Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 21 of 24
Found at i:2767598 original size:34 final size:34
Alignment explanation
Indices: 2767542--2767624 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
2767532 TATTTAAAAA
* *
2767542 TAAATTATGTATATTATTATATAA-GAATTATTT
1 TAAATTATGTATATTAATATATAATAAATTATTT
2767575 TAAATTTATAGTATA-TAATATATAATAAATTA-TT
1 TAAA-TTAT-GTATATTAATATATAATAAATTATTT
*
2767609 T-AATT-TTTATATTAAT
1 TAAATTATGTATATTAAT
2767625 TATGTTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
30 4 0.09
31 5 0.12
32 2 0.05
33 6 0.14
34 16 0.37
35 10 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (34 bp):
TAAATTATGTATATTAATATATAATAAATTATTT
Found at i:2767619 original size:35 final size:35
Alignment explanation
Indices: 2767542--2767609 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
2767532 TATTTAAAAA
* *
2767542 TAAA-TTAT-GTATATTATTATATAAGAATTATTT
1 TAAATTTATAGTATATTAATATATAAAAATTATTT
2767575 TAAATTTATAGTATA-TAATATATAATAAATTATTT
1 TAAATTTATAGTATATTAATATATAA-AAATTATTT
2767610 AATTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 4 0.13
34 13 0.43
35 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (35 bp):
TAAATTTATAGTATATTAATATATAAAAATTATTT
Found at i:2768580 original size:14 final size:13
Alignment explanation
Indices: 2768534--2768581 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
2768524 TAAATAACAT
*
2768534 AAATATTAAATTA
1 AAATATTTAATTA
2768547 AAATAATTTAAATTTA
1 AAAT-ATTT-AA-TTA
2768563 AAATATTTAATATA
1 AAATATTTAAT-TA
2768577 AAATA
1 AAATA
2768582 ACATTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 6 0.20
16 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATTTAATTA
Found at i:2770205 original size:3 final size:3
Alignment explanation
Indices: 2770197--2770231 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2770187 TTGTCGGCAG
2770197 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2770232 TGCGTAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2773070 original size:21 final size:21
Alignment explanation
Indices: 2773044--2773086 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2773034 TTTTTAATTT
2773044 TTAAATTTAATTAATTTAAAA
1 TTAAATTTAATTAATTTAAAA
* *
2773065 TTAAATTTGATTGATTTAAAA
1 TTAAATTTAATTAATTTAAAA
2773086 T
1 T
2773087 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAAATTTAATTAATTTAAAA
Found at i:2774496 original size:8 final size:7
Alignment explanation
Indices: 2774485--2774543 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
2774475 TTGAATTCAT
2774485 AAATTTAA
1 AAATTT-A
*
2774493 AAATTTT
1 AAATTTA
*
2774500 AAATTTT
1 AAATTTA
*
2774507 AAATTTT
1 AAATTTA
*
2774514 AAATCTA
1 AAATTTA
2774521 AAATTTTA
1 AAA-TTTA
2774529 AAATTT-
1 AAATTTA
2774535 AAATTTA
1 AAATTTA
2774542 AA
1 AA
2774544 TCTAAATCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
6 6 0.13
7 27 0.60
8 12 0.27
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
AAATTTA
Found at i:2774505 original size:7 final size:7
Alignment explanation
Indices: 2774493--2774544 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
2774483 ATAAATTTAA
2774493 AAATTTT
1 AAATTTT
2774500 AAATTTT
1 AAATTTT
2774507 AAATTTT
1 AAATTTT
* *
2774514 AAATCTA
1 AAATTTT
2774521 AAATTTT
1 AAATTTT
*
2774528 AAAATTT
1 AAATTTT
2774535 AAA-TTT
1 AAATTTT
2774541 AAAT
1 AAAT
2774545 CTAAATCCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (7 bp):
AAATTTT
Found at i:2774530 original size:28 final size:27
Alignment explanation
Indices: 2774492--2774549 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 27
2774482 CATAAATTTA
*
2774492 AAAATTTTAAATTTTAAATTTTAAATCT
1 AAAATTTTAAAATTTAAA-TTTAAATCT
2774520 AAAATTTTAAAATTTAAATTTAAATCT
1 AAAATTTTAAAATTTAAATTTAAATCT
2774547 AAA
1 AAA
2774550 TCCAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATTTTAAAATTTAAATTTAAATCT
Found at i:2774914 original size:16 final size:16
Alignment explanation
Indices: 2774902--2774934 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2774892 TTAAAATATC
2774902 AAATC-AAATAAATTA
1 AAATCTAAATAAATTA
*
2774917 AAATCTAAATAATTTA
1 AAATCTAAATAAATTA
2774933 AA
1 AA
2774935 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATCTAAATAAATTA
Found at i:2774942 original size:16 final size:16
Alignment explanation
Indices: 2774923--2774973 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2774913 ATTAAAATCT
2774923 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
* *
2774939 AAATAATCTAAATTCA
1 AAATAATTTAAATTTA
* *
2774955 AAATGATCTTAAATATA
1 AAATAAT-TTAAATTTA
2774972 AA
1 AA
2774974 TTTTATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:2776379 original size:36 final size:33
Alignment explanation
Indices: 2776338--2776403 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
2776328 AAAAATTTTA
*
2776338 AATTAAATTTAATTAATTTATATAATTATTTTTAAG
1 AATTAAA-TTAATAAATTT-TAT-ATTATTTTTAAG
*
2776374 AATTAAATTAATAAATTTTATCTTATTTTT
1 AATTAAATTAATAAATTTTATATTATTTTT
2776404 GAGTTATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 8 0.29
34 3 0.11
35 10 0.36
36 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (33 bp):
AATTAAATTAATAAATTTTATATTATTTTTAAG
Found at i:2777410 original size:17 final size:16
Alignment explanation
Indices: 2777369--2777407 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
2777359 CATGAAATAT
2777369 AAAAATTAAAAATTAA
1 AAAAATTAAAAATTAA
2777385 AAATAATTAAGTAAATTAA
1 AAA-AATTAA--AAATTAA
2777404 AAAA
1 AAAA
2777408 TTAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.15
17 6 0.30
18 1 0.05
19 10 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATTAAAAATTAA
Found at i:2779007 original size:20 final size:19
Alignment explanation
Indices: 2778980--2779055 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 19
2778970 ATTATTAATA
2778980 AAAATATATATTTAAATTT
1 AAAATATATATTTAAATTT
* *
2778999 AATAATATA-ATTTTTAATAT
1 AA-AATATATA-TTTAAATTT
2779019 AAAATTAATATATTTAAGATTT
1 AAAA-T-ATATATTTAA-ATTT
* *
2779041 AAAATTTATTTTTAA
1 AAAATATATATTTAA
2779056 TTTTTTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
19 5 0.11
20 24 0.53
21 8 0.18
22 8 0.18
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
AAAATATATATTTAAATTT
Found at i:2779052 original size:40 final size:38
Alignment explanation
Indices: 2778963--2779056 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 38
2778953 AGTAATAAAT
*
2778963 ATAATA-AATTATTAATAAAAATATATATTTAAATTTA
1 ATAATATAATTTTTAATAAAAATATATATTTAAATTTA
2779000 ATAATATAATTTTTAATATAAAATTAATATATTTAAGATTTA
1 ATAATATAATTTTTAATA-AAAA-T-ATATATTTAA-ATTTA
*
2779042 A-AAT-TTATTTTTAAT
1 ATAATATAATTTTTAAT
2779057 TTTTTTAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
37 6 0.12
38 10 0.20
39 4 0.08
40 11 0.22
41 13 0.26
42 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
ATAATATAATTTTTAATAAAAATATATATTTAAATTTA
Found at i:2779101 original size:20 final size:20
Alignment explanation
Indices: 2779052--2779099 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
2779042 AAATTTATTT
2779052 TTAATTTTT-TTAATTAAAAA
1 TTAATTTTTATTAATT-AAAA
2779072 TTAATTTTTATTAATT-AAA
1 TTAATTTTTATTAATTAAAA
2779091 TTAATTTTT
1 TTAATTTTT
2779100 TAATATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.44
20 9 0.33
21 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATTTTTATTAATTAAAA
Found at i:2779109 original size:20 final size:19
Alignment explanation
Indices: 2779069--2779109 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2779059 TTTTAATTAA
*
2779069 AAATTAATTTTTATTAATT
1 AAATTAATTTTTAATAATT
*
2779088 AAATTAATTTTTTAATATTT
1 AAATTAA-TTTTTAATAATT
2779108 AA
1 AA
2779110 TATCGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTAATTTTTAATAATT
Found at i:2780020 original size:15 final size:15
Alignment explanation
Indices: 2779989--2780027 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2779979 AGTTGTTGAT
*
2779989 ATTTATATATAAATA
1 ATTTATATTTAAATA
2780004 ATTT-TATTTAAATTA
1 ATTTATATTTAAA-TA
2780019 ATTTATATT
1 ATTTATATT
2780028 ATATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 10 0.48
16 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTATATTTAAATA
Found at i:2780043 original size:14 final size:14
Alignment explanation
Indices: 2780026--2780085 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
2780016 TTAATTTATA
*
2780026 TTATATTTATTAAT
1 TTATATTTAATAAT
* *
2780040 TTATTTTTAAAAAT
1 TTATATTTAATAAT
* **
2780054 ATAT-TTTTTTAAT
1 TTATATTTAATAAT
2780067 TTAATATTTAATAAT
1 TT-ATATTTAATAAT
2780082 TTAT
1 TTAT
2780086 TTTTTAAGTT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
13 7 0.21
14 18 0.53
15 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATTTAATAAT
Found at i:2780086 original size:28 final size:27
Alignment explanation
Indices: 2780026--2780090 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
2780016 TTAATTTATA
* *
2780026 TTATATTTATTAATTTATTTTTAAAAAT
1 TTAT-TTTTTTAATTTATATTTAAAAAT
* *
2780054 ATATTTTTTTAATTTAATATTTAATAAT
1 TTATTTTTTTAATTT-ATATTTAAAAAT
2780082 TTATTTTTT
1 TTATTTTTT
2780091 AAGTTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTTTTTAATTTATATTTAAAAAT
Found at i:2780088 original size:27 final size:27
Alignment explanation
Indices: 2780027--2780097 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2780017 TAATTTATAT
* *
2780027 TATATTTATTAATTT-ATTTTTAAAAA
1 TATATTTTTTAATTTAATATTTAAAAA
*
2780053 TATATTTTTTTAATTTAATATTTAATAA
1 TATA-TTTTTTAATTTAATATTTAAAAA
* *
2780081 TTTATTTTTTAAGTTAA
1 TATATTTTTTAATTTAA
2780098 AAATAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 4 0.11
27 22 0.58
28 12 0.32
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (27 bp):
TATATTTTTTAATTTAATATTTAAAAA
Found at i:2780228 original size:14 final size:15
Alignment explanation
Indices: 2780209--2780251 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2780199 TCTTTTTAAA
*
2780209 TAAATTTTAT-TTTT
1 TAAATTTAATATTTT
2780223 TAAATTTAATATTTT
1 TAAATTTAATATTTT
*
2780238 T-AATTTAAAATTTT
1 TAAATTTAATATTTT
2780252 CTAATGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAAATTTAATATTTT
Found at i:2781420 original size:17 final size:18
Alignment explanation
Indices: 2781390--2781432 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2781380 AAATATATAC
*
2781390 ATTAAAT-TTATATTTAT
1 ATTAAATATTATATTTAA
2781407 ATTAAATATT-TATTTAA
1 ATTAAATATTATATTTAA
2781424 ATTTAAATA
1 A-TTAAATA
2781433 ACATAAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAATATTATATTTAA
Found at i:2784135 original size:14 final size:14
Alignment explanation
Indices: 2784116--2784143 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2784106 GGTGAATCCC
2784116 GCGTGCAGGGCTGG
1 GCGTGCAGGGCTGG
2784130 GCGTGCAGGGCTGG
1 GCGTGCAGGGCTGG
2784144 CCCGCCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.57, T:0.14
Consensus pattern (14 bp):
GCGTGCAGGGCTGG
Found at i:2785399 original size:19 final size:21
Alignment explanation
Indices: 2785372--2785411 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2785362 TAGTAATTAT
2785372 GCTAATTTTT-ATTA-TAAAA
1 GCTAATTTTTCATTATTAAAA
*
2785391 GCTATTTTTTCATTATTAAAA
1 GCTAATTTTTCATTATTAAAA
2785412 TTTTTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
GCTAATTTTTCATTATTAAAA
Found at i:2788559 original size:10 final size:11
Alignment explanation
Indices: 2788536--2788573 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2788526 TAATTGTTAC
*
2788536 TTAAATCAAAA
1 TTAAATAAAAA
*
2788547 TTAAAT-TAAA
1 TTAAATAAAAA
2788557 TTAAATAAAAA
1 TTAAATAAAAA
2788568 TTAAAT
1 TTAAAT
2788574 GGAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
TTAAATAAAAA
Found at i:2789404 original size:13 final size:13
Alignment explanation
Indices: 2789386--2789412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2789376 ATATTTATAT
2789386 TTTTAAATATGAA
1 TTTTAAATATGAA
2789399 TTTTAAATATGAA
1 TTTTAAATATGAA
2789412 T
1 T
2789413 ATAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTAAATATGAA
Found at i:2789439 original size:19 final size:19
Alignment explanation
Indices: 2789391--2789427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2789381 TATATTTTTA
* *
2789391 AATATGAATTTTAAATATG
1 AATATAAATATTAAATATG
2789410 AATATAAATATTAAATAT
1 AATATAAATATTAAATAT
2789428 ATATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AATATAAATATTAAATATG
Found at i:2790005 original size:2 final size:2
Alignment explanation
Indices: 2789998--2790024 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2789988 GTTTTTGGTT
2789998 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
2790025 GCAAGATTTG
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:2790498 original size:2 final size:2
Alignment explanation
Indices: 2790491--2790521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2790481 TTCTTACTCT
2790491 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 T
2790522 GTTCGAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2791359 original size:3 final size:3
Alignment explanation
Indices: 2791351--2791375 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2791341 TCCGTGTATG
2791351 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2791376 GACTTCTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2795724 original size:23 final size:24
Alignment explanation
Indices: 2795687--2795734 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2795677 TAATATTTTC
* *
2795687 AATTTATAAATATTTTTTTAAAAA
1 AATTTATAAATATTTATATAAAAA
*
2795711 AATTTA-ATATATTTATATAAAAA
1 AATTTATAAATATTTATATAAAAA
2795734 A
1 A
2795735 TATATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTATAAATATTTATATAAAAA
Found at i:2803973 original size:2 final size:2
Alignment explanation
Indices: 2803968--2804010 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2803958 TATATCTGCG
2803968 TA TA TA TA TA 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 TA TA TA TA TA
2804010 T
1 T
2804011 TAAGTTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2804183 original size:22 final size:22
Alignment explanation
Indices: 2804153--2804218 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 22
2804143 ATAAAAAAAG
*
2804153 TTATAAATATTAAATTTTAAAT
1 TTATTAATATTAAATTTTAAAT
2804175 TTATTAATATTAATTAATTTTATAAAT
1 TTATTAATATT-A--AA-TTT-TAAAT
*
2804202 TAATTAA-ATTAAATTTT
1 TTATTAATATTAAATTTT
2804219 TGTTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
21 1 0.03
22 13 0.35
23 3 0.08
25 3 0.08
26 6 0.16
27 11 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTAATATTAAATTTTAAAT
Found at i:2804216 original size:27 final size:26
Alignment explanation
Indices: 2804161--2804213 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2804151 AGTTATAAAT
*
2804161 ATTAAATTTTAAATTTATTAATATTA
1 ATTAAATTTTAAATTAATTAATATTA
*
2804187 ATTAATTTTATAAATTAATTAA-ATTA
1 ATTAAATTT-TAAATTAATTAATATTA
2804213 A
1 A
2804214 ATTTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTAAATTTTAAATTAATTAATATTA
Found at i:2805110 original size:25 final size:23
Alignment explanation
Indices: 2805064--2805122 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
2805054 ATTATAAAAA
2805064 TTATTAAATATAA--ATATAATAT
1 TTATTAAATA-AATTATATAATAT
*
2805086 TTAATTTAAATAAATTATATCATAT
1 TT-A-TTAAATAAATTATATAATAT
2805111 TTATTAAATAAA
1 TTATTAAATAAA
2805123 CATAACCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 2 0.06
23 12 0.38
24 8 0.25
25 10 0.31
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATTAAATAAATTATATAATAT
Found at i:2806301 original size:4 final size:4
Alignment explanation
Indices: 2806288--2806317 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2806278 ATTAACATTA
2806288 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2806318 AGCATCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2807106 original size:19 final size:19
Alignment explanation
Indices: 2807082--2807119 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2807072 ACATTAAAAT
2807082 TTATTA-AATTACTTATAAA
1 TTATTATAATTA-TTATAAA
*
2807101 TTATTATATTTATTATAAA
1 TTATTATAATTATTATAAA
2807120 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTATAATTATTATAAA
Found at i:2807517 original size:45 final size:49
Alignment explanation
Indices: 2807462--2807557 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 49
2807452 TATTCATATC
*
2807462 ATATTCATAT-ATTTTATTATA-TCATAA-TTATATT-TA-AAATATTTT
1 ATATTCATATAATTTTATTATATTAATAATTTATATTATATAAA-ATTTT
*
2807507 ATATTTATATAAATTTTATTATATTAATAATTTATATTATATAAAATTTT
1 ATATTCATAT-AATTTTATTATATTAATAATTTATATTATATAAAATTTT
2807557 A
1 A
2807558 AAATATCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
45 9 0.21
47 11 0.26
48 5 0.12
49 7 0.16
50 8 0.19
51 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (49 bp):
ATATTCATATAATTTTATTATATTAATAATTTATATTATATAAAATTTT
Found at i:2807544 original size:18 final size:17
Alignment explanation
Indices: 2807472--2807555 Score: 74
Period size: 16 Copynumber: 5.2 Consensus size: 17
2807462 ATATTCATAT
*
2807472 ATTT-TATTATATCATA
1 ATTTATATTATATAATA
*
2807488 A-TTATATT-TAAAATA
1 ATTTATATTATATAATA
*
2807503 TTTTATATT-TAT-ATAA
1 ATTTATATTATATAAT-A
2807519 ATTT-TATTATATTAATA
1 ATTTATATTATA-TAATA
2807536 ATTTATATTATATAA-A
1 ATTTATATTATATAATA
2807552 ATTT
1 ATTT
2807556 TAAAATATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
15 13 0.23
16 25 0.45
17 9 0.16
18 9 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATATTATATAATA
Found at i:2807573 original size:33 final size:34
Alignment explanation
Indices: 2807500--2807579 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
2807490 TATATTTAAA
** *
2807500 ATAT-TTTATATT-TATATAAATTTTATTATATT
1 ATATATTTATATTATATATAAATTTTAAAATATC
2807532 A-ATAATTTATATTATATA-AAATTTTAAAATATC
1 ATAT-ATTTATATTATATATAAATTTTAAAATATC
*
2807565 ATATATTTATTTTAT
1 ATATATTTATATTAT
2807580 TTTTTCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 2 0.05
32 1 0.03
33 31 0.77
34 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
ATATATTTATATTATATATAAATTTTAAAATATC
Found at i:2807589 original size:26 final size:24
Alignment explanation
Indices: 2807560--2807607 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2807550 AAATTTTAAA
*
2807560 ATATCATATATTTATTTTATTTTTTC
1 ATATCATAT-TTTA-ATTATTTTTTC
*
2807586 ATATTATATTTTAATTATTTTT
1 ATATCATATTTTAATTATTTTT
2807608 ATCTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 4 0.20
26 8 0.40
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATCATATTTTAATTATTTTTTC
Found at i:2816053 original size:26 final size:25
Alignment explanation
Indices: 2816003--2816054 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
2815993 AAATATAAAG
* *
2816003 TAATAAATTAATGATTTTTTTATTT
1 TAATAAATAAATGATTTTTTAATTT
2816028 TAATAAAGTAAAT-ATTTTTTAAATTT
1 TAATAAA-TAAATGATTTTTT-AATTT
2816054 T
1 T
2816055 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TAATAAATAAATGATTTTTTAATTT
Found at i:2816086 original size:87 final size:87
Alignment explanation
Indices: 2815982--2816192 Score: 248
Period size: 85 Copynumber: 2.4 Consensus size: 87
2815972 TATATTTTTA
* * *
2815982 TTTAATTTTTAAAATATAAAGTAATAAATTAATGATTTTTTTATTTTAATAAAGT-AAATATTTT
1 TTTAA-TTTAAAAATATAAAGTAATAAATTAAT--TATTTTTATTTGAA-AAAGTGAAATATTTT
2816046 TTAAATTTTTTTAATAAT-A-ATTTC
62 TTAAATTTTTTTAATAATAATATTTC
* * * *
2816070 TTTAATTTAAAAATATAAATTAATAAATTAATTATTTTTATTTGAACAAGTGAATTATTTTTTTA
1 TTTAATTTAAAAATATAAAGTAATAAATTAATTATTTTTATTTGAAAAAGTGAAATATTTTTTAA
*
2816135 ATTTTTTTAATAATAATATTTT
66 ATTTTTTTAATAATAATATTTC
* *
2816157 TAAATTAATTTAAAAATAGAAAGTGATAAATTAATT
1 T---TTAATTTAAAAATATAAAGTAATAAATTAATT
2816193 TTTATAATTA
Statistics
Matches: 106, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
84 4 0.04
85 37 0.35
86 1 0.01
87 30 0.28
88 5 0.05
90 29 0.27
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (87 bp):
TTTAATTTAAAAATATAAAGTAATAAATTAATTATTTTTATTTGAAAAAGTGAAATATTTTTTAA
ATTTTTTTAATAATAATATTTC
Found at i:2816237 original size:5 final size:5
Alignment explanation
Indices: 2816227--2816264 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
2816217 TTTTTTAAAA
2816227 AAATT AAATT AAATT -AATT AAATT -AATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
2816265 TTTACACCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:2816238 original size:14 final size:14
Alignment explanation
Indices: 2816221--2816264 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2816211 TAATAATTTT
*
2816221 TTAAAAAAATTAAA
1 TTAAATAAATTAAA
*
2816235 TTAAATTAATTAAA
1 TTAAATAAATTAAA
*
2816249 TTAATTAAATTAAA
1 TTAAATAAATTAAA
2816263 TT
1 TT
2816265 TTTACACCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAATAAATTAAA
Found at i:2816245 original size:9 final size:9
Alignment explanation
Indices: 2816227--2816261 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
2816217 TTTTTTAAAA
2816227 AAATTAAATT
1 AAATT-AATT
2816237 AAATTAATT
1 AAATTAATT
2816246 AAATTAATT
1 AAATTAATT
2816255 AAATTAA
1 AAATTAA
2816262 ATTTTTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATTAATT
Found at i:2816362 original size:22 final size:21
Alignment explanation
Indices: 2816337--2816380 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
2816327 GGGAGAAATA
2816337 AAGAAGAAAAAAACACTAAGTT
1 AAGAAGAAAAAAA-ACTAAGTT
2816359 AAGAAGAAAAAAAACTAAGTT
1 AAGAAGAAAAAAAACTAAGTT
2816380 A
1 A
2816381 GATCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (21 bp):
AAGAAGAAAAAAAACTAAGTT
Found at i:2816370 original size:21 final size:22
Alignment explanation
Indices: 2816337--2816380 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2816327 GGGAGAAATA
*
2816337 AAGAAGAAAAAAACACTAAGTT
1 AAGAAGAAAAAAAAACTAAGTT
2816359 AAGAAG-AAAAAAAACTAAGTT
1 AAGAAGAAAAAAAAACTAAGTT
2816380 A
1 A
2816381 GATCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (22 bp):
AAGAAGAAAAAAAAACTAAGTT
Found at i:2816540 original size:19 final size:19
Alignment explanation
Indices: 2816502--2816540 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2816492 ATCCGTATTT
*
2816502 ATATTATTTTTTATTTAAA
1 ATATTATTTTTTATTAAAA
2816521 ATATTATATTTTTA-TAAAA
1 ATATTAT-TTTTTATTAAAA
2816540 A
1 A
2816541 AATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATTTTTTATTAAAA
Found at i:2816541 original size:20 final size:19
Alignment explanation
Indices: 2816502--2816541 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2816492 ATCCGTATTT
**
2816502 ATATTATTTTTTATTTAAA
1 ATATTATTTTTTATAAAAA
2816521 ATATTATATTTTTATAAAAA
1 ATATTAT-TTTTTATAAAAA
2816541 A
1 A
2816542 ATTTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTTTTTATAAAAA
Found at i:2816778 original size:19 final size:20
Alignment explanation
Indices: 2816756--2816794 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2816746 TGTATTCATA
2816756 TCATATT-TATATTATTTTT
1 TCATATTGTATATTATTTTT
* *
2816775 TCATGTTGTGTATTATTTTT
1 TCATATTGTATATTATTTTT
2816795 ATATATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (20 bp):
TCATATTGTATATTATTTTT
Found at i:2816881 original size:17 final size:15
Alignment explanation
Indices: 2816856--2816901 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
2816846 GAAGTTTTAA
*
2816856 TATTTATAAAATTTT
1 TATTAATAAAATTTT
*
2816871 TAATTAAATAAAATTAT
1 T-ATT-AATAAAATTTT
2816888 TATTAATAAAATTT
1 TATTAATAAAATTT
2816902 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 10 0.38
16 6 0.23
17 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATAAAATTTT
Found at i:2816903 original size:16 final size:16
Alignment explanation
Indices: 2816851--2816904 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
2816841 TGTTAGAAGT
* *
2816851 TTTAATATTTATAAAA
1 TTTATTATTAATAAAA
2816867 TTT-TTAATTAAATAAAA
1 TTTATT-ATT-AATAAAA
2816884 -TTATTATTAATAAAA
1 TTTATTATTAATAAAA
2816899 TTTATT
1 TTTATT
2816905 TAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.25
16 16 0.50
17 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATTATTAATAAAA
Found at i:2817280 original size:59 final size:60
Alignment explanation
Indices: 2817158--2817280 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 60
2817148 ATAAAAAAAC
* * * *
2817158 ATACTTTTTAATTAAATCACTATAACAAATTATGAAAAAAATATCATGAATTGAGATATG
1 ATACTTTTAAATTAAATCACTATAACAAATTATGAAAAAAATATCATGAATAGAAATACG
* * * * * *
2817218 ATAC-TTTAAATTAAATTATTATGACAAATTATGCAAAATATGTCATGAATAGAAATACG
1 ATACTTTTAAATTAAATCACTATAACAAATTATGAAAAAAATATCATGAATAGAAATACG
2817277 ATAC
1 ATAC
2817281 GATCATAACT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 49 0.92
60 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (60 bp):
ATACTTTTAAATTAAATCACTATAACAAATTATGAAAAAAATATCATGAATAGAAATACG
Found at i:2817360 original size:18 final size:19
Alignment explanation
Indices: 2817326--2817373 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2817316 AAATAATATT
*
2817326 TTTTATATTTT-A-TTTTTA
1 TTTTA-ATTTTAACTTTTAA
2817344 TTTTAATTTTAACTTTTAA
1 TTTTAATTTTAACTTTTAA
2817363 TTTT-ATTTTAA
1 TTTTAATTTTAA
2817374 AATAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 13 0.48
19 9 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTAACTTTTAA
Found at i:2817790 original size:20 final size:20
Alignment explanation
Indices: 2817754--2817791 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2817744 TAGTAAAATA
*
2817754 TTAAAATATATTTTTTTATT
1 TTAAAATATATTATTTTATT
2817774 TTAAAATA-ATATATTTTA
1 TTAAAATATAT-TATTTTA
2817792 AATTATCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAAATATATTATTTTATT
Found at i:2820264 original size:24 final size:22
Alignment explanation
Indices: 2820212--2820264 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
2820202 CCAGAAAAAC
2820212 CACCACCACCAAATCCTCCATA
1 CACCACCACCAAATCCTCCATA
*
2820234 -ACTACCACCAAAATCAGCTCCA-A
1 CACCACCACC-AAATC--CTCCATA
2820257 CACCACCA
1 CACCACCA
2820265 TAACCACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.32
22 5 0.20
23 1 0.04
24 11 0.44
ACGTcount: A:0.40, C:0.47, G:0.02, T:0.11
Consensus pattern (22 bp):
CACCACCACCAAATCCTCCATA
Found at i:2820349 original size:9 final size:9
Alignment explanation
Indices: 2820337--2820375 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2820327 AAAACCACTG
2820337 CCACCAAAA
1 CCACCAAAA
*
2820346 CCACCATAA
1 CCACCAAAA
* *
2820355 TCACCAAAT
1 CCACCAAAA
2820364 CCACCAAAA
1 CCACCAAAA
2820373 CCA
1 CCA
2820376 TGATTGTACG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.44, G:0.00, T:0.08
Consensus pattern (9 bp):
CCACCAAAA
Found at i:2822796 original size:3 final size:3
Alignment explanation
Indices: 2822788--2822828 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2822778 GCTTTATTTG
2822788 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2822829 AATTACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2823820 original size:23 final size:22
Alignment explanation
Indices: 2823778--2823820 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
2823768 ATGTGACAAA
*
2823778 AAAATATCATATCATTAATTTT
1 AAAATATCATATCATCAATTTT
2823800 AAAATGATGCATATCA-CAATT
1 AAAAT-AT-CATATCATCAATT
2823821 AAATTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 6 0.33
24 7 0.39
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAATATCATATCATCAATTTT
Found at i:2824306 original size:2 final size:2
Alignment explanation
Indices: 2824299--2824333 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2824289 ATAATGAAAT
2824299 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 T
2824334 GTAAGCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2824415 original size:2 final size:2
Alignment explanation
Indices: 2824408--2824432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2824398 CCCCGCATAC
2824408 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 A
2824433 AAAGAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2824650 original size:15 final size:16
Alignment explanation
Indices: 2824630--2824663 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2824620 TCATATAAAA
2824630 ATTATATTA-ATTTAT
1 ATTATATTATATTTAT
*
2824645 ATTATATTATTTTTAT
1 ATTATATTATATTTAT
2824661 ATT
1 ATT
2824664 GATTAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATATTATATTTAT
Found at i:2824668 original size:15 final size:15
Alignment explanation
Indices: 2824640--2824708 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
2824630 ATTATATTAA
2824640 TTTATATTATATTATT
1 TTTATATT-TATTATT
* *
2824656 TTTATATTGATTAGT
1 TTTATATTTATTATT
*
2824671 TTAATATTTATT-TT
1 TTTATATTTATTATT
2824685 TTTA-A--TATTATT
1 TTTATATTTATTATT
2824697 TTTAATATTTAT
1 TTT-ATATTTAT
2824709 CATATTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 4 0.10
12 5 0.12
13 2 0.05
14 5 0.12
15 15 0.36
16 11 0.26
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTATATTTATTATT
Found at i:2824700 original size:27 final size:29
Alignment explanation
Indices: 2824639--2824717 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
2824629 AATTATATTA
2824639 ATTT-ATATTATATTATTTTTATATTGATT
1 ATTTAATATT-TATTATTTTTATATTGATT
2824668 AGTTTAATATTTATT-TTTTTAATATT-ATT
1 A-TTTAATATTTATTATTTTT-ATATTGATT
*
2824697 -TTTAATATTTATCATATTTTA
1 ATTTAATATTTATTAT-TTTTA
2824718 ATAAAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
27 12 0.27
28 2 0.05
29 13 0.30
30 12 0.27
31 5 0.11
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (29 bp):
ATTTAATATTTATTATTTTTATATTGATT
Found at i:2824716 original size:29 final size:29
Alignment explanation
Indices: 2824639--2824720 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
2824629 AATTATATTA
*
2824639 ATTT-ATATTATATTATTTTTATATTGATT
1 ATTTAATATT-TATTATTTTAATATTGATT
*
2824668 AGTTTAATATTTATTTTTTTAATATT-ATT
1 A-TTTAATATTTATTATTTTAATATTGATT
2824697 -TTTAATATTTATCATATTTTAATA
1 ATTTAATATTTAT--TATTTTAATA
2824721 AAAAAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 12 0.26
29 13 0.28
30 16 0.35
31 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTTAATATTTATTATTTTAATATTGATT
Found at i:2826416 original size:3 final size:3
Alignment explanation
Indices: 2826408--2826433 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2826398 AAAGCAATTG
2826408 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2826434 GATATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2836703 original size:24 final size:25
Alignment explanation
Indices: 2836668--2836720 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2836658 AATCTTATTC
2836668 TTGGGGGGGGGGGTAATGTTTTAGT
1 TTGGGGGGGGGGGTAATGTTTTAGT
2836693 TTGGGGGGGGGGGTAATGTTTTAGT
1 TTGGGGGGGGGGGTAATGTTTTAGT
2836718 TTG
1 TTG
2836721 TTCATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.51, T:0.38
Consensus pattern (25 bp):
TTGGGGGGGGGGGTAATGTTTTAGT
Found at i:2836861 original size:15 final size:15
Alignment explanation
Indices: 2836829--2836871 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
2836819 ATTGGACGGA
2836829 TTGAATTAATTTTGAG
1 TTGAATT-ATTTTGAG
*
2836845 TT-AGATTATTTTTAG
1 TTGA-ATTATTTTGAG
2836860 TTGAATTATTTT
1 TTGAATTATTTT
2836872 AGATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (15 bp):
TTGAATTATTTTGAG
Found at i:2836945 original size:16 final size:16
Alignment explanation
Indices: 2836901--2836945 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2836891 TCATTTTTTA
*
2836901 GTTCGGATCATTTTGG
1 GTTCAGATCATTTTGG
* * *
2836917 ATTCAAATTATTTTGG
1 GTTCAGATCATTTTGG
2836933 GTTCAGATCATTT
1 GTTCAGATCATTT
2836946 CGAGTTTGGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47
Consensus pattern (16 bp):
GTTCAGATCATTTTGG
Found at i:2837540 original size:6 final size:7
Alignment explanation
Indices: 2837504--2837544 Score: 55
Period size: 7 Copynumber: 5.4 Consensus size: 7
2837494 CAATAATAAT
2837504 TTAAAAA
1 TTAAAAA
2837511 TTTAAACTAA
1 -TTAAA--AA
2837521 TTAAAAA
1 TTAAAAA
2837528 TTAAAAA
1 TTAAAAA
2837535 TTAAAAA
1 TTAAAAA
2837542 TTA
1 TTA
2837545 TTATAATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 19 0.61
8 5 0.16
9 5 0.16
10 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (7 bp):
TTAAAAA
Found at i:2837826 original size:16 final size:16
Alignment explanation
Indices: 2837802--2837887 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
2837792 TATCTGAATT
* *
2837802 ATTTAAAGTTCGGATC
1 ATTTTAAGTTCAGATC
*
2837818 ATTTTAAGTT-TGAATC
1 ATTTTAAGTTCAG-ATC
** *
2837834 ATTTTGGGTTAAGATC
1 ATTTTAAGTTCAGATC
* *
2837850 ATTTTGAA-TT-TGATT
1 ATTTT-AAGTTCAGATC
*
2837865 ATTTTAAATTCAGATC
1 ATTTTAAGTTCAGATC
2837881 ATTTTAA
1 ATTTTAA
2837888 ATTTTAGATC
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.04
15 11 0.20
16 40 0.74
17 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (16 bp):
ATTTTAAGTTCAGATC
Found at i:2837832 original size:32 final size:31
Alignment explanation
Indices: 2837796--2837887 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 31
2837786 GTTAATTATC
*
2837796 TGAATTATTTAAAGTTCGGATCATTTTAAGTT
1 TGAATTATTTAAAGTTCAGATCATTTTAA-TT
* *** *
2837828 TGAATCATTTTGGGTTAAGATCATTTTGAATT
1 TGAATTATTTAAAGTTCAGATCATTTT-AATT
2837860 TG-ATTATTTTAAA-TTCAGATCATTTTAA
1 TGAATTA-TTTAAAGTTCAGATCATTTTAA
2837888 ATTTTAGATC
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
30 2 0.04
31 15 0.32
32 28 0.60
33 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (31 bp):
TGAATTATTTAAAGTTCAGATCATTTTAATT
Found at i:2837874 original size:15 final size:15
Alignment explanation
Indices: 2837814--2837891 Score: 57
Period size: 16 Copynumber: 5.0 Consensus size: 15
2837804 TTAAAGTTCG
*
2837814 GATCATTTTAAGTTT
1 GATCATTTTAAATTT
*** *
2837829 GAATCATTTTGGGTTAA
1 G-ATCATTTTAAATT-T
*
2837846 GATCATTTTGAATTT
1 GATCATTTTAAATTT
* *
2837861 GATTATTTTAAATTCA
1 GATCATTTTAAATT-T
2837877 GATCATTTTAAATTT
1 GATCATTTTAAATTT
2837892 TAGATCAATC
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
15 13 0.27
16 35 0.71
17 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (15 bp):
GATCATTTTAAATTT
Found at i:2837891 original size:23 final size:22
Alignment explanation
Indices: 2837865--2837917 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
2837855 GAATTTGATT
2837865 ATTTTAAATTCAGATC-ATTTTAA
1 ATTTTAAA-TCA-ATCAATTTTAA
*
2837888 ATTTTAGATCAATCAATTTTAA
1 ATTTTAAATCAATCAATTTTAA
2837910 ATTATTAA
1 ATT-TTAA
2837918 TTTTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 13 0.50
23 10 0.38
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTTTAAATCAATCAATTTTAA
Found at i:2838098 original size:2 final size:2
Alignment explanation
Indices: 2838091--2838117 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2838081 CTGCCTCCTT
2838091 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
2838118 TCTCCTTTCT
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:2838382 original size:40 final size:40
Alignment explanation
Indices: 2838338--2838413 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2838328 ATTTTTTTAT
2838338 ATTAATAA-TATAAATATAAAAATAATAAAATTATTATTAA
1 ATTAA-AATTATAAATATAAAAATAATAAAATTATTATTAA
* * * *
2838378 ATTAAAATTTTAAATATTAAAATAATATATTTATTA
1 ATTAAAATTATAAATATAAAAATAATAAAATTATTA
2838414 AAAATATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
ATTAAAATTATAAATATAAAAATAATAAAATTATTATTAA
Found at i:2838434 original size:14 final size:13
Alignment explanation
Indices: 2838403--2838478 Score: 64
Period size: 14 Copynumber: 5.7 Consensus size: 13
2838393 ATTAAAATAA
*
2838403 TATATTTATTAAA
1 TATATTTATTAAT
*
2838416 AATATGTTATTAAT
1 TATAT-TTATTAAT
**
2838430 TATATTTAAAAAAT
1 TATATTT-ATTAAT
*
2838444 TATATTTTATTTAT
1 TATA-TTTATTAAT
*
2838458 TATA-TTATTTAT
1 TATATTTATTAAT
2838470 TATATTTAT
1 TATATTTAT
2838479 CATATAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 12 0.24
13 10 0.20
14 26 0.51
15 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TATATTTATTAAT
Found at i:2838467 original size:12 final size:12
Alignment explanation
Indices: 2838450--2838475 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2838440 AAATTATATT
2838450 TTATTTATTATA
1 TTATTTATTATA
2838462 TTATTTATTATA
1 TTATTTATTATA
2838474 TT
1 TT
2838476 TATCATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTATTATA
Found at i:2839168 original size:39 final size:40
Alignment explanation
Indices: 2839081--2839169 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 40
2839071 TGGTTAAGGT
* ** **
2839081 AATATTTAAAAAAATATATATAAATAATATATTATTTTTT
1 AATAATTAAAAAAATATATATAAATAATATAAAATTTTAA
*
2839121 AATGAATTAAAATAATATAT-TAAATAA-ATAAAATTTTAAA
1 AAT-AATTAAAAAAATATATATAAATAATATAAAATTTT-AA
2839161 AATAATTAA
1 AATAATTAA
2839170 TTAATGTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
39 14 0.34
40 13 0.32
41 14 0.34
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (40 bp):
AATAATTAAAAAAATATATATAAATAATATAAAATTTTAA
Found at i:2842200 original size:251 final size:251
Alignment explanation
Indices: 2841757--2842258 Score: 995
Period size: 251 Copynumber: 2.0 Consensus size: 251
2841747 CCATTCAAGA
*
2841757 ACATCGTTCAAGAGAGGGGAATCAATCAATGGAGTAGAATATGATGGATTAGGCTTTCACCAGGA
1 ACATCGTTCAAGAGAGGGGAATCAATCAATGGAGTAGAATATGATGGATTAGGCTTTAACCAGGA
2841822 GTTTTTAACCTTTAAGAGGTGCTATTTACTACCTCGAGGGTGTGTTGTATATGTTGATCCTGATC
66 GTTTTTAACCTTTAAGAGGTGCTATTTACTACCTCGAGGGTGTGTTGTATATGTTGATCCTGATC
2841887 CTCGTGTATATGTATAAGAAAACCTATGTCATCATGCTTGTACATTTCCACTGATGAAATCATAG
131 CTCGTGTATATGTATAAGAAAACCTATGTCATCATGCTTGTACATTTCCACTGATGAAATCATAG
2841952 GAGAGGCTGCAGAGAATTTAAGGTTGTGACCAAATACTCTTTTGATCAAAGTTGTT
196 GAGAGGCTGCAGAGAATTTAAGGTTGTGACCAAATACTCTTTTGATCAAAGTTGTT
2842008 ACATCGTTCAAGAGAGGGGAATCAATCAATGGAGTAGAATATGATGGATTAGGCTTTAACCAGGA
1 ACATCGTTCAAGAGAGGGGAATCAATCAATGGAGTAGAATATGATGGATTAGGCTTTAACCAGGA
2842073 GTTTTTAACCTTTAAGAGGTGCTATTTACTACCTCGAGGGTGTGTTGTATATGTTGATCCTGATC
66 GTTTTTAACCTTTAAGAGGTGCTATTTACTACCTCGAGGGTGTGTTGTATATGTTGATCCTGATC
2842138 CTCGTGTATATGTATAAGAAAACCTATGTCATCATGCTTGTACATTTCCACTGATGAAATCATAG
131 CTCGTGTATATGTATAAGAAAACCTATGTCATCATGCTTGTACATTTCCACTGATGAAATCATAG
2842203 GAGAGGCTGCAGAGAATTTAAGGTTGTGACCAAATACTCTTTTGATCAAAGTTGTT
196 GAGAGGCTGCAGAGAATTTAAGGTTGTGACCAAATACTCTTTTGATCAAAGTTGTT
2842259 TAAAACTCCA
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 250 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (251 bp):
ACATCGTTCAAGAGAGGGGAATCAATCAATGGAGTAGAATATGATGGATTAGGCTTTAACCAGGA
GTTTTTAACCTTTAAGAGGTGCTATTTACTACCTCGAGGGTGTGTTGTATATGTTGATCCTGATC
CTCGTGTATATGTATAAGAAAACCTATGTCATCATGCTTGTACATTTCCACTGATGAAATCATAG
GAGAGGCTGCAGAGAATTTAAGGTTGTGACCAAATACTCTTTTGATCAAAGTTGTT
Found at i:2845466 original size:2 final size:2
Alignment explanation
Indices: 2845459--2845486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2845449 AAAGGGCGCA
2845459 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2845487 TAAATTATGT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2845735 original size:2 final size:2
Alignment explanation
Indices: 2845728--2845762 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2845718 GGTAGACATA
2845728 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 A
2845763 CTCACATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2854883 original size:19 final size:20
Alignment explanation
Indices: 2854859--2854904 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2854849 TATTAAACAC
2854859 ATATTTAAAATATTA-TATT
1 ATATTTAAAATATTATTATT
** *
2854878 ATATTTATTATATTATTTTT
1 ATATTTAAAATATTATTATT
2854898 ATATTTA
1 ATATTTA
2854905 TTAAATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTAAAATATTATTATT
Found at i:2854886 original size:14 final size:14
Alignment explanation
Indices: 2854869--2854899 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2854859 ATATTTAAAA
2854869 TATTATATTATATT
1 TATTATATTATATT
*
2854883 TATTATATTATTTT
1 TATTATATTATATT
2854897 TAT
1 TAT
2854900 ATTTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:2855389 original size:32 final size:31
Alignment explanation
Indices: 2855353--2855442 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 31
2855343 GAAAAAATAA
2855353 TTAAAAGTTATATAAAATATAAAATAAATATT
1 TTAAAA-TTATATAAAATATAAAATAAATATT
* *
2855385 TTAAAATT-TATATAATATAAATTATAAATGTT
1 TTAAAATTATATAAAATATAAA--ATAAATATT
* *
2855417 TTTAAATT-TATATATATATAAAATAA
1 TTAAAATTATATA-AAATATAAAATAA
2855443 TTTAAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 12 0.24
31 6 0.12
32 25 0.50
33 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAATTATATAAAATATAAAATAAATATT
Found at i:2855467 original size:30 final size:25
Alignment explanation
Indices: 2855417--2855478 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 25
2855407 TATAAATGTT
2855417 TTTAAATTTATATATATATAAAATAA
1 TTTAAATTTATATATATATAAAAT-A
2855443 TTTAAATTTAATTATAATATTATAAAATA
1 TTTAAATTT-A-TAT-ATA-TATAAAATA
2855472 TTTAAAT
1 TTTAAAT
2855479 ATAAATACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.28
27 1 0.03
28 3 0.09
29 11 0.34
30 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTAAATTTATATATATATAAAATA
Found at i:2855475 original size:29 final size:27
Alignment explanation
Indices: 2855399--2855478 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 27
2855389 AATTTATATA
* *
2855399 ATATAA-ATTATAAATGTTTTTAAATTT
1 ATATAATATTATAAA-ATATTTAAATTT
2855426 ATAT-ATA-TATAAAATAATTTAAATTT
1 ATATAATATTATAAAAT-ATTTAAATTT
2855452 AATTATAATATTATAAAATATTTAAAT
1 -A-TATAATATTATAAAATATTTAAAT
2855479 ATAAATACAC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
25 1 0.02
26 16 0.36
27 6 0.13
28 3 0.07
29 11 0.24
30 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATAATATTATAAAATATTTAAATTT
Found at i:2855973 original size:3 final size:3
Alignment explanation
Indices: 2855965--2856002 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2855955 CAATTCCGAC
* *
2855965 GAG GAG GAG GAG GAG GAG GAG GAG CAG GAG CAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
2856003 AAAGGAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.61, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:2861903 original size:40 final size:40
Alignment explanation
Indices: 2861871--2861949 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 40
2861861 ACAACTTTAA
2861871 TGAACTTGAACTTTACCAACAACTAGAATTACAACCCAAG
1 TGAACTTGAACTTTACCAACAACTAGAATTACAACCCAAG
* *
2861911 TGAACTTGTACTTTACCAATAACTAGAACTTACAACCCA
1 TGAACTTGAACTTTACCAACAACTAGAA-TTACAACCCA
2861950 TTCATCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 26 0.72
41 10 0.28
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (40 bp):
TGAACTTGAACTTTACCAACAACTAGAATTACAACCCAAG
Found at i:2867230 original size:36 final size:36
Alignment explanation
Indices: 2867170--2867241 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
2867160 TTTTATATAA
2867170 AAAATATAATATAAATATGATATATTTAATAAATAT
1 AAAATATAATATAAATATGATATATTTAATAAATAT
* *
2867206 AAAA-ATAATATAATATATGATATATTTTATATATAT
1 AAAATATAATATAA-ATATGATATATTTAATAAATAT
2867242 TTAAAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (36 bp):
AAAATATAATATAAATATGATATATTTAATAAATAT
Found at i:2879091 original size:20 final size:18
Alignment explanation
Indices: 2879059--2879103 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2879049 ATTATTATAT
* *
2879059 TTATTTTTAAT-TTTTAA
1 TTATATTTAATATTTTTA
2879076 TATATATTTAATATTTTTA
1 T-TATATTTAATATTTTTA
2879095 TTATATTTA
1 TTATATTTA
2879104 TGTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTAATATTTTTA
Found at i:2881452 original size:20 final size:20
Alignment explanation
Indices: 2881408--2881453 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2881398 TTTATTTAAA
2881408 TTTAATAATAAAAAATATAT
1 TTTAATAATAAAAAATATAT
* *
2881428 ATTAAT-ATAAAAATTAATAT
1 TTTAATAATAAAAAAT-ATAT
2881448 TTTAAT
1 TTTAAT
2881454 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAATAATAAAAAATATAT
Found at i:2881805 original size:21 final size:20
Alignment explanation
Indices: 2881766--2881806 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2881756 CAACTTTTAA
*
2881766 AAATTTTATTAAATAAATAT
1 AAATTTAATTAAATAAATAT
*
2881786 AAATTTAATCTAAATTAATAT
1 AAATTTAAT-TAAATAAATAT
2881807 TTGATTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTAATTAAATAAATAT
Found at i:2882451 original size:13 final size:13
Alignment explanation
Indices: 2882433--2882457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2882423 TATTGATAAA
2882433 TATTTAATATATG
1 TATTTAATATATG
2882446 TATTTAATATAT
1 TATTTAATATAT
2882458 ATTTAAATAT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TATTTAATATATG
Found at i:2882480 original size:23 final size:22
Alignment explanation
Indices: 2882449--2882506 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
2882439 ATATATGTAT
2882449 TTAATATATATTTAAAT-ATAAA
1 TTAA-ATATATTTAAATAATAAA
*
2882471 TATAAAATATAATTAAATAAATAAA
1 T-T-AAATATATTTAAAT-AATAAA
2882496 TTAAATATATT
1 TTAAATATATT
2882507 CATATGCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.03
23 20 0.67
24 3 0.10
25 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATATATTTAAATAATAAA
Found at i:2882497 original size:13 final size:14
Alignment explanation
Indices: 2882461--2882502 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2882451 AATATATATT
* *
2882461 TAAATATAAATATA
1 TAAATATAATTAAA
2882475 -AAATATAATTAAA
1 TAAATATAATTAAA
2882488 TAAATA-AATTAAA
1 TAAATATAATTAAA
2882501 TA
1 TA
2882503 TATTCATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:2882727 original size:25 final size:24
Alignment explanation
Indices: 2882698--2882759 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
2882688 ATTTATAAAT
* *
2882698 TATTAATAAATTAAATTATATTATC
1 TATTAATAAATAAAATTAT-TTATA
2882723 TATTAATAAATAAAATTATTTATA
1 TATTAATAAATAAAATTATTTATA
**
2882747 TATTTTTAAATAA
1 TATTAATAAATAA
2882760 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTAATAAATAAAATTATTTATA
Found at i:2888589 original size:22 final size:21
Alignment explanation
Indices: 2888539--2888590 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2888529 TATATTTATT
*
2888539 TTAAAACTTACTAAAATAAAA
1 TTAAAAATTACTAAAATAAAA
* *
2888560 TTATAAAATTACTAAAGGTTAAA
1 TTA-AAAATTACTAAA-ATAAAA
2888583 TTAAAAAT
1 TTAAAAAT
2888591 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAAAAATTACTAAAATAAAA
Found at i:2888645 original size:21 final size:21
Alignment explanation
Indices: 2888619--2888671 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2888609 AAAAGTATAA
*
2888619 ATAAATTTAAACT-ATTTATTT
1 ATAAATTTAAA-TAATTTAATT
*
2888640 ATAAATATAAATAAATTTAATT
1 ATAAATTTAAAT-AATTTAATT
2888662 A-AAATTTAAA
1 ATAAATTTAAA
2888672 ACTCATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 18 0.67
22 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTTAAATAATTTAATT
Found at i:2889840 original size:9 final size:9
Alignment explanation
Indices: 2889826--2889878 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
2889816 TTTAATTAAC
2889826 TTTTAAAAT
1 TTTTAAAAT
*
2889835 TTTTAAAAA
1 TTTTAAAAT
*
2889844 TTTTAAATAA
1 TTTTAAA-AT
*
2889854 TTTT-AACT
1 TTTTAAAAT
2889862 TTTTAAAACT
1 TTTTAAAA-T
2889872 TTTTAAA
1 TTTTAAA
2889879 TATTAAACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 4 0.11
9 19 0.51
10 14 0.38
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:2890456 original size:12 final size:13
Alignment explanation
Indices: 2890437--2890476 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
2890427 ATATTTTATT
*
2890437 TATTTTTAATTAA
1 TATTTTTAATAAA
2890450 T-TTTTTAATAAA
1 TATTTTTAATAAA
2890462 TATTTTTAA-AAA
1 TATTTTTAATAAA
2890474 TAT
1 TAT
2890477 ATGTTATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTTTAATAAA
Found at i:2891692 original size:11 final size:11
Alignment explanation
Indices: 2891676--2891710 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2891666 ATTATAATAA
2891676 TATTTAAATTT
1 TATTTAAATTT
2891687 TATTTAAATTT
1 TATTTAAATTT
* *
2891698 TAATAAAATTT
1 TATTTAAATTT
2891709 TA
1 TA
2891711 ATGTATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAAATTT
Found at i:2893048 original size:12 final size:12
Alignment explanation
Indices: 2893026--2893059 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2893016 GTAATATAAT
2893026 ATATAATTAAAAA
1 ATATAA-TAAAAA
2893039 ATATAATAAAAA
1 ATATAATAAAAA
2893051 ATAT-ATAAA
1 ATATAATAAA
2893060 TATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 10 0.48
13 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATAATAAAAA
Found at i:2893070 original size:16 final size:16
Alignment explanation
Indices: 2893049--2893140 Score: 66
Period size: 16 Copynumber: 5.7 Consensus size: 16
2893039 ATATAATAAA
2893049 AAATATATAAATATAT
1 AAATATATAAATATAT
* *
2893065 AAATATTTATATAATAT
1 AAATATATAAAT-ATAT
*
2893082 AAAT-TATTAATATATT
1 AAATATATAAATATA-T
2893098 AAAATTTATATAAATATA-
1 -AAA--TATATAAATATAT
* *
2893116 AAATATTTTAA-ATAT
1 AAATATATAAATATAT
2893131 -AATATATAAA
1 AAATATATAAA
2893141 AAGTAAATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
14 11 0.19
15 9 0.15
16 15 0.25
17 14 0.24
19 1 0.02
20 9 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATATAAATATAT
Found at i:2893077 original size:34 final size:34
Alignment explanation
Indices: 2893039--2893131 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 34
2893029 TAATTAAAAA
2893039 ATATAATAAAAAATATATAAATATA-TAAATATTT
1 ATATAATAAAAAATATATAAATATATTAAA-ATTT
* *
2893073 ATATAAT-ATAAAT-TATTAATATATTAAAATTT
1 ATATAATAAAAAATATATAAATATATTAAAATTT
* *
2893105 ATATAAATATAAAATATTTTAAATATA
1 ATAT-AATAAAAAATA-TATAAATATA
2893132 ATATATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 17 0.35
33 12 0.25
34 11 0.23
36 8 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATAATAAAAAATATATAAATATATTAAAATTT
Found at i:2893089 original size:18 final size:17
Alignment explanation
Indices: 2893039--2893137 Score: 75
Period size: 18 Copynumber: 5.9 Consensus size: 17
2893029 TAATTAAAAA
* *
2893039 ATATAATA-AAAAATAT
1 ATATAATATAAATATTT
*
2893055 ATAAATATATAAATATTT
1 ATATA-ATATAAATATTT
*
2893073 ATATAATATAAATTATTA
1 ATATAATATAAA-TATTT
2893091 ATAT-AT-TAAA-ATTT
1 ATATAATATAAATATTT
2893105 ATATAAATATAAAATATTT
1 ATAT-AATAT-AAATATTT
2893124 -TA-AATATAATATAT
1 ATATAATATAA-ATAT
2893138 AAAAAGTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 19 0.28
17 13 0.19
18 23 0.34
19 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAATATAAATATTT
Found at i:2893101 original size:52 final size:52
Alignment explanation
Indices: 2893019--2893142 Score: 146
Period size: 52 Copynumber: 2.4 Consensus size: 52
2893009 TTTAGACGTA
2893019 ATATAATATATAATTAAAAAATATAATAAAAAATATATAAATATATAAATATTT
1 ATATAATATA-AATTAAAAAATATAATAAAAAATATATAAATATA-AAATATTT
** * **
2893073 ATATAATATAAATT-ATTAATATATTAAAATTTATATAAATATAAAATATTT
1 ATATAATATAAATTAAAAAATATAATAAAAAATATATAAATATAAAATATTT
2893124 -TA-AATATAATATATAAAAA
1 ATATAATATAA-AT-TAAAAA
2893143 GTAAATTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
49 7 0.12
50 4 0.07
51 9 0.15
52 26 0.43
53 4 0.07
54 10 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (52 bp):
ATATAATATAAATTAAAAAATATAATAAAAAATATATAAATATAAAATATTT
Found at i:2894294 original size:3 final size:3
Alignment explanation
Indices: 2894286--2894316 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2894276 GGCTATCAAA
2894286 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2894317 TGTTTCAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2897305 original size:19 final size:21
Alignment explanation
Indices: 2897267--2897305 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2897257 TTTAAAAATA
2897267 AATATAAATAATTATCTTTTT
1 AATATAAATAATTATCTTTTT
2897288 AATA-AAATAA-TAT-TTTTT
1 AATATAAATAATTATCTTTTT
2897306 GATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 6 0.33
21 4 0.22
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATTATCTTTTT
Found at i:2898417 original size:2 final size:2
Alignment explanation
Indices: 2898410--2898435 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2898400 TTCCCATTTC
2898410 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2898436 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2898440 original size:2 final size:2
Alignment explanation
Indices: 2898435--2898462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2898425 ACACACACAC
2898435 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
2898463 CACTTGTAGT
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:2900168 original size:21 final size:21
Alignment explanation
Indices: 2900138--2900179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2900128 TAACATGTCT
*
2900138 ATTATTTTTATTATAT-TTTA
1 ATTATTTTTATAATATATTTA
2900158 ATTATTTTTTATAATATATTTA
1 ATTA-TTTTTATAATATATTTA
2900180 TAGTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTTTTATAATATATTTA
Found at i:2900394 original size:50 final size:50
Alignment explanation
Indices: 2900290--2900525 Score: 287
Period size: 50 Copynumber: 4.7 Consensus size: 50
2900280 TTTTATTAAC
* * * * *
2900290 CTTTGACCATTGAGATAGGTGACCGT-ATTATTGATTATTCTTCACC-AA
1 CTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAAA
* * *
2900338 CTTTTGACAATTGAGAGAGGTGGCCGTAATTGTTGACTATTCTTTACCAAA
1 C-TTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAAA
* * * *
2900389 CTTTGACAATCGATAGAGGTGACCGTAATTGTTAACTATTTTTCACCAAC
1 CTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAAA
* * *
2900439 CTTTGACAATCGAGAGAGGTGACCATAATTGTTGACTATTCTTCACTAAC
1 CTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAAA
* * *
2900489 CTTTGACAATAGAGACAGGTGACTGTAATTGTTGACT
1 CTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACT
2900526 CTAAACATCT
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
48 1 0.01
49 22 0.13
50 137 0.84
51 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (50 bp):
CTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAAA
Found at i:2905121 original size:50 final size:50
Alignment explanation
Indices: 2904899--2905144 Score: 251
Period size: 50 Copynumber: 4.9 Consensus size: 50
2904889 TGATTTGATA
* * * *
2904899 ATTCTTCATCAACCTTTGACAATCGAGAGAAGTGACAGTAATTATTGACT
1 ATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTATTGACT
* * * * * * *
2904949 ATTATTCACCAACTTTTGATAATCGAGAGAGATGGCCTTAATTATTTACT
1 ATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTATTGACT
* * *
2904999 ATTCTTCACCAA-ACTTTGACAATTGAGAGAGGTGGCCGTAATTGTTGACT
1 ATTCTTCACCAACA-TTTGACAATCGAGAGAGGTGACCGTAATTATTGACT
* * * * *
2905049 GTTCTTCACTAACCTTTGACAATCGAGAGAGGTAACCGTAATTGTTGACT
1 ATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTATTGACT
* * * * **
2905099 ATTCTTCACCAATATTTAACAATAGAGAAAGGTGACTATAATTATT
1 ATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTATT
2905145 AACTCTAAGC
Statistics
Matches: 159, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
50 159 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (50 bp):
ATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTATTGACT
Found at i:2905834 original size:31 final size:32
Alignment explanation
Indices: 2905809--2905876 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
2905799 ATTTTTTTAT
2905809 ATTAA-AATATTATA-AATATAAATTTTAATAA
1 ATTAATAAT-TTATATAATATAAATTTTAATAA
*
2905840 ATTAATAATTTATATTATATAAATTTTAATACA
1 ATTAATAATTTATATAATATAAATTTTAATA-A
2905873 ATTA
1 ATTA
2905877 TATCAGCTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 10 0.30
32 18 0.55
33 5 0.15
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTAATAATTTATATAATATAAATTTTAATAA
Found at i:2905839 original size:16 final size:16
Alignment explanation
Indices: 2905820--2905870 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2905810 TTAAAATATT
2905820 ATAAATATAAATTTTA
1 ATAAATATAAATTTTA
*
2905836 ATAAAT-TAATAATTT-
1 ATAAATATAA-ATTTTA
*
2905851 ATATTATATAAATTTTA
1 ATA-AATATAAATTTTA
2905868 ATA
1 ATA
2905871 CAATTATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.21
16 16 0.57
17 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAATATAAATTTTA
Found at i:2917795 original size:12 final size:12
Alignment explanation
Indices: 2917791--2917822 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2917781 TATGTATCTA
2917791 TATATATGTATG
1 TATATATGTATG
2917803 TATATATGTATG
1 TATATATGTATG
2917815 TATATATG
1 TATATATG
2917823 CTTACCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:2917797 original size:14 final size:13
Alignment explanation
Indices: 2917778--2917821 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
2917768 ATACGAAAGC
2917778 ATATATGTATCTAT
1 ATATATGTAT-TAT
*
2917792 ATATATGTA-TGT
1 ATATATGTATTAT
2917804 ATATATGTATGTAT
1 ATATATGTAT-TAT
2917818 ATAT
1 ATAT
2917822 GCTTACCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 11 0.42
14 15 0.58
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (13 bp):
ATATATGTATTAT
Found at i:2922217 original size:2 final size:2
Alignment explanation
Indices: 2922210--2922247 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2922200 AAATAAAAAC
2922210 AT AT AT AT AT AT AT AT A- AT AT AT AT A- 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
2922248 TGCAAAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.