Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 8 of 59
Found at i:2862913 original size:22 final size:23
Alignment explanation
Indices: 2862874--2862920 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2862864 AACTAAGTCA
2862874 GATAAACGTTGGAGCAAAACCAG
1 GATAAACGTTGGAGCAAAACCAG
*
2862897 GATAAACGTT-GAGCAAAACTAG
1 GATAAACGTTGGAGCAAAACCAG
2862919 GA
1 GA
2862921 GAACCAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.15, G:0.26, T:0.15
Consensus pattern (23 bp):
GATAAACGTTGGAGCAAAACCAG
Found at i:2870766 original size:19 final size:18
Alignment explanation
Indices: 2870707--2870757 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
2870697 TGTCCAACAG
2870707 AAATATTCTTTTGAGACA
1 AAATATTCTTTTGAGACA
2870725 AAATATTCTTTTGAGACA
1 AAATATTCTTTTGAGACA
2870743 AAATATTCATTTTGA
1 AAATATTC-TTTTGA
2870758 AAACAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (18 bp):
AAATATTCTTTTGAGACA
Found at i:2873591 original size:16 final size:16
Alignment explanation
Indices: 2873570--2873603 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2873560 CTAATAAATT
*
2873570 AATATAAACATTTAAA
1 AATATAAACAATTAAA
2873586 AATATAAACAATTAAA
1 AATATAAACAATTAAA
2873602 AA
1 AA
2873604 GTTATGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AATATAAACAATTAAA
Found at i:2875246 original size:9 final size:9
Alignment explanation
Indices: 2875229--2875286 Score: 100
Period size: 9 Copynumber: 6.6 Consensus size: 9
2875219 CACTGTCTTT
*
2875229 TTTTCTCAA
1 TTTTATCAA
2875238 TTTTATCAA
1 TTTTATCAA
2875247 TTTTATCAA
1 TTTTATCAA
2875256 TTTTATCAA
1 TTTTATCAA
2875265 -TTTATCAA
1 TTTTATCAA
2875273 TTTTATCAA
1 TTTTATCAA
2875282 TTTTA
1 TTTTA
2875287 ATTTTAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
8 8 0.17
9 39 0.83
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTATCAA
Found at i:2875270 original size:17 final size:17
Alignment explanation
Indices: 2875234--2875292 Score: 95
Period size: 17 Copynumber: 3.5 Consensus size: 17
2875224 TCTTTTTTTC
2875234 TCAATTTTATCAATTTTA
1 TCAATTTTATCAA-TTTA
2875252 TCAATTTTATCAATTTA
1 TCAATTTTATCAATTTA
2875269 TCAATTTTATCAATTT-
1 TCAATTTTATCAATTTA
2875285 T-AATTTTA
1 TCAATTTTA
2875293 ATTTGGAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.17
16 1 0.02
17 20 0.49
18 13 0.32
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
TCAATTTTATCAATTTA
Found at i:2875275 original size:26 final size:26
Alignment explanation
Indices: 2875234--2875292 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
2875224 TCTTTTTTTC
2875234 TCAATTTTATCAATTTTATCAATTTT
1 TCAATTTTATCAATTTTATCAATTTT
2875260 ATCAA-TTTATCAATTTTATCAA-TTT
1 -TCAATTTTATCAATTTTATCAATTTT
2875285 T-AATTTTA
1 TCAATTTTA
2875293 ATTTGGAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.06
24 5 0.16
25 3 0.10
26 17 0.55
27 4 0.13
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (26 bp):
TCAATTTTATCAATTTTATCAATTTT
Found at i:2912302 original size:21 final size:21
Alignment explanation
Indices: 2912253--2912296 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2912243 CCTTTACGCA
*
2912253 GTAACGAAAGGAGACAGTCCT
1 GTAATGAAAGGAGACAGTCCT
*
2912274 GTAATGAAAGGAGACCGTCCT
1 GTAATGAAAGGAGACAGTCCT
2912295 GT
1 GT
2912297 TTTGAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (21 bp):
GTAATGAAAGGAGACAGTCCT
Found at i:2913349 original size:12 final size:12
Alignment explanation
Indices: 2913332--2913356 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2913322 TTTTCTACGA
2913332 CTAGTCATAAGC
1 CTAGTCATAAGC
2913344 CTAGTCATAAGC
1 CTAGTCATAAGC
2913356 C
1 C
2913357 GACTTTGGAG
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CTAGTCATAAGC
Found at i:2915271 original size:4 final size:4
Alignment explanation
Indices: 2915249--2915297 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
2915239 CTATCTCTCA
* *
2915249 ATTT TTTT ATTT CTTT ATTT ATTT -TTT ATATT ATTT ATTT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT A-TTT ATTT
2915298 CCTTCAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
4 27 0.71
5 8 0.21
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
ATTT
Found at i:2915274 original size:20 final size:21
Alignment explanation
Indices: 2915249--2915293 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2915239 CTATCTCTCA
*
2915249 ATTTTTTTAT-TTCTTTATTT
1 ATTTTTTTATATTATTTATTT
2915269 A-TTTTTTATATTATTTATTT
1 ATTTTTTTATATTATTTATTT
2915289 ATTTT
1 ATTTT
2915294 ATTTCCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 11 0.50
21 3 0.14
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTTTTTATATTATTTATTT
Found at i:2919680 original size:30 final size:30
Alignment explanation
Indices: 2919646--2919707 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2919636 TTTAAAATTT
2919646 TTGTAAGAGTGAAATTATT-AAATT-TTGAAA
1 TTGTAAGAGTGAAATT-TTGAAATTATT-AAA
2919676 TTGTAAGAGTGAAATTTTGAAATTATTAAA
1 TTGTAAGAGTGAAATTTTGAAATTATTAAA
2919706 TT
1 TT
2919708 ATTAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 2 0.07
30 26 0.87
31 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (30 bp):
TTGTAAGAGTGAAATTTTGAAATTATTAAA
Found at i:2923575 original size:12 final size:12
Alignment explanation
Indices: 2923558--2923592 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2923548 TAATTAATTA
*
2923558 GAAGATGAAGAT
1 GAAGATGAAAAT
2923570 GAAGATGAAAAT
1 GAAGATGAAAAT
*
2923582 GAAAATGAAAA
1 GAAGATGAAAA
2923593 GCAGACAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (12 bp):
GAAGATGAAAAT
Found at i:2926550 original size:14 final size:15
Alignment explanation
Indices: 2926523--2926551 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2926513 TGGTGCCTAT
2926523 GGTAGAGACACGTGA
1 GGTAGAGACACGTGA
2926538 GGTAGAG-CACGTGA
1 GGTAGAGACACGTGA
2926552 TGTCTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.14, G:0.41, T:0.14
Consensus pattern (15 bp):
GGTAGAGACACGTGA
Found at i:2935739 original size:33 final size:31
Alignment explanation
Indices: 2935675--2935763 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 31
2935665 TTAAATTTTA
2935675 AAAAAT-TAAATTTAAATATGTATAATTAAAATAT
1 AAAAATATAAATTTAAAT-T-TAT--TTAAAATAT
2935709 AAAAATATAATATTTTAAATTTATTTAAAATAT
1 AAAAATATAA-A-TTTAAATTTATTTAAAATAT
* **
2935742 TAATTTATAAATTTAAATTTAT
1 AAAAATATAAATTTAAATTTAT
2935764 AATTTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 11 0.22
32 1 0.02
33 16 0.33
34 6 0.12
35 6 0.12
36 2 0.04
37 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAAATATAAATTTAAATTTATTTAAAATAT
Found at i:2935757 original size:13 final size:13
Alignment explanation
Indices: 2935720--2935765 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
2935710 AAAATATAAT
2935720 ATTT-TAAATTT-
1 ATTTATAAATTTA
2935731 ATTTA-AAATATTA
1 ATTTATAAAT-TTA
2935744 ATTTATAAATTTAA
1 ATTTATAAATTT-A
2935758 ATTTATAA
1 ATTTATAA
2935766 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 7 0.23
14 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTATAAATTTA
Found at i:2939141 original size:24 final size:23
Alignment explanation
Indices: 2939097--2939148 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
2939087 ATTCATCTAT
2939097 AAATATTATATATATAAATAATA
1 AAATATTATATATATAAATAATA
*
2939120 AAATATTATATTATATATATAATA
1 AAATATTATA-TATATAAATAATA
2939144 AAATA
1 AAATA
2939149 ATTAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATTATATATATAAATAATA
Found at i:2943437 original size:59 final size:59
Alignment explanation
Indices: 2943341--2943456 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
2943331 ACTTTAAATT
2943341 GTTCGAATCATTCCCTTTACTCAAAGCGAGCAATTGCAGCGGGCGTGAGTCAGGTGTAA
1 GTTCGAATCATTCCCTTTACTCAAAGCGAGCAATTGCAGCGGGCGTGAGTCAGGTGTAA
* *
2943400 GTTCGAATCATTCCCTTTACTCAAAGCGAGCAGTTGCAGCGGGCGTGAGTCATGTGT
1 GTTCGAATCATTCCCTTTACTCAAAGCGAGCAATTGCAGCGGGCGTGAGTCAGGTGT
2943457 GATACAAAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (59 bp):
GTTCGAATCATTCCCTTTACTCAAAGCGAGCAATTGCAGCGGGCGTGAGTCAGGTGTAA
Found at i:2947735 original size:27 final size:27
Alignment explanation
Indices: 2947667--2947725 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
2947657 CTACATTGGG
*
2947667 CACTTATATACAAGTTACATTACAAGA
1 CACTTACATACAAGTTACATTACAAGA
2947694 CACTTACATACAAGTTACATTACAAGA
1 CACTTACATACAAGTTACATTACAAGA
2947721 -ACTTA
1 CACTTA
2947726 GCCTGCAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (27 bp):
CACTTACATACAAGTTACATTACAAGA
Found at i:2957655 original size:20 final size:20
Alignment explanation
Indices: 2957630--2957670 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2957620 TCCATCAAAG
2957630 TTCCTCCTAACTTTTCAGGC
1 TTCCTCCTAACTTTTCAGGC
2957650 TTCCTCCTAACTTTTCAGGC
1 TTCCTCCTAACTTTTCAGGC
2957670 T
1 T
2957671 CTATTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.34, G:0.10, T:0.41
Consensus pattern (20 bp):
TTCCTCCTAACTTTTCAGGC
Found at i:2963427 original size:70 final size:70
Alignment explanation
Indices: 2963337--2963525 Score: 272
Period size: 70 Copynumber: 2.7 Consensus size: 70
2963327 GAGGCGCAAC
* *
2963337 TTGTGAGACAAAATCGTGAAGCCAGCGGGCCAAAGCAGATAATACTTCACAGGGGTTTGTTTGGA
1 TTGTGAGACAAAATCGTGAAGCCAGCGGGCCAAAGCAGATAATACTTCACAGAGGTTTGTATGGA
2963402 G-TCAT
66 GCT-AT
* * * * * *
2963407 TTGTGAGACAAAACCTTGAAGCCAACGAGCCAAAACAGATAATACTTCACAGAGGTTTGTATGGC
1 TTGTGAGACAAAATCGTGAAGCCAGCGGGCCAAAGCAGATAATACTTCACAGAGGTTTGTATGGA
2963472 GCTAT
66 GCTAT
* *
2963477 TTGTGAGACAAAATCGTGAAGCCAGCGGGTCAAAGCAGATAATATTTCA
1 TTGTGAGACAAAATCGTGAAGCCAGCGGGCCAAAGCAGATAATACTTCA
2963526 TAAGGGTCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 102 0.99
71 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (70 bp):
TTGTGAGACAAAATCGTGAAGCCAGCGGGCCAAAGCAGATAATACTTCACAGAGGTTTGTATGGA
GCTAT
Found at i:3003148 original size:3 final size:3
Alignment explanation
Indices: 3003140--3003169 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3003130 CGGGAGGTGG
3003140 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3003170 GTCGTTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3022109 original size:228 final size:218
Alignment explanation
Indices: 3021711--3022157 Score: 671
Period size: 228 Copynumber: 2.0 Consensus size: 218
3021701 CATGTTTTGC
3021711 TGTGTTGTCCACAACAGTATCAATATGTGGCAAAGAGAAGCTATCCTTCGGACTTGCTCTGTTCA
1 TGTGTTGTCCACAACAGTATCAATATGTGGCAAAGAGAAGCTATCCTTCGGACTTGCTCTGTTCA
* * * * * *
3021776 AATCTCTATAATCGACGCACATTCGAATTTTTCCATCCTTCTTAGGAACTGGAATTATATTAGCC
66 AATCCCTATAATCGACGCACATTCAAACTTTTCCATCATTCTTAGGAACTGAAACTATATTAGCC
*
3021841 ACCCATTCAGGGTACTAGGCCACCTCTAAAAATCCAGCATCAAATTGCTTCTTTACTTCTTCTTT
131 ACCCATTCAGGGTACTAGGCCACCTCTAAAAATCCAGCATCAAATTGCTTCTTTACTTCCTCTTT
*
3021906 AATTTTCAGCAACATTTCTGGCT
196 AATCTTCAGCAACATTTCTGGCT
* *
3021929 TNNNNNNNNNNGTGTTGTCCACAAGAGTATCAATATGTGGCAAAGGGAAGCTATCCTTCGGACTT
1 T----------GTGTTGTCCACAACAGTATCAATATGTGGCAAAGAGAAGCTATCCTTCGGACTT
*
3021994 GCTCTGTTCAAATCCCTATAATTGACGCACATTCAAACTTTTCCATCATTCTTAGGAACTGAAAC
56 GCTCTGTTCAAATCCCTATAATCGACGCACATTCAAACTTTTCCATCATTCTTAGGAACTGAAAC
* *
3022059 TATATTAGCCACCCATTCAGGGTACTTA-GCCACCTCTAAAAATCCAGCATCGAATTGCTTTTTT
121 TATATTAGCCACCCATTCAGGGTAC-TAGGCCACCTCTAAAAATCCAGCATCAAATTGCTTCTTT
3022123 ACTTCCTCTTTAATCTTCAGCAACATTTCTGGCT
185 ACTTCCTCTTTAATCTTCAGCAACATTTCTGGCT
3022157 T
1 T
3022158 CATCCTTCTC
Statistics
Matches: 205, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
218 1 0.00
228 202 0.99
229 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.33
Consensus pattern (218 bp):
TGTGTTGTCCACAACAGTATCAATATGTGGCAAAGAGAAGCTATCCTTCGGACTTGCTCTGTTCA
AATCCCTATAATCGACGCACATTCAAACTTTTCCATCATTCTTAGGAACTGAAACTATATTAGCC
ACCCATTCAGGGTACTAGGCCACCTCTAAAAATCCAGCATCAAATTGCTTCTTTACTTCCTCTTT
AATCTTCAGCAACATTTCTGGCT
Found at i:3029944 original size:22 final size:22
Alignment explanation
Indices: 3029913--3029970 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3029903 AATTGTTCCA
*
3029913 TTTATATATTTTTTTATTATTAT-
1 TTTAT-TATTTTTTT-TTACTATC
*
3029936 TTTATTATTTATTTTTACTATC
1 TTTATTATTTTTTTTTACTATC
*
3029958 ATTATTATTTTTT
1 TTTATTATTTTTT
3029971 GATTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 5 0.17
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTATTTTTTTTTACTATC
Found at i:3029977 original size:27 final size:25
Alignment explanation
Indices: 3029922--3029979 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
3029912 ATTTATATAT
* *
3029922 TTTTTTATTATTATTTTATTATTTA
1 TTTTTTACTATCATTTTATTATTTA
*
3029947 -TTTTTACTATCATTATTATTTTTTGA
1 TTTTTTACTATCATT-TTATTATTT-A
3029973 TTTTTTA
1 TTTTTTA
3029980 ATATTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 12 0.44
25 8 0.30
26 1 0.04
27 6 0.22
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTTTACTATCATTTTATTATTTA
Found at i:3030669 original size:19 final size:19
Alignment explanation
Indices: 3030645--3030684 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3030635 CCCCTTTTCT
*
3030645 TTTTTTGGTTTTTGTTTTG
1 TTTTTTAGTTTTTGTTTTG
* *
3030664 TTTTTTATTTTTTTTTTTG
1 TTTTTTAGTTTTTGTTTTG
3030683 TT
1 TT
3030685 GCTAGGCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (19 bp):
TTTTTTAGTTTTTGTTTTG
Found at i:3037578 original size:2 final size:2
Alignment explanation
Indices: 3037573--3037600 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3037563 TATATATATA
3037573 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3037601 GCTGAAGATT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3042198 original size:2 final size:2
Alignment explanation
Indices: 3042191--3042216 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3042181 ATTATTTACT
3042191 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
3042217 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3072411 original size:2 final size:2
Alignment explanation
Indices: 3072406--3072438 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3072396 ACACACACAC
3072406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3072439 CCTTACACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3073898 original size:3 final size:3
Alignment explanation
Indices: 3073892--3073916 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3073882 TGATGCATAG
3073892 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3073917 TGTTAAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3074941 original size:111 final size:112
Alignment explanation
Indices: 3074726--3074953 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 112
3074716 TAAATATGGT
** *
3074726 CCTAATACCTAAATGGGGGCTCAAGAAAACCATTGGGGATGCTTTATCATAGTTCTAGGATTGAA
1 CCTAATACCTAAATAAGGGCTCAAGAAAACCATTGGGGATGCTTTATCACAGTTCTAGGATTGAA
* * *
3074791 TTTTCCAAATCGAACAGCTCACTGTGCACAAACAGTGAAGATTCTCC
66 TTTTCCAAATCAAACAGCTCACTGTGCACAAACACTGAAGACTCTCC
* * *
3074838 CCTAATACCT-AATAAGGGCTCGAGAAAACCA-TGGGGATGCTTTGTTACAGTTCTAGGGATTGA
1 CCTAATACCTAAATAAGGGCTCAAGAAAACCATTGGGGATGCTTTATCACAGTTCTA-GGATTGA
* *
3074901 ATTTTCCAAATCAAACAGGTCACTGTGTACAAACACTGAAGACTCTCC
65 ATTTTCCAAATCAAACAGCTCACTGTGCACAAACACTGAAGACTCTCC
3074949 CCTAA
1 CCTAA
3074954 AAATCTAAAG
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
110 21 0.20
111 73 0.70
112 10 0.10
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (112 bp):
CCTAATACCTAAATAAGGGCTCAAGAAAACCATTGGGGATGCTTTATCACAGTTCTAGGATTGAA
TTTTCCAAATCAAACAGCTCACTGTGCACAAACACTGAAGACTCTCC
Found at i:3080995 original size:18 final size:18
Alignment explanation
Indices: 3080962--3081001 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3080952 AGTTTCACAA
**
3080962 ATAATTCATAGGTAACAC
1 ATAATTCATAAATAACAC
*
3080980 ATAATTCATAAATAACTC
1 ATAATTCATAAATAACAC
3080998 ATAA
1 ATAA
3081002 ATTAACGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAATTCATAAATAACAC
Found at i:3083329 original size:14 final size:14
Alignment explanation
Indices: 3083310--3083345 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
3083300 ATCAGCTTCA
3083310 ATGGTTCCCATCTC
1 ATGGTTCCCATCTC
3083324 ATGGTTCCCATCTC
1 ATGGTTCCCATCTC
3083338 ATGGTTCC
1 ATGGTTCC
3083346 AACCTAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.33, G:0.17, T:0.36
Consensus pattern (14 bp):
ATGGTTCCCATCTC
Found at i:3088147 original size:2 final size:2
Alignment explanation
Indices: 3088140--3088178 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3088130 ATTACTTTGC
*
3088140 AT AT AT AT GT 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
3088179 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3090328 original size:46 final size:46
Alignment explanation
Indices: 3090275--3090369 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
3090265 TTGTCGTATA
*
3090275 ACCTAACTAGGCCTCATATCTACGTTCAAATTAATATAGAAACAAC
1 ACCTAACTAGGCCTCATATCTACGTCCAAATTAATATAGAAACAAC
**
3090321 ACCTAACTAGTTCTCATATCTACGTCCAAATTAATATAGAAACAAC
1 ACCTAACTAGGCCTCATATCTACGTCCAAATTAATATAGAAACAAC
3090367 ACC
1 ACC
3090370 AAGCAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (46 bp):
ACCTAACTAGGCCTCATATCTACGTCCAAATTAATATAGAAACAAC
Found at i:3094101 original size:18 final size:18
Alignment explanation
Indices: 3094078--3094116 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3094068 TTTTTTTTTT
3094078 AAAAATT-TTGTTCTTAAA
1 AAAAATTATT-TTCTTAAA
*
3094096 AAAAATTATTTTTTTAAA
1 AAAAATTATTTTCTTAAA
3094114 AAA
1 AAA
3094117 CTTTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAAATTATTTTCTTAAA
Found at i:3099263 original size:2 final size:2
Alignment explanation
Indices: 3099256--3099296 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3099246 CAAGATGTAC
3099256 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3099297 CCTCCCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3112050 original size:12 final size:12
Alignment explanation
Indices: 3112012--3112069 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
3112002 GAAATATAAT
3112012 TAAAA-AAACAAA
1 TAAAATAAA-AAA
3112024 -AAAATAATAAAA
1 TAAAATAA-AAAA
*
3112036 TAAAATAAGAAA
1 TAAAATAAAAAA
*
3112048 TAAATTAAAAAA
1 TAAAATAAAAAA
3112060 TGAAAA-AAAA
1 T-AAAATAAAA
3112070 GGGAAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 4 0.11
12 23 0.61
13 11 0.29
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (12 bp):
TAAAATAAAAAA
Found at i:3112712 original size:19 final size:18
Alignment explanation
Indices: 3112683--3112724 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
3112673 GAGGAAAGGA
* *
3112683 AAAGGCGTCGGCAGTGAG
1 AAAGACGTCGGCAGGGAG
3112701 AGAAGACGTCGGCAGGGAG
1 A-AAGACGTCGGCAGGGAG
3112720 AAAGA
1 AAAGA
3112725 GAAAGAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.14, G:0.43, T:0.07
Consensus pattern (18 bp):
AAAGACGTCGGCAGGGAG
Found at i:3112768 original size:22 final size:24
Alignment explanation
Indices: 3112720--3112786 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 24
3112710 CGGCAGGGAG
3112720 AAAGAGAAAGAGAGAAAAGGAAAGA
1 AAAGA-AAAGAGAGAAAAGGAAAGA
3112745 AAAGAAAAGAGAGAAAGAAGGAAAAGAA
1 AAAGAAAAGAGAG-AA-AAGG-AAAG-A
3112773 AAAGAAAGAGAGAG
1 AAAGAAA-AGAGAG
3112787 GGAAAGGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 8 0.22
25 7 0.19
26 4 0.11
27 4 0.11
28 8 0.22
29 6 0.16
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (24 bp):
AAAGAAAAGAGAGAAAAGGAAAGA
Found at i:3112775 original size:23 final size:23
Alignment explanation
Indices: 3112720--3112791 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
3112710 CGGCAGGGAG
* *
3112720 AAAGAGAAAGAGAGAAAAGGAAAGA
1 AAAGAAAAAGAGAG-AAA-GAAGGA
3112745 AAAG-AAAAGAGAGAAAGAAGGA
1 AAAGAAAAAGAGAGAAAGAAGGA
* * *
3112767 AAAGAAAAAGAAAGAGAGAGGGA
1 AAAGAAAAAGAGAGAAAGAAGGA
3112790 AA
1 AA
3112792 GGAGAGACGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.22
23 20 0.49
24 8 0.20
25 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAGAGAGAAAGAAGGA
Found at i:3115795 original size:24 final size:23
Alignment explanation
Indices: 3115754--3115805 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
3115744 CAAAGGTTTG
* *
3115754 TTTTCAATAGACACAATTGTCTAT
1 TTTTCAACAAACACAATTGT-TAT
*
3115778 TTTTCAACAAACATAATTGTTAT
1 TTTTCAACAAACACAATTGTTAT
3115801 TTTTC
1 TTTTC
3115806 CACCATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTTCAACAAACACAATTGTTAT
Found at i:3127073 original size:28 final size:30
Alignment explanation
Indices: 3127029--3127084 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
3127019 TTTGATTTGA
*
3127029 AATAAAAATATAAAAATTTGA-TTAAATAT
1 AATAAAAATATAAAAATTTAATTTAAATAT
3127058 AATAAAAA-ATAAAAATTTAATTTAAAT
1 AATAAAAATATAAAAATTTAATTTAAAT
3127085 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AATAAAAATATAAAAATTTAATTTAAATAT
Found at i:3128875 original size:17 final size:17
Alignment explanation
Indices: 3128850--3128883 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3128840 ATATTTAATC
*
3128850 AATTCAATTTTTTTTAA
1 AATTCAATTTGTTTTAA
*
3128867 AATTTAATTTGTTTTAA
1 AATTCAATTTGTTTTAA
3128884 TTAATGTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
AATTCAATTTGTTTTAA
Found at i:3139292 original size:2 final size:2
Alignment explanation
Indices: 3139285--3139326 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3139275 TTATGGTAGA
*
3139285 CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3139327 GTAATCTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3148500 original size:2 final size:2
Alignment explanation
Indices: 3148493--3148589 Score: 123
Period size: 2 Copynumber: 50.0 Consensus size: 2
3148483 CCATACATAC
*
3148493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AGT -T GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
3148534 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT -T AT GAT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
3148575 -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3148590 GTACTGTATN
Statistics
Matches: 85, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
1 5 0.06
2 77 0.91
3 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3148636 original size:2 final size:2
Alignment explanation
Indices: 3148629--3148687 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
3148619 NNNNNNNNNN
* *
3148629 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3148671 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3148688 GTATGTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3156266 original size:29 final size:28
Alignment explanation
Indices: 3156221--3156276 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3156211 ATCTTTAATG
*
3156221 TATTTTTTATGATTATTTGAATATGTTAA
1 TATTTTTTATGAATA-TTGAATATGTTAA
*
3156250 TATTTTTTAAT-AATATTGAATTTGTTA
1 TATTTTTT-ATGAATATTGAATATGTTA
3156277 CATTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 11 0.46
30 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (28 bp):
TATTTTTTATGAATATTGAATATGTTAA
Found at i:3158518 original size:22 final size:22
Alignment explanation
Indices: 3158493--3158537 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3158483 TTTTATTTCA
3158493 TATTATCATATATTCTATTTTT
1 TATTATCATATATTCTATTTTT
* * *
3158515 TATTCTCCTATATTTTATTTTT
1 TATTATCATATATTCTATTTTT
3158537 T
1 T
3158538 TATATTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATCATATATTCTATTTTT
Found at i:3158801 original size:15 final size:15
Alignment explanation
Indices: 3158775--3158830 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3158765 CATTATTGTT
*
3158775 TTATTTTATTTATTTT
1 TTATTTT-TTTATTTA
*
3158791 TTATTTTTTTATCTA
1 TTATTTTTTTATTTA
*
3158806 TTATTTGTTTATTTA
1 TTATTTTTTTATTTA
3158821 TTATTTTTTT
1 TTATTTTTTT
3158831 GATGATTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
15 28 0.80
16 7 0.20
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (15 bp):
TTATTTTTTTATTTA
Found at i:3158831 original size:19 final size:19
Alignment explanation
Indices: 3158774--3158831 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
3158764 TCATTATTGT
3158774 TTTATTTTATTTATTTTTTAT-
1 TTTA-TTTA-TTATTTTTT-TG
*
3158795 TTT-TTTATCTA-TTATTTG
1 TTTATTTAT-TATTTTTTTG
3158813 TTTATTTATTATTTTTTTG
1 TTTATTTATTATTTTTTTG
3158832 ATGATTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 1 0.03
18 10 0.32
19 17 0.55
21 3 0.10
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTATTTATTATTTTTTTG
Found at i:3159836 original size:18 final size:18
Alignment explanation
Indices: 3159795--3159842 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3159785 CTTTTATTTA
*
3159795 TTATTATTTTATTATATAC
1 TTATT-TTTTATCATATAC
* *
3159814 ATATTTTTTATCATATAT
1 TTATTTTTTATCATATAC
*
3159832 TTATTTATTAT
1 TTATTTTTTAT
3159843 TTTTTAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTTTATCATATAC
Found at i:3162812 original size:20 final size:20
Alignment explanation
Indices: 3162787--3162824 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3162777 AAAGACTAAA
*
3162787 CAAAACAAAGAAAAAAGCAC
1 CAAAACAAACAAAAAAGCAC
3162807 CAAAACAAACAAAAAAGC
1 CAAAACAAACAAAAAAGC
3162825 TAAGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.21, G:0.08, T:0.00
Consensus pattern (20 bp):
CAAAACAAACAAAAAAGCAC
Found at i:3169787 original size:13 final size:14
Alignment explanation
Indices: 3169755--3169795 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
3169745 GATTTAGATC
*
3169755 AATTTTAAATATTA
1 AATTTTAAAAATTA
*
3169769 TAAATTTAAAAATTA
1 -AATTTTAAAAATTA
3169784 AATTTTAAAAAT
1 AATTTTAAAAAT
3169796 CACAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTTAAAAATTA
Found at i:3170411 original size:30 final size:31
Alignment explanation
Indices: 3170372--3170438 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
3170362 TTCATTTCTT
*
3170372 AAATGAAATTAAAATAAAAATTT-TAATTAAA
1 AAAT-AAATTAAAATAAAAATTTAAAATTAAA
** * *
3170403 AAATAAATTGCATTAAACATTTAAAATTAAA
1 AAATAAATTAAAATAAAAATTTAAAATTAAA
3170434 AAATA
1 AAATA
3170439 TTTTAAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATAAATTAAAATAAAAATTTAAAATTAAA
Found at i:3170934 original size:20 final size:20
Alignment explanation
Indices: 3170911--3170960 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3170901 TATATATATT
* *
3170911 TTTATTATTTTATATTTTAG
1 TTTATTATTTTATAATTTAA
3170931 TTTATT-TTATTATAATTTAA
1 TTTATTATT-TTATAATTTAA
*
3170951 TTTTTTATTT
1 TTTATTATTT
3170961 ATTTATGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATTATTTTATAATTTAA
Found at i:3170940 original size:22 final size:22
Alignment explanation
Indices: 3170890--3170941 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
3170880 TTTTTTTTAA
3170890 ATTTTATTTTATATATATATTT
1 ATTTTATTTTATATATATATTT
*
3170912 -TTATTATTTTATAT-TTTAGTTT
1 ATT-TTATTTTATATATATA-TTT
3170934 ATTTTATT
1 ATTTTATT
3170942 ATAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 19 0.73
23 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
ATTTTATTTTATATATATATTT
Found at i:3174649 original size:14 final size:14
Alignment explanation
Indices: 3174630--3174672 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3174620 AAATAGATAG
*
3174630 ATTTAATTTTTAAT
1 ATTTAATTTTTAAA
* *
3174644 ATTTAAATTTAAAA
1 ATTTAATTTTTAAA
*
3174658 ATTAAATTTTTAAA
1 ATTTAATTTTTAAA
3174672 A
1 A
3174673 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAATTTTTAAA
Found at i:3174669 original size:15 final size:15
Alignment explanation
Indices: 3174634--3174679 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3174624 AGATAGATTT
* *
3174634 AATTTTTAATATTTA
1 AATTTTTAAAAATTA
3174649 AA--TTTAAAAATTA
1 AATTTTTAAAAATTA
*
3174662 AATTTTTAAAAATCA
1 AATTTTTAAAAATTA
3174677 AAT
1 AAT
3174680 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTTTAAAAATTA
Found at i:3174711 original size:20 final size:21
Alignment explanation
Indices: 3174678--3174721 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
3174668 TAAAAATCAA
3174678 ATAAAAATAAAAAT-ATTG-T
1 ATAAAAATAAAAATGATTGAT
*
3174697 ATAAAAATTACAAATGATTGAT
1 ATAAAAA-TAAAAATGATTGAT
3174719 ATA
1 ATA
3174722 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 4 0.19
22 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
ATAAAAATAAAAATGATTGAT
Found at i:3175289 original size:30 final size:31
Alignment explanation
Indices: 3175250--3175316 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
3175240 TTCATTTCTT
*
3175250 AAATGAAATTAAAATAAAAATTT-TAATTAAA
1 AAAT-AAATTAAAATAAAAATTTAAAATTAAA
** * *
3175281 AAATAAATTGCATTAAACATTTAAAATTAAA
1 AAATAAATTAAAATAAAAATTTAAAATTAAA
3175312 AAATA
1 AAATA
3175317 TTTTAAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATAAATTAAAATAAAAATTTAAAATTAAA
Found at i:3175791 original size:33 final size:34
Alignment explanation
Indices: 3175750--3175820 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
3175740 CTCTCTTTCC
3175750 TTTTTTTTTAATTA--TTTTATTATATATATAATT
1 TTTTTTTTTAATTATTTTTTATTATA-ATATAATT
** *
3175783 TTTTTTTTTTTTTATTTTTTATTATAATTTAATT
1 TTTTTTTTTAATTATTTTTTATTATAATATAATT
3175817 TTTT
1 TTTT
3175821 ATTTATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 12 0.36
34 11 0.33
35 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (34 bp):
TTTTTTTTTAATTATTTTTTATTATAATATAATT
Found at i:3175793 original size:35 final size:34
Alignment explanation
Indices: 3175750--3175829 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
3175740 CTCTCTTTCC
3175750 TTTTTTTTTAATTATTTTATTATATATATAATTTTT
1 TTTTTTTTTAATT-TTTTATTATA-ATATAATTTTT
* *
3175786 TTTTTTTTTTATTTTTTATTATAATTTAATTTTT
1 TTTTTTTTTAATTTTTTATTATAATATAATTTTT
* *
3175820 TATTTATTTA
1 TTTTTTTTTA
3175830 TCATGAATGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 17 0.44
35 10 0.26
36 12 0.31
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (34 bp):
TTTTTTTTTAATTTTTTATTATAATATAATTTTT
Found at i:3175808 original size:29 final size:28
Alignment explanation
Indices: 3175750--3175828 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
3175740 CTCTCTTTCC
*
3175750 TTTTTTTTTAATTATTTTATTATATATATAA
1 TTTTTTTTT--TT-TTTTATTTTATATATAA
*
3175781 TTTTTTTTTTTTTTTATTTTTTATTATAA
1 TTTTTTTTTTTTTTTATTTTATA-TATAA
** *
3175810 TTTAATTTTTTATTTATTT
1 TTTTTTTTTTTTTTTATTT
3175829 ATCATGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 10 0.24
29 23 0.55
31 9 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTATTTTATATATAA
Found at i:3177084 original size:30 final size:31
Alignment explanation
Indices: 3177045--3177111 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
3177035 TTCATTTCTT
*
3177045 AAATGAAATTAAAATAAAAATTT-TAATTAAA
1 AAAT-AAATTAAAATAAAAATTTAAAATTAAA
** * *
3177076 AAATAAATTGCATTAAACATTTAAAATTAAA
1 AAATAAATTAAAATAAAAATTTAAAATTAAA
3177107 AAATA
1 AAATA
3177112 TTTTAAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATAAATTAAAATAAAAATTTAAAATTAAA
Found at i:3180852 original size:3 final size:3
Alignment explanation
Indices: 3180844--3180892 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
3180834 TTTATTCAAG
* * * *
3180844 TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT CAT TATT TAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
3180890 TAT
1 TAT
3180893 ATTTTTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3180960 original size:27 final size:26
Alignment explanation
Indices: 3180928--3181013 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
3180918 TGCTTGCAAT
3180928 TAGGAACATCCTTGTGCATTATGCAC
1 TAGGAACATCCTTGTGCATTATGCAC
*
3180954 TCAGGAACATCCTTG-GACATTATCCAC
1 T-AGGAACATCCTTGTG-CATTATGCAC
* * * * *
3180981 TTGGAACGTCCTTATGAATTACGCAC
1 TAGGAACATCCTTGTGCATTATGCAC
3181007 TTAGGAA
1 -TAGGAA
3181014 TGTCCCTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
26 19 0.40
27 29 0.60
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (26 bp):
TAGGAACATCCTTGTGCATTATGCAC
Found at i:3181108 original size:26 final size:26
Alignment explanation
Indices: 3181050--3181108 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
3181040 ATGTCTTTAA
*
3181050 CGCACTTGGAACATCCCTATGCGTTG
1 CGCACTTGGAACATCCCTAGGCGTTG
** * * *
3181076 CAAACTTGGAACATCCCTGGGTGTTT
1 CGCACTTGGAACATCCCTAGGCGTTG
3181102 CGCACTT
1 CGCACTT
3181109 AGAGCATTTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (26 bp):
CGCACTTGGAACATCCCTAGGCGTTG
Found at i:3181490 original size:5 final size:5
Alignment explanation
Indices: 3181480--3181558 Score: 52
Period size: 5 Copynumber: 15.2 Consensus size: 5
3181470 AAGTTATAAT
* * * *
3181480 TAAAA TAAAA TATAT TAAAA TAAAA T-ATA TAATA TAAAAA TCAAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA T--AAAA
* * *
3181527 TTAAAA TAAAA TAAAA TATAA GAAAT TAAAA T
1 -TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
3181559 TTATATAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
4 3 0.05
5 41 0.71
6 8 0.14
7 5 0.09
8 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:3181498 original size:15 final size:15
Alignment explanation
Indices: 3181478--3181606 Score: 72
Period size: 15 Copynumber: 8.8 Consensus size: 15
3181468 GTAAGTTATA
3181478 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
3181493 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
3181508 A-TAATATAAAA-AT
1 ATTAAAATAAAATAT
*
3181521 CA--AAAATTAAAATAA
1 -ATTAAAA-TAAAATAT
* * * *
3181536 AATAAAATATAAGAA
1 ATTAAAATAAAATAT
**
3181551 ATTAAAAT-TTATAT
1 ATTAAAATAAAATAT
* ** *
3181565 AATATAAGCAAAAGAT
1 ATTA-AAATAAAATAT
3181581 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
*
3181596 A-TAATATAAAA
1 ATTAAAATAAAA
3181607 AATTATATTA
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
13 5 0.06
14 31 0.36
15 41 0.47
16 10 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:3181511 original size:33 final size:33
Alignment explanation
Indices: 3181474--3181557 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
3181464 TTTTGTAAGT
3181474 TATAAT-T-AAAATAAAATATATTAAAATAAAATA
1 TATAATATAAAAATAAAA-A-ATTAAAATAAAATA
*
3181507 TATAATATAAAAATCAAAAATTAAAATAAAATA
1 TATAATATAAAAATAAAAAATTAAAATAAAATA
*
3181540 -A-AATATAAGAAATTAAAA
1 TATAATATAA-AAATAAAAA
3181558 TTTATATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
31 7 0.15
32 9 0.20
33 20 0.43
34 2 0.04
35 8 0.17
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (33 bp):
TATAATATAAAAATAAAAAATTAAAATAAAATA
Found at i:3181686 original size:33 final size:33
Alignment explanation
Indices: 3181584--3181686 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 33
3181574 AAAAGATATT
* * * *
3181584 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAATATATGACATTAAAAA-TATATTTA
* * * *
3181618 AAAATAAAAAATATGAGATTATAATAAGA-A-ATA
1 AAAATAAAATATATGACATTA-AA-AATATATTTA
3181651 AAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATATGACATTAAAAATATATTTA
3181684 AAA
1 AAA
3181687 GATGATATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
31 3 0.06
32 3 0.06
33 25 0.46
34 18 0.33
35 3 0.06
36 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (33 bp):
AAAATAAAATATATGACATTAAAAATATATTTA
Found at i:3181915 original size:15 final size:15
Alignment explanation
Indices: 3181897--3181936 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
3181887 AGATTGCTTA
3181897 CAATCACATTACATG
1 CAATCACATTACATG
*
3181912 CAATCACATTACCTG
1 CAATCACATTACATG
*
3181927 TAATCACATT
1 CAATCACATT
3181937 GCATTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.30
Consensus pattern (15 bp):
CAATCACATTACATG
Found at i:3185403 original size:42 final size:42
Alignment explanation
Indices: 3185331--3185422 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
3185321 GCAATACTTA
*** * *
3185331 TTCTTCTCTTGAGGGTGTTTTGAATACTACTCAAAATGTTTC
1 TTCTTCTCTTGAGGGTGTTCCAAATACTACTCAAAATGCTCC
* **
3185373 TTCTTCTCTTG-GGTGTGTTCCAAATGCTACTCGTAATGCTCC
1 TTCTTCTCTTGAGG-GTGTTCCAAATACTACTCAAAATGCTCC
3185415 TTCTTCTC
1 TTCTTCTC
3185423 CTAGAGGTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (42 bp):
TTCTTCTCTTGAGGGTGTTCCAAATACTACTCAAAATGCTCC
Found at i:3186346 original size:45 final size:45
Alignment explanation
Indices: 3186217--3186334 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
3186207 TCCCTTTATG
* *
3186217 AAATAGCTATTTCATGCTTATTCTTATTCTGTAGCACAACATATA
1 AAATAGCTATTTCATGCTTATTCTTATTCTGTAGCACAATATAGA
* * * * * * * *
3186262 AAACAGTTGTTCCATACTTATTCATATTCTGTAACACAATGTAGA
1 AAATAGCTATTTCATGCTTATTCTTATTCTGTAGCACAATATAGA
3186307 AAATAGCTATTTCATGCTTATTCTTATT
1 AAATAGCTATTTCATGCTTATTCTTATT
3186335 TTATTGCACA
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (45 bp):
AAATAGCTATTTCATGCTTATTCTTATTCTGTAGCACAATATAGA
Found at i:3200404 original size:25 final size:25
Alignment explanation
Indices: 3200366--3200416 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3200356 GAGTGGGTAG
* *
3200366 AATGTCATGGAGATCATATGTTGTC
1 AATGTCACGAAGATCATATGTTGTC
*
3200391 AATGTCACGAAGATCTTATGTTGTC
1 AATGTCACGAAGATCATATGTTGTC
3200416 A
1 A
3200417 TAAGTTACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (25 bp):
AATGTCACGAAGATCATATGTTGTC
Found at i:3204486 original size:23 final size:23
Alignment explanation
Indices: 3204460--3204543 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
3204450 GCAGTGCCTA
*
3204460 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* *
3204483 AGTCTA-GCAATACTTTACTAACT
1 AGTC-ACGCAATGCCTTACTAACT
* *
3204506 AGTCACGCAATACCTTACTAACC
1 AGTCACGCAATGCCTTACTAACT
3204529 AGTCACGCAATGCCT
1 AGTCACGCAATGCCT
3204544 ATCAACTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 51 0.96
24 1 0.02
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:3204585 original size:23 final size:22
Alignment explanation
Indices: 3204525--3204585 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
3204515 ATACCTTACT
*
3204525 AACCAGTCACGCAATGCCTATC
1 AACCAGTCACACAATGCCTATC
* * *
3204547 AACTAATCATACAATGCCATATC
1 AACCAGTCACACAATGCC-TATC
*
3204570 AACCAGTCACATAATG
1 AACCAGTCACACAATG
3204586 GCTAAAAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (22 bp):
AACCAGTCACACAATGCCTATC
Found at i:3204659 original size:22 final size:22
Alignment explanation
Indices: 3204502--3204660 Score: 104
Period size: 22 Copynumber: 7.1 Consensus size: 22
3204492 ATACTTTACT
* **
3204502 AACTAGTCACGCAATACCTTACT
1 AACTAGTCACGCAATGCC-TAAA
* **
3204525 AACCAGTCACGCAATGCCTATC
1 AACTAGTCACGCAATGCCTAAA
* ** **
3204547 AACTAATCATACAATGCCATATC
1 AACTAGTCACGCAATGCC-TAAA
* ** *
3204570 AACCAGTCACATAATGGCTAAA
1 AACTAGTCACGCAATGCCTAAA
* *
3204592 AACTAATCACGTAATGCCT-AA
1 AACTAGTCACGCAATGCCTAAA
* *
3204613 AACTTAGTAATGCAATGCCTAAA
1 AAC-TAGTCACGCAATGCCTAAA
*
3204636 AACTAGTCACACAATGCCTAAA
1 AACTAGTCACGCAATGCCTAAA
3204658 AAC
1 AAC
3204661 CGATTACATA
Statistics
Matches: 107, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
21 5 0.05
22 64 0.60
23 38 0.36
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (22 bp):
AACTAGTCACGCAATGCCTAAA
Found at i:3204872 original size:50 final size:51
Alignment explanation
Indices: 3204818--3204914 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
3204808 TTTCTTCATA
*
3204818 TATCAAAAA-TCACTTCAAAATGCTCAAAACGCTCAAA-GTATTTCTTCTCG
1 TATCAAAAACT-ACTCCAAAATGCTCAAAACGCTCAAACGTATTTCTTCTCG
* * *
3204868 TATCAAAAACTACTCCAAAATGCTCAAAATGCTTAAACGTTTTTCTT
1 TATCAAAAACTACTCCAAAATGCTCAAAACGCTCAAACGTATTTCTT
3204915 TCTGGTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 32 0.78
51 9 0.22
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (51 bp):
TATCAAAAACTACTCCAAAATGCTCAAAACGCTCAAACGTATTTCTTCTCG
Found at i:3216128 original size:19 final size:20
Alignment explanation
Indices: 3216101--3216146 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3216091 AGGAGACAAG
*
3216101 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
3216120 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
3216139 ATAATATT
1 ATAATATT
3216147 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:3219195 original size:2 final size:2
Alignment explanation
Indices: 3219190--3219235 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3219180 CCTCTCAAGC
* *
3219190 AT AT AT AT AT AT AT AT AT AT AT AT AT CT CT 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
3219232 AT AT
1 AT AT
3219236 CTCTACTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3219236 original size:20 final size:20
Alignment explanation
Indices: 3219199--3219240 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3219189 CATATATATA
3219199 TATATATATATATATATCTC
1 TATATATATATATATATCTC
3219219 TATATATATATATATATCTC
1 TATATATATATATATATCTC
3219239 TA
1 TA
3219241 CTATTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATATATATATATATCTC
Found at i:3223049 original size:23 final size:23
Alignment explanation
Indices: 3223011--3223055 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3223001 TTTTTTATAA
3223011 TAAAAAACAAAAAAAT-AGAAAT
1 TAAAAAACAAAAAAATAAGAAAT
*
3223033 TAAAAAATAAAATAAATAAGAAA
1 TAAAAAACAAAA-AAATAAGAAA
3223056 AGAAAGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
TAAAAAACAAAAAAATAAGAAAT
Found at i:3230147 original size:161 final size:162
Alignment explanation
Indices: 3229848--3230280 Score: 498
Period size: 161 Copynumber: 2.7 Consensus size: 162
3229838 CCATCTATTA
** ** *
3229848 TGATATATTAACTTACCATGTCAACATTATGTGACATAAAATAAGAAATGATGTTTTAATTGTCA
1 TGATATATTAACTTACCATGTCAACATTATGTGGTATAAAATAAGAAATGACATTTTAACTGTCA
* * * * * *
3229913 TGAGTAAAAATATCATTTGTCATTTTATACTCATATAACACTAATGTGAAAGGTAAAAATATCAT
66 TTAGT-TAAATATCACTTGTCATTTTATACTCATGTGACACTAACGTGAAAGGTAAAAATATCAT
* *
3229978 ACAACTATGTCATTATGTCATATCAAT-ATGTCAC
130 ACAACTATGTCATGATGTCATATC-ATCAT-CCAC
* **
3230012 -G-TATGTTAACTTACCATGTCAGTATTATGTGGTATAAAATAA-AAAGTGACATTTTAACTGTC
1 TGATATATTAACTTACCATGTCAACATTATGTGGTATAAAATAAGAAA-TGACATTTTAACTGTC
* * * * * **
3230074 ATTAGTTAAACATCACTTATCATTTTATGCTCATGTGACACTAACGTGAAGGGTGAAAATATTGT
65 ATTAGTTAAATATCACTTGTCATTTTATACTCATGTGACACTAACGTGAAAGGTAAAAATATCAT
3230139 ACAACTATGTCATGATGTCATATCATCATCCAC
130 ACAACTATGTCATGATGTCATATCATCATCCAC
* *
3230172 TATGATATATTAACTTGA-CATGTCAACATTATGTAGTATAAAATAAGAAATAACATTTTAACTG
1 --TGATATATTAACTT-ACCATGTCAACATTATGTGGTATAAAATAAGAAATGACATTTTAACTG
* * * *
3230236 TCGTTAATTATAATGTCACTTGTCATTTTATATTCATGTGACACT
63 TCATTAGTTA-AATATCACTTGTCATTTTATACTCATGTGACACT
3230281 GATATGAAAG
Statistics
Matches: 225, Mismatches: 35, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
160 5 0.02
161 75 0.33
162 54 0.24
163 2 0.01
164 56 0.25
165 33 0.15
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (162 bp):
TGATATATTAACTTACCATGTCAACATTATGTGGTATAAAATAAGAAATGACATTTTAACTGTCA
TTAGTTAAATATCACTTGTCATTTTATACTCATGTGACACTAACGTGAAAGGTAAAAATATCATA
CAACTATGTCATGATGTCATATCATCATCCAC
Found at i:3230314 original size:164 final size:162
Alignment explanation
Indices: 3229846--3230327 Score: 469
Period size: 164 Copynumber: 3.0 Consensus size: 162
3229836 ATCCATCTAT
* ** *
3229846 TATGATATATTAACTTACCATGTCAACATTATGTGACATAAAATAAGAAATGATGTTTTAATTGT
1 TATGATATATTAACTTACCATGTCAACATTATGTG-TATAAAATAAGAAATGACATTTTAACTGT
* * * * * **
3229911 CATGAGTAAAAATATCATTTGTCATTTTATACTCATATAACACTAATGTGAAAGGTAAAAATATC
65 CATTAGT-TAAATATCACTTGTCATTTTATACTCATGTGACACTAATGTGAAA-GTTGAAATATC
** * *
3229976 ATACAACTATGTCATTATGTCATATCAATATGTCAC
128 ATGTAACTATGTCATCATGTCATATC-ATATGCCAC
* **
3230012 ---G-TATGTTAACTTACCATGTCAGTATTATGTGGTATAAAATAA-AAAGTGACATTTTAACTG
1 TATGATATATTAACTTACCATGTCAACATTATGT-GTATAAAATAAGAAA-TGACATTTTAACTG
* * * * * *
3230072 TCATTAGTTAAACATCACTTATCATTTTATGCTCATGTGACACTAACGTGAAGGGTGAAA-AT-A
64 TCATTAGTTAAATATCACTTGTCATTTTATACTCATGTGACACTAATGTGAAAGTTGAAATATCA
*
3230135 TTGTACAACTATGTCATGATGTCATATCATCAT-CCAC
129 -TGT--AACTATGTCATCATGTCATATCAT-ATGCCAC
*
3230172 TATGATATATTAACTTGA-CATGTCAACATTATGTAGTATAAAATAAGAAATAACATTTTAACTG
1 TATGATATATTAACTT-ACCATGTCAACATTATGT-GTATAAAATAAGAAATGACATTTTAACTG
* * * * * *
3230236 TCGTTAATTATAATGTCACTTGTCATTTTATATTCATGTGACACTGATATGAAAGTTGAAATATC
64 TCATTAGTTA-AATATCACTTGTCATTTTATACTCATGTGACACTAATGTGAAAGTTGAAATATC
* * *
3230301 ACGTAATTATGTCATCATATCATATCA
128 ATGTAACTATGTCATCATGTCATATCA
3230328 GCATGTCATA
Statistics
Matches: 256, Mismatches: 45, Indels: 32
0.77 0.14 0.10
Matches are distributed among these distances:
158 1 0.00
159 3 0.01
160 9 0.04
161 62 0.24
162 53 0.21
163 3 0.01
164 76 0.30
165 44 0.17
166 4 0.02
167 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (162 bp):
TATGATATATTAACTTACCATGTCAACATTATGTGTATAAAATAAGAAATGACATTTTAACTGTC
ATTAGTTAAATATCACTTGTCATTTTATACTCATGTGACACTAATGTGAAAGTTGAAATATCATG
TAACTATGTCATCATGTCATATCATATGCCAC
Found at i:3230470 original size:30 final size:29
Alignment explanation
Indices: 3230427--3230501 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
3230417 TTTTTTTATT
* * *
3230427 AAAATAAAGATTTATTTGGTATAAA-ATAA
1 AAAATAAAAATTTATTT-GAACAAAGATAA
*
3230456 AAATATAAAAATTTA-TTGAACAAAGTTAA
1 AAA-ATAAAAATTTATTTGAACAAAGATAA
3230485 AAAATAAAAATTTATTT
1 AAAATAAAAATTTATTT
3230502 ATATAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 16 0.41
29 13 0.33
30 10 0.26
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATAAAAATTTATTTGAACAAAGATAA
Found at i:3238338 original size:31 final size:31
Alignment explanation
Indices: 3238273--3238338 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3238263 AATTAATCAA
*
3238273 TTAAAATTATTTCATAAAAATATATTAAAGT
1 TTAAAATTATTTCATAAAAATATAATAAAGT
* * *
3238304 TTAAAATTATATTTATAATAAT-TAATAAATT
1 TTAAAATTAT-TTCATAAAAATATAATAAAGT
3238335 TTAA
1 TTAA
3238339 TAAGTATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 21 0.70
32 9 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
TTAAAATTATTTCATAAAAATATAATAAAGT
Found at i:3239103 original size:2 final size:2
Alignment explanation
Indices: 3239091--3239150 Score: 95
Period size: 2 Copynumber: 30.0 Consensus size: 2
3239081 AATTCCTATC
3239091 TA TA T- 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
*
3239132 TA TA TA GTA TA CA TA TA TA
1 TA TA TA -TA TA TA TA TA TA
3239151 GAATTCTCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 1 0.02
2 51 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3244774 original size:122 final size:119
Alignment explanation
Indices: 3244559--3244799 Score: 313
Period size: 122 Copynumber: 2.0 Consensus size: 119
3244549 CAATTTGGAT
* *
3244559 TTTTGTCAAGATTTTTCTTCAATTTACACTTTGTTATTTTCCTTTAAAAGCAAAATTTTTGTATA
1 TTTTGTCAAAATTTTTCTCCAATTTACACTTTGTTATTTTCCTTTAAAAGCAAAA-TTTTGTATA
* * *
3244624 TTAACTAAAATTAAAATTACATGAATGTCAAATCTAGTCTATATCTAATGAACAC
65 TTAACTAAAATTAAAATTACACGAATGTCAAATCAAATCTATATCTAATGAACAC
* * **
3244679 TTTTGTCAAAATTTTTCTCCAATTTACACCTTGTTTTTTTTTTTTTTGAAAAGCAACAA-TTTGT
1 TTTTGTCAAAATTTTTCTCCAATTTACA-CTT-TGTTATTTTCCTTT-AAAAGCAA-AATTTTGT
* * * *
3244743 ATATTAATTAAAATTAAAATTATACGAATGTCAAATCAAATCTGTATTTAATGAACA
62 ATATTAACTAAAATTAAAATTACACGAATGTCAAATCAAATCTATATCTAATGAACA
3244800 GACATTTAAC
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
120 26 0.25
121 3 0.03
122 65 0.62
123 8 0.08
124 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (119 bp):
TTTTGTCAAAATTTTTCTCCAATTTACACTTTGTTATTTTCCTTTAAAAGCAAAATTTTGTATAT
TAACTAAAATTAAAATTACACGAATGTCAAATCAAATCTATATCTAATGAACAC
Found at i:3246768 original size:18 final size:17
Alignment explanation
Indices: 3246747--3246780 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3246737 TCAACTTTTG
*
3246747 GTGTAGCGACATATTTCT
1 GTGTAGCAACAT-TTTCT
3246765 GTGTAGCAACATTTTC
1 GTGTAGCAACATTTTC
3246781 ATCCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (17 bp):
GTGTAGCAACATTTTCT
Found at i:3250050 original size:50 final size:50
Alignment explanation
Indices: 3249970--3250070 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
3249960 TCAAGTTTTC
* * *
3249970 CCCAGATTCTCTTATGCTTTATATCCGAATTTATTTCTATATTTAGCTGT
1 CCCAGATTCTCTTATGCCTTACATCAGAATTTATTTCTATATTTAGCTGT
* * * *
3250020 CCCAGATTCTCTTATGCCTTACGTCAGAATTTCTTTTTATATTTTGCTGT
1 CCCAGATTCTCTTATGCCTTACATCAGAATTTATTTCTATATTTAGCTGT
3250070 C
1 C
3250071 GGGAAGATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.48
Consensus pattern (50 bp):
CCCAGATTCTCTTATGCCTTACATCAGAATTTATTTCTATATTTAGCTGT
Found at i:3252720 original size:25 final size:26
Alignment explanation
Indices: 3252657--3252720 Score: 62
Period size: 29 Copynumber: 2.4 Consensus size: 26
3252647 TTTCAAACAT
*
3252657 AAAAATTTA-CATTCAAAATTTAAGA
1 AAAAAATTATCATTCAAAATTTAAGA
3252682 AAAAATATAATATCATTCAATAA-TTAA-A
1 AAAAA-AT--TATCATTCAA-AATTTAAGA
3252710 AAAAAATTATC
1 AAAAAATTATC
3252721 TAAAAACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
25 9 0.27
26 1 0.03
27 2 0.06
28 8 0.24
29 11 0.33
30 2 0.06
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAAATTATCATTCAAAATTTAAGA
Found at i:3253708 original size:66 final size:66
Alignment explanation
Indices: 3253602--3253800 Score: 326
Period size: 66 Copynumber: 3.0 Consensus size: 66
3253592 TGAACAGGAA
* *
3253602 GAACCGCAGCTGGTGGTCTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
1 GAACCTCAGCTGGTGGTTTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
3253667 T
66 T
**
3253668 GAACCTTGGCTGGTGGTTTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
1 GAACCTCAGCTGGTGGTTTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
3253733 T
66 T
* * * *
3253734 GAACCTCAGTTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGGGGAGACTCTTGGGGAGAA
1 GAACCTCAGCTGGTGGTTTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
3253799 T
66 T
3253800 G
1 G
3253801 GCTCATCTTC
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 123 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (66 bp):
GAACCTCAGCTGGTGGTTTTCCTGACTCTGGATAAGCATCCTTTGGAGGAGACTCTTGGGGAGAA
T
Found at i:3254771 original size:27 final size:28
Alignment explanation
Indices: 3254739--3254791 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
3254729 TTCAAAAAAA
*
3254739 ATTTAATAAGTTATTAT-TTTTTATTAT
1 ATTTAATAAATTATTATATTTTTATTAT
*
3254766 ATTTAATAAATTTTTATATTTTTATT
1 ATTTAATAAATTATTATATTTTTATT
3254792 TTAAGTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
ATTTAATAAATTATTATATTTTTATTAT
Found at i:3255369 original size:12 final size:12
Alignment explanation
Indices: 3255352--3255378 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3255342 TACTGTAATC
3255352 ACATCAAGAAAA
1 ACATCAAGAAAA
3255364 ACATCAAGAAAA
1 ACATCAAGAAAA
3255376 ACA
1 ACA
3255379 ATAATCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (12 bp):
ACATCAAGAAAA
Found at i:3259634 original size:17 final size:17
Alignment explanation
Indices: 3259605--3259660 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
3259595 AATTAATTAT
3259605 ATTAAAA-ATATATAAA
1 ATTAAAATATATATAAA
3259621 ATTAAAATATATATATAA
1 ATTAAAATATATATA-AA
*
3259639 ATAAAAATA-ATTAATAAA
1 ATTAAAATATA-T-ATAAA
3259657 ATTA
1 ATTA
3259661 TTTGTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.21
17 8 0.24
18 16 0.47
19 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAATATATATAAA
Found at i:3260141 original size:9 final size:10
Alignment explanation
Indices: 3260128--3260165 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
3260118 TATAATTAAT
3260128 TATATTAAAAA
1 TATA-TAAAAA
3260139 TATATAAAAA
1 TATATAAAAA
3260149 T-TA-AAAAA
1 TATATAAAAA
3260157 TATATAAAA
1 TATATAAAA
3260166 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 11 0.44
11 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:3260153 original size:17 final size:17
Alignment explanation
Indices: 3260131--3260175 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
3260121 AATTAATTAT
3260131 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
3260148 ATTAAAAAATATATAAAA
1 ATT-AAAAATATATAAAA
* *
3260166 GTAAAAAATA
1 ATTAAAAATA
3260176 ATTGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:3260157 original size:18 final size:17
Alignment explanation
Indices: 3260134--3260175 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
3260124 TAATTATATT
*
3260134 AAAAATATATAAAAATTA
1 AAAAATATAT-AAAAGTA
3260152 AAAAATATATAAAAGTA
1 AAAAATATATAAAAGTA
3260169 AAAAATA
1 AAAAATA
3260176 ATTGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAAGTA
Found at i:3260614 original size:45 final size:44
Alignment explanation
Indices: 3260543--3260633 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
3260533 ATTTTCATAA
*
3260543 AGTCATTAGCCTCATTTGCAGTTTGCAATAAGCATTCAACAATT
1 AGTCATAAGCCTCATTTGCAGTTTGCAATAAGCATTCAACAATT
* * *
3260587 AGNTCATAAGCCTCGTTTGCGGTTTGCAATAAGCATTCAGCAATT
1 AG-TCATAAGCCTCATTTGCAGTTTGCAATAAGCATTCAACAATT
3260632 AG
1 AG
3260634 GTACTATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
AGTCATAAGCCTCATTTGCAGTTTGCAATAAGCATTCAACAATT
Found at i:3264368 original size:3 final size:3
Alignment explanation
Indices: 3264362--3264397 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3264352 AGTGCGTGGG
*
3264362 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGG GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
3264398 ACATACAGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3264674 original size:78 final size:78
Alignment explanation
Indices: 3264580--3264737 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
3264570 GCGCCTGCTT
3264580 CTTGGGAAAAATACCTTGTGCAGTACTTGGCACAGGTAAATTGGTTTTTGTAGGAGGCGGCAGAG
1 CTTGGGAAAAATACCTTGTGCAGTACTTGGCACAGGTAAATTGGTTTTTGTAGGAGGCGGCAGAG
3264645 CTGAAGGAAGGTC
66 CTGAAGGAAGGTC
3264658 CTTGGGAAAAATACCTTGTGCAGTACTTGGCACAGGTAAATTGGTTTTTGTAGGAGGCGGCAGAG
1 CTTGGGAAAAATACCTTGTGCAGTACTTGGCACAGGTAAATTGGTTTTTGTAGGAGGCGGCAGAG
3264723 CTGAAGGAAGGTC
66 CTGAAGGAAGGTC
3264736 CT
1 CT
3264738 GCTGAGAATA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.26
Consensus pattern (78 bp):
CTTGGGAAAAATACCTTGTGCAGTACTTGGCACAGGTAAATTGGTTTTTGTAGGAGGCGGCAGAG
CTGAAGGAAGGTC
Found at i:3278838 original size:17 final size:16
Alignment explanation
Indices: 3278816--3278867 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
3278806 ATATATATAA
3278816 ATTACTATAAATTTTTT
1 ATTACTAT-AATTTTTT
*
3278833 ATTACTATTATTTTTT
1 ATTACTATAATTTTTT
* *
3278849 ATT-TTATAATGTTTT
1 ATTACTATAATTTTTT
3278864 ATTA
1 ATTA
3278868 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.40
16 10 0.33
17 8 0.27
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
ATTACTATAATTTTTT
Found at i:3278847 original size:16 final size:17
Alignment explanation
Indices: 3278816--3278851 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3278806 ATATATATAA
3278816 ATTACTATAAATTTTTT
1 ATTACTATAAATTTTTT
*
3278833 ATTACTAT-TATTTTTT
1 ATTACTATAAATTTTTT
3278849 ATT
1 ATT
3278852 TTATAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTACTATAAATTTTTT
Found at i:3285041 original size:54 final size:54
Alignment explanation
Indices: 3284983--3285177 Score: 229
Period size: 54 Copynumber: 3.6 Consensus size: 54
3284973 CAGTGCTACT
* * *
3284983 AGCATTAGAGCCT-GCTGAAACACT-ACTAGCATGAGAATTCGCTGCAACACAAGA
1 AGCATTAGA-ACTAGCTGCAACACTAAC-AGCATTAGAATTCGCTGCAACACAAGA
3285037 AGCATTAGAACTCA-CTGCAACACTAACAGCATTAGAACTT-GCTGCAACACAAGA
1 AGCATTAGAACT-AGCTGCAACACTAACAGCATTAGAA-TTCGCTGCAACACAAGA
* * *
3285091 AGTATTAGAACTAGCTGCAACACTAACAGCATTAGAACTCGCTGCAACAC-TGA
1 AGCATTAGAACTAGCTGCAACACTAACAGCATTAGAATTCGCTGCAACACAAGA
* * *
3285144 CAGCATTAGAACTTGCTGCAATACTACCAGCATT
1 -AGCATTAGAACTAGCTGCAACACTAACAGCATT
3285178 CACATTCAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
53 6 0.05
54 114 0.92
55 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (54 bp):
AGCATTAGAACTAGCTGCAACACTAACAGCATTAGAATTCGCTGCAACACAAGA
Found at i:3285068 original size:81 final size:81
Alignment explanation
Indices: 3284983--3285176 Score: 237
Period size: 81 Copynumber: 2.4 Consensus size: 81
3284973 CAGTGCTACT
* * * * * *
3284983 AGCATTAGAGCCTGCTGAAACACTACTAGCATGAGAATTCGCTGCAACAC-AAGAAGCATTAGAA
1 AGCATTAGAACTTGCTGCAACACTACAAGCATGAGAACTAGCTGCAACACTAA-AAGCATTAGAA
3285047 CTCACTGCAACACTAAC
65 CTCACTGCAACACTAAC
* * * * *
3285064 AGCATTAGAACTTGCTGCAACACAAGAAGTATTAGAACTAGCTGCAACACTAACAGCATTAGAAC
1 AGCATTAGAACTTGCTGCAACACTACAAGCATGAGAACTAGCTGCAACACTAAAAGCATTAGAAC
* *
3285129 TCGCTGCAACACTGAC
66 TCACTGCAACACTAAC
* *
3285145 AGCATTAGAACTTGCTGCAATACTACCAGCAT
1 AGCATTAGAACTTGCTGCAACACTACAAGCAT
3285177 TCACATTCAA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 92 0.98
82 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (81 bp):
AGCATTAGAACTTGCTGCAACACTACAAGCATGAGAACTAGCTGCAACACTAAAAGCATTAGAAC
TCACTGCAACACTAAC
Found at i:3285174 original size:27 final size:27
Alignment explanation
Indices: 3284978--3285177 Score: 188
Period size: 27 Copynumber: 7.4 Consensus size: 27
3284968 TTCCACAGTG
* * * *
3284978 CTACTAGCATTAGAGCCTGCTGAAACA
1 CTACCAGCATTAGAACTTGCTGCAACA
* *
3285005 CTACTAGCATGAGAA-TTCGCTGCAACA
1 CTACCAGCATTAGAACTT-GCTGCAACA
* ** **
3285032 CAAGAAGCATTAGAACTCACTGCAACA
1 CTACCAGCATTAGAACTTGCTGCAACA
*
3285059 CTAACAGCATTAGAACTTGCTGCAACA
1 CTACCAGCATTAGAACTTGCTGCAACA
* ** * *
3285086 CAAGAAGTATTAGAACTAGCTGCAACA
1 CTACCAGCATTAGAACTTGCTGCAACA
* *
3285113 CTAACAGCATTAGAACTCGCTGCAACA
1 CTACCAGCATTAGAACTTGCTGCAACA
*
3285140 CTGA-CAGCATTAGAACTTGCTGCAATA
1 CT-ACCAGCATTAGAACTTGCTGCAACA
3285167 CTACCAGCATT
1 CTACCAGCATT
3285178 CACATTCAAA
Statistics
Matches: 142, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.01
27 138 0.97
28 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (27 bp):
CTACCAGCATTAGAACTTGCTGCAACA
Found at i:3285307 original size:27 final size:27
Alignment explanation
Indices: 3285277--3285334 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3285267 AACTCACTCC
*
3285277 AACAACACTGATGTTTGAACTAGCTAA
1 AACAACACAGATGTTTGAACTAGCTAA
* * * *
3285304 AACACCGCAGGTGTTTGAACTCGCTAA
1 AACAACACAGATGTTTGAACTAGCTAA
3285331 AACA
1 AACA
3285335 CTGCCAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (27 bp):
AACAACACAGATGTTTGAACTAGCTAA
Found at i:3285335 original size:27 final size:27
Alignment explanation
Indices: 3285288--3285355 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
3285278 ACAACACTGA
*
3285288 TGTTTGAACTAGCTAAAACACCG-CAGG
1 TGTTTGAACTCGCTAAAACACCGCCA-G
*
3285315 TGTTTGAACTCGCTAAAACACTGCCAG
1 TGTTTGAACTCGCTAAAACACCGCCAG
*
3285342 TGTTTGAGCTCGCT
1 TGTTTGAACTCGCT
3285356 GTGACAGTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (27 bp):
TGTTTGAACTCGCTAAAACACCGCCAG
Found at i:3285673 original size:14 final size:14
Alignment explanation
Indices: 3285654--3285681 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3285644 AAAAAAGAAT
3285654 AATAAAGATAGACA
1 AATAAAGATAGACA
3285668 AATAAAGATAGACA
1 AATAAAGATAGACA
3285682 CCTCTTCGTT
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:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAAAGATAGACA
Found at i:3285987 original size:21 final size:21
Alignment explanation
Indices: 3285962--3286002 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3285952 AGCTAAAGAG
*
3285962 AGGTT-CACAAAATAATTAAAT
1 AGGTTCCAC-AAATAAATAAAT
3285983 AGGTTCCACAAATAAATAAA
1 AGGTTCCACAAATAAATAAA
3286003 CTAGCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (21 bp):
AGGTTCCACAAATAAATAAAT
Found at i:3288847 original size:20 final size:21
Alignment explanation
Indices: 3288822--3288861 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3288812 CTAAAATATT
3288822 AATATT-TTATATAT-AATTTA
1 AATATTATTA-ATATCAATTTA
3288842 AATATTATTAATATCAATTT
1 AATATTATTAATATCAATTT
3288862 GATTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATTATTAATATCAATTTA
Found at i:3288886 original size:17 final size:17
Alignment explanation
Indices: 3288866--3288899 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3288856 CAATTTGATT
3288866 AAAATATTAATATTTTA
1 AAAATATTAATATTTTA
3288883 AAAATATTAATATTTTA
1 AAAATATTAATATTTTA
3288900 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATATTAATATTTTA
Found at i:3288894 original size:23 final size:23
Alignment explanation
Indices: 3288868--3288918 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3288858 ATTTGATTAA
3288868 AATATTAATATTT-TAAAAATATT
1 AATATT-ATATTTATAAAAATATT
* * *
3288891 AATATTTTATTTATTAAATTATT
1 AATATTATATTTATAAAAATATT
3288914 AATAT
1 AATAT
3288919 ATTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTATATTTATAAAAATATT
Found at i:3288894 original size:40 final size:41
Alignment explanation
Indices: 3288838--3288925 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 41
3288828 TTATATATAA
*
3288838 TTTAAATATTATTAATA-TCAATTTGATTAAAATATTAATAT
1 TTTAAATAATATTAATATTCAATTT-ATTAAAATATTAATAT
** *
3288879 TTTAAA-AATATTAATATTTTATTTATTAAATTATTAATAT
1 TTTAAATAATATTAATATTCAATTTATTAAAATATTAATAT
*
3288919 ATTAAAT
1 TTTAAAT
3288926 TTTTAATGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 29 0.73
41 11 0.28
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TTTAAATAATATTAATATTCAATTTATTAAAATATTAATAT
Found at i:3288931 original size:16 final size:16
Alignment explanation
Indices: 3288864--3288932 Score: 61
Period size: 16 Copynumber: 4.3 Consensus size: 16
3288854 ATCAATTTGA
*
3288864 TTAAAATATTAATATTT
1 TTAATATATTAA-ATTT
* *
3288881 TAAAAATATT-AATATT
1 TTAATATATTAAAT-TT
* *
3288897 TT-ATTTATTAAATTA
1 TTAATATATTAAATTT
3288912 TTAATATATTAAATTT
1 TTAATATATTAAATTT
3288928 TTAAT
1 TTAAT
3288933 GAGTATAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
15 10 0.24
16 23 0.55
17 9 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATATATTAAATTT
Found at i:3292148 original size:125 final size:125
Alignment explanation
Indices: 3292019--3292275 Score: 315
Period size: 125 Copynumber: 2.1 Consensus size: 125
3292009 TTGAGTATTT
* *
3292019 TATATTTGGGTTTTG-GATAAACTCGAGTAAAAATTTTACTATCCATATCGGATTCAGATAAGGT
1 TATATTTGGG-TTTGAGACAAACTCGAGTAAAAATTTTACTATCAATATCGGATTCAGATAAGGT
* * *
3292083 A-ATTTGAATA-TTCAATA-TCTGAACCTATTTATATATAAATATGTATAAAATATATTGTATG
65 ACATTTG-ATACCT-AATACT-TGAACCTATTTATATATAAATATGTATAAAATATATTATATA
** * * * * * *
3292144 TATATTTGGGTTTGAGACAAGGTCGGGTAAAAATTTTACTATTAATCTCGGGTTCATATAGGGTA
1 TATATTTGGGTTTGAGACAAACTCGAGTAAAAATTTTACTATCAATATCGGATTCAGATAAGGTA
* *
3292209 CCTTTGATACCTAATACTTGAACCTGTTTATATATAAATATGTATAAAATATATTATATA
66 CATTTGATACCTAATACTTGAACCTATTTATATATAAATATGTATAAAATATATTATATA
3292269 TATATTT
1 TATATTT
3292276 AAGTTTGGGA
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
124 4 0.04
125 103 0.91
126 6 0.05
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (125 bp):
TATATTTGGGTTTGAGACAAACTCGAGTAAAAATTTTACTATCAATATCGGATTCAGATAAGGTA
CATTTGATACCTAATACTTGAACCTATTTATATATAAATATGTATAAAATATATTATATA
Found at i:3292746 original size:19 final size:20
Alignment explanation
Indices: 3292718--3292757 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
3292708 AATAAAAAAA
*
3292718 TAAATTATTTAAAAAT-TTT
1 TAAATAATTTAAAAATATTT
3292737 TAAATAATTTAAAAATATTT
1 TAAATAATTTAAAAATATTT
3292757 T
1 T
3292758 CAAGCATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATAATTTAAAAATATTT
Found at i:3301708 original size:2 final size:2
Alignment explanation
Indices: 3301701--3301725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3301691 TTCTCCCCCA
3301701 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3301726 ACACTCTTCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3311608 original size:22 final size:22
Alignment explanation
Indices: 3311565--3311608 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3311555 TTTTATATAT
* *
3311565 TTATTTAATAATTAATTTTTTA
1 TTATTTAATAATAAATTATTTA
3311587 TTATTTAAT-ATAAATATATTTA
1 TTATTTAATAATAAAT-TATTTA
3311609 ATAAACACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTTAATAATAAATTATTTA
Done.