TGGCATCCTTTTAAAGTCCACAA
Found at i:4508714 original size:79 final size:81
Alignment explanation
Indices: 4508603--4508814 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 81
4508593 ATATATAGTA
* *
4508603 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAAGTCTACAACTCCGTTGTAATC-TTTTAAAG
1 TTTTAAAGTCCACAA--C--TGGCATCTTTTTAAAGTCTACAACTCCGTTGGAATCTTTTTAAAG
* *
4508667 TCCACAATTCCGTGGCATCC
62 TCCACAATTCCGTGACAACC
* * * *
4508687 TTTTAAAGTCCACAA-TGGCATCTTTTTAAAGT-TCACAATTTCG-TGGCATCTTTTTAAAGTCT
1 TTTTAAAGTCCACAACTGGCATCTTTTTAAAGTCT-ACAACTCCGTTGGAATCTTTTTAAAGTCC
*
4508749 ATAATTCCGTGACAACC
65 ACAATTCCGTGACAACC
* *
4508766 TTTTAAAGTCCACAACTCCGTGACATCTTTTTAGAGTCCACAACTCCGT
1 TTTTAAAGTCCACAACT--G-G-CATCTTTTTAAAGTCTACAACTCCGT
4508815 GACATCCTTT
Statistics
Matches: 106, Mismatches: 13, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
78 6 0.06
79 62 0.58
80 1 0.01
82 1 0.01
83 1 0.01
84 35 0.33
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (81 bp):
TTTTAAAGTCCACAACTGGCATCTTTTTAAAGTCTACAACTCCGTTGGAATCTTTTTAAAGTCCA
CAATTCCGTGACAACC
Found at i:4508742 original size:107 final size:107
Alignment explanation
Indices: 4508603--4508808 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 107
4508593 ATATATAGTA
* *
4508603 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAAGTCTACAACTCCGTTG-TAATCTTTTAAAG
1 TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAAGTCTACAACTCCG-TGACAACCTTTTAAAG
* *
4508667 TCCACAATTCCGTGGCATCCTTTTAAAGTCCACAATGGCATCT
65 TCCACAACTCCGTGACATCCTTTTAAAGTCCACAATGGCATCT
* * * * *
4508710 TTTTAAAGTTCACAA-TTTCGTGGCATCTTTTTAAAGTCTATAATTCCGTGACAACCTTTTAAAG
1 TTTTAAAGTCCACAACTCT-GTGGCATCCTTTTAAAGTCTACAACTCCGTGACAACCTTTTAAAG
* *
4508774 TCCACAACTCCGTGACATCTTTTTAGAGTCCACAA
65 TCCACAACTCCGTGACATCCTTTTAAAGTCCACAA
4508809 CTCCGTGACA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 4 0.05
107 82 0.95
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (107 bp):
TTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAAGTCTACAACTCCGTGACAACCTTTTAAAGT
CCACAACTCCGTGACATCCTTTTAAAGTCCACAATGGCATCT
Found at i:4509198 original size:40 final size:41
Alignment explanation
Indices: 4509119--4509206 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
4509109 AATTCAATAT
4509119 AAAATTTTAAGAAATTAAAAAATAATTAATAATTAATTTTA
1 AAAATTTTAAGAAATTAAAAAATAATTAATAATTAATTTTA
* * *
4509160 AAAATTTTAA-AAA-TAAAAAATTATCTTAATAATTATTTTTT
1 AAAATTTTAAGAAATTAAAAAA-TA-ATTAATAATTAATTTTA
4509201 AAAATT
1 AAAATT
4509207 GTATTTCTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 7 0.17
40 5 0.12
41 30 0.71
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (41 bp):
AAAATTTTAAGAAATTAAAAAATAATTAATAATTAATTTTA
Found at i:4509952 original size:19 final size:18
Alignment explanation
Indices: 4509911--4509952 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
4509901 AATTTAATTA
4509911 ATAATTTTATAAAAAAAT
1 ATAATTTTATAAAAAAAT
4509929 A-AATTTT-TAATATAAAAT
1 ATAATTTTATAA-A-AAAAT
4509947 ATAATT
1 ATAATT
4509953 AAAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 7 0.33
19 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTTTATAAAAAAAT
Found at i:4510420 original size:13 final size:15
Alignment explanation
Indices: 4510402--4510433 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4510392 ATTTTATATC
4510402 AATTTAT-T-AATTA
1 AATTTATATCAATTA
4510415 AATTTATATCAATTA
1 AATTTATATCAATTA
4510430 AATT
1 AATT
4510434 ATAGATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTATATCAATTA
Found at i:4510708 original size:2 final size:2
Alignment explanation
Indices: 4510701--4510730 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4510691 ATGCTATGCC
4510701 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
4510731 GCTGACAGAA
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:4510952 original size:3 final size:3
Alignment explanation
Indices: 4510944--4510974 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4510934 GATTATTGAT
4510944 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4510975 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4511208 original size:12 final size:12
Alignment explanation
Indices: 4511182--4511214 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4511172 AAACAGTTCT
4511182 TTTTTATT-TTA
1 TTTTTATTATTA
4511193 -TTTTATTATTA
1 TTTTTATTATTA
4511204 TTTTTATTATT
1 TTTTTATTATT
4511215 TTCAAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 3 0.15
12 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:4512357 original size:2 final size:2
Alignment explanation
Indices: 4512350--4512377 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4512340 ACATAAATGC
4512350 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
4512378 TAATTAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4512945 original size:21 final size:23
Alignment explanation
Indices: 4512921--4512962 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
4512911 TTATTTAAAA
4512921 AAATTTAAAA-TAT-TATTTTTT
1 AAATTTAAAATTATATATTTTTT
4512942 AAATTTAAAATTATATATTTT
1 AAATTTAAAATTATATATTTT
4512963 ATAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTTAAAATTATATATTTTTT
Found at i:4512963 original size:21 final size:21
Alignment explanation
Indices: 4512921--4512968 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
4512911 TTATTTAAAA
*
4512921 AAATTTAAAATATTATTTTTT
1 AAATTTAAAATATTATATTTT
4512942 AAATTTAAAAT-TATATATTTT
1 AAATTTAAAATAT-TATATTTT
4512963 ATAATT
1 A-AATT
4512969 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATTTAAAATATTATATTTT
Found at i:4517534 original size:9 final size:9
Alignment explanation
Indices: 4517474--4517565 Score: 57
Period size: 9 Copynumber: 10.6 Consensus size: 9
4517464 GGGTTTCACT
*
4517474 TCTTCTTCC
1 TCTTCTTCA
4517483 TCTTCTTC-
1 TCTTCTTCA
4517491 TC--CTTCA
1 TCTTCTTCA
*
4517498 T-TATCATCA
1 TCT-TCTTCA
* *
4517507 TCATCATCA
1 TCTTCTTCA
* * *
4517516 TCATCATCT
1 TCTTCTTCA
*
4517525 TCTTCTTCT
1 TCTTCTTCA
*
4517534 TCTTCTCCA
1 TCTTCTTCA
4517543 TCTTCTTCA
1 TCTTCTTCA
*
4517552 TCATCTTCA
1 TCTTCTTCA
4517561 TCTTC
1 TCTTC
4517566 GTCTTCCTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
6 4 0.06
7 1 0.01
8 2 0.03
9 61 0.90
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:4519047 original size:2 final size:2
Alignment explanation
Indices: 4519040--4519075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4519030 CAGTAGCTAC
4519040 AT 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 AT
4519076 TAACCAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4519737 original size:50 final size:50
Alignment explanation
Indices: 4519680--4519781 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
4519670 AAATCCCTAG
** *
4519680 AATTCGACTATGTAATTGGAATTTCACAAACTAATGAATTCGAAACTGAA
1 AATTCGACTATGTAACGGGAATTTCACAAACTAATGAATTCGAAACTCAA
*
4519730 AATTCGACTATGTAACGGGAATTTCACAAACTTATGAATTCGAAACTCAA
1 AATTCGACTATGTAACGGGAATTTCACAAACTAATGAATTCGAAACTCAA
4519780 AA
1 AA
4519782 CCTAGTTAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (50 bp):
AATTCGACTATGTAACGGGAATTTCACAAACTAATGAATTCGAAACTCAA
Found at i:4520075 original size:2 final size:2
Alignment explanation
Indices: 4520068--4520094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4520058 AGACACGGGA
4520068 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
4520095 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4523407 original size:18 final size:19
Alignment explanation
Indices: 4523364--4523409 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4523354 TGTTTGTGTG
*
4523364 TTTTATTATGTTATATAAA
1 TTTTAATATGTTATATAAA
4523383 TTTTAATATGTTA-AT-AA
1 TTTTAATATGTTATATAAA
4523400 TTTATAATAT
1 TTT-TAATAT
4523410 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTAATATGTTATATAAA
Found at i:4530794 original size:13 final size:14
Alignment explanation
Indices: 4530758--4530795 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4530748 ATAAATTAAT
*
4530758 ATATATTATTTATA
1 ATATTTTATTTATA
4530772 ATAATTTTATTTATA
1 AT-ATTTTATTTATA
4530787 AT-TTTTATT
1 ATATTTTATT
4530796 ATATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTTATTTATA
Found at i:4531213 original size:14 final size:15
Alignment explanation
Indices: 4531183--4531213 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4531173 GATGTCTTTG
4531183 TTTTTAATTAAATAT
1 TTTTTAATTAAATAT
4531198 TTTTTAATTAAA-AT
1 TTTTTAATTAAATAT
4531212 TT
1 TT
4531214 GATATTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAATTAAATAT
Found at i:4531447 original size:2 final size:2
Alignment explanation
Indices: 4531440--4531478 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4531430 TTCCCTCCGA
4531440 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4531479 CTTAGACAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:4540409 original size:2 final size:2
Alignment explanation
Indices: 4540402--4540435 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4540392 TAATAGTCCC
4540402 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
4540436 CCGAACTTGA
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:4540780 original size:2 final size:2
Alignment explanation
Indices: 4540773--4540811 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4540763 TTAATTGATT
4540773 TA TA TA TA TA 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 TA TA TA TA TA T
4540812 CATTTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4541065 original size:2 final size:2
Alignment explanation
Indices: 4541058--4541087 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4541048 AAACCAAGGG
4541058 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4541088 AAGATTAATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4541133 original size:13 final size:13
Alignment explanation
Indices: 4541115--4541154 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4541105 TTAATTTACG
4541115 AAAATAAAATTTA
1 AAAATAAAATTTA
*
4541128 AAAATAAAATTCA
1 AAAATAAAATTTA
* *
4541141 TAATTAAAATTTA
1 AAAATAAAATTTA
4541154 A
1 A
4541155 TAATTAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATAAAATTTA
Found at i:4542270 original size:10 final size:10
Alignment explanation
Indices: 4542255--4542316 Score: 72
Period size: 10 Copynumber: 6.1 Consensus size: 10
4542245 ACCTGAAGTC
4542255 TGTAAATATA
1 TGTAAATATA
4542265 TGTAAATATGA
1 TGTAAATAT-A
4542276 T-TCAAATATA
1 TGT-AAATATA
4542286 TGTAAATATA
1 TGTAAATATA
*
4542296 TGTATATATA
1 TGTAAATATA
* *
4542306 TATATATATA
1 TGTAAATATA
4542316 T
1 T
4542317 AATGATTCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
10 38 0.81
11 9 0.19
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (10 bp):
TGTAAATATA
Found at i:4545400 original size:2 final size:2
Alignment explanation
Indices: 4545393--4545426 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4545383 TCACTAGAAA
4545393 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
4545427 GAAAAATATC
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:4546986 original size:4 final size:4
Alignment explanation
Indices: 4546964--4547000 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
4546954 CTATTTTTGT
4546964 TTTA TTTTA TTTCA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTT
4547001 TGTTTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:4547564 original size:17 final size:18
Alignment explanation
Indices: 4547529--4547570 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4547519 ATTAAAATAT
4547529 AATATATAATATGAAAAA
1 AATATATAATATGAAAAA
4547547 AATATA-AATAT-AATAAA
1 AATATATAATATGAA-AAA
4547564 AAT-TATA
1 AATATATA
4547571 TGAAATGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AATATATAATATGAAAAA
Found at i:4547711 original size:48 final size:51
Alignment explanation
Indices: 4547652--4547746 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 51
4547642 ATTAAACATG
** *
4547652 AAAATAATATAAATATAATTTAAATATAT-AA-ATTATCAAATTTAATTTT
1 AAAATAATATAAATATAATAAAAATATATGAATATTATAAAATTTAATTTT
*
4547701 AAAA-AATATAAATATAATAAAAATATATGAATATTTTAAAATTTAA
1 AAAATAATATAAATATAATAAAAATATATGAATATTATAAAATTTAA
4547747 ATAGTATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 22 0.55
49 6 0.15
50 12 0.30
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (51 bp):
AAAATAATATAAATATAATAAAAATATATGAATATTATAAAATTTAATTTT
Found at i:4547740 original size:19 final size:18
Alignment explanation
Indices: 4547696--4547741 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
4547686 ATCAAATTTA
4547696 ATTTTAAAAAATATAAAT
1 ATTTTAAAAAATATAAAT
** *
4547714 ATAATAAAAATATATGAAT
1 ATTTTAAAAA-ATATAAAT
4547733 ATTTTAAAA
1 ATTTTAAAA
4547742 TTTAAATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTTTAAAAAATATAAAT
Found at i:4547845 original size:158 final size:157
Alignment explanation
Indices: 4547543--4547868 Score: 355
Period size: 158 Copynumber: 2.1 Consensus size: 157
4547533 TATAATATGA
* *
4547543 AAAAAATATAAATATAATAAAAATTATATGAAATGCGTTAAAAGTTATATAACATAAGTTATTAT
1 AAAAAATATAAATATAATAAAAATTATATGAAAT-CGTTAAAAGTTAAATAACATAAATTATTAT
*
4547608 TATATCAAAATTTTTATATATATATATATAAATTATTAAACATGAAAATAATATAAATATAATTT
65 TATATCAAAATTTTTATATAAATATATATAAATTATTAAACATGAAAATAATATAAATATAATTT
* * *
4547673 AAATATATAAATTATCAAAT-TTAATTTT
130 AAAAAAATAAATTAT-AAATAATAATTTT
* * **
4547701 AAAAAATATAAATATAATAAAAA-TATATGAATAT-TTTAAAATTTAAATAGTATAAATTATTAT
1 AAAAAATATAAATATAATAAAAATTATATGAA-ATCGTTAAAAGTTAAATAACATAAATTATTAT
* * *
4547764 T-TAT-AAAA-TTTTATATAAATATGTATACTATT-TTAAATACAAT-ACGAAT-ATATAAATAT
65 TATATCAAAATTTTTATATAAATATATATA-AATTATT-AA-AC-ATGA-AAATAATATAAATAT
* *
4547823 CAAATTTAAAAAAATATTATTATATATAATAATTTT
125 --AATTTAAAAAAATA-AATTATAAATAATAATTTT
4547859 AAAAAATATA
1 AAAAAATATA
4547869 TTACTAAAAT
Statistics
Matches: 143, Mismatches: 15, Indels: 20
0.80 0.08 0.11
Matches are distributed among these distances:
153 19 0.13
154 9 0.06
155 16 0.11
156 29 0.20
157 23 0.16
158 47 0.33
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (157 bp):
AAAAAATATAAATATAATAAAAATTATATGAAATCGTTAAAAGTTAAATAACATAAATTATTATT
ATATCAAAATTTTTATATAAATATATATAAATTATTAAACATGAAAATAATATAAATATAATTTA
AAAAAATAAATTATAAATAATAATTTT
Found at i:4551081 original size:13 final size:12
Alignment explanation
Indices: 4551033--4551077 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
4551023 TTTTTTAAAT
*
4551033 ATTTAATAATTA
1 ATTTAATATTTA
4551045 A-TT-ATATTTA
1 ATTTAATATTTA
4551055 TATTTAATATTTA
1 -ATTTAATATTTA
4551068 ATTTAA-ATTT
1 ATTTAATATTT
4551078 TTAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.21
11 7 0.24
12 9 0.31
13 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTAATATTTA
Found at i:4551224 original size:4 final size:4
Alignment explanation
Indices: 4551215--4551239 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4551205 TGCAGGACTA
4551215 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
4551240 GGGATTGCAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:4552030 original size:19 final size:20
Alignment explanation
Indices: 4551993--4552032 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
4551983 AAATAAATTA
*
4551993 AATATTAAATATATGATTTC
1 AATATTAAATATATAATTTC
*
4552013 AATA-TAAATATTTAATTTC
1 AATATTAAATATATAATTTC
4552032 A
1 A
4552033 TTGACTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATTAAATATATAATTTC
Found at i:4552277 original size:19 final size:18
Alignment explanation
Indices: 4552241--4552278 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
4552231 AACTTTTTAA
*
4552241 ATTTAATTAAATTAAATT
1 ATTTAATTAAAATAAATT
4552259 ATTTAATTAAAAATAAATT
1 ATTTAATT-AAAATAAATT
4552278 A
1 A
4552279 AATATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTAATTAAAATAAATT
Found at i:4552477 original size:286 final size:282
Alignment explanation
Indices: 4551815--4552591 Score: 794
Period size: 286 Copynumber: 2.7 Consensus size: 282
4551805 TGATTAAGTT
* *
4551815 AATATCTTTAATTAA--TTTTT-TTATTTAAAAGGGAGTACTTAATCACAAATTTGTTTGATTAC
1 AATAT-TTTAATTAATTTTTTTATTATTTAAATGGGAGTACTTAGTCACAAATTTGTTTGATTAC
* * **
4551877 AATTAATAAATTAATTAGTTACTTTATAAGAATATAATAAAAAAACTAGATTGAGGATCAAATCG
65 AATTAATAAATTAATTAGTTTCTTTATAAGAA-ATAAT-AAAAAATTAGATTGAAAATCAAATC-
* * *
4551942 TTTAAAA-TTTCATACCTAATTAAATTGAATTATTTAATTAAAAATAAATTAAATATTAAATATA
127 ATTAAAACTTTTATATCTAATTAAATTGAATTATTTAATTAAAAATAAATTAAATATTAAATATA
* * * * *
4552006 TGATTTCAATATAAATATTTAATTTCATTGACTAAGTTTATATGCGATTAATTTTTGATACTACT
192 TGATTTTAATATAAATATTTAACTTCACTAACTAAGTTTATATGCAATTAATTTTTGATACTACT
* * ** * *
4552071 TTGATTAGTCTTCTTAATATAAAATA
257 TCGATCAAACTTCTAAAGATAAAATA
* * * * *
4552097 AATATTTTCAA-T--TTTTTTTATTATTTAAAAGTGAGCACTTAATACTTAGTGATAGATTTGTT
1 AATATTTT-AATTAATTTTTTTATTATTT-AAA-TG-G----GAGTACTTAGTCACAAATTTGTT
* *
4552159 TGATTACAATTAAT-AA--AATTAGTTTTTTTATAAGAAACTAATAAAAAATTAGATTGAAAATT
58 TGATTACAATTAATAAATTAATTAGTTTCTTTATAAGAAA-TAATAAAAAATTAGATTGAAAATC
* * * *
4552221 AAATCATTGAAACTTTTTAAATTTAATTAAATTAAATTATTTAATTAAAAATAAATTAAATATTA
122 AAATCATTAAAAC-TTTTATATCTAATTAAATTGAATTATTTAATTAAAAATAAATTAAATATTA
* * * * *
4552286 AATATATGATTTTGATATAAATATTTAACTTCACTAATTGAA-TTTATTTTCAATTAATTTTTTA
186 AATATATGATTTTAATATAAATATTTAACTTCACTAACT-AAGTTTATATGCAATTAATTTTTGA
* *
4552350 TGCTAAC-TCGATCAAACTT-TGAAAGATAATATA
250 TACT-ACTTCGATCAAACTTCT-AAAGATAAAATA
*
4552383 GATAATTTTAATTAATTTTTTATATTATTTAAATGGGAGTACTTAGTCACAAATTTGTTTGATTA
1 AAT-ATTTTAATTAATTTTTT-TATTATTTAAATGGGAGTACTTAGTCACAAATTTGTTTGATTA
* * * *
4552448 CAATTAATAAATTAATTAATTTCTTTATAAGAAAATATTAAAAATTTAGATTGAAAGTCAAATCA
64 CAATTAATAAATTAATTAGTTTCTTTATAAG-AAATAATAAAAAATTAGATTGAAAATCAAATCA
* * * ** * *
4552513 TTAAAAC-TTTATATGTAATTGAATCGGGTTGTTTGATTAAAAATAAATT--ATATTAAATATAT
128 TTAAAACTTTTATATCTAATTAAATTGAATTATTTAATTAAAAATAAATTAAATATTAAATATAT
*
4552575 AATTTTAATATTAAATA
193 GATTTTAATA-TAAATA
4552592 CATAGTAAAT
Statistics
Matches: 406, Mismatches: 62, Indels: 53
0.78 0.12 0.10
Matches are distributed among these distances:
281 9 0.02
282 34 0.08
283 41 0.10
284 41 0.10
285 24 0.06
286 191 0.47
287 14 0.03
288 4 0.01
289 40 0.10
290 8 0.02
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (282 bp):
AATATTTTAATTAATTTTTTTATTATTTAAATGGGAGTACTTAGTCACAAATTTGTTTGATTACA
ATTAATAAATTAATTAGTTTCTTTATAAGAAATAATAAAAAATTAGATTGAAAATCAAATCATTA
AAACTTTTATATCTAATTAAATTGAATTATTTAATTAAAAATAAATTAAATATTAAATATATGAT
TTTAATATAAATATTTAACTTCACTAACTAAGTTTATATGCAATTAATTTTTGATACTACTTCGA
TCAAACTTCTAAAGATAAAATA
Found at i:4553984 original size:2 final size:2
Alignment explanation
Indices: 4553977--4554007 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4553967 ATTAACTCTA
*
4553977 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4554008 CTGAACTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4555997 original size:39 final size:39
Alignment explanation
Indices: 4555928--4556014 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
4555918 TTCAAGTTTT
* * * *
4555928 GGTTCATTTGTTTGGTTTATGAGTTCAATTCATG-GTTC
1 GGTTCATGTGTTTGATTCATGAGCTCAATTCATGAGTTC
4555966 GGGTTCATGTGTTTGATTCAT-AGCTCTAATTCATGAGTTC
1 -GGTTCATGTGTTTGATTCATGAGCTC-AATTCATGAGTTC
*
4556006 AGTTCATGT
1 GGTTCATGT
4556015 ACCTATTCAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.10
39 33 0.80
40 4 0.10
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (39 bp):
GGTTCATGTGTTTGATTCATGAGCTCAATTCATGAGTTC
Found at i:4557922 original size:23 final size:21
Alignment explanation
Indices: 4557896--4557937 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
4557886 AAAAGAATAA
4557896 ATTTAAATAATATAATAAAATTT
1 ATTTAAA-AA-ATAATAAAATTT
*
4557919 ATTTAAAAAATAATTAAAT
1 ATTTAAAAAATAATAAAAT
4557938 ATTGATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTAAAAAATAATAAAATTT
Found at i:4557945 original size:23 final size:23
Alignment explanation
Indices: 4557896--4557950 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
4557886 AAAAGAATAA
*
4557896 ATTTAAATAATATAATAAAATTT
1 ATTTAAATAATATAATAAAATTG
4557919 ATTTAAA-AA-ATAATTAAATATTG
1 ATTTAAATAATATAA-TAAA-ATTG
4557942 ATTTTAAAT
1 A-TTTAAAT
4557951 TTATTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 11 0.41
24 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTAAATAATATAATAAAATTG
Found at i:4558024 original size:19 final size:19
Alignment explanation
Indices: 4558002--4558040 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4557992 ATTTAAAAAT
4558002 TTTAAATAAAAATA-TTAAA
1 TTTAAA-AAAAATATTTAAA
*
4558021 TTTAAAAAATATATTTAAA
1 TTTAAAAAAAATATTTAAA
4558040 T
1 T
4558041 AAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAAAAATATTTAAA
Found at i:4559537 original size:21 final size:21
Alignment explanation
Indices: 4559511--4559563 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4559501 AAATCAAAAA
*
4559511 AATATTAAATTAAATTTAATT
1 AATATTAAATTAAATTTAAAT
*
4559532 ATTATTAAATTAAATTTAAAT
1 AATATTAAATTAAATTTAAAT
4559553 AAT-TTAAATTA
1 AATATTAAATTA
4559564 TCAATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTAAATTAAATTTAAAT
Found at i:4560747 original size:2 final size:2
Alignment explanation
Indices: 4560742--4560770 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4560732 TTTTAAAATT
4560742 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
4560771 TCCTGGCAAC
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:4562375 original size:2 final size:2
Alignment explanation
Indices: 4562368--4562397 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4562358 AAATGAGGTC
4562368 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4562398 ATTTATGTAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4565359 original size:50 final size:50
Alignment explanation
Indices: 4565288--4565384 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
4565278 ATGGGGTATC
4565288 TTTGAAAAATTTTAATGTCATAATTCAATTTTTTCAAATAAAAGCTTCTT
1 TTTGAAAAATTTTAATGTCATAATTCAATTTTTTCAAATAAAAGCTTCTT
*
4565338 TTTGAAAAATTTTAATGTCATAATTCAATTTTTTCAAATGAAAGCTT
1 TTTGAAAAATTTTAATGTCATAATTCAATTTTTTCAAATAAAAGCTT
4565385 TCTTAGGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (50 bp):
TTTGAAAAATTTTAATGTCATAATTCAATTTTTTCAAATAAAAGCTTCTT
Found at i:4568288 original size:5 final size:5
Alignment explanation
Indices: 4568278--4568303 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4568268 AATTCAATCG
4568278 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
4568304 AGAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:4569517 original size:12 final size:12
Alignment explanation
Indices: 4569497--4569530 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
4569487 GTGAAATTTG
4569497 ACCCTAACCCCA
1 ACCCTAACCCCA
*
4569509 ACCCCAACCCCA
1 ACCCTAACCCCA
4569521 ACCCTAACCC
1 ACCCTAACCC
4569531 TATATTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.62, G:0.00, T:0.06
Consensus pattern (12 bp):
ACCCTAACCCCA
Found at i:4569532 original size:6 final size:6
Alignment explanation
Indices: 4569497--4569530 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4569487 GTGAAATTTG
* *
4569497 ACCCTA ACCCCA ACCCCA ACCCCA ACCCTA ACCC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
4569531 TATATTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.62, G:0.00, T:0.06
Consensus pattern (6 bp):
ACCCCA
Found at i:4569676 original size:6 final size:6
Alignment explanation
Indices: 4569667--4569700 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4569657 GTGAAATTTG
4569667 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
1 ACCCCA ACCCCA ACCCCA ACCCCA ACCCCA ACCC
4569701 TATATTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCCCA
Found at i:4569733 original size:170 final size:156
Alignment explanation
Indices: 4569570--4569927 Score: 448
Period size: 161 Copynumber: 2.3 Consensus size: 156
4569560 CCCCCCCCCC
*
4569570 CCCCCCCCTCTCATGTGAGTGTGACTCGC-TACTTTGATTGTGTTTCAAATACACTCCCACAGCT
1 CCCCCCCCTCTCATGTGAGTGTGACTCGCATACTTTGATTGTGATTCAAATACACTCCCACAGCT
*
4569634 AAAATTTGGTCCATGATGAGGATGTGAAATTTGACCCCAACCCCAACCCCAACCCCAACCCCAAC
66 AAAATTTGGTCCATGATGAGGATGTGAAATTTGACCCTAACCCCAACCCCAACCCCAACCCCAAC
4569699 CCTATATTGGAAAACAGACAGCCCCTTG-T
131 CCTATATTGGAAAAC--A-A-CCCCTTGCT
*
4569728 CCCCCCCTTCTCATGTGAGTGTGACTCGCTAATACTTTGATTGTGATTCAAATACACTCCCACAG
1 CCCCCCCCTCTCATGTGAGTGTGACTCGC--ATACTTTGATTGTGATTCAAATACACTCCCACAG
* * * *
4569793 CTAAAATTTGGTCCATGATGAGGATGTGAAACTTGACCCT------AACCCTAACCCTAGCCCCA
64 CTAAAATTTGGTCCATGATGAGGATGTGAAATTTGACCCTAACCCCAACCCCAACCCCAACCCCA
*
4569852 ACCCTATATTGGAAAGACAATCCCTTCTTTCT
129 ACCCTATATTGGAAA-ACAA-CCC--CTTGCT
*
4569884 CCCCACCCC-C-CATGTGAGTGTGACTGGCTACTACTTTGATTGTG
1 CCCC-CCCCTCTCATGTGAGTGTGACTCGC-A-TACTTTGATTGTG
4569928 TTTCCCTTTC
Statistics
Matches: 179, Mismatches: 12, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
153 4 0.02
154 2 0.01
155 64 0.36
156 8 0.04
157 3 0.02
158 28 0.16
161 70 0.39
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (156 bp):
CCCCCCCCTCTCATGTGAGTGTGACTCGCATACTTTGATTGTGATTCAAATACACTCCCACAGCT
AAAATTTGGTCCATGATGAGGATGTGAAATTTGACCCTAACCCCAACCCCAACCCCAACCCCAAC
CCTATATTGGAAAACAACCCCTTGCT
Found at i:4571674 original size:331 final size:332
Alignment explanation
Indices: 4571012--4571675 Score: 1158
Period size: 334 Copynumber: 2.0 Consensus size: 332
4571002 AATTAAAAAA
*
4571012 TAATCAATTGAAACTGTTGTCTATTCCTGGAGATTCTCCTTATAGTTACTTTGCATAAATAATTT
1 TAATCAATTGAAACTGTTGTCTATTCCTGGAGATTCTCCTTACAGTTACTTTGCATAAATAATTT
*
4571077 TTTTTTTTTTGCTAATAATGATGCATTAGACTTTTAATTTTAATAATCAAAATTTAATTTTTAAT
66 TTTTTTTTTTGCTAATAATGATGCATTAGACTTTTAATTTTAATAATCAAAATTTAATCTTTAAT
4571142 AATTTAAAATATATATAAAAAATATTTTAACCTTAAAAAAGAACAGATCTTATTAAATACATATT
131 AATTTAAAATATATATAAAAAATATTTTAACCTT-AAAAAGAACAGATCTTATTAAATACATATT
4571207 AAAATTAAAAATTTAAATTTAACTTTATTAATTTATAAAATTATATTAAAAATAATTTTTAATTA
195 AAAATTAAAAATTTAAATTTAACTTTATTAATTTATAAAATTATATTAAAAATAATTTTTAATTA
*
4571272 TTTTAAATTTTAAATTTTAATATCTACAATTTTTTTCTCATTCCAAACTATAATCTCTTTTTATA
260 ATTTAAATTTTAAATTTTAATATCTACAATTTTTTTCTCATTCCAAACTATAATCTCTTTTTATA
4571337 CCATCAAG
325 CCATCAAG
*
4571345 TAATCAATTGAAACTGTTGTCTATTCCTTGAGATTCTCCTTACAGTTACTTTGCATAAATAAATT
1 TAATCAATTGAAACTGTTGTCTATTCCTGGAGATTCTCCTTACAGTTACTTTGCATAAAT-AATT
*
4571410 TTTTTTTTTTTGCTAATAATGATGCATTAGATTTTTAATTTTAATAATCAAAATTTAATCTTTAA
65 TTTTTTTTTTTGCTAATAATGATGCATTAGACTTTTAATTTTAATAATCAAAATTTAATCTTTAA
*
4571475 TAATTTAAAATATATATAAAAAAATATTTTAACCTT-TAAA-AA-A-ATCTTATTAAATACATAT
130 TAATTTAAAATATATAT-AAAAAATATTTTAACCTTAAAAAGAACAGATCTTATTAAATACATAT
* * *
4571536 TAAAATTAAAATTTTAAATTTAACTTTATTAATTTATATAATTATTTTTAAAAATAATTTTTAAT
194 TAAAATTAAAAATTTAAATTTAACTTTATTAATTTATAAAATTA-TATTAAAAATAATTTTTAAT
*
4571601 TAATTTAAATTTTAAGTTTTAATATCTACGAATTTTTTT-TCATTCCAAACTATAATCTCTTTTT
258 TAATTTAAATTTTAAATTTTAATATCTAC-AATTTTTTTCTCATTCCAAACTATAATCTCTTTTT
4571665 ATACCATCAAG
322 ATACCATCAAG
4571676 AACATGTATG
Statistics
Matches: 317, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
330 60 0.19
331 83 0.26
332 11 0.03
333 61 0.19
334 84 0.26
335 18 0.06
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.46
Consensus pattern (332 bp):
TAATCAATTGAAACTGTTGTCTATTCCTGGAGATTCTCCTTACAGTTACTTTGCATAAATAATTT
TTTTTTTTTTGCTAATAATGATGCATTAGACTTTTAATTTTAATAATCAAAATTTAATCTTTAAT
AATTTAAAATATATATAAAAAATATTTTAACCTTAAAAAGAACAGATCTTATTAAATACATATTA
AAATTAAAAATTTAAATTTAACTTTATTAATTTATAAAATTATATTAAAAATAATTTTTAATTAA
TTTAAATTTTAAATTTTAATATCTACAATTTTTTTCTCATTCCAAACTATAATCTCTTTTTATAC
CATCAAG
Done.