Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 15 of 17
Found at i:3199732 original size:5 final size:5
Alignment explanation
Indices: 3199722--3199749 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3199712 GCCGTCCGTC
3199722 TCGGG TCGGG TCGGG TCGGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG
3199750 TGGGCGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.57, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:3210565 original size:14 final size:14
Alignment explanation
Indices: 3210546--3210582 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3210536 ATGGTGTGGA
3210546 GACTTTGTTCGAAG
1 GACTTTGTTCGAAG
*
3210560 GACTTTGGTCGAAG
1 GACTTTGTTCGAAG
3210574 GACTTTGTT
1 GACTTTGTT
3210583 GTTTCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.38
Consensus pattern (14 bp):
GACTTTGTTCGAAG
Found at i:3212764 original size:11 final size:11
Alignment explanation
Indices: 3212748--3212774 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3212738 AAAATTACAT
3212748 TATTAAAAATA
1 TATTAAAAATA
3212759 TATTAAAAATA
1 TATTAAAAATA
3212770 TATTA
1 TATTA
3212775 TTGATAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3219275 original size:35 final size:37
Alignment explanation
Indices: 3219236--3219311 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
3219226 GAATACTCAC
3219236 ATCCTATCATTCATAGT-ATTT-TTGAAATCACAAAA
1 ATCCTATCATTCATAGTGATTTATTGAAATCACAAAA
*
3219271 ATCCTATCATTCATAGTGTTTTAACTTGAAATCACAAAA
1 ATCCTATCATTCATAGTGATTT-A-TTGAAATCACAAAA
3219310 AT
1 AT
3219312 AACAATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 17 0.47
36 3 0.08
39 16 0.44
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (37 bp):
ATCCTATCATTCATAGTGATTTATTGAAATCACAAAA
Found at i:3230469 original size:34 final size:32
Alignment explanation
Indices: 3230430--3230499 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3230420 TTTTGTAAAG
*
3230430 GGGAAAGATTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGATTCTAGCTAAGCCCG-GTAAAA-CTA
* * *
3230464 GGGAAAGGTTCTAGTTTAGCCCGGTAAAACTA
1 GGGAAAGATTCTAGCTAAGCCCGGTAAAACTA
3230496 GGGA
1 GGGA
3230500 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 6 0.19
34 19 0.59
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGATTCTAGCTAAGCCCGGTAAAACTA
Found at i:3233244 original size:31 final size:31
Alignment explanation
Indices: 3233177--3233236 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3233167 CAATTTAAGG
*
3233177 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3233208 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3233237 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3233334 original size:19 final size:19
Alignment explanation
Indices: 3233306--3233347 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3233296 TTTTATAAAT
*
3233306 AGTAATTTACTATTTGAAC
1 AGTAAATTACTATTTGAAC
3233325 AGTAAATTACTATTTGAAC
1 AGTAAATTACTATTTGAAC
3233344 AGTA
1 AGTA
3233348 TCCCGAGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AGTAAATTACTATTTGAAC
Found at i:3233479 original size:21 final size:21
Alignment explanation
Indices: 3233453--3233494 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3233443 ATTTGAATAT
* *
3233453 TATGAAGGGGTATCGATTCCC
1 TATGAAAGGGTACCGATTCCC
3233474 TATGAAAGGGTACCGATTCCC
1 TATGAAAGGGTACCGATTCCC
3233495 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAAGGGTACCGATTCCC
Found at i:3233556 original size:21 final size:21
Alignment explanation
Indices: 3233523--3233562 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3233513 TTTTTGTAGA
*
3233523 AAAATCATTCCCAAACGGCTCT
1 AAAATCATCCCCAAA-GGCTCT
3233545 AAAA-CATCCCCAAAGGCT
1 AAAATCATCCCCAAAGGCT
3233563 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.40, C:0.33, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAAAGGCTCT
Found at i:3233816 original size:34 final size:32
Alignment explanation
Indices: 3233777--3233846 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3233767 TTTTGTAAAG
*
3233777 GGGAAAGATTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGATTCTAGCTAAGCCCG-GTAAAA-CTA
* * *
3233811 GGGAAAGGTTCTAGTTTAGCCCGGTAAAACTA
1 GGGAAAGATTCTAGCTAAGCCCGGTAAAACTA
3233843 GGGA
1 GGGA
3233847 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 6 0.19
34 19 0.59
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGATTCTAGCTAAGCCCGGTAAAACTA
Found at i:3235654 original size:2 final size:2
Alignment explanation
Indices: 3235644--3235715 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
3235634 TTTTATCTGG
*
3235644 AT AT GT 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
3235686 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
3235716 TGTTTGTTGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3249380 original size:2 final size:2
Alignment explanation
Indices: 3249373--3249425 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3249363 TAATTGAATA
3249373 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
3249415 AT AT AT AT AT A
1 AT AT AT AT AT A
3249426 CTCTACCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3249610 original size:2 final size:2
Alignment explanation
Indices: 3249603--3249649 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3249593 GGTTATACCA
3249603 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
3249645 AT AT A
1 AT AT A
3249650 CTCAACAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3256756 original size:78 final size:74
Alignment explanation
Indices: 3256649--3256799 Score: 230
Period size: 78 Copynumber: 2.0 Consensus size: 74
3256639 AGGGTAATTT
* * *
3256649 ACGTTTTGAGTCATCCATGCTTATTAAATTTTGTTAATTAGCTATATTTTGTTTTTTTAAAGAAT
1 ACGTTTTGAGTCATCCATGCTTATAAAATTTTGTTAATTAGCCATA---T-TTTTTTAAAAGAAT
3256714 TATTATATATATA
62 TATTATATATATA
*
3256727 ACGTTTTGAGTCATCCATGTTTATAAAATTTTGTTAATTAGCCATATTTTTTTAAAAGAATTATT
1 ACGTTTTGAGTCATCCATGCTTATAAAATTTTGTTAATTAGCCATATTTTTTTAAAAGAATTATT
3256792 ATATATAT
66 ATATATAT
3256800 CTATGTTACA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
74 25 0.36
75 1 0.01
78 43 0.62
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (74 bp):
ACGTTTTGAGTCATCCATGCTTATAAAATTTTGTTAATTAGCCATATTTTTTTAAAAGAATTATT
ATATATATA
Found at i:3279723 original size:42 final size:42
Alignment explanation
Indices: 3279664--3279783 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
3279654 TTTCCCCGAA
*
3279664 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
3279706 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
3279748 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
3279784 TGTAAAGTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:3280008 original size:22 final size:23
Alignment explanation
Indices: 3279961--3280021 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
3279951 TAATTATTAA
* *
3279961 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
3279982 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
3280005 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
3280022 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:3280017 original size:31 final size:31
Alignment explanation
Indices: 3279972--3280120 Score: 96
Period size: 31 Copynumber: 5.1 Consensus size: 31
3279962 ATATTTAAAA
3279972 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TTAATATTTATAATAATATAATAT
*
3280004 TATATTTTTAATA-TTAT-ATAAAAT-A-AT
1 TATATTTTTAATATTTATAATAATATAATAT
*
3280031 CA-A---TT-ATA-TTATAATAATATAAGATAT
1 TATATTTTTAATATTTATAATAATAT-A-ATAT
3280058 TATATTTTT-AT-TTTAATAAT-ATATAATAAT
1 TATATTTTTAATATTT-ATAATAATATAAT-AT
*
3280088 T-T-TTTTTATATATTTAATAATGA-ATAATAT
1 TATATTTTTA-ATATTT-ATAATAATATAATAT
3280118 TAT
1 TAT
3280121 TTATATATTT
Statistics
Matches: 96, Mismatches: 4, Indels: 35
0.71 0.03 0.26
Matches are distributed among these distances:
22 7 0.07
23 8 0.08
26 2 0.02
27 6 0.06
28 7 0.07
29 9 0.09
30 13 0.14
31 31 0.32
32 13 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TATATTTTTAATATTTATAATAATATAATAT
Found at i:3280081 original size:24 final size:23
Alignment explanation
Indices: 3280049--3280095 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3280039 TTATAATAAT
* *
3280049 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
3280073 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
3280096 TATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:3280094 original size:29 final size:29
Alignment explanation
Indices: 3280037--3280139 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
3280027 TAATCAATTA
* *
3280037 TATTATAATAATATA-AGATATTATATTTT
1 TATTTTAATAATATATA-ATATTATTTTTT
3280066 TATTTTAATAATATATAATAATT-TTTTTT
1 TATTTTAATAATATATAAT-ATTATTTTTT
* *
3280095 ATATATTTAATAATGA-ATAATATTATTTATA
1 -TAT-TTTAATAAT-ATATAATATTATTTTTT
*
3280126 TATTTCAATAATAT
1 TATTTTAATAATAT
3280140 TTTAGTAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.02
29 29 0.47
30 13 0.21
31 18 0.29
32 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (29 bp):
TATTTTAATAATATATAATATTATTTTTT
Found at i:3280105 original size:28 final size:28
Alignment explanation
Indices: 3280074--3280137 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
3280064 TTTATTTTAA
* *
3280074 TAATATAT-AATAATTTTTTTTATATATT
1 TAATA-ATGAATAATATTATTTATATATT
3280102 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAATATTATTTATATATT
3280130 TCAATAAT
1 T-AATAAT
3280138 ATTTTAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
TAATAATGAATAATATTATTTATATATT
Found at i:3280324 original size:15 final size:15
Alignment explanation
Indices: 3280304--3280385 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
3280294 TTTCAGAAAA
3280304 TGAATTACTGGAATT
1 TGAATTACTGGAATT
3280319 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3280334 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
3280349 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
3280364 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
3280378 TGAATTAC
1 TGAATTAC
3280386 ATTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:3280340 original size:30 final size:30
Alignment explanation
Indices: 3280304--3280385 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
3280294 TTTCAGAAAA
**
3280304 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
3280334 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
3280364 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
3280386 ATTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:3280348 original size:45 final size:44
Alignment explanation
Indices: 3280299--3280385 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
3280289 TGGTTTTTCA
**
3280299 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
3280344 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
3280386 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:3280391 original size:20 final size:20
Alignment explanation
Indices: 3280368--3280417 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3280358 GGAATTTGAA
3280368 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3280388 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3280408 TTCTGGAAAA
1 TTCTGGAAAA
3280418 CATCTGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:3280640 original size:30 final size:28
Alignment explanation
Indices: 3280583--3280685 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
3280573 CTTTACTAAA
*
3280583 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
3280612 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATAT-AAAAAA-TATTAT
3280642 ATATTATTAAA-ATA-AAATATAATATCT-T
1 ATATTATTAAATATATAAA-A-AATAT-TAT
3280670 ATATTATTATAATATA
1 ATATTATTA-AATATA
3280686 ATTGATTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
27 3 0.05
28 23 0.36
29 19 0.30
30 18 0.28
31 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:3280671 original size:23 final size:22
Alignment explanation
Indices: 3280627--3280671 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3280617 ATTAAATATA
* *
3280627 TAAAAAAATTATTATATATTAT
1 TAAAAAAAATATAATATATTAT
*
3280649 TAAAATAAAATATAATATCTTAT
1 TAAAA-AAAATATAATATATTAT
3280672 ATTATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAAAAATATAATATATTAT
Found at i:3280681 original size:52 final size:52
Alignment explanation
Indices: 3280625--3280734 Score: 129
Period size: 52 Copynumber: 2.1 Consensus size: 52
3280615 TTATTAAATA
3280625 TATAAAAAAATT-ATTATATATTAT-TAA-AAT-AAAATATAATATCTTATATTAT
1 TATAAAAAAATTGATTAT-T-TTATATAATAATAAAAATATAATA--TTATATTAT
* * *
3280677 TATAATATAATTGATTATTTTATATAATATTAAAAATATAATATTATATTAT
1 TATAAAAAAATTGATTATTTTATATAATAATAAAAATATAATATTATATTAT
3280729 TATAAA
1 TATAAA
3280735 TATTAATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
51 4 0.08
52 28 0.56
53 7 0.14
54 11 0.22
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (52 bp):
TATAAAAAAATTGATTATTTTATATAATAATAAAAATATAATATTATATTAT
Found at i:3280683 original size:28 final size:27
Alignment explanation
Indices: 3280636--3280733 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
3280626 ATAAAAAAAT
*
3280636 TATTATATATTATTAAAATAAAATATAA
1 TATT-TATATTATTATAATAAAATATAA
* *
3280664 TATCTTATATTATTATAATATAAT-TGAT
1 TAT-TTATATTATTATAATAAAATAT-AA
* *
3280692 TATTT-TA-TATAATATTAAAAATATAA
1 TATTTATATTATTATAAT-AAAATATAA
3280718 TA-TTATATTATTATAA
1 TATTTATATTATTATAA
3280734 ATATTAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
25 9 0.16
26 11 0.20
27 10 0.18
28 24 0.44
29 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTTATATTATTATAATAAAATATAA
Found at i:3280724 original size:22 final size:23
Alignment explanation
Indices: 3280699--3280742 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3280689 GATTATTTTA
3280699 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3280721 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3280743 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:3280747 original size:22 final size:22
Alignment explanation
Indices: 3280703--3280759 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3280693 ATTTTATATA
* *
3280703 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
3280724 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
3280746 ATATTTTAAATATT
1 ATATTATAAATATT
3280760 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:3280758 original size:52 final size:50
Alignment explanation
Indices: 3280640--3280759 Score: 122
Period size: 54 Copynumber: 2.3 Consensus size: 50
3280630 AAAAATTATT
**
3280640 ATATATTATTAAA-A-TAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAATATAATA-CTTATATTATTATAATATAATAA
3280690 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATT-AAAATATAATACTTATATTATTAT-AATA-TAATAA
3280744 ATATATTTTAAATATT
1 ATATATTTTAAATATT
3280760 TTAATAATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 2 0.03
52 19 0.32
53 7 0.12
54 20 0.34
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (50 bp):
ATATATTTTAAATATTAAAATATAATACTTATATTATTATAATATAATAA
Found at i:3281011 original size:42 final size:42
Alignment explanation
Indices: 3280948--3281067 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
3280938 ATGAATTACA
* *
3280948 TTCCGGAAAACGAATTGCGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
3280990 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
3281032 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
3281068 TTCGAGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:3281232 original size:14 final size:15
Alignment explanation
Indices: 3281211--3281262 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
3281201 TTACAGAAAT
3281211 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
3281226 G-AATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
3281240 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
3281255 GTAATTCA
1 GTAATTCA
3281263 AATTCCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:3281236 original size:20 final size:20
Alignment explanation
Indices: 3281159--3281228 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3281149 TTTCCAGATG
3281159 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3281179 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
3281199 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3281219 TTTTCCAGAA
1 TTTTCCAGAA
3281229 TTCAAATTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3281245 original size:15 final size:15
Alignment explanation
Indices: 3281227--3281271 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
3281217 CATTTTCCAG
3281227 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
*
3281242 AATTC-ATTTTCCAGT
1 AATTCAAATTT-CAGT
*
3281257 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
3281272 TTTCTGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 18 0.72
16 3 0.12
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:3281253 original size:29 final size:30
Alignment explanation
Indices: 3281211--3281271 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
3281201 TTACAGAAAT
*
3281211 GTAATTCATTTTCCAG-AATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
3281240 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
3281270 GT
1 GT
3281272 TTTCTGGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:3281806 original size:31 final size:31
Alignment explanation
Indices: 3281771--3281840 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
3281761 ACTATTAAAA
3281771 GTTACAAAATGGTCATCTAACTATCCATTAT
1 GTTACAAAATGGTCATCTAACTATCCATTAT
3281802 GTTACAAAATGGTCATCTAACTATCCATTAT
1 GTTACAAAATGGTCATCTAACTATCCATTAT
*
3281833 GTTCCAAA
1 GTTACAAA
3281841 CTCATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (31 bp):
GTTACAAAATGGTCATCTAACTATCCATTAT
Found at i:3286713 original size:4 final size:4
Alignment explanation
Indices: 3286704--3286737 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
3286694 TCCAAATTGT
3286704 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
3286738 ATGCTTGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3286768 original size:2 final size:2
Alignment explanation
Indices: 3286761--3286787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3286751 GTATAAATTG
3286761 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 T
3286788 GTGCGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3291332 original size:2 final size:2
Alignment explanation
Indices: 3291325--3291351 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3291315 ATAAATTGTG
3291325 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 T
3291352 GGGTAAAGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3293246 original size:18 final size:17
Alignment explanation
Indices: 3293214--3293247 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3293204 TTAGCCGGTC
3293214 CGGTTTGAACGGTTCAG
1 CGGTTTGAACGGTTCAG
*
3293231 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
3293248 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAG
Found at i:3293258 original size:24 final size:24
Alignment explanation
Indices: 3293229--3293284 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
3293219 TGAACGGTTC
3293229 AGCGGTTCTGACCGGTTCACTAAT
1 AGCGGTTCTGACCGGTTCACTAAT
3293253 AGCGGTTCTGACCGGTTCACTAAT
1 AGCGGTTCTGACCGGTTCACTAAT
*
3293277 AACGGTTC
1 AGCGGTTC
3293285 AACCGGTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (24 bp):
AGCGGTTCTGACCGGTTCACTAAT
Found at i:3304551 original size:16 final size:16
Alignment explanation
Indices: 3304530--3304590 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
3304520 TAATAAATAA
3304530 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3304546 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
3304562 ACGAATATAAATGAAC
1 ACGAACATAAACGAAC
3304578 ACGAACATAAACG
1 ACGAACATAAACG
3304591 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3305705 original size:14 final size:14
Alignment explanation
Indices: 3305688--3305714 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3305678 GAACATAAAC
3305688 GAACATAATCGAAT
1 GAACATAATCGAAT
3305702 GAACATAATCGAA
1 GAACATAATCGAA
3305715 CGTTCACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (14 bp):
GAACATAATCGAAT
Found at i:3305724 original size:24 final size:24
Alignment explanation
Indices: 3305665--3305715 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3305655 GATTGGGTTA
3305665 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAATGAACATAAACG
*
3305689 AACATAATCGAATGAACATAATCG
1 AACATAATCGAATGAACATAAACG
3305713 AAC
1 AAC
3305716 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.18
Consensus pattern (24 bp):
AACATAATCGAATGAACATAAACG
Found at i:3309254 original size:13 final size:13
Alignment explanation
Indices: 3309238--3309262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3309228 GGTATCCACT
3309238 TTAAAATTTTATA
1 TTAAAATTTTATA
3309251 TTAAAATTTTAT
1 TTAAAATTTTAT
3309263 TCGTATTTAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAAATTTTATA
Found at i:3312379 original size:20 final size:20
Alignment explanation
Indices: 3312351--3312396 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3312341 TTTTCTTAGA
* *
3312351 AAATATATAAATTAATCATT
1 AAATTTATAAAATAATCATT
3312371 AAATTTATAAAATAATCATT
1 AAATTTATAAAATAATCATT
3312391 AAATTT
1 AAATTT
3312397 TATTGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTTATAAAATAATCATT
Found at i:3315630 original size:2 final size:2
Alignment explanation
Indices: 3315623--3315661 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3315613 CATGAGTTAG
3315623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3315662 GGAATTGGTA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3316387 original size:22 final size:22
Alignment explanation
Indices: 3316359--3316402 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3316349 AGAGTCTAGG
3316359 GTATCCAGTGGTCCTTCGGGAC
1 GTATCCAGTGGTCCTTCGGGAC
3316381 GTATCCAGTGGTCCTTCGGGAC
1 GTATCCAGTGGTCCTTCGGGAC
3316403 ATAATAGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (22 bp):
GTATCCAGTGGTCCTTCGGGAC
Found at i:3317430 original size:16 final size:16
Alignment explanation
Indices: 3317411--3317447 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3317401 CGATCACTAA
3317411 TGTTTGATTAAGATTT
1 TGTTTGATTAAGATTT
3317427 TGTTTGATTAAGATTT
1 TGTTTGATTAAGATTT
3317443 TGTTT
1 TGTTT
3317448 TCACCACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (16 bp):
TGTTTGATTAAGATTT
Found at i:3337759 original size:60 final size:60
Alignment explanation
Indices: 3337662--3337774 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
3337652 TAGTTAGGTG
* * * *
3337662 ACTATTTTGTAACTTTTAATAGTTGAGGGACTTAATAAAGTAATA-CTCTATAGCCAGAAC
1 ACTATTTTATAACTTTTAATAGTCGAGGGACTAAATAAAGCAATATC-CTATAGCCAGAAC
3337722 ACTATTTTATAACTTTTAATAGTCGAGTGG-CTAAATAAAGCAATATCCTATAG
1 ACTATTTTATAACTTTTAATAGTCGAG-GGACTAAATAAAGCAATATCCTATAG
3337775 TCGGGGACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (60 bp):
ACTATTTTATAACTTTTAATAGTCGAGGGACTAAATAAAGCAATATCCTATAGCCAGAAC
Found at i:3338903 original size:2 final size:2
Alignment explanation
Indices: 3338896--3338943 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3338886 CAATGATTAG
3338896 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
3338938 AT AT AT
1 AT AT AT
3338944 CCAAATGCGC
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:3339650 original size:16 final size:17
Alignment explanation
Indices: 3339615--3339651 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3339605 CCCGTCGCAG
3339615 GAATAATTTTTTTAGTTT
1 GAATAATTTTTTTAG-TT
3339633 GAATAATTTTTTTA-TT
1 GAATAATTTTTTTAGTT
3339649 GAA
1 GAA
3339652 ACTCGTCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (17 bp):
GAATAATTTTTTTAGTT
Found at i:3340250 original size:41 final size:41
Alignment explanation
Indices: 3340190--3340338 Score: 144
Period size: 41 Copynumber: 3.7 Consensus size: 41
3340180 TCAAATTCGC
* *
3340190 AAATCGCAATGCGA-ATACGTAAATCGCATTGCGAATTAGG
1 AAATCGCAATGCGATTTACGTAAATCGCATTGCGAATTACG
* *
3340230 AAAATCGCAATGCGA-TTACGTATATCGCAATGCG-ATTACG
1 -AAATCGCAATGCGATTTACGTAAATCGCATTGCGAATTACG
* * * * * * *
3340270 TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACG
1 AAATCGCAATGCGATTTACGTAAATCGCATTGCGAATTACG
* *
3340311 TAATCGCATTGCGATTTA-GTAAATCGCA
1 AAATCGCAATGCGATTTACGTAAATCGCA
3340339 ACGAGATTCT
Statistics
Matches: 89, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 11 0.12
40 27 0.30
41 51 0.57
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
AAATCGCAATGCGATTTACGTAAATCGCATTGCGAATTACG
Found at i:3340272 original size:20 final size:20
Alignment explanation
Indices: 3340190--3340339 Score: 135
Period size: 20 Copynumber: 7.5 Consensus size: 20
3340180 TCAAATTCGC
*
3340190 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGATTACGT
* * *
3340210 AAATCGCATTGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGT
3340231 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGT
*
3340251 ATATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGT
* * * *
3340271 -ATTCGCATTGCGATTTTCCT
1 AAATCGCAATGCGA-TTACGT
* *
3340291 AATTCGCATTGCGATTTACGT
1 AAATCGCAATGCGA-TTACGT
*
3340312 -AATCGCATTGCGATTTA-GT
1 AAATCGCAATGCGA-TTACGT
3340331 AAATCGCAA
1 AAATCGCAA
3340340 CGAGATTCTG
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
19 12 0.11
20 63 0.58
21 34 0.31
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGT
Found at i:3340297 original size:21 final size:21
Alignment explanation
Indices: 3340254--3340328 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
3340244 ATTACGTATA
* *
3340254 TCGCAATGCGA-TTACGT-AT
1 TCGCATTGCGATTTACCTAAT
*
3340273 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
3340294 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
3340314 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
3340329 GTAAATCGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.20
20 19 0.39
21 20 0.41
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:3340304 original size:60 final size:61
Alignment explanation
Indices: 3340191--3340338 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 61
3340181 CAAATTCGCA
* **
3340191 AATCGCAATGCGAATACGTAAATCGCATTGCGAATTAGGAAAATCGCAATGCGA-TTACGT
1 AATCGCAATGCGATTACGTAAATCGCATTGCGAATTACCAAAATCGCAATGCGATTTACGT
* * * * * *
3340251 ATATCGCAATGCGATTACGT-ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
1 A-ATCGCAATGCGATTACGTAAATCGCATTGCGAATTACCAAAATCGCAATGCGATTTACGT
*
3340312 AATCGCATTGCGATTTA-GTAAATCGCA
1 AATCGCAATGCGA-TTACGTAAATCGCA
3340339 ACGAGATTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
60 40 0.55
61 33 0.45
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (61 bp):
AATCGCAATGCGATTACGTAAATCGCATTGCGAATTACCAAAATCGCAATGCGATTTACGT
Found at i:3341205 original size:24 final size:24
Alignment explanation
Indices: 3341178--3341231 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3341168 GTATTCAAAA
3341178 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3341202 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3341226 TTTGAT
1 TTTGAT
3341232 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3343777 original size:19 final size:18
Alignment explanation
Indices: 3343755--3343904 Score: 108
Period size: 19 Copynumber: 8.7 Consensus size: 18
3343745 GGAAATTACT
3343755 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3343774 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
3343788 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3343807 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
3343821 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* **
3343840 ATCGCAA-CG---GGGGA
1 ATCGCAAGCGAAATGAAA
3343854 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
*
3343873 ATCACAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
3343892 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
3343905 TTTAGTTTCG
Statistics
Matches: 103, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
14 27 0.26
15 4 0.04
16 6 0.06
17 6 0.06
18 4 0.04
19 56 0.54
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:3343792 original size:14 final size:14
Alignment explanation
Indices: 3343773--3343827 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3343763 GCGAAATGAA
3343773 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3343787 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3343806 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3343820 AATCGCAA
1 AATCGCAA
3343828 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3343797 original size:33 final size:33
Alignment explanation
Indices: 3343755--3343881 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
3343745 GGAAATTACT
3343755 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3343788 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3343821 ATCGCAATGCGAAATGAAAATCGCAACGGGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3343854 ATCGCAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3343882 CGAAATGAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3343922 original size:19 final size:19
Alignment explanation
Indices: 3343900--3343974 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
3343890 AAATCGCAAC
*
3343900 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCATT
*
3343919 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
*
3343938 GCG-A-TTC-TCTCG--TT
1 GCGAATTTCATTTCGCATT
*
3343952 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
3343971 GCGA
1 GCGA
3343975 TAGTCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.11
16 7 0.16
17 7 0.16
19 24 0.55
20 1 0.02
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:3343983 original size:19 final size:19
Alignment explanation
Indices: 3343910--3343975 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
3343900 GCGAATTTAG
*
3343910 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
3343929 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
3343945 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
3343962 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3343976 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:3344101 original size:14 final size:13
Alignment explanation
Indices: 3344082--3344120 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
3344072 CATCAATTAA
3344082 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
3344096 ACAAATCATATTTT
1 ACAAATCA-ATTTT
3344110 ACAAATCAATT
1 ACAAATCAATT
3344121 AAACAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:3345519 original size:21 final size:21
Alignment explanation
Indices: 3345453--3345519 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3345443 GTGAATCGGG
*
3345453 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * * * *
3345473 CCTCTTCAACGATGGCAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3345495 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3345516 CTCT
1 CTCT
3345520 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3345538 original size:42 final size:42
Alignment explanation
Indices: 3345492--3345575 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3345482 CGATGGCAGT
* * *
3345492 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
3345534 GGCCTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
3345576 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3346042 original size:33 final size:33
Alignment explanation
Indices: 3345990--3346083 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
3345980 AAAAATGACT
* *
3345990 ATCGTAACGCGAAACGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
3346023 ATTGCAACGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
3346056 ATCGCAATGCGGAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
3346084 CGATTATAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:3346105 original size:19 final size:19
Alignment explanation
Indices: 3346083--3346126 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3346073 AAATCGCAAC
3346083 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
3346102 GCGATTTTCGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
3346121 GCGATT
1 GCGATT
3346127 TTCATTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:3346142 original size:20 final size:19
Alignment explanation
Indices: 3346093--3346154 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
3346083 GCGATTATAG
*
3346093 TTTCGCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
3346112 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
3346131 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
3346151 TTTC
1 TTTC
3346155 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 22 0.55
20 18 0.45
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:3346361 original size:94 final size:94
Alignment explanation
Indices: 3346245--3346713 Score: 754
Period size: 94 Copynumber: 5.1 Consensus size: 94
3346235 ATGGATTGCA
* * * *
3346245 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3346309 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
3346338 TTACTTTCAACCAAAGGACAAAACAAAGACAAATACTAACTTCACATTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3346403 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3346432 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3346497 TTAGCAGAATTGGCATCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3346526 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3346591 TTAGCAGAATTGGCAACAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
3346620 TTAC-TTCAACCAAAAGACAACA-AAAGACAAATACTAACTTCGCAGTGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3346679 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3346708 TTACTT
1 TTACTT
3346714 ACCTCGTTGC
Statistics
Matches: 357, Mismatches: 17, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
88 40 0.11
89 1 0.00
92 26 0.07
93 21 0.06
94 269 0.75
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3348371 original size:19 final size:19
Alignment explanation
Indices: 3348307--3348419 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
3348297 TCTTTTGGTT
*
3348307 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
3348326 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3348346 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
3348366 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3348385 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3348404 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3348420 TGAGATTTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
19 50 0.60
20 31 0.37
21 2 0.02
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3348494 original size:33 final size:33
Alignment explanation
Indices: 3348431--3348512 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
3348421 GAGATTTTGG
*
3348431 TTTCGCGTTGCGATTATATCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTATATCATTGCAATTTTCA
* * * *
3348464 TTTCGCGTTGCGATTCTCTCATTGCGATTTTTA
1 TTTCGCGTTGCGATTATATCATTGCAATTTTCA
*
3348497 TCTCTCTCGTTGCGAT
1 T-T-TCGCGTTGCGAT
3348513 AGTCATTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 29 0.71
34 1 0.02
35 11 0.27
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATATCATTGCAATTTTCA
Found at i:3348553 original size:20 final size:20
Alignment explanation
Indices: 3348505--3348555 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3348495 TATCTCTCTC
** *
3348505 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
3348525 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
3348545 GTTGCGATTTT
1 GTTGCGATTTT
3348556 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:3349112 original size:21 final size:21
Alignment explanation
Indices: 3349088--3349224 Score: 100
Period size: 20 Copynumber: 6.7 Consensus size: 21
3349078 GGCGCTATGT
3349088 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* *
3349109 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
* **
3349129 AAATCGCATTGCG-ATTCTGA
1 AAATCGCAATGCGAATTAGGA
** * * *
3349149 CTATCGCATTGCGATTTACG-
1 AAATCGCAATGCGAATTAGGA
* * * *
3349169 TATTCGCATTGCGATTTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
3349190 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
3349211 AAATCGCAATGCGA
1 AAATCGCAATGCGA
3349225 TAGTCAGAAT
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
20 48 0.53
21 43 0.47
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:3349212 original size:22 final size:21
Alignment explanation
Indices: 3349182--3349224 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3349172 TCGCATTGCG
3349182 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
3349204 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
3349225 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:3358245 original size:2 final size:2
Alignment explanation
Indices: 3358199--3358233 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3358189 CCATAAATGA
*
3358199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3358234 AGCGTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3359072 original size:22 final size:23
Alignment explanation
Indices: 3359046--3359096 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
3359036 TTTTCAATCG
*
3359046 TTATTTTAACATATTATTATTA-
1 TTATTTTAAAATATTATTATTAT
*
3359068 TTATTATAAAATATTATTATTAT
1 TTATTTTAAAATATTATTATTAT
3359091 TTATTT
1 TTATTT
3359097 ACAAACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATTTTAAAATATTATTATTAT
Found at i:3361149 original size:29 final size:30
Alignment explanation
Indices: 3361117--3361188 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
3361107 TTGCATTTAG
3361117 GTCCCCCAACTTTTAAAAC-TTGCAATACA
1 GTCCCCCAACTTTTAAAACGTTGCAATACA
* *** *
3361146 GTCCCCCAACATTTATTTCGTTTGCAATATA
1 GTCCCCCAACTTTTAAAACG-TTGCAATACA
3361177 GTCCCCCAACTT
1 GTCCCCCAACTT
3361189 AAATCACTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 15 0.43
31 20 0.57
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (30 bp):
GTCCCCCAACTTTTAAAACGTTGCAATACA
Found at i:3361556 original size:16 final size:18
Alignment explanation
Indices: 3361524--3361556 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3361514 TATTAATGTA
3361524 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
3361542 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
3361557 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:3362265 original size:125 final size:124
Alignment explanation
Indices: 3362021--3362255 Score: 355
Period size: 125 Copynumber: 1.9 Consensus size: 124
3362011 TTTTCTTCTA
* * *
3362021 ATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCATATCC
1 ATTAGGTGGTGACA-GTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
* *
3362086 TGTTAAATGATTAATTATTAAATTTTATTTAATTTAGGACCAAATGATAGATATATAAAT
65 TATTAAATGATTAATTATTAAATTCTATTTAATTTAGGACCAAATGATAGATATATAAAT
* * * *
3362146 ATTAGGTGGTGACA-TGTCACCAATGACACGTGTCTTGATCATGTGCTAACACATGTCAGATCCT
1 ATTAGGTGGTGACAGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCT
3362210 AATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAAT
66 -ATTAAATGATTAA-TTATTAAATTCTATTTAATTTAGGACCAAAT
3362256 TGATTATATA
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
123 43 0.43
124 12 0.12
125 44 0.44
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (124 bp):
ATTAGGTGGTGACAGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCCT
ATTAAATGATTAATTATTAAATTCTATTTAATTTAGGACCAAATGATAGATATATAAAT
Found at i:3362683 original size:35 final size:35
Alignment explanation
Indices: 3362644--3362725 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 35
3362634 TGACATAATT
* *
3362644 GAATTTAATTGAATTA-TTTTAAAATTTAGGGTTTA
1 GAATTAAATTGAATTACTTTGAAAA-TTAGGGTTTA
*
3362679 GAATTAAATTGAATTACTTTGGAAATTAGGGTTTA
1 GAATTAAATTGAATTACTTTGAAAATTAGGGTTTA
*
3362714 GAATGAAATTGA
1 GAATTAAATTGA
3362726 GGGTTGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 36 0.86
36 6 0.14
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.41
Consensus pattern (35 bp):
GAATTAAATTGAATTACTTTGAAAATTAGGGTTTA
Found at i:3366756 original size:15 final size:16
Alignment explanation
Indices: 3366736--3366769 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3366726 TATGAAAAAT
3366736 AATATTTTA-TTTTAA
1 AATATTTTACTTTTAA
3366751 AATATTTTACTTTTAA
1 AATATTTTACTTTTAA
3366767 AAT
1 AAT
3366770 TTTAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATTTTACTTTTAA
Found at i:3372406 original size:23 final size:23
Alignment explanation
Indices: 3372362--3372406 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3372352 ATCACTTTAC
* *
3372362 TGATGTTGATTGGTTTCTTGAAG
1 TGATGTTGATTGGCTTCATGAAG
3372385 TGATGTATGATT-GCTTCATGAA
1 TGATGT-TGATTGGCTTCATGAA
3372407 CTATTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (23 bp):
TGATGTTGATTGGCTTCATGAAG
Found at i:3373082 original size:21 final size:20
Alignment explanation
Indices: 3373058--3373100 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3373048 GAGGGTTAAT
3373058 TATA-AACTAACCCTTTTTA
1 TATATAACTAACCCTTTTTA
3373077 TATATAACTAACCCTTTTTA
1 TATATAACTAACCCTTTTTA
3373097 TATA
1 TATA
3373101 GGAGTTGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAACTAACCCTTTTTA
Found at i:3375257 original size:60 final size:58
Alignment explanation
Indices: 3375092--3375272 Score: 172
Period size: 60 Copynumber: 3.0 Consensus size: 58
3375082 ATGAACATGG
* * *
3375092 GGATGAAATTAGAA-GATTCAAAAGTTT-GGTGAC-CAATCTACAATGAGAGTCATAGTTTAA
1 GGATGAAATTGGAATG-TTCAAAAGTTTAAG-GACTC-ATTTACAATGAGA-TCATAGTTT-A
* *
3375152 GGATGGAATTGGAATGTTCAAAAGTTTAAGGACTCATTTAGAATGAGATTCATAGATTTA
1 GGATGAAATTGGAATGTTCAAAAGTTTAAGGACTCATTTACAATGAGA-TCATAG-TTTA
* * * *
3375212 GGATGAAATTGGAATTTTTATAAGTTTAAGGAC-CATTTCCCAATGAAGATCATAGTTTA
1 GGATGAAATTGGAATGTTCAAAAGTTTAAGGACTCATTT-ACAATG-AGATCATAGTTTA
3375271 GG
1 GG
3375273 GGCATATCAG
Statistics
Matches: 103, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
59 11 0.11
60 83 0.81
61 9 0.09
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (58 bp):
GGATGAAATTGGAATGTTCAAAAGTTTAAGGACTCATTTACAATGAGATCATAGTTTA
Found at i:3376698 original size:20 final size:20
Alignment explanation
Indices: 3376673--3376761 Score: 133
Period size: 20 Copynumber: 4.5 Consensus size: 20
3376663 GAATTTGAAA
3376673 ATCGCAATGTAAACAGTACT
1 ATCGCAATGTAAACAGTACT
* *
3376693 ATCGCAATGTAAACAATTCT
1 ATCGCAATGTAAACAGTACT
3376713 ATCGCAATGTAAACAGTACT
1 ATCGCAATGTAAACAGTACT
* * *
3376733 ATGGTAATGTAAATAGTACT
1 ATCGCAATGTAAACAGTACT
3376753 ATCGCAATG
1 ATCGCAATG
3376762 CGATTTTCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (20 bp):
ATCGCAATGTAAACAGTACT
Found at i:3376811 original size:77 final size:77
Alignment explanation
Indices: 3376721--3376881 Score: 252
Period size: 77 Copynumber: 2.1 Consensus size: 77
3376711 CTATCGCAAT
* * * * *
3376721 GTAAACAGTACTATGGT-AATGTAAATAGTACTATCGCAATGCGATTTTCAAATTCGTAATGTTA
1 GTAAACAGTACTAT-CTCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTA
3376785 ATTACCGATATAG
65 ATTACCGATATAG
*
3376798 GTAAACAGTACTATCTCAGTGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
1 GTAAACAGTACTATCTCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
3376863 TTACCGATATAG
66 TTACCGATATAG
3376875 GTAAACA
1 GTAAACA
3376882 CAACTATCGC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
76 1 0.01
77 76 0.99
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (77 bp):
GTAAACAGTACTATCTCAATGTAAACAGTACTATCGCAATGCGATTTTCAAATTCGCAACGCTAA
TTACCGATATAG
Found at i:3376919 original size:21 final size:20
Alignment explanation
Indices: 3376895--3376962 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
3376885 CTATCGCAAC
3376895 GCGAATTTCCGAAACTGAGTT
1 GCGAATTT-CGAAACTGAGTT
* * *
3376916 GCGAATTTGTGAAATTCGCGTT
1 GCGAATTT-CGAAACT-GAGTT
* *
3376938 GCGAATTTGGAAACTGTGTT
1 GCGAATTTCGAAACTGAGTT
3376958 GCGAA
1 GCGAA
3376963 ATTAGAGTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 9 0.23
21 18 0.46
22 12 0.31
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (20 bp):
GCGAATTTCGAAACTGAGTT
Found at i:3376959 original size:42 final size:40
Alignment explanation
Indices: 3376895--3376986 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
3376885 CTATCGCAAC
* * *
3376895 GCGAATTTCCGAAACTGAGTTGCGAATTTGTGAAATTCGCGTT
1 GCGAATTT-GGAAACTGAGTTGCGAAATT-AG-AATTCGCGTT
* *
3376938 GCGAATTTGGAAACTGTGTTGCGAAATTAGAGTTCGCGTT
1 GCGAATTTGGAAACTGAGTTGCGAAATTAGAATTCGCGTT
3376978 GCGAATTTG
1 GCGAATTTG
3376987 TTAATCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 18 0.41
41 1 0.02
42 17 0.39
43 8 0.18
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
GCGAATTTGGAAACTGAGTTGCGAAATTAGAATTCGCGTT
Found at i:3379373 original size:21 final size:20
Alignment explanation
Indices: 3379289--3379444 Score: 73
Period size: 21 Copynumber: 7.7 Consensus size: 20
3379279 AATGACCAAC
** *
3379289 AAATCGCAACGCGA-AATAA
1 AAATCGCAACGCGATTTTCA
***
3379308 AAATCGCAACGCGATCCCCA
1 AAATCGCAACGCGATTTTCA
* ** *
3379328 GAATCGCAAATC-AGTTTCCA
1 AAATCGCAACGCGA-TTTTCA
*
3379348 AAATCGCAACGCGATTCTTGA
1 AAATCGCAACGCGATT-TTCA
* * * *
3379369 AAATCGCGATGCGATAGTACA
1 AAATCGCAACGCGAT-TTTCA
* **
3379390 AATTCGCATTGCGATTTTCA
1 AAATCGCAACGCGATTTTCA
* * *
3379410 ATAATCGCAACGCGAATATGA
1 A-AATCGCAACGCGATTTTCA
3379431 AAATCGCAACGCGA
1 AAATCGCAACGCGA
3379445 ACACATAAAT
Statistics
Matches: 101, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 15 0.15
20 42 0.42
21 44 0.44
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGATTTTCA
Found at i:3379437 original size:20 final size:20
Alignment explanation
Indices: 3379412--3379605 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
3379402 GATTTTCAAT
* *
3379412 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
3379432 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
3379452 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3379472 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
3379492 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
3379512 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
3379532 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
3379552 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
3379573 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
3379593 AATCGCAACGCGA
1 AATCGCAACGCGA
3379606 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:3379457 original size:40 final size:39
Alignment explanation
Indices: 3379412--3379605 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
3379402 GATTTTCAAT
* ** *
3379412 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
3379452 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
3379492 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
3379532 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
3379573 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
3379606 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:3379495 original size:60 final size:60
Alignment explanation
Indices: 3379412--3379604 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
3379402 GATTTTCAAT
* ** * *
3379412 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
3379472 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
3379532 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
3379593 AATCGCAACGCG
1 AATCGCAACGCG
3379605 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:3380028 original size:33 final size:33
Alignment explanation
Indices: 3379986--3380056 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3379976 TTCACTTAGA
3379986 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
***
3380019 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
3380052 TTTCA
1 TTTCA
3380057 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTAAGATTCTCTCGTTGCGAT
Found at i:3380196 original size:14 final size:14
Alignment explanation
Indices: 3380177--3380231 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3380167 AGAATGACTG
3380177 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3380191 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
3380210 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3380224 TCGCAACG
1 TCGCAACG
3380232 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:3380214 original size:33 final size:33
Alignment explanation
Indices: 3380177--3380247 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3380167 AGAATGACTG
**
3380177 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3380210 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3380243 TCGCA
1 TCGCA
3380248 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:3380265 original size:19 final size:19
Alignment explanation
Indices: 3380243--3380340 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3380233 GAAACCAAAA
*
3380243 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3380262 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3380276 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3380295 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3380309 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3380328 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3380341 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3380284 original size:14 final size:14
Alignment explanation
Indices: 3380265--3380354 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3380255 TTTCATTTCG
3380265 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3380279 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3380298 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3380312 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3380329 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3380345 CGTTGCGATT
1 CGTTGCGATT
3380355 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3380290 original size:33 final size:33
Alignment explanation
Indices: 3380248--3380362 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3380238 CAAAATCGCA
3380248 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3380281 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3380314 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3380347 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3380363 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3382462 original size:93 final size:92
Alignment explanation
Indices: 3382056--3382710 Score: 1267
Period size: 92 Copynumber: 7.1 Consensus size: 92
3382046 TAGATTGCTT
*
3382056 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3382121 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3382149 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3382214 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3382241 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3382306 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3382333 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3382398 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3382426 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3382491 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3382518 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
3382582 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3382609 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
3382674 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3382702 AGTAAATTT
1 AGTAAATTT
3382711 ATCCATTCAA
Statistics
Matches: 558, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
91 91 0.16
92 275 0.49
93 192 0.34
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3382794 original size:19 final size:19
Alignment explanation
Indices: 3382756--3382882 Score: 121
Period size: 19 Copynumber: 7.2 Consensus size: 19
3382746 GTTTACTTTT
* *
3382756 GCAACACGAAACTTAAAATC
1 GCAACGCGAAAC-CAAAATC
3382776 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACCAAAATC
**
3382795 GCAACGCGAAATGAAAATC
1 GCAACGCGAAACCAAAATC
*
3382814 GCAA--CG--A-CAGAATC
1 GCAACGCGAAACCAAAATC
3382828 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACCAAAATC
*
3382847 GCAA--CG--A-CAAGATC
1 GCAACGCGAAACCAAAATC
3382861 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACCAAAATC
3382880 GCA
1 GCA
3382883 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 46 0.52
20 11 0.12
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAACCAAAATC
Found at i:3382833 original size:33 final size:32
Alignment explanation
Indices: 3382790--3382882 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3382780 CGCGAAACCA
**
3382790 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3382822 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3382855 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3382883 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3382880 original size:52 final size:51
Alignment explanation
Indices: 3382755--3382882 Score: 136
Period size: 52 Copynumber: 2.5 Consensus size: 51
3382745 AGTTTACTTT
**
3382755 TGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3382806 TG-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3382859 TCGCAACGCGAAAC-CAAAATCGCA
1 T-GCAACACGAAACACAAAATCGCA
3382883 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
50 3 0.05
51 7 0.11
52 41 0.66
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (51 bp):
TGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3382900 original size:19 final size:19
Alignment explanation
Indices: 3382878--3383012 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3382868 GAAACCAAAA
*
3382878 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3382897 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3382913 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3382930 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3382946 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3382963 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3382982 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3383002 TCGTGTTGCGA
1 TCGCGTTGCGA
3383013 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3382919 original size:14 final size:14
Alignment explanation
Indices: 3382900--3382956 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3382890 TTTCATTTCG
3382900 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3382914 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3382931 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3382947 CGTTGCGATT
1 CGTTGCGATT
3382957 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3382925 original size:33 final size:33
Alignment explanation
Indices: 3382883--3382975 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3382873 CAAAATCGCA
*
3382883 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3382916 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3382949 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3382976 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3384928 original size:14 final size:14
Alignment explanation
Indices: 3384909--3384944 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3384899 ATTGTTTAAT
3384909 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3384923 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3384937 TGATTTGT
1 TGATTTGT
3384945 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3385119 original size:20 final size:19
Alignment explanation
Indices: 3385051--3385133 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
3385041 AAAAATGACT
3385051 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3385070 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3385084 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3385103 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3385123 ATCGCAATGCG
1 ATCGCAATGCG
3385134 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3385186 original size:19 final size:19
Alignment explanation
Indices: 3385162--3385416 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
3385152 GATTATCTCG
3385162 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3385181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3385200 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3385214 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3385233 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3385252 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3385271 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3385290 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3385309 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
3385323 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3385342 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3385356 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3385376 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3385390 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3385409 TTGCGATT
1 TTGCGATT
3385417 GTATTTTCCG
Statistics
Matches: 207, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
14 29 0.14
16 24 0.12
17 21 0.10
18 3 0.01
19 118 0.57
20 12 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3385202 original size:52 final size:52
Alignment explanation
Indices: 3385140--3385349 Score: 348
Period size: 52 Copynumber: 3.9 Consensus size: 52
3385130 TGCGTTTATA
3385140 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3385192 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3385244 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT--ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
3385301 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT
3385350 CTCTCGTTGC
Statistics
Matches: 149, Mismatches: 4, Indels: 10
0.91 0.02 0.06
Matches are distributed among these distances:
52 91 0.61
53 2 0.01
54 5 0.03
55 5 0.03
56 2 0.01
57 44 0.30
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3385332 original size:33 final size:33
Alignment explanation
Indices: 3385181--3385416 Score: 276
Period size: 33 Copynumber: 6.8 Consensus size: 33
3385171 TCATTTCGCA
* *
3385181 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
3385214 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG
* *
3385250 CATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG
3385288 CATTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
3385323 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
3385356 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTATC-TCG
* *
3385390 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
3385417 GTATTTTCCG
Statistics
Matches: 188, Mismatches: 8, Indels: 14
0.90 0.04 0.07
Matches are distributed among these distances:
33 83 0.44
34 29 0.15
35 8 0.04
36 7 0.04
38 61 0.32
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCG
Found at i:3387712 original size:12 final size:12
Alignment explanation
Indices: 3387695--3387719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3387685 TCTTCGGGGA
3387695 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3387707 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3387719 C
1 C
3387720 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3387928 original size:24 final size:24
Alignment explanation
Indices: 3387894--3387940 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3387884 CTGAAACATC
3387894 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3387918 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3387941 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3388644 original size:20 final size:20
Alignment explanation
Indices: 3388616--3388966 Score: 408
Period size: 20 Copynumber: 17.4 Consensus size: 20
3388606 AAATTTCAGT
* * * *
3388616 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3388636 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3388656 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3388676 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3388696 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3388716 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3388736 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3388756 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3388776 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3388796 GTTGCGATTTACGCATACAC
1 GTTGCGATTTACGGATACGC
3388816 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
3388836 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
3388857 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3388877 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3388897 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
3388917 GTTGCGATTTACGGATA--C
1 GTTGCGATTTACGGATACGC
3388935 GTTGCGATTTACGGATATTGCGC
1 GTTGCGATTTACGGATA---CGC
3388958 GTTGCGATT
1 GTTGCGATT
3388967 ATTGAAAATC
Statistics
Matches: 287, Mismatches: 30, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
18 18 0.06
19 7 0.02
20 232 0.81
21 18 0.06
22 2 0.01
23 10 0.03
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3389584 original size:3 final size:3
Alignment explanation
Indices: 3389576--3389602 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3389566 AAAAATAAAT
3389576 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3389603 CAACTTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3390381 original size:60 final size:60
Alignment explanation
Indices: 3390253--3390369 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
3390243 AATAGTCGGG
* * * *
3390253 TGACCATTTTGTAACTTTTAATAGTTGAAGGACTTAACAAAGCAACATTCTATTATCAAA
1 TGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAGAAACACTCTATAATCAAA
* * ** *
3390313 TGATCATTTTGTAAGTTTTAATAGTCGAATTACTTAATAAAGAAACACTCTATAATC
1 TGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAGAAACACTCTATAATC
3390370 GAGAGACCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAGAAACACTCTATAATCAAA
Found at i:3399082 original size:94 final size:94
Alignment explanation
Indices: 3398918--3399114 Score: 335
Period size: 94 Copynumber: 2.1 Consensus size: 94
3398908 CCATAAATAA
3398918 TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATTGGAAAAAAATAATATATAGAGAGATA
1 TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATTGGAAAAAAATAATATATAGAGAGATA
3398983 TTATTTTGATTATTCATAAATATATAAGG
66 TTATTTTGATTATTCATAAATATATAAGG
* * * *
3399012 TAAAAATTTGTTTTTATTCAATAAAAATAATGATTTAATT-GAAAAAAATAATATATAGAGGGGT
1 TAAAAA-TTATTTTTATTCAATAAAAACAATGATTTAATTGGAAAAAAATAATATATAGAGAGAT
3399076 ATTATTTTGATTATTCATAAATATATAAGG
65 ATTATTTTGATTATTCATAAATATATAAGG
3399106 T-AAAATTAT
1 TAAAAATTAT
3399115 ATATTTTTAG
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
92 3 0.03
93 4 0.04
94 59 0.61
95 31 0.32
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (94 bp):
TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATTGGAAAAAAATAATATATAGAGAGATA
TTATTTTGATTATTCATAAATATATAAGG
Found at i:3404193 original size:15 final size:15
Alignment explanation
Indices: 3404167--3404236 Score: 86
Period size: 15 Copynumber: 4.5 Consensus size: 15
3404157 CGGGTGTTAT
*
3404167 GGGTACCTGGTAATC
1 GGGTACCCGGTAATC
*
3404182 GGGTATCCGGTAATC
1 GGGTACCCGGTAATC
**
3404197 GGGTACCCGGATGTTAC
1 GGGTACCCGG-TAAT-C
3404214 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
3404229 GGGTACCC
1 GGGTACCC
3404237 AGATTTTATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
15 31 0.67
16 4 0.09
17 11 0.24
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (15 bp):
GGGTACCCGGTAATC
Found at i:3404224 original size:32 final size:32
Alignment explanation
Indices: 3404181--3404251 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
3404171 ACCTGGTAAT
* *
3404181 CGGGTATCCGGTAATCGGGTACCCGGATGTTA
1 CGGGTACCCGGTAATCGGGTACCCAGATGTTA
*
3404213 CGGGTACCCGGTAATCGGGTACCCAGATTTTA
1 CGGGTACCCGGTAATCGGGTACCCAGATGTTA
*
3404245 TGGGTAC
1 CGGGTAC
3404252 TTGATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (32 bp):
CGGGTACCCGGTAATCGGGTACCCAGATGTTA
Found at i:3404505 original size:28 final size:28
Alignment explanation
Indices: 3404472--3404527 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3404462 CGGGTCCTAT
*
3404472 CGGGAAATGTCGGGCCGGGTATCCGACC
1 CGGGAAATGTCGGGCCGGGTACCCGACC
*
3404500 CGGGAAATGTCGGGTCGGGTACCCGACC
1 CGGGAAATGTCGGGCCGGGTACCCGACC
3404528 TTGCCGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (28 bp):
CGGGAAATGTCGGGCCGGGTACCCGACC
Done.