Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 13 of 230
Found at i:3535094 original size:28 final size:29
Alignment explanation
Indices: 3535054--3535109 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3535044 AAGTTTTTCC
3535054 TTTTTACTAAAAAA-CTAAAATTAATTCT
1 TTTTTACTAAAAAAGCTAAAATTAATTCT
* *
3535082 TTTTTACTTAAAAAGCTAAAGTTAATTC
1 TTTTTACTAAAAAAGCTAAAATTAATTC
3535110 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTTTACTAAAAAAGCTAAAATTAATTCT
Found at i:3535100 original size:29 final size:28
Alignment explanation
Indices: 3535054--3535109 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
3535044 AAGTTTTTCC
3535054 TTTTTACTAAAAAACTAAAATTAATTCT
1 TTTTTACTAAAAAACTAAAATTAATTCT
* *
3535082 TTTTTACTTAAAAAGCTAAAGTTAATTC
1 TTTTTAC-TAAAAAACTAAAATTAATTC
3535110 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTTTACTAAAAAACTAAAATTAATTCT
Found at i:3535131 original size:18 final size:18
Alignment explanation
Indices: 3535089--3535135 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
3535079 TCTTTTTTAC
* **
3535089 TTAAAAAGCTAAAGTTAA
1 TTAAAAAGATAAAGGAAA
3535107 TTCAAAAAGATAAAGGAAA
1 TT-AAAAAGATAAAGGAAA
3535126 TTAAAAAGAT
1 TTAAAAAGAT
3535136 CGAATGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (18 bp):
TTAAAAAGATAAAGGAAA
Found at i:3536479 original size:61 final size:61
Alignment explanation
Indices: 3536362--3536512 Score: 160
Period size: 61 Copynumber: 2.5 Consensus size: 61
3536352 AATGGTTGAC
* * * * * *
3536362 TAATAAAATTAGTCTTCAATGTTTATAAAATTTGTCATTTTAATTTTATTTTTAAAAAATT
1 TAATAAATTTAGTCTTCAATATTTATAAAATTTGTCATTTTAATTCTAATTCTAAAAAACT
* * *
3536423 TAATAAATTTAGTCTTCATTATTTATAAAAGTTT-TCATTTTAGTTCTAATTCTAAAAGACT
1 TAATAAATTTAGTCTTCAATATTTATAAAA-TTTGTCATTTTAATTCTAATTCTAAAAAACT
* * * * *
3536484 CAATAAATTTGGCCCTCAACATTTATAAA
1 TAATAAATTTAGTCTTCAATATTTATAAA
3536513 TTCTATCAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
61 71 0.96
62 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (61 bp):
TAATAAATTTAGTCTTCAATATTTATAAAATTTGTCATTTTAATTCTAATTCTAAAAAACT
Found at i:3545244 original size:9 final size:9
Alignment explanation
Indices: 3545230--3545255 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3545220 TTAAGTGATG
3545230 AATTTAATC
1 AATTTAATC
3545239 AATTTAATC
1 AATTTAATC
3545248 AATTTAAT
1 AATTTAAT
3545256 TAACAGCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTTAATC
Found at i:3546720 original size:18 final size:18
Alignment explanation
Indices: 3546699--3546736 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3546689 CTTCTACCCT
3546699 TTCCCCTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
*
3546717 TTCCCTTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
3546735 TT
1 TT
3546737 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCCCCTTTCCCTTCCCC
Found at i:3546830 original size:25 final size:25
Alignment explanation
Indices: 3546796--3546845 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3546786 CAGGTAAGGC
*
3546796 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
3546821 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
3546846 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:3550214 original size:15 final size:15
Alignment explanation
Indices: 3550175--3550227 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
3550165 GAACATTTGG
3550175 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
3550192 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
3550209 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
3550225 AAT
1 AAT
3550228 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:3550301 original size:22 final size:20
Alignment explanation
Indices: 3550258--3550296 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3550248 TAATTTAAAA
3550258 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
3550278 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
3550297 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:3550420 original size:20 final size:20
Alignment explanation
Indices: 3550395--3550434 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3550385 AATATTTTCC
*
3550395 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3550415 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3550435 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3550440 original size:34 final size:35
Alignment explanation
Indices: 3550383--3550449 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3550373 CAAACACTAG
*
3550383 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3550418 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3550450 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3550441 original size:14 final size:14
Alignment explanation
Indices: 3550418--3550457 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3550408 ACAGAAAAGT
*
3550418 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3550432 AAATCATTTTACGG
1 AAAACATTTTACAG
3550446 AAAACATTTTAC
1 AAAACATTTTAC
3550458 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3551686 original size:86 final size:87
Alignment explanation
Indices: 3551587--3551800 Score: 229
Period size: 88 Copynumber: 2.4 Consensus size: 87
3551577 TTAAGGTTTT
* * * *
3551587 AAAAAGCAATCAAAATTTTCTAAAAAAACAATTAAGCTT-TTATTTTTTTTTCACTCAATTGGGT
1 AAAAAGCTATCAAAATTTTCAAAAAAAACAATTAAGCTTGCT-TTTTTTTTTCACTCAATCGGGT
**
3551651 ACTTGAACTTTCAAAATGCAT-A
65 ACTTGAACTGCCAAAATGCATAA
* * ***
3551673 AAAAAGCTTTCAAACTTAAAAAAAAAAACAATTAAGCCCTTGCTTTTTTTTTTCACTCAATCGGG
1 AAAAAGCTATCAAAATTTTCAAAAAAAACAATTAAG--CTTGCTTTTTTTTTTCACTCAATCGGG
3551738 TACTTGAACTGCCAAAATGCATCAA
64 TACTTGAACTGCCAAAATGCAT-AA
*
3551763 AAAAAG-TCCTCAAAATTTTTCCAAAAAAAA-AATTAAGC
1 AAAAAGCT-ATCAAAA-TTTT-CAAAAAAAACAATTAAGC
3551801 CATTTTTTCA
Statistics
Matches: 104, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
86 29 0.28
88 43 0.41
89 3 0.03
90 12 0.12
91 9 0.09
92 8 0.08
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (87 bp):
AAAAAGCTATCAAAATTTTCAAAAAAAACAATTAAGCTTGCTTTTTTTTTTCACTCAATCGGGTA
CTTGAACTGCCAAAATGCATAA
Found at i:3551972 original size:28 final size:27
Alignment explanation
Indices: 3551934--3552032 Score: 92
Period size: 28 Copynumber: 3.6 Consensus size: 27
3551924 ATAAAAATCA
* *
3551934 ATAAAAGTTATAGAATTATAAAATTTT
1 ATAAAAATTATAAAATTATAAAATTTT
* *
3551961 ATTAAAAATTATAAAAATATATAAAA-ATC
1 A-TAAAAATTAT-AAAAT-TATAAAATTTT
* *
3551990 ATAAAAATATAAAAAATTGTAAAATTTT
1 ATAAAAAT-TATAAAATTATAAAATTTT
*
3552018 ATAAAAATAATAAAA
1 ATAAAAATTATAAAA
3552033 AAATTATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 12 0.21
28 30 0.53
29 8 0.14
30 7 0.12
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (27 bp):
ATAAAAATTATAAAATTATAAAATTTT
Found at i:3551977 original size:9 final size:9
Alignment explanation
Indices: 3551910--3552033 Score: 85
Period size: 9 Copynumber: 13.6 Consensus size: 9
3551900 TGACATGAGG
*
3551910 AAAAAATAT
1 AAAAATTAT
3551919 AAAAA--AT
1 AAAAATTAT
*
3551926 AAAAATCAAT
1 AAAAAT-TAT
*
3551936 AAAAGTTAT
1 AAAAATTAT
*
3551945 -AGAATTAT
1 AAAAATTAT
*
3551953 AAAATTTTATT
1 AAAA-ATTA-T
3551964 AAAAATTAT
1 AAAAATTAT
3551973 AAAAATATAT
1 AAAAAT-TAT
*
3551983 AAAAATCAT
1 AAAAATTAT
3551992 AAAAA-TAT
1 AAAAATTAT
*
3552000 AAAAAATTGT
1 -AAAAATTAT
*
3552010 AAAATTTTAT
1 AAAA-ATTAT
*
3552020 AAAAATAAT
1 AAAAATTAT
3552029 AAAAA
1 AAAAA
3552034 AATTATATAA
Statistics
Matches: 91, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
7 7 0.08
8 8 0.09
9 40 0.44
10 31 0.34
11 5 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3551987 original size:19 final size:19
Alignment explanation
Indices: 3551947--3552033 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
3551937 AAAGTTATAG
* *
3551947 AATTATAAAATTTTATTAAA
1 AATTATAAAAATATA-TAAA
3551967 AATTATAAAAATATATAAA
1 AATTATAAAAATATATAAA
*
3551986 AATCATAAAAATATA-AAA
1 AATTATAAAAATATATAAA
* * *
3552004 AATTGTAAAATTTTATAAA
1 AATTATAAAAATATATAAA
*
3552023 AATAATAAAAA
1 AATTATAAAAA
3552034 AATTATATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
18 14 0.25
19 29 0.52
20 13 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AATTATAAAAATATATAAA
Found at i:3552004 original size:8 final size:8
Alignment explanation
Indices: 3551911--3552004 Score: 55
Period size: 8 Copynumber: 10.6 Consensus size: 8
3551901 GACATGAGGA
3551911 AAAAATAT
1 AAAAATAT
3551919 AAAAA-AT
1 AAAAATAT
3551926 AAAAATCAAT
1 AAAAAT--AT
*
3551936 AAAAGTTAT
1 AAAA-ATAT
* *
3551945 AGAATTAT
1 AAAAATAT
*
3551953 AAAATTTTATT
1 AAAA--ATA-T
3551964 AAAAATTAT
1 AAAAA-TAT
3551973 AAAAATATAT
1 -AAAA-ATAT
3551983 AAAAATCAT
1 AAAAAT-AT
3551992 AAAAATAT
1 AAAAATAT
3552000 AAAAA
1 AAAAA
3552005 ATTGTAAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
7 7 0.10
8 21 0.30
9 18 0.25
10 18 0.25
11 7 0.10
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAAATAT
Found at i:3552034 original size:57 final size:59
Alignment explanation
Indices: 3551924--3552043 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 59
3551914 AATATAAAAA
* * * *
3551924 ATAAAAATCAATAAAAGTTATAGAATTATAAAATTTTATTAAAAATTAT-AAAAA-TAT
1 ATAAAAATCAATAAAAATTAAAAAATTATAAAATTTTATTAAAAATAATAAAAAATTAT
*
3551981 ATAAAAATC-ATAAAAATATAAAAAATTGTAAAATTTTA-TAAAAATAATAAAAAAATTAT
1 ATAAAAATCAATAAAAAT-TAAAAAATTATAAAATTTTATTAAAAATAAT-AAAAAATTAT
3552040 ATAA
1 ATAA
3552044 TGCATCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
56 16 0.30
57 26 0.48
58 5 0.09
59 7 0.13
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.33
Consensus pattern (59 bp):
ATAAAAATCAATAAAAATTAAAAAATTATAAAATTTTATTAAAAATAATAAAAAATTAT
Found at i:3552270 original size:21 final size:20
Alignment explanation
Indices: 3552215--3552286 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 20
3552205 TTGGAACGAT
3552215 AGTTTTTATAATTTTTTTTTAC
1 AGTTTTTATAA--TTTTTTTAC
**
3552237 AAATTTTAT-ATTTTTTTAC
1 AGTTTTTATAATTTTTTTAC
*
3552256 AGTTCTTTATAATTTTCTTAC
1 AGTT-TTTATAATTTTTTTAC
*
3552277 -GATTTTATAA
1 AGTTTTTATAA
3552287 AATTTTATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 18 0.43
20 7 0.17
21 10 0.24
22 7 0.17
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (20 bp):
AGTTTTTATAATTTTTTTAC
Found at i:3552293 original size:29 final size:30
Alignment explanation
Indices: 3552261--3552332 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
3552251 TTTACAGTTC
3552261 TTTATAATTTTCTTACGAT-TTTATA-AAAT
1 TTTATAATTTT-TTACGATATTTATATAAAT
* * *
3552290 TTTAT-ATTTTTT-CTATATTTCTATATAT
1 TTTATAATTTTTTACGATATTTATATAAAT
3552318 TTTATAATTTTTTAC
1 TTTATAATTTTTTAC
3552333 TTTTTTTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.08
27 7 0.19
28 13 0.36
29 12 0.33
30 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTATAATTTTTTACGATATTTATATAAAT
Found at i:3552301 original size:19 final size:20
Alignment explanation
Indices: 3552278--3552324 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
3552268 TTTTCTTACG
3552278 ATTTTATAAAATTT-TATAT
1 ATTTTATAAAATTTCTATAT
* * *
3552297 TTTTTCT-ATATTTCTATAT
1 ATTTTATAAAATTTCTATAT
3552316 ATTTTATAA
1 ATTTTATAA
3552325 TTTTTTACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 3
0.72 0.17 0.10
Matches are distributed among these distances:
18 5 0.24
19 15 0.71
20 1 0.05
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATAAAATTTCTATAT
Found at i:3552327 original size:8 final size:9
Alignment explanation
Indices: 3552278--3552328 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
3552268 TTTTCTTACG
*
3552278 ATTTTATAAA
1 ATTTTAT-AT
3552288 ATTTTATAT
1 ATTTTATAT
* *
3552297 TTTTTCTAT
1 ATTTTATAT
3552306 ATTTCTATAT
1 ATTT-TATAT
3552316 ATTTTATA-
1 ATTTTATAT
3552324 ATTTT
1 ATTTT
3552329 TTACTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 5 0.14
9 15 0.43
10 15 0.43
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTATAT
Found at i:3552381 original size:19 final size:20
Alignment explanation
Indices: 3552357--3552410 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
3552347 AATTCTAATT
3552357 TTTAAT-ATTTTTATTAAAA
1 TTTAATAATTTTTATTAAAA
**
3552376 TTTAATAATTTTTA-TAACT
1 TTTAATAATTTTTATTAAAA
3552395 TTTAATAATTTTTATT
1 TTTAATAATTTTTATT
3552411 TTTTATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 23 0.74
20 8 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATAATTTTTATTAAAA
Found at i:3552389 original size:10 final size:10
Alignment explanation
Indices: 3552352--3552423 Score: 66
Period size: 9 Copynumber: 7.8 Consensus size: 10
3552342 AAAAAAATTC
3552352 TAATTTTTAA
1 TAATTTTTAA
*
3552362 T-ATTTTTAT
1 TAATTTTTAA
**
3552371 TAAAATTTAA
1 TAATTTTTAA
3552381 TAATTTTT-A
1 TAATTTTTAA
*
3552390 TAACTTTTAA
1 TAATTTTTAA
3552400 TAATTTTT-A
1 TAATTTTTAA
3552409 T--TTTTT-A
1 TAATTTTTAA
3552416 TAATTTTT
1 TAATTTTT
3552424 TGTCACATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
7 7 0.14
9 23 0.46
10 20 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:3570961 original size:21 final size:22
Alignment explanation
Indices: 3570919--3570967 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
3570909 AGCGGAAATT
3570919 AAAATATAAATTTTTTGAATGTA
1 AAAATATAAATTTTTT-AATGTA
3570942 AAAATAT-AATTTTATT-ATGTA
1 AAAATATAAATTTT-TTAATGTA
*
3570963 TAAAT
1 AAAAT
3570968 TTATGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 6 0.25
23 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
AAAATATAAATTTTTTAATGTA
Found at i:3584268 original size:15 final size:16
Alignment explanation
Indices: 3584242--3584276 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3584232 GGATTAATTG
3584242 TATATATTAATTAAAT
1 TATATATTAATTAAAT
*
3584258 TATAT-TTAATTATAT
1 TATATATTAATTAAAT
3584273 TATA
1 TATA
3584277 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTAATTAAAT
Found at i:3597257 original size:18 final size:18
Alignment explanation
Indices: 3597234--3597268 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3597224 ATAAGTTGAG
*
3597234 GGCGTCACCCACTGAACT
1 GGCGTCAACCACTGAACT
3597252 GGCGTCAACCACTGAAC
1 GGCGTCAACCACTGAAC
3597269 AAATACCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.14
Consensus pattern (18 bp):
GGCGTCAACCACTGAACT
Found at i:3601476 original size:37 final size:37
Alignment explanation
Indices: 3601435--3601514 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
3601425 TCCTCATATG
*
3601435 TGTTGTAGGACTTATGTCTCCTGACTTTCATACTCAA
1 TGTTGTAGGACTTATGCCTCCTGACTTTCATACTCAA
*
3601472 TGTTGTAGGACTTATGCCTCGTGACTTTCATACTCAA
1 TGTTGTAGGACTTATGCCTCCTGACTTTCATACTCAA
3601509 TGTTGT
1 TGTTGT
3601515 GAGGGTATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (37 bp):
TGTTGTAGGACTTATGCCTCCTGACTTTCATACTCAA
Found at i:3608760 original size:20 final size:21
Alignment explanation
Indices: 3608735--3608773 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3608725 AAATTAGATC
3608735 CATTCAAGGCCGG-GCTTGAA
1 CATTCAAGGCCGGAGCTTGAA
3608755 CATTCAAGGCCGGAGCTTG
1 CATTCAAGGCCGGAGCTTG
3608774 GTTTAGTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (21 bp):
CATTCAAGGCCGGAGCTTGAA
Found at i:3609864 original size:26 final size:26
Alignment explanation
Indices: 3609834--3609883 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3609824 ATTTTACATG
*
3609834 TTATAGAAGTGTTATAATATATTTAT
1 TTATAAAAGTGTTATAATATATTTAT
3609860 TTATAAAAGTGTTATAATATATTT
1 TTATAAAAGTGTTATAATATATTT
3609884 TACATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (26 bp):
TTATAAAAGTGTTATAATATATTTAT
Found at i:3610727 original size:15 final size:15
Alignment explanation
Indices: 3610701--3610734 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
3610691 CTAATATATG
3610701 AAAAAGGAAAAAGAAA
1 AAAAAGGAAAAA-AAA
3610717 AAAAAGGAAAAAAAA
1 AAAAAGGAAAAAAAA
3610732 AAA
1 AAA
3610735 TTTGGTGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAAAAAA
Found at i:3610859 original size:117 final size:114
Alignment explanation
Indices: 3610716--3611295 Score: 707
Period size: 119 Copynumber: 5.1 Consensus size: 114
3610706 GGAAAAAGAA
* * *
3610716 AAAAAAGGAAAAAAAAAAATTT-GGTGCTGGCCGGTCAATGGCCGGCACCCAACAGTAAAATTTT
1 AAAAAA-GTAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAA-TTT
3610780 TTTTTGAATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
64 TTTTTGAATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
**
3610831 AAAAAAGTAAAAAAAAATTGTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAA-AA
1 AAAAAAGTAAAAAAAAA-T-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAATTT
*** * *
3610895 AAATTGAA-------ATTTTTTTTCGTGTCAGAATTAGATATAAATATACG
64 TTTTTGAATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
* *
3610939 AAAAAAGTATTAAAAAAAAATTTT-GGTGCTGGCCTGTCAATGGTCGGCACCCAACCGTAAAAAT
1 AAAAAAG---TAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGT-AAAAT
**
3611003 TTTTTTAAAATTTTTTTCTTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
62 TTTTTTTGAA-TTTTTTC-TTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
* *
3611058 AAAAAAGTAAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCCAACAGTAAATTTT
1 AAAAAAGT--AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAA--AT
3611123 TTTTTTTGAATTTTTTCTTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
62 TTTTTTTGAATTTTTTC-TTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
** * ****
3611177 AAAAAAGTAAAAAAAAAAATTGGGTGCTAGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAAAT
1 AAAAAAGTAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTT
* * *
3611242 TTTG-ATTTTTT-TCTTTTTTTCGTGTTAGAATCAAATATAAATATACG
66 TTTGAATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
3611289 AAAAAAG
1 AAAAAAG
3611296 ATTTGTTTCG
Statistics
Matches: 404, Mismatches: 39, Indels: 47
0.82 0.08 0.10
Matches are distributed among these distances:
108 73 0.18
109 7 0.02
110 4 0.01
111 10 0.02
112 40 0.10
114 17 0.04
115 16 0.04
116 4 0.01
117 84 0.21
118 16 0.04
119 124 0.31
120 9 0.02
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (114 bp):
AAAAAAGTAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAAATTTTT
TTTGAATTTTTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
Found at i:3611436 original size:117 final size:115
Alignment explanation
Indices: 3611301--3611882 Score: 781
Period size: 117 Copynumber: 5.1 Consensus size: 115
3611291 AAAAGATTTG
* *
3611301 TTTCGTATATTTATATCTGATTCTGACATGAAAAAAAAAAGAAAAAAAATTTTAAACAAATTTTA
1 TTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAAAG-AAAAAAATTTTAAAAAAATTTTA
3611366 CTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTT
64 CTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTT
*****
3611418 TTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAAG-AAAAAA-TTTAATTTTTTTTTACT
1 TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTTAAAAAAATTTTACT
* *
3611480 GTTGGGTGTCGGCCATTGACAGGCCATCACCC--AATTTTTTTTTACTTT
66 GTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTT
* * * *
3611528 TTTCGTATATTTATATCTGGTTCTTACAC---AAAAAAAGAAAAAAATTTAAAAAAAAAATTTAC
1 TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTT-TAAAAAAATTTTAC
* *
3611590 TGTTGGGTGCCGGCCATTGACAGGCCCGCACCCAAATTTTTTTTTTACTTT
65 TGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTT
*
3611641 TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAATTTTTAAAAAAATTTTTTA
1 TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTTAAAAAAA--TTTTA
* *
3611706 CGGTTGGGTGCCGACCATTGACAGGCCAGCA-CCAAAATTTTTTTTTTTACTTT
64 CTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA--TTTTTTTTTACTTT
* ** *
3611759 TTTCGTATATTTATACCTGATTCTGACACG-AAAAAAAAG-AAAAAATTCAAAAAAAAATTTACT
1 TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTTAAAAAAATTTTACT
* * * *
3611822 GTTGGGTGCCGGCCATTGATAGGCCAGCACCCCCAAATTTTTTTTTTCCTT
66 GTTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTTTACTTT
3611873 TTTCGTATAT
1 TTTCGTATAT
3611883 CAGTATTATA
Statistics
Matches: 410, Mismatches: 41, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
108 8 0.02
109 6 0.01
110 45 0.11
111 37 0.09
112 42 0.10
113 48 0.12
114 54 0.13
115 16 0.04
116 41 0.10
117 70 0.17
118 43 0.10
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (115 bp):
TTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTTAAAAAAATTTTACT
GTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTT
Found at i:3611613 original size:223 final size:227
Alignment explanation
Indices: 3611301--3611882 Score: 816
Period size: 223 Copynumber: 2.5 Consensus size: 227
3611291 AAAAGATTTG
* * * *
3611301 TTTCGTATATTTATATCTGATTCTGACATGAAAAAAAAAAGAAAAAAAATTTTAAACAAATTTTA
1 TTTCGTATATTTATATCTGATTCTGAC----ACAAAAAAAG-AAAAAAATTTAAAAAAAAATTTA
3611366 CTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTTTTTCGTATATTTA
61 CTGTTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTTTTTCGTATATTTA
*** * * *
3611431 TATCTGATTCTGACACG-AAAAAAAAGAAAAAA-TTT-AATTTTTTTTTACTGTTGGGTGTCGGC
126 TATCTGATTCTGACACGAAAAAAAAAGAAAAAATTTTAAAAAATTTTTTACGGTTGGGTGCCGAC
* *
3611493 CATTGACAGGCCATCACC-CAA-TTTTTTTTTACTTT
191 CATTGACAGGCCAGCACCAAAATTTTTTTTTTACTTT
* *
3611528 TTTCGTATATTTATATCTGGTTCTTACACAAAAAAAGAAAAAAATTTAAAAAAAAAATTTACTGT
1 TTTCGTATATTTATATCTGATTCTGACACAAAAAAAGAAAAAAATTT-AAAAAAAAATTTACTGT
* *
3611593 TGGGTGCCGGCCATTGACAGGCCCGCACCCAAATTTTTTTTTTACTTTTTTCGTATATTTATATC
65 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTTTTTCGTATATTTATATC
3611658 TGATTCTGACACGAAAAAAAAAGAAAAAATTTTTAAAAAAATTTTTTACGGTTGGGTGCCGACCA
130 TGATTCTGACACGAAAAAAAAAGAAAAAA-TTTT-AAAAAATTTTTTACGGTTGGGTGCCGACCA
3611723 TTGACAGGCCAGCACCAAAATTTTTTTTTTTACTTT
193 TTGACAGGCCAGCACCAAAA-TTTTTTTTTTACTTT
* *
3611759 TTTCGTATATTTATACCTGATTCTGACACGAAAAAAA-AGAAAAAATTCAAAAAAAAATTTACTG
1 TTTCGTATATTTATATCTGATTCTGACAC-AAAAAAAGA-AAAAAATTTAAAAAAAAATTTACTG
* * * *
3611823 TTGGGTGCCGGCCATTGATAGGCCAGCACCCCCAAATTTTTTTTTTCCTTTTTCGTATAT
64 TTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTTTACTTTTTTCGTATAT
3611883 CAGTATTATA
Statistics
Matches: 317, Mismatches: 26, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
222 10 0.03
223 99 0.31
224 15 0.05
226 3 0.01
227 25 0.08
228 38 0.12
229 2 0.01
231 83 0.26
232 42 0.13
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (227 bp):
TTTCGTATATTTATATCTGATTCTGACACAAAAAAAGAAAAAAATTTAAAAAAAAATTTACTGTT
GGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTACTTTTTTCGTATATTTATATCT
GATTCTGACACGAAAAAAAAAGAAAAAATTTTAAAAAATTTTTTACGGTTGGGTGCCGACCATTG
ACAGGCCAGCACCAAAATTTTTTTTTTACTTT
Found at i:3614475 original size:30 final size:28
Alignment explanation
Indices: 3614434--3614492 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
3614424 AAACTATAAT
* *
3614434 TGGTATTCAAATAAGCCCTTAATCTTTAAC
1 TGGTATCCAAATAAG-CCTTAA-CCTTAAC
3614464 TGGTATCCAAATAAGCCTTAACCTTAAC
1 TGGTATCCAAATAAGCCTTAACCTTAAC
3614492 T
1 T
3614493 TATACCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 6 0.22
30 14 0.52
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (28 bp):
TGGTATCCAAATAAGCCTTAACCTTAAC
Found at i:3618595 original size:5 final size:5
Alignment explanation
Indices: 3618581--3618610 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3618571 CTATATGAAT
*
3618581 ATAAA ATAAA GTAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
3618611 TGAAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:3619806 original size:18 final size:17
Alignment explanation
Indices: 3619785--3619819 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3619775 TTATTATTAA
*
3619785 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3619803 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3619820 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3619958 original size:157 final size:157
Alignment explanation
Indices: 3619672--3619988 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
3619662 CTAAATACTC
* *
3619672 TTAGCATAAATTTGTTTTGGTTAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
3619737 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
3619802 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
3619829 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
3619894 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
3619959 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
3619986 TTA
1 TTA
3619989 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:3620060 original size:120 final size:121
Alignment explanation
Indices: 3619920--3620217 Score: 462
Period size: 120 Copynumber: 2.5 Consensus size: 121
3619910 ATTTAATCAT
* *
3619920 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
3619985 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
3620042 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
3620105 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * * * *
3620161 ATTTGAA-ATAATTAATA-CATCATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTA-AATATATTATAATTAAAATATATAATTTAATAAAATT
3620218 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
119 8 0.05
120 152 0.92
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:3620090 original size:14 final size:15
Alignment explanation
Indices: 3620041--3620092 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3620031 GTAAAATATA
3620041 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3620056 TATTAAATATATTAT
1 AATTAAATATATTAT
3620071 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3620084 AATTTAATA
1 AATTAAATA
3620093 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3620304 original size:24 final size:25
Alignment explanation
Indices: 3620258--3620305 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
3620248 TATGAATTTG
3620258 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
3620284 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
3620306 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:3620309 original size:92 final size:92
Alignment explanation
Indices: 3620213--3620441 Score: 227
Period size: 92 Copynumber: 2.5 Consensus size: 92
3620203 TGATTTAATA
* * *
3620213 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
3620275 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
3620305 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
3620370 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * * *
3620395 ATAATTTCATAAAATTCTTAAAAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
3620442 CTAAAATCAA
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
90 2 0.02
91 26 0.22
92 81 0.69
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:3624203 original size:23 final size:23
Alignment explanation
Indices: 3624169--3624213 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3624159 AGTGTCATTT
**
3624169 ATAATTTGATAATTTATTTGAAA
1 ATAATTTGATAATCAATTTGAAA
3624192 ATAATATT-ATAATCAATTTGAA
1 ATAAT-TTGATAATCAATTTGAA
3624214 TTAAATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (23 bp):
ATAATTTGATAATCAATTTGAAA
Found at i:3628457 original size:17 final size:19
Alignment explanation
Indices: 3628430--3628466 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
3628420 AATTGGTTTG
3628430 ATTTAAAAAATATT-AAAA
1 ATTTAAAAAATATTCAAAA
3628448 ATTT-AAAAATATTCAAAA
1 ATTTAAAAAATATTCAAAA
3628466 A
1 A
3628467 AAGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTTAAAAAATATTCAAAA
Found at i:3629467 original size:31 final size:30
Alignment explanation
Indices: 3629376--3629468 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
3629366 AGTACCTAAA
* * *
3629376 TTATACATGAACTTTT-ATCTAATGTACAATG
1 TTATACATGAA-TTTTAATTTGATGT-CAATT
*
3629407 TTATACATGAATTTTAATTTTATGT-AATT
1 TTATACATGAATTTTAATTTGATGTCAATT
*
3629436 TTATACATGAAAATTTTGATTTGAT-TCAATT
1 TTATACATG--AATTTTAATTTGATGTCAATT
3629467 TT
1 TT
3629469 CATAAATCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.23
30 5 0.09
31 36 0.68
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (30 bp):
TTATACATGAATTTTAATTTGATGTCAATT
Found at i:3630029 original size:21 final size:19
Alignment explanation
Indices: 3629998--3630042 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
3629988 CTCTTTCAAT
3629998 AAAAAATATAAAAAAATAA
1 AAAAAATATAAAAAAATAA
*
3630017 AAAAAATTCATAAAAGAATTAA
1 AAAAAA-T-ATAAAA-AAATAA
3630039 AAAA
1 AAAA
3630043 GAACAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 6 0.27
22 9 0.41
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAATATAAAAAAATAA
Found at i:3632969 original size:475 final size:475
Alignment explanation
Indices: 3632079--3633032 Score: 1908
Period size: 475 Copynumber: 2.0 Consensus size: 475
3632069 GGTGTTGGGA
3632079 TAAAGAAGGCAGAGAAAAGTGTAGAAGAAAAATCTTGGAAACTTAAAATATAGCTACAATCAAAA
1 TAAAGAAGGCAGAGAAAAGTGTAGAAGAAAAATCTTGGAAACTTAAAATATAGCTACAATCAAAA
3632144 TCTTCAACTTCTATGCACACAAAAAGAGATAAATATTACATACTAAATAATTGCATAATGTACAG
66 TCTTCAACTTCTATGCACACAAAAAGAGATAAATATTACATACTAAATAATTGCATAATGTACAG
3632209 TCGGCAAGGACACAAATCACATTCCCCGTCCCCATCACTCTGGATATTTGTTTTTTCATGTAGAA
131 TCGGCAAGGACACAAATCACATTCCCCGTCCCCATCACTCTGGATATTTGTTTTTTCATGTAGAA
3632274 CAGAGATAGGGAGAAGTGAGGGAGTTACTTGGCTCATACTGAAGGCTAAAGCAACTATGTAAATC
196 CAGAGATAGGGAGAAGTGAGGGAGTTACTTGGCTCATACTGAAGGCTAAAGCAACTATGTAAATC
3632339 TTATTCCTTGACAATAGCTTTATAGCGTGAGTCAATGAGATGTCACTGAAAATTTTTAATTGGAA
261 TTATTCCTTGACAATAGCTTTATAGCGTGAGTCAATGAGATGTCACTGAAAATTTTTAATTGGAA
3632404 TCTTAATTATAACCAATCCAATTTAATAAATCTTCAACAAGCAGTTAAAAACTTAAAAGTGACTT
326 TCTTAATTATAACCAATCCAATTTAATAAATCTTCAACAAGCAGTTAAAAACTTAAAAGTGACTT
3632469 AAATACATCTAAAACTACCCAATATATGAACAGAACTACAGTGACAATGCTGCAAAGAATCATGG
391 AAATACATCTAAAACTACCCAATATATGAACAGAACTACAGTGACAATGCTGCAAAGAATCATGG
3632534 AACAGCGACATTCTCAATTG
456 AACAGCGACATTCTCAATTG
3632554 TAAAGAAGGCAGAGAAAAGTGTAGAAGAAAAATCTTGGAAACTTAAAATATAGCTACAATCAAAA
1 TAAAGAAGGCAGAGAAAAGTGTAGAAGAAAAATCTTGGAAACTTAAAATATAGCTACAATCAAAA
3632619 TCTTCAACTTCTATGCACACAAAAAGAGATAAATATTACATACTAAATAATTGCATAATGTACAG
66 TCTTCAACTTCTATGCACACAAAAAGAGATAAATATTACATACTAAATAATTGCATAATGTACAG
3632684 TCGGCAAGGACACAAATCACATTCCCCGTCCCCATCACTCTGGATATTTGTTTTTTCATGTAGAA
131 TCGGCAAGGACACAAATCACATTCCCCGTCCCCATCACTCTGGATATTTGTTTTTTCATGTAGAA
3632749 CAGAGATAGGGAGAAGTGAGGGAGTTACTTGGCTCATACTGAAGGCTAAAGCAACTATGTAAATC
196 CAGAGATAGGGAGAAGTGAGGGAGTTACTTGGCTCATACTGAAGGCTAAAGCAACTATGTAAATC
3632814 TTATTCCTTGACAATAGCTTTATAGCGTGAGTCAATGAGATGTCACTGAAAATTTTTAATTGGAA
261 TTATTCCTTGACAATAGCTTTATAGCGTGAGTCAATGAGATGTCACTGAAAATTTTTAATTGGAA
3632879 TCTTAATTATAACCAATCCAATTTAATAAATCTTCAACAAGCAGTTAAAAACTTAAAAGTGACTT
326 TCTTAATTATAACCAATCCAATTTAATAAATCTTCAACAAGCAGTTAAAAACTTAAAAGTGACTT
3632944 AAATACATCTAAAACTACCCAATATATGAACAGAACTACAGTGACAATGCTGCAAAGAATCATGG
391 AAATACATCTAAAACTACCCAATATATGAACAGAACTACAGTGACAATGCTGCAAAGAATCATGG
3633009 AACAGCGACATTCTCAATTG
456 AACAGCGACATTCTCAATTG
3633029 TAAA
1 TAAA
3633033 TGAGAAACGT
Statistics
Matches: 479, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 479 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (475 bp):
TAAAGAAGGCAGAGAAAAGTGTAGAAGAAAAATCTTGGAAACTTAAAATATAGCTACAATCAAAA
TCTTCAACTTCTATGCACACAAAAAGAGATAAATATTACATACTAAATAATTGCATAATGTACAG
TCGGCAAGGACACAAATCACATTCCCCGTCCCCATCACTCTGGATATTTGTTTTTTCATGTAGAA
CAGAGATAGGGAGAAGTGAGGGAGTTACTTGGCTCATACTGAAGGCTAAAGCAACTATGTAAATC
TTATTCCTTGACAATAGCTTTATAGCGTGAGTCAATGAGATGTCACTGAAAATTTTTAATTGGAA
TCTTAATTATAACCAATCCAATTTAATAAATCTTCAACAAGCAGTTAAAAACTTAAAAGTGACTT
AAATACATCTAAAACTACCCAATATATGAACAGAACTACAGTGACAATGCTGCAAAGAATCATGG
AACAGCGACATTCTCAATTG
Found at i:3634756 original size:17 final size:18
Alignment explanation
Indices: 3634734--3634768 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3634724 GGAGAAACAT
*
3634734 AATTTGC-ATAAATATAA
1 AATTTGCAATAAAGATAA
3634751 AATTTGCAATAAAGATAA
1 AATTTGCAATAAAGATAA
3634769 TTTACATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTGCAATAAAGATAA
Found at i:3637269 original size:14 final size:13
Alignment explanation
Indices: 3637248--3637296 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
3637238 AAGGTAACCA
3637248 AATATTTAAATAT
1 AATATTTAAATAT
3637261 AATTATTT-AA-A-
1 AA-TATTTAAATAT
3637272 AATATTTAAATAT
1 AATATTTAAATAT
* *
3637285 AAAATATAAATA
1 AATATTTAAATA
3637297 ATCCTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 2 0.07
13 14 0.47
14 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:3664261 original size:152 final size:151
Alignment explanation
Indices: 3664062--3664646 Score: 833
Period size: 153 Copynumber: 3.9 Consensus size: 151
3664052 AGCATGTTCG
* * *
3664062 TATTTCAGCCCTTTATTCGTATTTTTTT-CCGAATTTTATTACTTTAAAAAAATATACTATTTTC
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATATTATTTTC
* * *
3664126 TAATTTTGTTATTTTACATTATTTTAGTAGATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
66 TAATTTTATTATTTTACATTATTTTAGTATATTATGCTTGAAATGTATTCATTTAGTGTGTTTTT
** *
3664191 ATTTAAATTAAAAAAAACCCT
131 AAATAAATTAAAAAAAACTCT
*
3664212 TATTTCGGCCCTTTGTTCGTATTTTTTTTCCCGGATTTTATTACTTTAAAAAAATATATTATTTT
1 TATTTCGGCCCTTTGTTCGTA-TTTTTTTCCCGAATTTTATTACTTTAAAAAAATATATTATTTT
* * * * *
3664277 CTAATTTTATTATTTTAAATTATTTTAGTACATTATGCTTAAAATGTATTAATTTACTGTGTTTT
65 CTAATTTTATTATTTTACATTATTTTAGTATATTATGCTTGAAATGTATTCATTTAGTGTG-TTT
3664342 TTAAATAAATTAAAAAAAACTCT
129 TTAAATAAATTAAAAAAAACTCT
*
3664365 TATTTCGGCCCTTTGTTTGTATTTTTTTCCCCGAATTTTATTACTTTAAAAAAATATATTATTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTT-CCCGAATTTTATTACTTTAAAAAAATATATTATTTT
* * *
3664430 CTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTGAAATGTAATTCATTTAGTATATTT
65 CTAATTTTATTATTTTACATTATTTTAGTATATTATGCTTGAAATGT-ATTCATTTAGTGT-GTT
* *
3664495 TTTAAATAAATTTTAAAAAAATTCT
128 TTTAAATAAA-TTAAAAAAAACTCT
* *
3664520 TATTTCGGCTCTTTGTTCGTA--TTTTTCCCAGAA-TTTATTACTTT-AAAAAATATAATA-TTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCCC-GAATTTTATTACTTTAAAAAAATATATTATTTT
*
3664580 CTAATTTTATTATTTTACATTTATTTT-GTATATTATGCTTGAAATGTATTCATTTAGTGTTTTT
65 CTAATTTTATTATTTTACA-TTATTTTAGTATATTATGCTTGAAATGTATTCATTTAGTGTGTTT
3664644 TTA
129 TTA
3664647 TTGAAAGTAA
Statistics
Matches: 395, Mismatches: 31, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
148 7 0.02
149 12 0.03
150 60 0.15
151 26 0.07
152 108 0.27
153 129 0.33
154 22 0.06
155 31 0.08
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (151 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATATTATTTTC
TAATTTTATTATTTTACATTATTTTAGTATATTATGCTTGAAATGTATTCATTTAGTGTGTTTTT
AAATAAATTAAAAAAAACTCT
Found at i:3664459 original size:305 final size:300
Alignment explanation
Indices: 3664062--3664646 Score: 863
Period size: 305 Copynumber: 1.9 Consensus size: 300
3664052 AGCATGTTCG
3664062 TATTTCAGCCCTTTATTCGTATTTTTTTCCGAATTTTATTACTTTAAAAAAATATACTATTTTCT
1 TATTTCAGCCCTTTATTCGTATTTTTTTCCGAATTTTATTACTTTAAAAAAATATACTATTTTCT
* *
3664127 AATTTTGTTATTTTACATTATTTTAGTAGATTATGTTTGAAATGT-ATTCATTTAGTGT-GTTTT
66 AATTTTATTATTTTACATTATTTTAGTAGATTATGTTTGAAATGTAATTCATTTAGTATAGTTTT
** * *
3664190 TATTTAAA-TTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTTCCCGGATTTTATT
131 TAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTA---TTTTTCCCAGAATTTATT
*
3664254 ACTTTAAAAAAATATATTATTTTCTAATTTTATTATTTTA-AATTATTTTAGTACATTATGCTTA
193 ACTTT-AAAAAATATAATA-TTTCTAATTTTATTATTTTACAATTATTTT-GTACATTATGCTTA
3664318 AAATGTATTAATTTACTGTGTTTTTTAAATAAATTAAAAAAAACTCT
255 AAATGTATTAATTTACTGT-TTTTTTAAATAAATTAAAAAAAACTCT
* * * *
3664365 TATTTCGGCCCTTTGTTTGTATTTTTTTCCCCGAATTTTATTACTTTAAAAAAATATATTATTTT
1 TATTTCAGCCCTTTATTCGTATTTTTTT--CCGAATTTTATTACTTTAAAAAAATATACTATTTT
* *
3664430 CTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTGAAATGTAATTCATTTAGTATATTT
64 CTAATTTTATTATTTTACATTATTTTAGTAGATTATGTTTGAAATGTAATTCATTTAGTATAGTT
* ** *
3664495 TTTAAATAAATTTTAAAAAAATTCTTATTTCGGCTCTTTGTTCGTATTTTTCCCAGAATTTATTA
129 TTTAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTCCCAGAATTTATTA
* * *
3664560 CTTTAAAAAATATAATATTTCTAATTTTATTATTTTACATTTATTTTGTATATTATGCTTGAAAT
194 CTTTAAAAAATATAATATTTCTAATTTTATTATTTTACAATTATTTTGTACATTATGCTTAAAAT
* *
3664625 GTATTCATTTAGTGTTTTTTTA
259 GTATTAATTTACTGTTTTTTTA
3664647 TTGAAAGTAA
Statistics
Matches: 254, Mismatches: 22, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
302 7 0.03
303 74 0.29
304 20 0.08
305 100 0.39
306 12 0.05
307 10 0.04
308 31 0.12
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (300 bp):
TATTTCAGCCCTTTATTCGTATTTTTTTCCGAATTTTATTACTTTAAAAAAATATACTATTTTCT
AATTTTATTATTTTACATTATTTTAGTAGATTATGTTTGAAATGTAATTCATTTAGTATAGTTTT
TAAATAAATTTAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTCCCAGAATTTATTACT
TTAAAAAATATAATATTTCTAATTTTATTATTTTACAATTATTTTGTACATTATGCTTAAAATGT
ATTAATTTACTGTTTTTTTAAATAAATTAAAAAAAACTCT
Found at i:3664980 original size:306 final size:304
Alignment explanation
Indices: 3664641--3665545 Score: 1315
Period size: 306 Copynumber: 3.0 Consensus size: 304
3664631 ATTTAGTGTT
*
3664641 TTTTTATTGAAAGTAATAAAATCCGGAAAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTT
1 TTTTTATTGAAAGTAATAAAATCTGGAAAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTT
* *
3664706 AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTATTAAAATAATATAAA
66 AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* *
3664771 ATAATAAAATTATAAAATATTATATTTTTTAAAAGTAATAAAATCTAGGGAAAAAATACGAACAA
131 ATAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCT-GGAAAAAAATACGAACAA
* * * * *
3664836 AAGGCCAAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACA
195 AGGGCCAAAATAAGGATTTTTTTTAATTTATTTAAAAAATACACTAAATGAATACATTTCAAACA
3664901 TAATGTACTAAAATAATGTAAAATAATAAAATACAAAAATAATATA
260 TAATGTACTAAAATAATGTAAAATAATAAAATA-AAAAATAATATA
* *
3664947 TTTTTATTGAAAGTAATAAAATCTGGGAAAAAATACGAACAAATGG-CAGAAATAAGGATTTTTT
1 TTTTTATTGAAAGTAATAAAATCTGGAAAAAAATACGAACAAATGGCCA-AAATAAGGGTTTTTT
*
3665011 TAAAATTTATTTAAAAAACACACTAAATGAATACATTCCAAACATAATGTACTAAAATAATGTAA
65 TAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
* *
3665076 AATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATCTGGAAAAAAATACGAAC
130 AATAATAAAATTAGAAAATATTATA-TTTT-TTAAAAGTAATAAAATCTGGAAAAAAATACGAAC
* * *
3665141 AAAGGGCCGAAATAA-GAATTTTTTAAATTTATTTAAAAAATACACTAAATGAATACATTTCAAA
193 AAAGGGCCAAAATAAGGATTTTTTTTAATTTATTTAAAAAATACACTAAATGAATACATTTCAAA
* *
3665205 CATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGTATA
258 CATAATGTACTAAAATAATGTAAAATAATAAAA-TAAAAAATAATATA
* * *
3665253 -TTTT-TT-AAAGTAATAAAATTTAGGAAAAAAATACGAACAAA-GGACCGAAATAATGGTTTTT
1 TTTTTATTGAAAGTAATAAAATCT-GGAAAAAAATACGAACAAATGG-CCAAAATAAGGGTTTTT
* * *
3665314 TT--AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAGCATAATGTACTAAAATAATGTA
64 TTAAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
*
3665377 AAATAATAAAATTAGAAAATAGTT-TATTTTTTAAAAGTAATAAAATTTCGGCAAAAAAATACGA
129 AAATAATAAAATTAGAAAATA-TTATATTTTTTAAAAGTAATAAAATCT-GG-AAAAAAATACGA
* * * * *
3665441 ACAAAGGGCTAAAATAAGAGTTTTTTTTTTAAATTCAAATAAAAAAATACACTAAATGAATACAT
191 ACAAAGGGCCAAAATAAG-G-ATTTTTTTT-AATT-TATTTAAAAAATACACTAAATGAATACAT
*
3665506 TTCAAACATAATCTACTAAAATAATGTAAAATAATAAAAT
252 TTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
3665546 TAGAAAAAAA
Statistics
Matches: 543, Mismatches: 41, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
300 16 0.03
301 6 0.01
302 107 0.20
303 17 0.03
304 35 0.06
305 13 0.02
306 234 0.43
307 98 0.18
308 17 0.03
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (304 bp):
TTTTTATTGAAAGTAATAAAATCTGGAAAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTT
AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
ATAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCTGGAAAAAAATACGAACAAA
GGGCCAAAATAAGGATTTTTTTTAATTTATTTAAAAAATACACTAAATGAATACATTTCAAACAT
AATGTACTAAAATAATGTAAAATAATAAAATAAAAAATAATATA
Found at i:3665059 original size:154 final size:152
Alignment explanation
Indices: 3664642--3665552 Score: 1264
Period size: 152 Copynumber: 6.0 Consensus size: 152
3664632 TTTAGTGTTT
* * *
3664642 TTTTATTGAAAGTAATAAAATC-CGGAAAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTT
1 TTTT-TTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCAAAATAAGGATTTTTTT
* *
3664706 AAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTATTAAAATAATATAAA
65 -AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* *
3664771 ATAATAAAATTATAAAATATTATA
129 ATAATAAAATTAGAAAATAATATA
* * * * *
3664795 TTTTTTAAAAGTAATAAAATCTAGGGAAAAAATACGAACAAAAGGCCAAAATAAGGGTTTTTTTT
1 TTTTTTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCAAAATAAGGATTTTTTTA
* *
3664860 AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
66 AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
*
3664925 AATAAAA-TACAAAAATAATATA
131 AATAAAATTA-GAAAATAATATA
* *
3664947 TTTTTATTGAAAGTAATAAAATCT-GGGAAAAAATACGAACAAATGG-CAGAAATAAGGATTTTT
1 -TTTT-TTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCA-AAATAAGGATTTTT
*
3665010 TTAAAATTTATTTAAAAAACACACTAAATGAATACATTCCAAACATAATGTACTAAAATAATGTA
63 TT-AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTA
3665075 AAATAATAAAATTAGAAAATAATATA
127 AAATAATAAAATTAGAAAATAATATA
* *
3665101 TTTTTATTGAAAGTAATAAAATCT-GGAAAAAAATACGAACAAAGGGCCGAAATAA-GAATTTTT
1 -TTTT-TTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCAAAATAAGGATTTTTT
*
3665164 TAAATTTATTTAAAAAATACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
64 TAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
*
3665229 ATAATAAAATTAGAAAATAGTATA
129 ATAATAAAATTAGAAAATAATATA
* * *
3665253 TTTTTT-AAAGTAATAAAATTTAGGAAAAAAATACGAACAAAGGACCGAAATAATGG-TTTTTTT
1 TTTTTTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCAAAATAA-GGATTTTTTT
* * *
3665316 -AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAGCATAATGTACTAAAATAATGTAAAA
65 AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
* *
3665380 TAATAAAATTAGAAAATAGTTTA
130 TAATAAAATTAGAAAATAATATA
* * * * *
3665403 TTTTTTAAAAGTAATAAAATTTCGGCAAAAAAATACGAACAAAGGGCTAAAATAAGAGTTTTTTT
1 TTTTTTGAAAGTAATAAAATCTAGG-AAAAAAATACGAACAAAGGGCCAAAATAAG-G--ATTTT
* * * * *
3665468 TTTAAATTCAAATAAAAAAATACACTAAATGAATACATTTCAAACATAATCTACTAAAATAATGT
62 TTTAAATT-TATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGT
3665533 AAAATAATAAAATTAGAAAA
126 AAAATAATAAAATTAGAAAA
3665553 AAATGTACTG
Statistics
Matches: 693, Mismatches: 46, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
149 14 0.02
150 120 0.17
151 30 0.04
152 209 0.30
153 91 0.13
154 147 0.21
155 10 0.01
156 4 0.01
157 68 0.10
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.31
Consensus pattern (152 bp):
TTTTTTGAAAGTAATAAAATCTAGGAAAAAAATACGAACAAAGGGCCAAAATAAGGATTTTTTTA
AATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
AATAAAATTAGAAAATAATATA
Found at i:3666869 original size:32 final size:33
Alignment explanation
Indices: 3666829--3666909 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
3666819 TCTTCATCTT
3666829 AATTTCTCTTAG-ATATCTTCATGAA-TCTT-AA
1 AATTTCTCTTAGAAT-TCTTCATGAATTCTTCAA
* *
3666860 AAGTTTCTCTAAGAATTCTTCATGAATTCTTCAT
1 AA-TTTCTCTTAGAATTCTTCATGAATTCTTCAA
3666894 AATTTCTCTTAGAATT
1 AATTTCTCTTAGAATT
3666910 TCTAATACAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 19 0.44
33 19 0.44
34 3 0.07
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (33 bp):
AATTTCTCTTAGAATTCTTCATGAATTCTTCAA
Found at i:3667588 original size:63 final size:63
Alignment explanation
Indices: 3667515--3667642 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
3667505 GAATATATTG
*
3667515 AGTTAGTTTCAAATTAAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATGGTTTA
1 AGTTAGTTTCAAATTAAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATGGTGTA
*
3667578 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATGGTGTA
1 AGTTAGTTTCAAATTAAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATGGTGTA
3667641 AG
1 AG
3667643 GTGGTAATCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (63 bp):
AGTTAGTTTCAAATTAAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCATGGTGTA
Found at i:3680087 original size:24 final size:24
Alignment explanation
Indices: 3680012--3680179 Score: 82
Period size: 24 Copynumber: 6.9 Consensus size: 24
3680002 CTGGGCTTAA
3680012 TAACGGGAAGCTCAC-AAGGAGC-CT
1 TAACGGGAAGCTC-CGAA-GAGCACT
* * *
3680036 ATATCGGGTAGCTCCGAAGAGCATT
1 -TAACGGGAAGCTCCGAAGAGCACT
*
3680061 TAACGGGAAGCTCCGAAGAGTACT
1 TAACGGGAAGCTCCGAAGAGCACT
* * * *
3680085 TAATCAGAAAGCACCGGATA-ACCA-T
1 TAA-CGGGAAGCTCC-GA-AGAGCACT
*
3680110 ATAACGGGAAG-TTC-AAGTACGCAC-
1 -TAACGGGAAGCTCCGAAG-A-GCACT
*
3680134 TAACGGGAAGCTCCGAGGAGC-CTT
1 TAACGGGAAGCTCCGAAGAGCAC-T
*
3680158 TAACGGGAAGCTCACAAAGAGC
1 TAACGGGAAGCTC-CGAAGAGC
3680180 CTATAAACAA
Statistics
Matches: 107, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 13 0.12
24 47 0.44
25 36 0.34
26 7 0.07
27 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.16
Consensus pattern (24 bp):
TAACGGGAAGCTCCGAAGAGCACT
Found at i:3682543 original size:21 final size:21
Alignment explanation
Indices: 3682519--3682565 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3682509 AAAAAAATAC
3682519 ATAAATATTT-TTGAAATATAT
1 ATAAATATTTATTG-AATATAT
* *
3682540 ATAATTTTTTATTGAATATAT
1 ATAAATATTTATTGAATATAT
3682561 A-AAAT
1 ATAAAT
3682566 TCTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 16 0.73
22 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATAAATATTTATTGAATATAT
Found at i:3686033 original size:13 final size:14
Alignment explanation
Indices: 3686005--3686038 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3685995 ACCTAAACAT
*
3686005 TTATAAAAACATAA
1 TTATAATAACATAA
3686019 TTATAATAA-ATAA
1 TTATAATAACATAA
3686032 TTATAAT
1 TTATAAT
3686039 TATAATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TTATAATAACATAA
Found at i:3688097 original size:20 final size:20
Alignment explanation
Indices: 3688074--3688544 Score: 105
Period size: 20 Copynumber: 23.6 Consensus size: 20
3688064 TTTATATCCT
3688074 CTCATAATTTTTGGTACTTC
1 CTCATAATTTTTGGTACTTC
** *
3688094 CTCAT-ATTTTTTTTATATTC
1 CTCATAATTTTTGGTA-CTTC
* **
3688114 CTCATAACTTTCCGTACATT-
1 CTCATAATTTTTGGTAC-TTC
* ** *
3688134 CTCGTGGTTTTTAGTA-TTC
1 CTCATAATTTTTGGTACTTC
* *
3688153 CATCATAAATTTTGATACTTC
1 C-TCATAATTTTTGGTACTTC
* *
3688174 CTCA-AGTTTTATAGTA-TTC
1 CTCATAATTTT-TGGTACTTC
** * *
3688193 TCTCGCAATTTTTTGTA-TAC
1 -CTCATAATTTTTGGTACTTC
* * *
3688213 ACTCATAACTTTTGTTACATC
1 -CTCATAATTTTTGGTACTTC
* * *
3688234 ATCAT--TTTTT-TTACATC
1 CTCATAATTTTTGGTACTTC
* *
3688251 CTCATATTTTTTTGTA-TTCC
1 CTCATAATTTTTGGTACTT-C
*
3688271 CTCATAATTTTTCGTACTTC
1 CTCATAATTTTTGGTACTTC
* * * *
3688291 ATCATACGTTTTGTGGCACATC
1 CTCATA-ATTTT-TGGTACTTC
* * * * *
3688313 TTTAAAAATTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
** *
3688333 CTCATTTTTTTTTGTA-TTC
1 CTCATAATTTTTGGTACTTC
*
3688352 CTTCATATTTTTTGGTACTTC
1 C-TCATAATTTTTGGTACTTC
* * *
3688373 CTCATATGTTTTATGGTGCATC
1 CTCATA-ATTTT-TGGTACTTC
* * * *
3688395 TTTAAAATTTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
**
3688415 CTCAT--TTTTTTATACTTC
1 CTCATAATTTTTGGTACTTC
* *
3688433 CT--TAGGTATTATGGTA-TTC
1 CTCATA-AT-TTTTGGTACTTC
* * *
3688452 TCTCATAATTTTTGATATTTT
1 -CTCATAATTTTTGGTACTTC
* * *
3688473 CTCGT-ATTTTTAGT-TTTC
1 CTCATAATTTTTGGTACTTC
* *
3688491 TCTCATAATTTTTTGTGCTTC
1 -CTCATAATTTTTGGTACTTC
* *
3688512 CTCAAAATTTTTGGTAATTC
1 CTCATAATTTTTGGTACTTC
*
3688532 CTTATAATCTTTT
1 CTCATAAT-TTTT
3688545 ATATCCCCTC
Statistics
Matches: 320, Mismatches: 98, Indels: 65
0.66 0.20 0.13
Matches are distributed among these distances:
16 1 0.00
17 11 0.03
18 21 0.07
19 40 0.12
20 177 0.55
21 49 0.15
22 21 0.07
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (20 bp):
CTCATAATTTTTGGTACTTC
Found at i:3688242 original size:17 final size:17
Alignment explanation
Indices: 3688202--3688260 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
3688192 CTCTCGCAAT
*
3688202 TTTTTGTATACACTCATAA
1 TTTTTGT-TACA-TCATCA
*
3688221 CTTTTGTTACATCATCA
1 TTTTTGTTACATCATCA
* *
3688238 TTTTTTTTACATCCTCA
1 TTTTTGTTACATCATCA
3688255 TATTTT
1 T-TTTT
3688261 TTTGTATTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 20 0.59
18 8 0.24
19 6 0.18
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTTGTTACATCATCA
Found at i:3688296 original size:40 final size:40
Alignment explanation
Indices: 3688061--3688384 Score: 119
Period size: 40 Copynumber: 8.1 Consensus size: 40
3688051 ATCCTCGTAA
*
3688061 TTTTT-TATATCCTCTCATAATTTTTGGTACTTCCTCATATT
1 TTTTTGTAT-TCC-CTCATAATTTTTCGTACTTCCTCATATT
* * * * **
3688102 TTTTT-TATATTCCTCATAACTTTCCGTACATT-CTCGTGGT
1 TTTTTGTAT-TCCCTCATAATTTTTCGTAC-TTCCTCATATT
* * *
3688142 TTTTAGTATTCCATCATAAATTTT-GATACTTCCTCA-AGTT
1 TTTTTGTATTCCCTCATAATTTTTCG-TACTTCCTCATA-TT
* * * ** * * *
3688182 TTATAGTATTCTCTCGCAATTTTTTGTA-TACACTCATA-A
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTC-CTCATATT
* * * * ** *
3688221 CTTTTG--TTACATCATCATTTTTTTTACATCCTCATATT
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
*
3688259 TTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTT
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATA--TT
* * * * * * * * * * *
3688301 TTGTGGCACAT-CTTTAAAAATTTTGGTACATCCTCATTTT
1 TTTTTGTA-TTCCCTCATAATTTTTCGTACTTCCTCATATT
* * * *
3688341 TTTTTGTATTCCTTCATATTTTTTGGTACTTCCTCATATG
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
3688381 TTTT
1 TTTT
3688385 ATGGTGCATC
Statistics
Matches: 200, Mismatches: 67, Indels: 33
0.67 0.22 0.11
Matches are distributed among these distances:
37 19 0.09
38 6 0.03
39 9 0.05
40 121 0.61
41 18 0.09
42 26 0.13
43 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (40 bp):
TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
Found at i:3688346 original size:82 final size:82
Alignment explanation
Indices: 3688245--3688425 Score: 272
Period size: 82 Copynumber: 2.2 Consensus size: 82
3688235 TCATTTTTTT
* *
3688245 TACATCCTCATATTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTGTGGCAC
1 TACATCCTCATTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCAC
3688310 ATCTTTAAAAATTTTGG
66 ATCTTTAAAAATTTTGG
* * * * * **
3688327 TACATCCTCATTTTTTTTTGTATTCCTTCATATTTTTTGGTACTTCCTCATATGTTTTATGGTGC
1 TACATCCTCATTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCAC
*
3688392 ATCTTTAAAATTTTTGG
66 ATCTTTAAAAATTTTGG
3688409 TACATCCTCATTTTTTT
1 TACATCCTCATTTTTTT
3688426 ATACTTCCTT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 89 1.00
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (82 bp):
TACATCCTCATTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCAC
ATCTTTAAAAATTTTGG
Found at i:3688418 original size:42 final size:41
Alignment explanation
Indices: 3688309--3688427 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 41
3688299 TTTTGTGGCA
* *
3688309 CATCTTTAAAAATTTTGGTACATCCTCATT-TTTT-T-TTG
1 CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTATGGTG
* * * * *
3688347 TATTCCTTCATATTTTTTGGTACTTCCTCATATGTTTTATGGTG
1 CA-T-CTTTAAAATTTTTGGTACATCCTCAT-TGTTTTATGGTG
*
3688391 CATCTTTAAAATTTTTGGTACATCCTCATTTTTTTAT
1 CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTAT
3688428 ACTTCCTTAG
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 21 0.34
41 8 0.13
42 26 0.42
43 2 0.03
44 3 0.05
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (41 bp):
CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTATGGTG
Found at i:3688502 original size:19 final size:21
Alignment explanation
Indices: 3688449--3688502 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
3688439 TATTATGGTA
*
3688449 TTCTCTCATAATTTTTGATAT
1 TTCTCTCATAATTTTAGATAT
* *
3688470 TT-TCTCGTATTTTTAG-T-T
1 TTCTCTCATAATTTTAGATAT
3688488 TTCTCTCATAATTTT
1 TTCTCTCATAATTTT
3688503 TTGTGCTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 11 0.41
21 2 0.07
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.61
Consensus pattern (21 bp):
TTCTCTCATAATTTTAGATAT
Found at i:3691480 original size:29 final size:28
Alignment explanation
Indices: 3691445--3691499 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
3691435 TGATATCTGA
3691445 AAAAGTAAAAAGAATAAAATTTTAAATAT
1 AAAAGTAAAAAGAAT-AAATTTTAAATAT
* * *
3691474 AAAAGTATAGAGACTAAATTTTAAAT
1 AAAAGTAAAAAGAATAAATTTTAAAT
3691500 TTACAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAAGTAAAAAGAATAAATTTTAAATAT
Found at i:3701682 original size:21 final size:22
Alignment explanation
Indices: 3701656--3701702 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3701646 CTCTGCTCAA
*
3701656 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3701677 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3701699 ACTC
1 ACTC
3701703 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3706542 original size:3 final size:3
Alignment explanation
Indices: 3706534--3706565 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3706524 AATTCACCTT
*
3706534 TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3706566 CTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:3707177 original size:36 final size:37
Alignment explanation
Indices: 3707137--3707214 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
3707127 TTTTTCTTCG
*
3707137 TCTTTTTATCAG-AGCTTGAATCTGGGTTTTTGGGGT
1 TCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGGT
**
3707173 TCTTTTCATTTGTAGCTTGAATCTGGGTTTTTGGGGT
1 TCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGGT
*
3707210 ACTTT
1 TCTTT
3707215 CATTTGCAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 9 0.24
37 28 0.76
ACGTcount: A:0.13, C:0.12, G:0.26, T:0.50
Consensus pattern (37 bp):
TCTTTTCATCAGTAGCTTGAATCTGGGTTTTTGGGGT
Found at i:3707190 original size:37 final size:36
Alignment explanation
Indices: 3707149--3707220 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
3707139 TTTTTATCAG
*
3707149 AGCTTGAATCTGGGTTTTTGGGGTTCTTTTCATTTGT
1 AGCTTGAATCTGGGTTTTTGGGGTAC-TTTCATTTGT
3707186 AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTG
1 AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTG
3707221 CAGGAGTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 9 0.26
37 25 0.74
ACGTcount: A:0.12, C:0.11, G:0.28, T:0.49
Consensus pattern (36 bp):
AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTGT
Found at i:3709569 original size:184 final size:184
Alignment explanation
Indices: 3709260--3709627 Score: 664
Period size: 184 Copynumber: 2.0 Consensus size: 184
3709250 CCTATATGTT
*
3709260 TGTTTCTCTTTTTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
* *
3709325 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGT
66 GTGCATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
*
3709390 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCATGTATAAGTTTC
3709444 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
* *
3709509 GTGCATATCTACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTTTCTTTTATTTTGACTGA
66 GTGCATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
* *
3709574 AAGTGAGTGTTTCAAAATTTTTTTTATTGGAAATGACTCTCATGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCATGTATAAGTTTC
3709628 CAGTAACAAG
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (184 bp):
TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
GTGCATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCATGTATAAGTTTC
Found at i:3715889 original size:24 final size:24
Alignment explanation
Indices: 3715862--3715910 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3715852 CACTGAATTA
*
3715862 TTCAAAAGTTTTCATTTCAGTCAC
1 TTCAAAAGTCTTCATTTCAGTCAC
*
3715886 TTCAAAAGTCTTCATTTGAGTCAC
1 TTCAAAAGTCTTCATTTCAGTCAC
3715910 T
1 T
3715911 CGGATGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (24 bp):
TTCAAAAGTCTTCATTTCAGTCAC
Found at i:3716241 original size:31 final size:31
Alignment explanation
Indices: 3716205--3716266 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3716195 GTCTAGTGGC
* * *
3716205 TTAAATAGAAATTTTTAAATAGTTTAATGAT
1 TTAAATAAAAATTTTTAAATAATTCAATGAT
*
3716236 TTAAATAAAAATTTTTGAATAATTCAATGAT
1 TTAAATAAAAATTTTTAAATAATTCAATGAT
3716267 CAAATTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (31 bp):
TTAAATAAAAATTTTTAAATAATTCAATGAT
Found at i:3716525 original size:28 final size:28
Alignment explanation
Indices: 3716472--3716526 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3716462 CTTAATTCAA
*
3716472 TAGTTGGTCCTTAAATTATGATTTTTTT
1 TAGTTGGTACTTAAATTATGATTTTTTT
*
3716500 TAGTTAGGTACTTAAATTATTATTTTT
1 TAGTT-GGTACTTAAATTATGATTTTT
3716527 GGTCAAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.56
Consensus pattern (28 bp):
TAGTTGGTACTTAAATTATGATTTTTTT
Found at i:3716994 original size:16 final size:18
Alignment explanation
Indices: 3716973--3717018 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
3716963 GAAAATGAAG
3716973 AAAAAAATAATTAA-A-T
1 AAAAAAATAATTAATATT
*
3716989 AAAAAATTATATTAATATT
1 AAAAAAATA-ATTAATATT
3717008 AAATAAAATAA
1 AAA-AAAATAA
3717019 AAAATTCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 1 0.04
19 5 0.21
20 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAAATAATTAATATT
Found at i:3717508 original size:2 final size:2
Alignment explanation
Indices: 3717501--3717525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3717491 GCAAAGAAGG
3717501 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3717526 AAAAGCCTAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3725399 original size:15 final size:15
Alignment explanation
Indices: 3725357--3725398 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 15
3725347 GTACTTTATG
3725357 TAAATTTTTTGAATTTT
1 TAAATTTTTT--ATTTT
3725374 TAAATTTTTTATTTT
1 TAAATTTTTTATTTT
3725389 TATAATTTTT
1 TA-AATTTTT
3725399 AAAATAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TAAATTTTTTATTTT
Found at i:3731405 original size:102 final size:102
Alignment explanation
Indices: 3731225--3731416 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 102
3731215 TGATTAATGT
* * ** *
3731225 TATCCGGTACACATAGTAACCTACACTTAGTACTACACATGTGACCAATACCATCTAATACACGT
1 TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAATAAAATCTAATACACAT
* *
3731290 AGTAGCTTGCACATAGTACTACACACGTAACTAAAGC
66 AGTAGCCTACACATAGTACTACACACGTAACTAAAGC
* * * *
3731327 TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTTA-CAATAAAAATCTTATACTCA
1 TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAAT-AAAATCTAATACACA
*
3731391 TATTAGCCTACACATAGTACTACACA
65 TAGTAGCCTACACATAGTACTACACA
3731417 TGAGTTCTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 4 0.05
102 73 0.95
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.27
Consensus pattern (102 bp):
TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAATAAAATCTAATACACAT
AGTAGCCTACACATAGTACTACACACGTAACTAAAGC
Found at i:3734523 original size:33 final size:33
Alignment explanation
Indices: 3734480--3734544 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3734470 CTAATTTATA
* * *
3734480 ACAAAGTTTGTTGCAATGAATCT-AACTTAAATT
1 ACAAAATTTGTTCCAATAAATCTCAA-TTAAATT
3734513 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
1 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
3734545 AAATACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (33 bp):
ACAAAATTTGTTCCAATAAATCTCAATTAAATT
Found at i:3739615 original size:31 final size:31
Alignment explanation
Indices: 3739580--3739662 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
3739570 CAGCTCAGTG
* *
3739580 ACTTAAATAAAATTTTTTAAATAGTTTATTA
1 ACTTAAATAAAATTTTTTAAATAATTTAATA
** *
3739611 ACTTAAATAAAAACTTTTGAATAATTTAATA
1 ACTTAAATAAAATTTTTTAAATAATTTAATA
*
3739642 AC-TAAATTGTAAATTTTTTAA
1 ACTTAAA-T-AAAATTTTTTAA
3739663 TTAAATAACC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.10
31 29 0.71
32 8 0.20
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (31 bp):
ACTTAAATAAAATTTTTTAAATAATTTAATA
Found at i:3740931 original size:28 final size:28
Alignment explanation
Indices: 3740891--3740957 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
3740881 CTGTGACAAC
3740891 TGGTATCCGAGCCAAGTTTTGAACCAAG
1 TGGTATCCGAGCCAAGTTTTGAACCAAG
*
3740919 TGGTATCCGAGCCAAGTTTTGAGCCAAG
1 TGGTATCCGAGCCAAGTTTTGAACCAAG
* *
3740947 TGCTATTCGAG
1 TGGTATCCGAG
3740958 TTGGTTCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (28 bp):
TGGTATCCGAGCCAAGTTTTGAACCAAG
Found at i:3744664 original size:88 final size:88
Alignment explanation
Indices: 3744515--3744692 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
3744505 ATAGTTATGA
* * *
3744515 GTCATCTAAGGAATTATAAAAGATTAAAAAGGATAAGATGGTAATTAGTCAAGTAGATATTTTTA
1 GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3744580 GACATAATGATTAGGACTAAAGT
66 GACATAATGATTAGGACTAAAGT
*
3744603 GTCATCCAAGGAATTATAAAAGATGAAAAATGATAAGATGATAATTAGTCAAGTAGATATTTTTA
1 GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3744668 GACATAATGATTAGGACTAAAGT
66 GACATAATGATTAGGACTAAAGT
3744691 GT
1 GT
3744693 AAAGCTGGAT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.30
Consensus pattern (88 bp):
GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
GACATAATGATTAGGACTAAAGT
Found at i:3746543 original size:75 final size:75
Alignment explanation
Indices: 3746453--3746638 Score: 336
Period size: 75 Copynumber: 2.5 Consensus size: 75
3746443 CCGGATTACA
* *
3746453 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATT
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
3746518 CCACCGTATC
66 CCACCGTATC
*
3746528 TTAAGTGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
3746593 CCACCGTATC
66 CCACCGTATC
*
3746603 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3746639 CGAGGGGTTG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 106 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (75 bp):
TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
CCACCGTATC
Found at i:3746559 original size:42 final size:41
Alignment explanation
Indices: 3746500--3746636 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 41
3746490 ATTCATTGGT
3746500 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAGTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAA-TGTGAAAGG
* *
3746542 GGTTGCTAAGTGCTGATTCC-CCG-A-C-TCAT-T---AGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
*
3746575 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGG
3746617 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
3746637 CCCGAGGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 22 0.27
34 3 0.04
35 1 0.01
36 2 0.02
37 2 0.02
38 4 0.05
39 2 0.02
40 1 0.01
41 3 0.04
42 41 0.51
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
Found at i:3746660 original size:102 final size:102
Alignment explanation
Indices: 3746539--3746740 Score: 361
Period size: 102 Copynumber: 2.0 Consensus size: 102
3746529 TAAGTGTGAA
*
3746539 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCC-ACCGTATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGA-TCCTACCGTATC
*
3746603 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
*
3746641 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCTACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATCCTACCGTATCT
3746706 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3746741 GACTCATTGG
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 3 0.03
102 93 0.97
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATCCTACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3746760 original size:177 final size:176
Alignment explanation
Indices: 3746464--3746952 Score: 888
Period size: 177 Copynumber: 2.8 Consensus size: 176
3746454 TAAATGTGAA
*
3746464 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGA-TCCACCGTATCT
* *
3746529 TAAGTGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
65 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC
3746594 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
130 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
3746641 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCTACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCC-ACCGTATCT
3746706 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC
65 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC
3746771 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
130 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
3746818 AGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAT-CCACCGTATCT
* * *
3746883 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTAGTTGTTAAGTGCTGAATC
65 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC
3746948 CACCG
130 CACCG
3746953 ATAACGGATA
Statistics
Matches: 303, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
176 3 0.01
177 298 0.98
178 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (176 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCACCGTATCTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCC
ACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3746764 original size:75 final size:75
Alignment explanation
Indices: 3746641--3746815 Score: 316
Period size: 75 Copynumber: 2.3 Consensus size: 75
3746631 GATTCCCCCG
3746641 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGA-TCCTACCGTATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCC-ACCGTATC
3746705 TTAAATGTGAA
65 TTAAATGTGAA
*
3746716 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
3746781 TAAATGTGAA
66 TAAATGTGAA
*
3746791 GGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
3746816 CGAGGGGTTG
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
75 94 0.97
76 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (75 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
TAAATGTGAA
Found at i:3746822 original size:102 final size:102
Alignment explanation
Indices: 3746716--3746917 Score: 368
Period size: 102 Copynumber: 2.0 Consensus size: 102
3746706 TAAATGTGAA
* *
3746716 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
3746781 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
*
3746818 AGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
3746883 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3746918 GACTCATTGG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3748658 original size:22 final size:22
Alignment explanation
Indices: 3748596--3748660 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
3748586 CTCAGATTAT
* *
3748596 TAGCACATTAGTGCTCTTCGTT
1 TAGCACATTAGTGCTCTTTGTA
3748618 TAGCACATTCA-TGCTCTTTGTA
1 TAGCACATT-AGTGCTCTTTGTA
*
3748640 TAGCACCTTAGTGCTCTTTGT
1 TAGCACATTAGTGCTCTTTGT
3748661 TCATTAGTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTTTGTA
Found at i:3753784 original size:23 final size:23
Alignment explanation
Indices: 3753758--3753878 Score: 179
Period size: 23 Copynumber: 5.3 Consensus size: 23
3753748 ATAAGTGCCA
*
3753758 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
3753781 CACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
3753804 AACTGAAATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3753827 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3753850 CGCTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3753873 CGCTGA
1 CACTGA
3753879 TCAATAACAC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 92 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:3755824 original size:18 final size:19
Alignment explanation
Indices: 3755801--3755851 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
3755791 AGGTAAATTG
3755801 TATTATTTATTAT-TTTTA
1 TATTATTTATTATATTTTA
3755819 TATTA-TTATT-TATTTTA
1 TATTATTTATTATATTTTA
*
3755836 TTTTATTTTATTATAT
1 TATTA-TTTATTATAT
3755852 ATACTTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 14 0.50
18 5 0.18
19 5 0.18
20 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTATTTATTATATTTTA
Found at i:3755832 original size:10 final size:10
Alignment explanation
Indices: 3755801--3755847 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3755791 AGGTAAATTG
3755801 TATTATTTAT
1 TATTATTTAT
*
3755811 TATTTTTATAT
1 TATTATT-TAT
3755822 TATTATTTAT
1 TATTATTTAT
3755832 T-TTATTTTAT
1 TATTA-TTTAT
3755842 T-TTATT
1 TATTATT
3755848 ATATATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 5 0.15
10 19 0.58
11 9 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTATTTAT
Found at i:3758201 original size:6 final size:6
Alignment explanation
Indices: 3758192--3758242 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
3758182 TATATATATC
* * *
3758192 AAATAA AAATAA AAATAA AAATAT ATAT-C AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
3758239 AAAT
1 AAAT
3758243 CACATTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 3 0.08
6 36 0.92
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:3758225 original size:29 final size:29
Alignment explanation
Indices: 3758183--3758242 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3758173 AATATAATAT
3758183 ATATATATCAAATAAAAATAAAAATAAAA
1 ATATATATCAAATAAAAATAAAAATAAAA
3758212 ATATATATCAAATAAAAATAAAAATAAAA
1 ATATATATCAAATAAAAATAAAAATAAAA
3758241 AT
1 AT
3758243 CACATTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (29 bp):
ATATATATCAAATAAAAATAAAAATAAAA
Found at i:3758226 original size:17 final size:17
Alignment explanation
Indices: 3758183--3758231 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
3758173 AATATAATAT
3758183 ATATATATCAAAT-AAA
1 ATATATATCAAATAAAA
3758199 A-ATA-A--AAATAAAA
1 ATATATATCAAATAAAA
3758212 ATATATATCAAATAAAA
1 ATATATATCAAATAAAA
3758229 ATA
1 ATA
3758232 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 4 0.14
15 4 0.14
16 1 0.04
17 11 0.39
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATATATCAAATAAAA
Found at i:3758244 original size:23 final size:23
Alignment explanation
Indices: 3758198--3758244 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3758188 TATCAAATAA
* *
3758198 AAATAAAAATAAAAATATATATC
1 AAATAAAAATAAAAATAAAAATC
3758221 AAATAAAAATAAAAATAAAAATC
1 AAATAAAAATAAAAATAAAAATC
3758244 A
1 A
3758245 CATTCTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATAAAAATAAAAATAAAAATC
Found at i:3761646 original size:22 final size:20
Alignment explanation
Indices: 3761587--3761647 Score: 50
Period size: 22 Copynumber: 2.9 Consensus size: 20
3761577 TTAAAATTGA
* *
3761587 AAAAATTTTGAAAAAATATTT
1 AAAAATTTTAAAAAAATA-AT
* *
3761608 AAAATTTTTCAATAAAATAAAT
1 AAAAATTTT-AAAAAAAT-AAT
3761630 AAAAATTTATAAAAAAAT
1 AAAAATTT-TAAAAAAAT
3761648 GAATTCATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.26
22 21 0.68
23 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTTTAAAAAAATAAT
Found at i:3766654 original size:52 final size:54
Alignment explanation
Indices: 3766586--3766746 Score: 188
Period size: 52 Copynumber: 3.0 Consensus size: 54
3766576 TGGTGGTACT
* * *
3766586 AGTGTAGGAA-TTTTTTATTAATCTTTGGTG-CTGCCTCCTTCAATGGAGG-ACC
1 AGTGTAGGAATTTTTTTATTATTTTTTGGTGTC-GCCTCCTTCAATAGAGGCACC
* * * *
3766638 AGT-TAGGAATTTTTTTAATATTTTTTGGTGTCGCCTACTTCTATTGAGGCACC
1 AGTGTAGGAATTTTTTTATTATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACC
*
3766691 AGTGTAGGAGTTTTTTT-TCATATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACC
1 AGTGTAGGAATTTTTTTAT--TATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACC
3766746 A
1 A
3766747 AATTTTAGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
51 6 0.07
52 34 0.37
53 7 0.08
54 12 0.13
55 33 0.36
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (54 bp):
AGTGTAGGAATTTTTTTATTATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACC
Found at i:3766714 original size:55 final size:53
Alignment explanation
Indices: 3766590--3766746 Score: 185
Period size: 55 Copynumber: 3.0 Consensus size: 53
3766580 GGTACTAGTG
* * * *
3766590 TAGGAA-TTTTTTATTAATCTTTGGTG-CTGCCTCCTTCAATGGAGG-ACCAGT
1 TAGGAATTTTTTTAATATTTTTTGGTGTC-GCCTCCTTCAATAGAGGCACCAGT
* * *
3766641 TAGGAATTTTTTTAATATTTTTTGGTGTCGCCTACTTCTATTGAGGCACCAGT
1 TAGGAATTTTTTTAATATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACCAGT
* *
3766694 GTAGGAGTTTTTTTTCATATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACCA
1 -TAGGA-ATTTTTTTAATATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACCA
3766747 AATTTTAGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 6 0.07
52 31 0.34
53 7 0.08
54 5 0.06
55 41 0.46
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (53 bp):
TAGGAATTTTTTTAATATTTTTTGGTGTCGCCTCCTTCAATAGAGGCACCAGT
Found at i:3767617 original size:15 final size:16
Alignment explanation
Indices: 3767589--3767619 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3767579 TCAACTTTTT
3767589 TGGCCCGAGCCCGGCC
1 TGGCCCGAGCCCGGCC
3767605 TGGCCCG-GCCCGGCC
1 TGGCCCGAGCCCGGCC
3767620 CGAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.03, C:0.52, G:0.39, T:0.06
Consensus pattern (16 bp):
TGGCCCGAGCCCGGCC
Found at i:3767653 original size:13 final size:14
Alignment explanation
Indices: 3767635--3767668 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3767625 ATAATAAATA
3767635 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
3767648 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
3767662 TAATTTT
1 TATTTTT
3767669 AAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:3767660 original size:14 final size:13
Alignment explanation
Indices: 3767635--3767668 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3767625 ATAATAAATA
3767635 TATTTTTTATTTT
1 TATTTTTTATTTT
3767648 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
3767662 TAATTTT
1 T-ATTTT
3767669 AAAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:3774343 original size:19 final size:18
Alignment explanation
Indices: 3774321--3774391 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
3774311 AATTTATATC
3774321 TTTTAATAATTTTTACAAT
1 TTTTAATAATTTTTA-AAT
* * *
3774340 TTTTTATACTTATTAAAT
1 TTTTAATAATTTTTAAAT
* * *
3774358 TTTTATATTATTTATAAGT
1 TTTTA-ATAATTTTTAAAT
*
3774377 TTTTATTAATTTTTA
1 TTTTAATAATTTTTA
3774392 TAGAATTTTA
Statistics
Matches: 39, Mismatches: 12, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTTAATAATTTTTAAAT
Found at i:3774433 original size:16 final size:19
Alignment explanation
Indices: 3774408--3774444 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
3774398 TTTAAATATA
3774408 TTTTATTAATT-TT-ATTT
1 TTTTATTAATTATTGATTT
3774425 TTTTA-TAATTATTGATTT
1 TTTTATTAATTATTGATTT
3774443 TT
1 TT
3774445 GTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTTATTAATTATTGATTT
Found at i:3774563 original size:10 final size:10
Alignment explanation
Indices: 3774517--3774665 Score: 85
Period size: 10 Copynumber: 14.9 Consensus size: 10
3774507 TTAAAAAAAT
*
3774517 TAAATGTTTA
1 TAAATTTTTA
*
3774527 TAATTTTTTA
1 TAAATTTTTA
*
3774537 -AGAATTCTTA
1 TA-AATTTTTA
*
3774547 TACATTTTTA
1 TAAATTTTTA
3774557 TAAATTTTTAA
1 TAAATTTTT-A
3774568 TAAA-TTTTA
1 TAAATTTTTA
*
3774577 TTAATTTTTA
1 TAAATTTTTA
*
3774587 TAAAATTTTA
1 TAAATTTTTA
* *
3774597 TAACTTATTA
1 TAAATTTTTA
*
3774607 -GAA-TTTTA
1 TAAATTTTTA
*
3774615 T-AATATTTA
1 TAAATTTTTA
3774624 TAAGTTATTTTT-
1 TAA---ATTTTTA
*
3774636 TATAACTTTTA
1 TA-AATTTTTA
*
3774647 TAAATTTATA
1 TAAATTTTTA
*
3774657 TCAATTTTT
1 TAAATTTTT
3774666 TAATAATTTT
Statistics
Matches: 104, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
8 6 0.06
9 11 0.11
10 71 0.68
11 8 0.08
12 2 0.02
13 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
TAAATTTTTA
Found at i:3774623 original size:27 final size:27
Alignment explanation
Indices: 3774574--3774632 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3774564 TTAATAAATT
*
3774574 TTATTAATTTTTATAAAATTTTATAAC
1 TTATTAAATTTTATAAAATTTTATAAC
* *
3774601 TTATTAGAATTTTATAATA-TTTATAAG
1 TTATTA-AATTTTATAAAATTTTATAAC
3774628 TTATT
1 TTATT
3774633 TTTTATAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TTATTAAATTTTATAAAATTTTATAAC
Found at i:3774645 original size:9 final size:8
Alignment explanation
Indices: 3774570--3774656 Score: 52
Period size: 9 Copynumber: 10.1 Consensus size: 8
3774560 ATTTTTAATA
3774570 AATTTTATT
1 AATTTTA-T
3774579 AATTTTTAT
1 AA-TTTTAT
3774588 AAAATTTTAT
1 --AATTTTAT
*
3774598 AACTTATTAG
1 AA-TT-TTAT
3774608 AATTTTAT
1 AATTTTAT
3774616 AATATTTAT
1 AAT-TTTAT
*
3774625 AA-GTTAT
1 AATTTTAT
*
3774632 -TTTTTAT
1 AATTTTAT
3774639 AACTTTTAT
1 AA-TTTTAT
*
3774648 AAATTTAT
1 AATTTTAT
3774656 A
1 A
3774657 TCAATTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
7 8 0.13
8 14 0.23
9 22 0.35
10 16 0.26
11 2 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (8 bp):
AATTTTAT
Found at i:3774675 original size:10 final size:10
Alignment explanation
Indices: 3774526--3774694 Score: 57
Period size: 10 Copynumber: 16.7 Consensus size: 10
3774516 TTAAATGTTT
3774526 ATAATTTTTTA
1 ATAA-TTTTTA
* *
3774537 AGAATTCTT-
1 ATAATTTTTA
3774546 ATACATTTTT-
1 ATA-ATTTTTA
3774556 ATAAATTTTTA
1 AT-AATTTTTA
*
3774567 ATAAATTTTA
1 ATAATTTTTA
*
3774577 TTAATTTTT-
1 ATAATTTTTA
*
3774586 ATAAAATTTT-
1 AT-AATTTTTA
*
3774596 ATAACTTATT-
1 ATAA-TTTTTA
*
3774606 AGAATTTTATA
1 ATAATTTT-TA
*
3774617 AT-ATTTATA
1 ATAATTTTTA
* *
3774626 AGTTATTTTTT
1 A-TAATTTTTA
*
3774637 ATAACTTTT-
1 ATAATTTTTA
*
3774646 ATAA-ATTTA
1 ATAATTTTTA
3774655 TATCAATTTTTTA
1 -AT-AA-TTTTTA
3774668 ATAATTTTTA
1 ATAATTTTTA
* *
3774678 GTGATTTTTA
1 ATAATTTTTA
*
3774688 ATCATTT
1 ATAATTT
3774695 ATTATGAGAA
Statistics
Matches: 119, Mismatches: 25, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
8 3 0.03
9 15 0.13
10 78 0.66
11 17 0.14
12 2 0.02
13 4 0.03
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:3781440 original size:40 final size:39
Alignment explanation
Indices: 3781396--3781485 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 39
3781386 AAAAAAATAT
*
3781396 TTATATT-AAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
3781436 TTATATTTAAAAAACACAAATAAATATAATAAATATTTTA
1 TTATA-TTAAAAAACACAAATAAATATAATAAATATTTTA
*
3781476 TTGTATTAAA
1 TTATATTAAA
3781486 TATATTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 5 0.11
40 30 0.65
41 3 0.07
42 8 0.17
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:3782373 original size:20 final size:21
Alignment explanation
Indices: 3782342--3782388 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
3782332 AAATCGTAGC
3782342 AAAATAGTGAAAAAATAA-TAA
1 AAAATAGTGAAAAAA-AAGTAA
3782363 AAAATAG-GAAAAAAAAGTAA
1 AAAATAGTGAAAAAAAAGTAA
3782383 AAAATA
1 AAAATA
3782389 AAATAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (21 bp):
AAAATAGTGAAAAAAAAGTAA
Found at i:3786311 original size:43 final size:43
Alignment explanation
Indices: 3786210--3786499 Score: 307
Period size: 43 Copynumber: 6.8 Consensus size: 43
3786200 AAGGTCATGG
* * *** **
3786210 CCTTTAGCGGTGCTTTTCCCACAAACGCCGCT-AAGGCCATGA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
* * *
3786252 CCTTTAACGGCACTTTTCTCACAAACGCCGCTAAAAATTGCGA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
*** **
3786295 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGCCCATGA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
* *
3786338 CCTTTAACGGCGCTTTTCTCACAAACGCCGCTAAAAATCGCAA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
* * * * * *
3786381 CTTTTAGC-ACGCTTTT-CCACAAATGCCACTAAAAGTCGCGA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
* * ** *
3786422 CCTTTAACGACGCTTTTCCCACAAACGTCGCTAAAAGCCGTGA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
3786465 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
3786500 GGTCATGAAA
Statistics
Matches: 203, Mismatches: 42, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
41 26 0.13
42 43 0.21
43 134 0.66
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (43 bp):
CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCGA
Found at i:3786455 original size:127 final size:128
Alignment explanation
Indices: 3786189--3786499 Score: 382
Period size: 127 Copynumber: 2.4 Consensus size: 128
3786179 TATTTTAAAA
* * * * * **
3786189 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAGGCCAT-G-A
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAA--AAATCGCA
* * * * *
3786252 CCTTTAACGGCA--CTTTTCTCACAAACGCCGCTAAAAATTGCGACCTTTAACGGCGCTTTTCCC
64 ACTTTTA--GCACGCTTTTCTCACAAACGCCACTAAAAATCGCGACCTTTAACGACGCTTTTCCC
3786315 AC
127 AC
*
3786317 AAACGCCGCT-AAAGCCCATGACCTTTAACGGCGCTTTTCTCACAAACGCCGCTAAAAATCGCAA
1 AAACGCCGCTAAAAG-CCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCAA
* *
3786381 CTTTTAGCACGCTTTTC-CACAAATGCCACTAAAAGTCGCGACCTTTAACGACGCTTTTCCCAC
65 CTTTTAGCACGCTTTTCTCACAAACGCCACTAAAAATCGCGACCTTTAACGACGCTTTTCCCAC
* *
3786444 AAACGTCGCTAAAAGCCGTGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
3786500 GGTCATGAAA
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
126 5 0.03
127 93 0.58
128 61 0.38
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (128 bp):
AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAATCGCAAC
TTTTAGCACGCTTTTCTCACAAACGCCACTAAAAATCGCGACCTTTAACGACGCTTTTCCCAC
Found at i:3786573 original size:40 final size:40
Alignment explanation
Indices: 3786496--3786574 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
3786486 CAAACGCCGC
** *
3786496 TAAAGGTCATGAAATTTTAAAATATATATATATAATATTA
1 TAAAGGTCATGAAAAATTAAAATATATATATAAAATATTA
3786536 TAAAGGTCATGAAAAATTAAAAT-TCAT-TATCAAAATATT
1 TAAAGGTCATGAAAAATTAAAATAT-ATATAT-AAAATATT
3786575 GAGGAGAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.37
Consensus pattern (40 bp):
TAAAGGTCATGAAAAATTAAAATATATATATAAAATATTA
Found at i:3790780 original size:48 final size:45
Alignment explanation
Indices: 3790688--3790782 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 45
3790678 CTTCAAATAC
*
3790688 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAACCA
*
3790733 TAGTTAACTCATAAACTGCTTTAAACCCT-AATCATATATCTTAAACCA
1 TAGTTAACTCATAAAC--C-TTAAACCCTAAACCATATATCTT-AACCA
3790781 TA
1 TA
3790783 AACCTTAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
45 15 0.34
47 13 0.30
48 16 0.36
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (45 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAACCA
Found at i:3791055 original size:40 final size:41
Alignment explanation
Indices: 3790956--3791150 Score: 231
Period size: 41 Copynumber: 4.9 Consensus size: 41
3790946 ATATGACTTT
* **
3790956 AAGCGCTGCTAATGCTCAAGTTTTTAGCGGCGTTTTACCAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
* *
3790997 AAGCGCCGCTAATGCTCTGGTTTTTAGCTGCGTTTTACC-C
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
* *
3791037 AAGCGCCGCTAATACTCTGGTTTTTAGCGGCATTTTACCAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
* * *
3791078 AAGCACCGCTAATGCTCT-GTTTTTAGTGGCGTTTTTA-CTA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG-TTTTACCAA
**
3791118 AA-CGCCGCTGTTGCTCT--TTTTTAGCGGCGTTTT
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTT
3791151 TTGATAAAAC
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.03
38 11 0.08
39 12 0.09
40 51 0.38
41 56 0.42
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
Found at i:3791115 original size:81 final size:81
Alignment explanation
Indices: 3790956--3791112 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 81
3790946 ATATGACTTT
* * * *
3790956 AAGCGCTGCTAATGCTCAAGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTTTT
1 AAGCGCCGCTAATACTCAAGTTTTTAGCGGCATTTTACCAAAAGCACCGCTAATGCTCTGGTTTT
3791021 TAGCTGCGTTTTACCC
66 TAGCTGCGTTTTACCC
**
3791037 AAGCGCCGCTAATACTCTGGTTTTTAGCGGCATTTTACCAAAAGCACCGCTAATGCTCT-GTTTT
1 AAGCGCCGCTAATACTCAAGTTTTTAGCGGCATTTTACCAAAAGCACCGCTAATGCTCTGGTTTT
3791101 TAG-TGGCGTTTT
66 TAGCT-GCGTTTT
3791113 TACTAAACGC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 1 0.01
80 15 0.22
81 53 0.77
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (81 bp):
AAGCGCCGCTAATACTCAAGTTTTTAGCGGCATTTTACCAAAAGCACCGCTAATGCTCTGGTTTT
TAGCTGCGTTTTACCC
Found at i:3806745 original size:11 final size:11
Alignment explanation
Indices: 3806729--3806754 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3806719 TAAAAATTAA
3806729 AAAAGTATTTT
1 AAAAGTATTTT
3806740 AAAAGTATTTT
1 AAAAGTATTTT
3806751 AAAA
1 AAAA
3806755 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3806769 original size:16 final size:17
Alignment explanation
Indices: 3806738--3806838 Score: 71
Period size: 16 Copynumber: 5.7 Consensus size: 17
3806728 AAAAAGTATT
*
3806738 TTAAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAA
3806755 TTAAAAATA-TTTAAAA
1 TTAAAAATATTTTAAAA
***
3806771 TTAAAAATAATAAAAAAAGTA
1 TTAAAAAT-AT-TTTAAA--A
3806792 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
*
3806811 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTTAAAA
* *
3806827 ATAAATATATTT
1 TTAAAAATATTT
3806839 ATTATATCGG
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
16 28 0.42
17 20 0.30
19 4 0.06
21 4 0.06
22 2 0.03
23 8 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:3811777 original size:31 final size:29
Alignment explanation
Indices: 3811735--3811815 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
3811725 TACTTTGTAA
3811735 AAATTATAAATTTAAT-CTCCATACTATTC
1 AAATTATAAATTTAATCCT-CATACTATTC
* *
3811764 AAATTGATCAAATTTAATCCTTATACTTTTC
1 AAATT-AT-AAATTTAATCCTCATACTATTC
*
3811795 AAATTTTAAAATTTTAATCCT
1 AAATTAT-AAA-TTTAATCCT
3811816 AACTCAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 5 0.11
30 6 0.14
31 31 0.70
32 2 0.05
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (29 bp):
AAATTATAAATTTAATCCTCATACTATTC
Found at i:3818884 original size:10 final size:10
Alignment explanation
Indices: 3818871--3818938 Score: 57
Period size: 10 Copynumber: 6.4 Consensus size: 10
3818861 AATAACAAAT
3818871 AAAGAAAGAA
1 AAAGAAAGAA
3818881 AAAGAAATAGAA
1 AAAG-AA-AGAA
*
3818893 AGAACAAACGAA
1 A-AAGAAA-GAA
3818905 AAAGAAAGAA
1 AAAGAAAGAA
* *
3818915 ACAGAAAG-G
1 AAAGAAAGAA
3818924 AAAGAAAAGAA
1 AAAG-AAAGAA
3818935 AAAG
1 AAAG
3818939 GGAAGGAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.07
10 18 0.39
11 12 0.26
12 11 0.24
13 2 0.04
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:3818905 original size:18 final size:16
Alignment explanation
Indices: 3818871--3818938 Score: 77
Period size: 15 Copynumber: 4.2 Consensus size: 16
3818861 AATAACAAAT
3818871 AAAGAAAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
*
3818887 ATAGAAAGAACAAACGAA
1 AAAGAAAGAA-AAA-GAA
*
3818905 AAAGAAAGAAACAG-A
1 AAAGAAAGAAAAAGAA
*
3818920 AAGGAAAG-AAAAGAA
1 AAAGAAAGAAAAAGAA
3818935 AAAG
1 AAAG
3818939 GGAAGGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 4 0.09
15 12 0.28
16 10 0.23
17 5 0.12
18 12 0.28
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.01
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Done.