Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 134 of 335
Found at i:39657269 original size:13 final size:14
Alignment explanation
Indices: 39657253--39657285 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39657243 GTATTTTTCC
39657253 TTATTTATT-TTAT
1 TTATTTATTATTAT
39657266 TTATTTATTATTAT
1 TTATTTATTATTAT
*
39657280 TAATTT
1 TTATTT
39657286 TAAAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:39657341 original size:23 final size:22
Alignment explanation
Indices: 39657297--39657375 Score: 90
Period size: 21 Copynumber: 3.6 Consensus size: 22
39657287 AAAAAACTTG
** **
39657297 AAATATATATTTGATATGTTTT
1 AAATATATATTTTTTAAATTTT
39657319 ATAATATATATTTTTTAAATTTT
1 A-AATATATATTTTTTAAATTTT
*
39657342 AAATAT-TATTTTTTAAATATT
1 AAATATATATTTTTTAAATTTT
39657363 AAATATAT-TTTTT
1 AAATATATATTTTT
39657376 AATAATATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 25 0.50
22 7 0.14
23 18 0.36
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
AAATATATATTTTTTAAATTTT
Found at i:39657353 original size:21 final size:21
Alignment explanation
Indices: 39657315--39657377 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
39657305 ATTTGATATG
39657315 TTTTATAATATATATTTTTTAAA
1 TTTTA-AATAT-TATTTTTTAAA
39657338 TTTTAAATATTATTTTTTAAA
1 TTTTAAATATTATTTTTTAAA
*
39657359 TATTAAATA-TATTTTTTAA
1 TTTTAAATATTATTTTTTAA
39657378 TAATATAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 10 0.26
21 19 0.49
22 5 0.13
23 5 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAATATTATTTTTTAAA
Found at i:39657386 original size:21 final size:20
Alignment explanation
Indices: 39657318--39657386 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
39657308 TGATATGTTT
*
39657318 TATAATATATATTTTTTAAAT
1 TATAA-ATATATTTTTTAAAA
*
39657339 TTTAAATATTATTTTTT-AAA
1 TATAAATA-TATTTTTTAAAA
39657359 TATTAAATATATTTTTTAATAA
1 TA-TAAATATATTTTTTAA-AA
39657381 TATAAA
1 TATAAA
39657387 ACATTTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 14 0.34
21 23 0.56
22 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAAATATATTTTTTAAAA
Found at i:39657649 original size:20 final size:20
Alignment explanation
Indices: 39657592--39657649 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
39657582 AAAAGAATTT
39657592 AATTAAAATATATATATT-AA
1 AATTAAAA-ATATATATTAAA
* * *
39657612 AAGTAAAAATTTAAATTAAA
1 AATTAAAAATATATATTAAA
39657632 AATTAAAAATATATATTA
1 AATTAAAAATATATATTA
39657650 TAACTTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTAAAAATATATATTAAA
Found at i:39657708 original size:14 final size:15
Alignment explanation
Indices: 39657691--39657723 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39657681 TATATTTTAA
*
39657691 ATAATTTATAAT-TT
1 ATAATTTAAAATATT
39657705 ATAATTTAAAATATT
1 ATAATTTAAAATATT
39657720 ATAA
1 ATAA
39657724 AATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTTAAAATATT
Found at i:39657733 original size:35 final size:34
Alignment explanation
Indices: 39657689--39657765 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
39657679 AATATATTTT
*
39657689 AAATAATTTATAATTTATA-ATTTAAAAT-ATTATA
1 AAATAATTTA-AA-ATATACATTTAAAATAATTATA
39657723 AAATATATTTAAAATATACATTTAAAATAATTATA
1 AAATA-ATTTAAAATATACATTTAAAATAATTATA
39657758 AAACTAAT
1 AAA-TAAT
39657766 AATAAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 4 0.11
34 16 0.42
35 16 0.42
36 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (34 bp):
AAATAATTTAAAATATACATTTAAAATAATTATA
Found at i:39657734 original size:21 final size:21
Alignment explanation
Indices: 39657679--39657739 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
39657669 CTTTAAAAAT
*
39657679 AATATATTTTAAATAATTTATAA
1 AATATATTTAAAAT-A-TTATAA
**
39657702 TTTATAATTTAAAATATTATAA
1 AATAT-ATTTAAAATATTATAA
39657724 AATATATTTAAAATAT
1 AATATATTTAAAATAT
39657740 ACATTTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 11 0.34
22 9 0.28
23 4 0.12
24 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATATTTAAAATATTATAA
Found at i:39657747 original size:13 final size:11
Alignment explanation
Indices: 39657679--39657760 Score: 62
Period size: 11 Copynumber: 7.2 Consensus size: 11
39657669 CTTTAAAAAT
*
39657679 AATATATTTTA
1 AATATATTTAA
39657690 AATA-ATTTATA
1 AATATATTTA-A
*
39657701 ATTTATAATTTAA
1 A-ATAT-ATTTAA
*
39657714 AATAT-TATAA
1 AATATATTTAA
39657724 AATATATTTAA
1 AATATATTTAA
39657735 AATATACATTTAA
1 AATAT--ATTTAA
39657748 AATA-ATTATAA
1 AATATATT-TAA
39657759 AA
1 AA
39657761 CTAATAATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
10 16 0.28
11 20 0.34
12 5 0.09
13 12 0.21
14 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (11 bp):
AATATATTTAA
Found at i:39657841 original size:21 final size:20
Alignment explanation
Indices: 39657817--39657902 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
39657807 TTTTATTATT
*
39657817 AAAAATATATTTAATATTTA
1 AAAAATATATTTAAAATTTA
39657837 AAAAATAATATTTAAAATTTA
1 AAAAAT-ATATTTAAAATTTA
*
39657858 GAAAAATA-A--T---A-TCA
1 -AAAAATATATTTAAAATTTA
39657872 AAAATATATATTTAAAATTTA
1 AAAA-ATATATTTAAAATTTA
39657893 AAAAATATAT
1 AAAAATATAT
39657903 ATTATAAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
13 4 0.08
14 5 0.09
15 2 0.04
17 1 0.02
18 1 0.02
20 14 0.26
21 20 0.38
22 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAATATATTTAAAATTTA
Found at i:39657865 original size:22 final size:21
Alignment explanation
Indices: 39657817--39657869 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
39657807 TTTTATTATT
*
39657817 AAAAAT-ATATTTAATATTTA
1 AAAAATAATATTTAAAATTTA
39657837 AAAAATAATATTTAAAATTTA
1 AAAAATAATATTTAAAATTTA
39657858 GAAAAATAATAT
1 -AAAAATAATAT
39657870 CAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 11 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAATATTTAAAATTTA
Found at i:39657875 original size:22 final size:21
Alignment explanation
Indices: 39657832--39657876 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
39657822 TATATTTAAT
**
39657832 ATTTAAAAAATAATATTTAAA
1 ATTTAAAAAATAATATCAAAA
39657853 ATTTAGAAAAATAATATCAAAA
1 ATTTA-AAAAATAATATCAAAA
39657875 AT
1 AT
39657877 ATATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTTAAAAAATAATATCAAAA
Found at i:39657876 original size:34 final size:35
Alignment explanation
Indices: 39657837--39657904 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
39657827 TTAATATTTA
39657837 AAAAATA-ATATTTAAAATTTAGAAAAATA-ATATC
1 AAAAATATATATTTAAAATTTA-AAAAATATATATC
39657871 AAAAATATATATTTAAAATTTAAAAAATATATAT
1 AAAAATATATATTTAAAATTTAAAAAATATATAT
39657905 TATAAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 14 0.44
35 18 0.56
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAAATATATATTTAAAATTTAAAAAATATATATC
Found at i:39657963 original size:14 final size:14
Alignment explanation
Indices: 39657940--39657979 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39657930 CAAGTTTTTT
* *
39657940 AAAATTAATAATAC
1 AAAATAAATAAAAC
*
39657954 AAAATAAATAAAAT
1 AAAATAAATAAAAC
39657968 AAAATAAATAAA
1 AAAATAAATAAA
39657980 GATAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAATAAAAC
Found at i:39659197 original size:3 final size:3
Alignment explanation
Indices: 39659183--39659236 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
39659173 GACAATAAAG
*
39659183 AAT AAT AGT AAT AAT AAT AAT -AT AGAT AAT AAT -AT ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT
39659227 AAT AAT AAT A
1 AAT AAT AAT A
39659237 GTTAGAGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.73
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39659459 original size:3 final size:3
Alignment explanation
Indices: 39659451--39659501 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
39659441 TATAAATATG
* * * *
39659451 ATA ATA ATA ATA ATG ATA ATG ATA ATA ATA ATA AT- ATA GTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39659498 ATA A
1 ATA A
39659502 AAGTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39659901 original size:17 final size:17
Alignment explanation
Indices: 39659846--39659905 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
39659836 AAATAATATT
39659846 AAAATATATACGAGTAATAA
1 AAAATATATAC-A-TAAT-A
* * * *
39659866 AAAATGTATCCGTATTA
1 AAAATATATACATAATA
39659883 AAAATATATACATAATA
1 AAAATATATACATAATA
39659900 AAAATA
1 AAAATA
39659906 CAATATTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 20 0.62
18 3 0.09
20 9 0.28
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (17 bp):
AAAATATATACATAATA
Found at i:39660071 original size:43 final size:41
Alignment explanation
Indices: 39659976--39660072 Score: 94
Period size: 41 Copynumber: 2.4 Consensus size: 41
39659966 TATTACATAG
*
39659976 ATATATACATATATAAAAAAATAAATACATGATAATATTAA
1 ATATATACATACATAAAAAAATAAATACATGATAATATTAA
* * *
39660017 A-AGTAT--GTACATAACATAAATATCATACAT-ATAATATCTAA
1 ATA-TATACATACATAA-AAAAATA-AATACATGATAATAT-TAA
39660058 ATATATACATACATA
1 ATATATACATACATA
39660073 TATATGTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
39 6 0.14
40 14 0.32
41 17 0.39
42 1 0.02
43 6 0.14
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (41 bp):
ATATATACATACATAAAAAAATAAATACATGATAATATTAA
Found at i:39660075 original size:22 final size:22
Alignment explanation
Indices: 39660033--39660075 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39660023 GTACATAACA
*
39660033 TAAATATCATACATATAATATC
1 TAAATATCATACATACAATATC
39660055 TAAATAT-ATACATACATATAT
1 TAAATATCATACATACA-ATAT
39660076 ATGTAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATCATACATACAATATC
Found at i:39660246 original size:15 final size:14
Alignment explanation
Indices: 39660221--39660256 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
39660211 TAATAATACT
39660221 ATATAATATATATA
1 ATATAATATATATA
39660235 ATATACATATATATA
1 ATATA-ATATATATA
39660250 AGTATAA
1 A-TATAA
39660257 CAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:39660964 original size:18 final size:18
Alignment explanation
Indices: 39660941--39660981 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39660931 TTCGAAATAA
39660941 AATAAAAAGGAAA-AAAAT
1 AATAAAAA-GAAAGAAAAT
*
39660959 AATAAATAGAAAGAAAAT
1 AATAAAAAGAAAGAAAAT
39660977 AATAA
1 AATAA
39660982 TAATGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (18 bp):
AATAAAAAGAAAGAAAAT
Found at i:39660980 original size:21 final size:22
Alignment explanation
Indices: 39660940--39660984 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
39660930 ATTCGAAATA
39660940 AAATAAAAAGGAAAAAAATAAT
1 AAATAAAAAGGAAAAAAATAAT
* *
39660962 AAATAGAAA-GAAAATAATAAT
1 AAATAAAAAGGAAAAAAATAAT
39660983 AA
1 AA
39660985 TGTAATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (22 bp):
AAATAAAAAGGAAAAAAATAAT
Found at i:39661952 original size:14 final size:14
Alignment explanation
Indices: 39661930--39661964 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
39661920 ACTGTTAGCA
*
39661930 AGTTATTAAGAAGT
1 AGTTATTAAAAAGT
*
39661944 AGTTGTTAAAAAGT
1 AGTTATTAAAAAGT
39661958 AGTTATT
1 AGTTATT
39661965 CCATAAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AGTTATTAAAAAGT
Found at i:39662079 original size:40 final size:40
Alignment explanation
Indices: 39662024--39662107 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
39662014 AGTCTAAATA
39662024 CAAAATTACTTTCTTCAGGTTATTATATTAATTTTCCCTT
1 CAAAATTACTTTCTTCAGGTTATTATATTAATTTTCCCTT
39662064 CAAAATTACTTTCTTCAGGTTATTATATTAATTTTCCCTT
1 CAAAATTACTTTCTTCAGGTTATTATATTAATTTTCCCTT
39662104 CAAA
1 CAAA
39662108 TTTTAGTGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (40 bp):
CAAAATTACTTTCTTCAGGTTATTATATTAATTTTCCCTT
Found at i:39663938 original size:21 final size:24
Alignment explanation
Indices: 39663896--39663940 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39663886 TTTGGGTTAA
39663896 TTTATTTTTTGTTCCAATTTTGGT
1 TTTATTTTTTGTTCCAATTTTGGT
39663920 TTTATTTTTT-TT-C-ATTTTGGT
1 TTTATTTTTTGTTCCAATTTTGGT
39663941 ATCTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 1 0.05
23 2 0.10
24 10 0.48
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.71
Consensus pattern (24 bp):
TTTATTTTTTGTTCCAATTTTGGT
Found at i:39664360 original size:16 final size:17
Alignment explanation
Indices: 39664335--39664368 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39664325 TATATTGATT
*
39664335 GTTTTTTTTAA-AAAAA
1 GTTTTATTTAAGAAAAA
39664351 GTTTTATTTAAGAAAAA
1 GTTTTATTTAAGAAAAA
39664368 G
1 G
39664369 AATAGTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
GTTTTATTTAAGAAAAA
Found at i:39664763 original size:2 final size:2
Alignment explanation
Indices: 39664756--39664780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39664746 GGTAACTTTC
39664756 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39664781 ACAAGAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39666385 original size:14 final size:14
Alignment explanation
Indices: 39666359--39666389 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39666349 ATCAAAACAA
39666359 TAACAATAAAATAG
1 TAACAATAAAATAG
*
39666373 TAACAATATAATAG
1 TAACAATAAAATAG
39666387 TAA
1 TAA
39666390 AATGACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAACAATAAAATAG
Found at i:39674355 original size:16 final size:17
Alignment explanation
Indices: 39674325--39674356 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39674315 GTTATCAGAT
39674325 AATTAAATATTTAAAAA
1 AATTAAATATTTAAAAA
39674342 AATTAAAT-TTTAAAA
1 AATTAAATATTTAAAA
39674357 TCTAAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATATTTAAAAA
Found at i:39680543 original size:18 final size:18
Alignment explanation
Indices: 39680512--39680546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39680502 ATAAAAAAAA
**
39680512 CTTTTAAATTTTTTTTAT
1 CTTTTAAAAGTTTTTTAT
39680530 CTTTTAAAAGTTTTTTA
1 CTTTTAAAAGTTTTTTA
39680547 AAAAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
CTTTTAAAAGTTTTTTAT
Found at i:39696801 original size:14 final size:14
Alignment explanation
Indices: 39696784--39696813 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39696774 AAAACTGGGC
39696784 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
39696798 AAGGAAAAATGGAA
1 AAGGAAAAATGGAA
39696812 AA
1 AA
39696814 AAAATGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
AAGGAAAAATGGAA
Found at i:39711569 original size:39 final size:39
Alignment explanation
Indices: 39711523--39711701 Score: 295
Period size: 39 Copynumber: 4.6 Consensus size: 39
39711513 GTTCTGATGA
39711523 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
**
39711562 GCTTCAGTTAGCCTTCACGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
39711601 GCTTCAGTTAGCCTCCGGGTTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
39711640 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
39711679 GCTTCAGCTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
39711702 AGATCATGAT
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 129 1.00
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:39716073 original size:26 final size:26
Alignment explanation
Indices: 39716037--39716172 Score: 245
Period size: 26 Copynumber: 5.2 Consensus size: 26
39716027 TGATACAAAT
* *
39716037 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
39716063 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39716089 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39716115 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39716141 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
39716167 TGATAA
1 TGATAA
39716173 GAATTTCATG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 108 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:39717680 original size:25 final size:26
Alignment explanation
Indices: 39717652--39717703 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
39717642 TTTACAGTTT
39717652 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
39717677 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
39717703 T
1 T
39717704 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:39718817 original size:2 final size:2
Alignment explanation
Indices: 39718810--39718835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39718800 GGGTGCTACA
39718810 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39718836 TAAATTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39719579 original size:11 final size:12
Alignment explanation
Indices: 39719555--39719580 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39719545 ATTATTTTAA
39719555 TTTTTAGAATTT
1 TTTTTAGAATTT
39719567 TTTTTAGAATTT
1 TTTTTAGAATTT
39719579 TT
1 TT
39719581 ATAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTAGAATTT
Found at i:39719591 original size:19 final size:20
Alignment explanation
Indices: 39719569--39719622 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
39719559 TAGAATTTTT
39719569 TTTAGAATTTTTATAAA-TA
1 TTTAGAATTTTTATAAATTA
*
39719588 TTTAGAA-TTTTAAAAATTA
1 TTTAGAATTTTTATAAATTA
*
39719607 TTTTGAATTTTT-TAAA
1 TTTAGAATTTTTATAAA
39719623 ATTGTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.27
19 18 0.60
20 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTAGAATTTTTATAAATTA
Found at i:39727854 original size:15 final size:15
Alignment explanation
Indices: 39727834--39727863 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39727824 GTTAGCAAAA
39727834 GGATGGTGGGGGAAG
1 GGATGGTGGGGGAAG
39727849 GGATGGTGGGGGAAG
1 GGATGGTGGGGGAAG
39727864 AGGGAGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.67, T:0.13
Consensus pattern (15 bp):
GGATGGTGGGGGAAG
Found at i:39729758 original size:22 final size:21
Alignment explanation
Indices: 39729714--39729758 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
39729704 ATTTTTATAC
*
39729714 TTTTTAATTTTTTAAAATATT
1 TTTTTAAATTTTTAAAATATT
*
39729735 TTTTATAAATTTTTAGAAT-TT
1 TTTT-TAAATTTTTAAAATATT
39729756 TTT
1 TTT
39729759 AAATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTAAATTTTTAAAATATT
Found at i:39731214 original size:24 final size:23
Alignment explanation
Indices: 39731143--39731216 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
39731133 TCTAGTTGAG
*
39731143 ATAATTATATATTTAAAAATAATT
1 ATAATTA-ATATTTAAAAATAAGT
* *
39731167 ATAATT--TA-ATAAAAAT-TGT
1 ATAATTAATATTTAAAAATAAGT
39731186 GATAATTACATATTTAAAAATAAGT
1 -ATAATTA-ATATTTAAAAATAAGT
39731211 ATAATT
1 ATAATT
39731217 TAATTTACAG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 1 0.03
20 13 0.33
21 2 0.05
23 2 0.05
24 19 0.49
25 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (23 bp):
ATAATTAATATTTAAAAATAAGT
Found at i:39734253 original size:3 final size:3
Alignment explanation
Indices: 39734247--39734571 Score: 189
Period size: 3 Copynumber: 106.0 Consensus size: 3
39734237 CTATTATTCC
* * * * *
39734247 TAT TAT TTT TAT TAT TACC TAT TAT CAA TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
39734293 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
39734341 TAT TAT TAT TAT TAT TAT TGT TGT TGT TGT TAT TAT TAT TAT GAT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * ** * * * * *
39734389 T-T T-T TGGT TAA TAT TGC TAT TAT GAT TA- TAC T-T TCT TTT TGT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
39734431 GT-T TATT TATT TAT TCAT T-T TAT TAT TAGT CCAT TAAT TCAT TGT TAC
1 -TAT TA-T TA-T TAT T-AT TAT TAT TAT TA-T -TAT T-AT T-AT TAT TAT
* * * * * * *
39734479 TAA CA- TAT TCT TAT TAT TTT TAT TAACG TAT TAT TAT TATT TGT TGCT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TA-T TAT T-AT
39734527 CTAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39734572 CAATATTTAC
Statistics
Matches: 259, Mismatches: 43, Indels: 40
0.76 0.13 0.12
Matches are distributed among these distances:
2 13 0.05
3 214 0.83
4 29 0.11
5 3 0.01
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:39734823 original size:37 final size:35
Alignment explanation
Indices: 39734781--39734878 Score: 87
Period size: 34 Copynumber: 2.8 Consensus size: 35
39734771 GTATTTCAAA
39734781 ATTATTGTTACTATTATTATTATTATTATTAATTTTT
1 ATTATT-TTACTATTATTATTATTATTATTAA-TTTT
* * * *
39734818 ATTATTTGAC-A-TATTATTGTTATCACTAATTTT
1 ATTATTTTACTATTATTATTATTATTATTAATTTT
* *
39734851 -TT-TTCTTACTGTCATTATTATTATTATT
1 ATTATT-TTACTATTATTATTATTATTATT
39734879 TTTCTATTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
31 2 0.04
32 5 0.10
33 4 0.08
34 27 0.56
35 1 0.02
36 3 0.06
37 6 0.12
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (35 bp):
ATTATTTTACTATTATTATTATTATTATTAATTTT
Found at i:39734833 original size:34 final size:36
Alignment explanation
Indices: 39734793--39734878 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 36
39734783 TATTGTTACT
*
39734793 ATTATTATTATTATTATTAATTTTTATTATT-TGAC
1 ATTATTATTATTATTACTAATTTTTATTATTATGAC
* * * * *
39734828 A-TATTATTGTTATCACTAATTTTTTTTCTTACTGTC
1 ATTATTATTATTATTACTAATTTTTATTATTA-TGAC
39734864 ATTATTATTATTATT
1 ATTATTATTATTATT
39734879 TTTCTATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
34 24 0.60
35 1 0.03
36 4 0.10
37 11 0.28
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (36 bp):
ATTATTATTATTATTACTAATTTTTATTATTATGAC
Found at i:39734835 original size:3 final size:3
Alignment explanation
Indices: 39734781--39734823 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
39734771 GTATTTCAAA
* * *
39734781 ATT ATT GTT ACT ATT ATT ATT ATT ATT ATT AATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
39734824 TGACATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39735002 original size:16 final size:17
Alignment explanation
Indices: 39734983--39735020 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
39734973 AGGTACTAAT
39734983 ATTATATTTTAC-TATC
1 ATTATATTTTACTTATC
*
39734999 ATTATATTTTTCTTATC
1 ATTATATTTTACTTATC
39735016 ATTAT
1 ATTAT
39735021 CATCACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATTTTACTTATC
Found at i:39738692 original size:20 final size:20
Alignment explanation
Indices: 39738669--39738707 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39738659 TAATTTCTCT
39738669 AATTTAATTTATAAAATTTG
1 AATTTAATTTATAAAATTTG
* *
39738689 AATTTACTTTATGAAATTT
1 AATTTAATTTATAAAATTT
39738708 AAAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
AATTTAATTTATAAAATTTG
Found at i:39742855 original size:7 final size:7
Alignment explanation
Indices: 39742844--39742873 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39742834 TTTTACACAC
39742844 ATCAACT
1 ATCAACT
*
39742851 TTCAACT
1 ATCAACT
39742858 ATCAACT
1 ATCAACT
39742865 ATCAACT
1 ATCAACT
39742872 AT
1 AT
39742874 ATTTTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (7 bp):
ATCAACT
Found at i:39743627 original size:21 final size:22
Alignment explanation
Indices: 39743577--39743632 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
39743567 AATTTATGTA
**
39743577 ATTATATTTGTTTATATGATTT
1 ATTATATTACTTTATATGATTT
* *
39743599 -TTAAATTACTTTATAT-TTTT
1 ATTATATTACTTTATATGATTT
39743619 ATTATATTAGCTTT
1 ATTATATTA-CTTT
39743633 TAATGGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTATATTACTTTATATGATTT
Found at i:39745495 original size:25 final size:22
Alignment explanation
Indices: 39745471--39745516 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39745461 AAAAAATTTA
*
39745471 AAATTATATATTTATATTATTTTT
1 AAATTA-ATATTTA-ATGATTTTT
*
39745495 AATTTAATATTTAATGATTTTT
1 AAATTAATATTTAATGATTTTT
39745517 TATTCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATTAATATTTAATGATTTTT
Found at i:39745633 original size:22 final size:22
Alignment explanation
Indices: 39745608--39745649 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39745598 AATTTTTATG
* *
39745608 TTTATAAATTACATAATATATT
1 TTTAAAAATAACATAATATATT
*
39745630 TTTAAAAATAATATAATATA
1 TTTAAAAATAACATAATATA
39745650 AAACCTTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAAAATAACATAATATATT
Found at i:39749407 original size:2 final size:2
Alignment explanation
Indices: 39749400--39749435 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39749390 GTTTTAGTTC
*
39749400 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39749436 TGCTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39749515 original size:18 final size:18
Alignment explanation
Indices: 39749488--39749526 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
39749478 TACAGGCTGC
39749488 AATCACTTATATAAATGG
1 AATCACTTATATAAATGG
*
39749506 AATCAGTTATATAAATGG
1 AATCACTTATATAAATGG
39749524 AAT
1 AAT
39749527 TGATCGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (18 bp):
AATCACTTATATAAATGG
Found at i:39750620 original size:3 final size:3
Alignment explanation
Indices: 39750612--39750647 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39750602 GAATATAGAA
39750612 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39750648 GACACAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39750720 original size:15 final size:15
Alignment explanation
Indices: 39750702--39750731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39750692 AAATTTTAAT
*
39750702 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
39750717 TTTTTATAATTTATA
1 TTTTTATAATTTATA
39750732 AATAATTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:39752384 original size:34 final size:34
Alignment explanation
Indices: 39752334--39752410 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
39752324 ATTTTCATCA
* *
39752334 TAAT-AAT-TTCTTTCAAAGTTGATCCATAATGT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
39752366 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
1 TAATGAATCTTCTTTCAAAATTGATCCATAATAT
39752400 TAATGAATCTT
1 TAATGAATCTT
39752411 TTACATGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 4 0.10
33 3 0.07
34 34 0.83
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (34 bp):
TAATGAATCTTCTTTCAAAATTGATCCATAATAT
Found at i:39755300 original size:19 final size:19
Alignment explanation
Indices: 39755246--39755294 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
39755236 GACATTGGAC
* *
39755246 TTTATTATTTAT-TTATTTA
1 TTTATTTTTTATATT-TTAA
39755265 TTTATTTTTTATATTTTAA
1 TTTATTTTTTATATTTTAA
*
39755284 TTTGTTTTTTA
1 TTTATTTTTTA
39755295 GTTTTTGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTATTTTTTATATTTTAA
Found at i:39755893 original size:12 final size:12
Alignment explanation
Indices: 39755876--39755913 Score: 53
Period size: 10 Copynumber: 3.2 Consensus size: 12
39755866 TATTTTGATA
39755876 ATTTATCATAAT
1 ATTTATCATAAT
39755888 ATTTATCAT--T
1 ATTTATCATAAT
39755898 ATTTATCATAAAT
1 ATTTATCAT-AAT
39755911 ATT
1 ATT
39755914 CAATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
12 9 0.39
13 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTATCATAAT
Found at i:39757513 original size:47 final size:47
Alignment explanation
Indices: 39757365--39757488 Score: 221
Period size: 47 Copynumber: 2.6 Consensus size: 47
39757355 GTACATAGTG
39757365 CTTCATCGGAACAAATCCGGAACTTTAACATTATAGTACACAAAGTA
1 CTTCATCGGAACAAATCCGGAACTTTAACATTATAGTACACAAAGTA
*
39757412 CTTCATCAGAACAAATCCGGAACTTTAACATTATAGTACACAAAGTA
1 CTTCATCGGAACAAATCCGGAACTTTAACATTATAGTACACAAAGTA
**
39757459 CTTCATCGGAACAAATCCAAAACTTTAACA
1 CTTCATCGGAACAAATCCGGAACTTTAACA
39757489 GTAGTCGACA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (47 bp):
CTTCATCGGAACAAATCCGGAACTTTAACATTATAGTACACAAAGTA
Found at i:39758011 original size:14 final size:14
Alignment explanation
Indices: 39757988--39758031 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
39757978 TCATAAATCT
39757988 ATATTCAATATAATA
1 ATATT-AATATAATA
39758003 ATATTAATA-ATATA
1 ATATTAATATA-ATA
*
39758017 ATATTATTATAATA
1 ATATTAATATAATA
39758031 A
1 A
39758032 AATAACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 19 0.73
15 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAATATAATA
Found at i:39759293 original size:19 final size:19
Alignment explanation
Indices: 39759257--39759312 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
39759247 ACGTGAGAGT
*
39759257 AATAA-AAGAA-ATAATAA
1 AATAACAAGAATAAAATAA
39759274 AATAACAAGAATAAAATAA
1 AATAACAAGAATAAAATAA
* *
39759293 AATAACGACAATAATAATAA
1 AATAACAAGAATAA-AATAA
39759313 CTGAGCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 18 0.55
20 5 0.15
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AATAACAAGAATAAAATAA
Found at i:39764879 original size:25 final size:27
Alignment explanation
Indices: 39764842--39764894 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39764832 TCAAACATGC
39764842 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
39764868 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
39764894 A
1 A
39764895 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:39766412 original size:26 final size:26
Alignment explanation
Indices: 39766376--39766459 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
39766366 CATGAAATTC
39766376 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39766402 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39766428 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39766454 TTATCA
1 TTATCA
39766460 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39767986 original size:136 final size:135
Alignment explanation
Indices: 39767741--39768024 Score: 525
Period size: 136 Copynumber: 2.1 Consensus size: 135
39767731 CATTGGGCCT
**
39767741 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39767806 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCA-T-AA
39767871 CATATGC
129 CATATGC
39767878 AAGCCCATTTGGGTAACAGTGGTACT-GGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
39767942 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCATAACA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCATAACA
39768007 TATGC
131 TATGC
39768012 AAGCCCATTTGGG
1 AAGCCCATTTGGG
39768025 GAGACTACTC
Statistics
Matches: 145, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
134 22 0.15
135 1 0.01
136 98 0.68
137 24 0.17
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (135 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCATAACA
TATGC
Found at i:39768309 original size:25 final size:27
Alignment explanation
Indices: 39768272--39768324 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39768262 TCAAACATGC
39768272 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
39768298 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
39768324 A
1 A
39768325 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:39769841 original size:26 final size:26
Alignment explanation
Indices: 39769805--39769939 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
39769795 CATGAAATTC
*
39769805 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
39769831 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
39769857 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
39769883 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
39769909 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
39769934 TTATCA
1 TTATCA
39769940 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 23 0.21
26 84 0.79
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:39773392 original size:17 final size:17
Alignment explanation
Indices: 39773370--39773407 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39773360 AAAAAGGAGA
39773370 AAAAAAACTATATGTAC
1 AAAAAAACTATATGTAC
39773387 AAAAAAACTATATGTAC
1 AAAAAAACTATATGTAC
39773404 AAAA
1 AAAA
39773408 TACATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAAACTATATGTAC
Found at i:39773850 original size:2 final size:2
Alignment explanation
Indices: 39773843--39773878 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39773833 ACTAAAAAGC
39773843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39773879 AGAACAACAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39775393 original size:40 final size:40
Alignment explanation
Indices: 39775331--39775407 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
39775321 AGACCATGTG
* *
39775331 GGGATGAAATCGACTCACCCAGCCCTACACACCAAGTATA
1 GGGATAAAATCGACCCACCCAGCCCTACACACCAAGTATA
* *
39775371 GGGATAAAATTGACCCATCCAGCCCTACACACCAAGT
1 GGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
39775408 GGTACTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.16
Consensus pattern (40 bp):
GGGATAAAATCGACCCACCCAGCCCTACACACCAAGTATA
Found at i:39782942 original size:30 final size:30
Alignment explanation
Indices: 39782908--39782966 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39782898 GCCCTTGTGG
* *
39782908 TTCACCCATGTGACCCACAAGCCCGTGCGA
1 TTCACCCATGTAACCCACAAGCCCATGCGA
**
39782938 TTCACCTGTGTAACCCACAAGCCCATGCG
1 TTCACCCATGTAACCCACAAGCCCATGCG
39782967 GTTTACACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.39, G:0.19, T:0.19
Consensus pattern (30 bp):
TTCACCCATGTAACCCACAAGCCCATGCGA
Found at i:39783979 original size:40 final size:40
Alignment explanation
Indices: 39783924--39784002 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
39783914 ACAAACCATG
*
39783924 TAGGGATAAAATCGACCCACCCAGCCTTACACACCAAGTA
1 TAGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
* *
39783964 TAGGGATAAAATCGACCCATCTAGCCCTACACACCAAGT
1 TAGGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
39784003 GGTACAGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.16
Consensus pattern (40 bp):
TAGGGATAAAATCGACCCACCCAGCCCTACACACCAAGTA
Found at i:39788164 original size:47 final size:47
Alignment explanation
Indices: 39788111--39788236 Score: 171
Period size: 47 Copynumber: 2.7 Consensus size: 47
39788101 TCGATAAATT
* * *
39788111 CCTATACCATGGCCTGTAGTCAAATCAAGGTAACTTATCCCGGAGTA
1 CCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGGAATA
* * * ***
39788158 CCTATACCATGACCCGTAGCCAAATCAAGGTAACTCCTCTTTGAATA
1 CCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGGAATA
39788205 CCTATACCATGACCTGTAGTCAAATCAAGGTA
1 CCTATACCATGACCTGTAGTCAAATCAAGGTA
39788237 TCATTCGCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (47 bp):
CCTATACCATGACCTGTAGTCAAATCAAGGTAACTCATCCCGGAATA
Found at i:39791693 original size:33 final size:33
Alignment explanation
Indices: 39791590--39791708 Score: 108
Period size: 33 Copynumber: 3.7 Consensus size: 33
39791580 TTGATCTCAT
* *
39791590 TATGAAAAGGAAATGTATACTTTGTGTGTACCA
1 TATGAAAAGGAAATGTATACTTTGTGTATACAA
* *
39791623 TGTGAAAAGG----G-ATAGCTTCG-GCTAT-CGAA
1 TATGAAAAGGAAATGTATA-CTTTGTG-TATAC-AA
*
39791652 TATGAAAAGGAAATGTATACTTTGTGTATACTA
1 TATGAAAAGGAAATGTATACTTTGTGTATACAA
*
39791685 TATGAAAAGGAAAGGTATACTTTG
1 TATGAAAAGGAAATGTATACTTTG
39791709 AAAAGGGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
28 5 0.07
29 17 0.25
33 41 0.60
34 5 0.07
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (33 bp):
TATGAAAAGGAAATGTATACTTTGTGTATACAA
Found at i:39793694 original size:33 final size:33
Alignment explanation
Indices: 39793629--39793697 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
39793619 ACAGTTAAGA
* *
39793629 GAGCTTGCAGTATCGACTCACAAGAGTTGAAGG
1 GAGCTCGCAGTATCGACTCACAAGAGTCGAAGG
* ** *
39793662 GAGCTCGCAGTATCGGCTTGCATGAGTCGAAGG
1 GAGCTCGCAGTATCGACTCACAAGAGTCGAAGG
39793695 GAG
1 GAG
39793698 TTCACGGTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.20
Consensus pattern (33 bp):
GAGCTCGCAGTATCGACTCACAAGAGTCGAAGG
Found at i:39795622 original size:12 final size:12
Alignment explanation
Indices: 39795605--39795638 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39795595 AAGGAGAAGC
*
39795605 AAAAAAGAATGA
1 AAAAAAGAAAGA
*
39795617 AAAAAAAAAAGA
1 AAAAAAGAAAGA
39795629 AAAAAAGAAA
1 AAAAAAGAAA
39795639 AGTTAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:39795639 original size:16 final size:17
Alignment explanation
Indices: 39795605--39795663 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 17
39795595 AAGGAGAAGC
**
39795605 AAAAAAGAATGAAAA-A
1 AAAAAAGAACAAAAAGA
39795621 AAAAAAGAA-AAAAAGA
1 AAAAAAGAACAAAAAGA
39795637 AAAGTTAAAGAACATAAAAGA
1 AAA---AAAGAACA-AAAAGA
39795658 AAAAAA
1 AAAAAA
39795664 ATTAAATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.11
16 13 0.36
18 3 0.08
19 6 0.17
20 1 0.03
21 9 0.25
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAAAAGAACAAAAAGA
Found at i:39797127 original size:3 final size:3
Alignment explanation
Indices: 39797085--39797117 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39797075 ACTAAATTTG
39797085 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39797118 TGGTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39803355 original size:31 final size:31
Alignment explanation
Indices: 39803317--39803377 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
39803307 AAATGAAGAG
39803317 AGTGGGTGTAACATCCCAAAAATTATGTTAT
1 AGTGGGTGTAACATCCCAAAAATTATGTTAT
39803348 AGTGGGTGTAACATCCCAAAAATTATGTTA
1 AGTGGGTGTAACATCCCAAAAATTATGTTA
39803378 GAAGAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTGGGTGTAACATCCCAAAAATTATGTTAT
Found at i:39804888 original size:42 final size:43
Alignment explanation
Indices: 39804807--39804922 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
39804797 TCTCAGACGT
* *
39804807 GGTCTTACATGTAATCAAACATCGATGCCACTATCCTAGATAG
1 GGTCTTACATGAAATCAAACATCGATGCCACTATCCTAGACAG
* * * *
39804850 GGTCTTACATGAAATCAAATA-CGATGTCGA-TGTCCTAGACAT
1 GGTCTTACATGAAATCAAACATCGATG-CCACTATCCTAGACAG
* * *
39804892 GGTCTTAAATGTAAAACAAAAATCGATGCCA
1 GGTCTTACATG-AAATCAAACATCGATGCCA
39804923 ATTTTCCAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 24 0.40
43 31 0.52
44 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGAAATCAAACATCGATGCCACTATCCTAGACAG
Found at i:39807730 original size:31 final size:31
Alignment explanation
Indices: 39807666--39807731 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
39807656 TAAATGCAAT
*
39807666 GTGATACACCATCATTGTCGGGCAACCTAGG
1 GTGATACACCATCATTGTCGGGCAACCCAGG
* * * *
39807697 GTGATAGATCATCATTGTTGGGCAACCCGGG
1 GTGATACACCATCATTGTCGGGCAACCCAGG
39807728 GTGA
1 GTGA
39807732 CCTGTTTGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.24
Consensus pattern (31 bp):
GTGATACACCATCATTGTCGGGCAACCCAGG
Found at i:39814552 original size:13 final size:13
Alignment explanation
Indices: 39814534--39814559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39814524 CTGTGCATTC
39814534 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39814547 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39814560 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:39816585 original size:5 final size:5
Alignment explanation
Indices: 39816547--39816572 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39816537 TAACCCAAGT
39816547 ACCCA ACCCA ACCCA ACCCA ACCCA A
1 ACCCA ACCCA ACCCA ACCCA ACCCA A
39816573 TTTCCCAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:39816631 original size:14 final size:14
Alignment explanation
Indices: 39816614--39816640 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39816604 AATTAATAAA
39816614 TAAAAATAAAAATC
1 TAAAAATAAAAATC
39816628 TAAAAATAAAAAT
1 TAAAAATAAAAAT
39816641 AAAAAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAAATAAAAATC
Found at i:39816638 original size:5 final size:6
Alignment explanation
Indices: 39816588--39816645 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
39816578 CAACCCAATC
* *
39816588 ATAAAA ATTACAA AT-AAA TTAATAA ATAAAA ATAAAA ATCTAAAA ATAAAA
1 ATAAAA A-TAAAA ATAAAA ATAA-AA ATAAAA ATAAAA A--TAAAA ATAAAA
39816639 ATAAAA A
1 ATAAAA A
39816646 ACATATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 3 0.07
6 24 0.56
7 10 0.23
8 6 0.14
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.22
Consensus pattern (6 bp):
ATAAAA
Found at i:39816688 original size:18 final size:18
Alignment explanation
Indices: 39816665--39816715 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
39816655 TTTATACAAA
**
39816665 TAATTCGGTTAATTTGGG
1 TAATTCGGTTAATTTAAG
* *
39816683 TAATTCAGG-TAATTCAAT
1 TAATTC-GGTTAATTTAAG
39816701 TAATTCGGTTAATTT
1 TAATTCGGTTAATTT
39816716 TATACTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (18 bp):
TAATTCGGTTAATTTAAG
Found at i:39819370 original size:61 final size:61
Alignment explanation
Indices: 39819275--39819403 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
39819265 GTGGGAAATC
* * * *
39819275 AACACTGCATGGACTTCCCTACACGGGTATACCACACGCCCGTATAGTGTT-AGCAGACTCT
1 AACACGGCATGGACTTCCCTACACGGGTAGACCACACGCCCGTAT-CTATTCAGCAGACTCT
* * * *
39819336 AACACGGCCTGGACTTCCTTACACGGGTAGACCACACGGCCGTGTCTATTCAGCAGACTCT
1 AACACGGCATGGACTTCCCTACACGGGTAGACCACACGCCCGTATCTATTCAGCAGACTCT
39819397 AACACGG
1 AACACGG
39819404 TTTGAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
60 3 0.05
61 56 0.95
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.21
Consensus pattern (61 bp):
AACACGGCATGGACTTCCCTACACGGGTAGACCACACGCCCGTATCTATTCAGCAGACTCT
Found at i:39820255 original size:13 final size:13
Alignment explanation
Indices: 39820237--39820262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39820227 CTGTGCATTC
39820237 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39820250 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
39820263 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:39824113 original size:40 final size:39
Alignment explanation
Indices: 39824069--39824164 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 39
39824059 ACGGTACCAT
* * *
39824069 TTGGTGTGTAGGGTTGGACAGGTTGATTTTATCCCTATA
1 TTGGTGTGTAGGGTTGGACAGGTCGATTCTATCCCAATA
* * **
39824108 CTTGGTGTGTAAGGCTGGGTAGGTCGATTCTATCCCAATA
1 -TTGGTGTGTAGGGTTGGACAGGTCGATTCTATCCCAATA
*
39824148 -TGGTGTGTTGGGTTGGA
1 TTGGTGTGTAGGGTTGGA
39824165 TGAATATAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 13 0.29
40 32 0.71
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.38
Consensus pattern (39 bp):
TTGGTGTGTAGGGTTGGACAGGTCGATTCTATCCCAATA
Found at i:39826042 original size:18 final size:19
Alignment explanation
Indices: 39826019--39826076 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
39826009 ACGTGGCAGT
*
39826019 CCAACTAGATTT-TAGATG
1 CCAACTAGATTTCTAAATG
*
39826037 CCAACTTGGATTTCTAAATG
1 CCAAC-TAGATTTCTAAATG
*
39826057 CCAACTTGGATTTCTAAATG
1 CCAAC-TAGATTTCTAAATG
39826077 GGATGAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.14
19 6 0.17
20 25 0.69
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (19 bp):
CCAACTAGATTTCTAAATG
Found at i:39826059 original size:20 final size:20
Alignment explanation
Indices: 39826034--39826076 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
39826024 TAGATTTTAG
39826034 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
39826054 ATGCCAACTTGGATTTCTAA
1 ATGCCAACTTGGATTTCTAA
39826074 ATG
1 ATG
39826077 GGATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGCCAACTTGGATTTCTAA
Found at i:39826813 original size:16 final size:17
Alignment explanation
Indices: 39826772--39826814 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
39826762 ATTTAGGGTT
39826772 TAAAATT-TTTAATTAA
1 TAAAATTATTTAATTAA
*
39826788 TTAAATTTATTTAATTAA
1 -TAAAATTATTTAATTAA
39826806 -AAAATTATT
1 TAAAATTATT
39826815 CTCATTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 6 0.26
18 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATTATTTAATTAA
Found at i:39831120 original size:18 final size:18
Alignment explanation
Indices: 39831089--39831123 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39831079 ATAACTCAAT
**
39831089 TATTTTATTTTATTTTTA
1 TATTTTATAATATTTTTA
39831107 TATTTTATAATATTTTT
1 TATTTTATAATATTTTT
39831124 TATCTATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTATAATATTTTTA
Found at i:39834376 original size:27 final size:28
Alignment explanation
Indices: 39834344--39834407 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
39834334 CATAAATTTT
* *
39834344 TAAAATATAG--AAATATAAAAAATAATC
1 TAAAATATAGTAAAAT-TAAAAAACAATA
39834371 TAAAATA-AGTAAAATTAAAAAACAATA
1 TAAAATATAGTAAAATTAAAAAACAATA
39834398 TAAAAATATA
1 T-AAAATATA
39834408 CAAAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 18 0.58
28 10 0.32
29 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (28 bp):
TAAAATATAGTAAAATTAAAAAACAATA
Found at i:39835393 original size:21 final size:22
Alignment explanation
Indices: 39835367--39835417 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
39835357 AAACTAGCTT
* *
39835367 AACTAATTTAATAAT-AAAATA
1 AACTAATATAAAAATAAAAATA
39835388 AACTAA-ATAAAAATAAAAATA
1 AACTAATATAAAAATAAAAATA
*
39835409 AAATAATAT
1 AACTAATAT
39835418 CTTCCTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
AACTAATATAAAAATAAAAATA
Found at i:39838230 original size:4 final size:4
Alignment explanation
Indices: 39838223--39838250 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
39838213 CATATATATA
39838223 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
39838251 GACAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:39838740 original size:2 final size:2
Alignment explanation
Indices: 39838733--39838772 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39838723 TTCTTACTTT
39838733 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39838773 AATAATCTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39839786 original size:2 final size:2
Alignment explanation
Indices: 39839781--39839810 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39839771 GAATGTGTGA
39839781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39839811 GGTAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39846695 original size:22 final size:22
Alignment explanation
Indices: 39846670--39846714 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39846660 ATCCTGGTCT
*
39846670 CGTCGTGATGACCATCACTTGA
1 CGTCGCGATGACCATCACTTGA
*
39846692 CGTCGCGATGACCATTACTTGA
1 CGTCGCGATGACCATCACTTGA
39846714 C
1 C
39846715 ATCATGACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (22 bp):
CGTCGCGATGACCATCACTTGA
Found at i:39847127 original size:22 final size:24
Alignment explanation
Indices: 39847102--39847145 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
39847092 GGCACGTTAT
39847102 TTTTTGTTC-TGT-TTCTTCTTGG
1 TTTTTGTTCTTGTGTTCTTCTTGG
39847124 TTTTTGTTCTTGTGTTCTTCTT
1 TTTTTGTTCTTGTGTTCTTCTT
39847146 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTGTTCTTGTGTTCTTCTTGG
Found at i:39851945 original size:20 final size:20
Alignment explanation
Indices: 39851883--39851946 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39851873 ATGAGCATTT
*
39851883 TTAAATT-ATGTTTAATATATA
1 TTAAATTAATCTTTAAT-TA-A
* *
39851904 TT-AATTAATTCATTAA-TCA
1 TTAAATTAA-TCTTTAATTAA
39851923 TTAAATTAATCTTTAATTAA
1 TTAAATTAATCTTTAATTAA
39851943 TTAA
1 TTAA
39851947 CCTTAATCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
19 9 0.26
20 17 0.50
21 3 0.09
22 5 0.15
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAAATTAATCTTTAATTAA
Found at i:39852064 original size:416 final size:399
Alignment explanation
Indices: 39851318--39852064 Score: 1036
Period size: 400 Copynumber: 1.8 Consensus size: 399
39851308 TAATACACGA
*
39851318 GCTAGCTAAATCAAGCTCCCGGTACCTCAAAAACATAAAAATTACAAGAAAATGACTTTAAATTA
1 GCTAGCTAAATCAAGCTCCCGG-ACCTCAAAAACATAAAAATTACAAGAAAATGACTTGAAATTA
* *
39851383 CTTACCTAATAGGGATCAATAGTGAAAAGCTTTCACGGGTTTTCTTCTTTTCTTAGAATTGGTGG
65 CTTACCTAATAGGGATCAATAGTGAAAAGCTTTCAAGGGTTTTCTTCTTTTCTTAGAATTAGTGG
* * * * *
39851448 TTCGGTTGAAGAAAGAAGAAAATATGAGCATTTTAACTTATGTTTAATAGATATACATTATTAAT
130 TTCGATTGAAGAAAAAAGAAAAGATGAGCATTTTAAATTATGTTTAATAGATATAAATTATTAAT
* *
39851513 TCATTAATCATTTAATTAATCTTAATCTCAATAAAAAATTAATGTATGATAACATCATCCTCCAC
195 TAATTAATCATTTAATTAATCTTAATCTCAATAAAAAATTAATGGATGATAACATCATCCTCCAC
* * * * *
39851578 TAATTGATGAAACAAAATGGTTTAATTACCATTTTGAACCTTTTGCTAATTAAAAATCTATAGTG
260 TAATTGATGAAACAAAATAGTTTAATTACCATTTTGAACCTTTTCCTAATTAAAAATATACAGCG
39851643 ATAAAAAATTACAATTTAATCATTGTGCTTTAATTAAACAATTAATAAGACCAAACTTTAACAAA
325 ATAAAAAATTACAATTTAATCATTGTGCTTTAATTAAACAATTAATAAGACCAAACTTTAACAAA
39851708 CTTTTATATG
390 CTTTTATATG
* *
39851718 GCTAGCTAAATTAAGCTCCCATGG-CCTCAAAAACATAAAAATTACAAGATAATGACTTGAAATT
1 GCTAGCTAAATCAAGCTCCC--GGACCTCAAAAACATAAAAATTACAAGAAAATGACTTGAAATT
* * *
39851782 ACTTACCTAATATGGACTGAATAGTGAAAAGCTTTCAAAGGGTTTTTTTCTTTTCTTAGCAA-TA
64 ACTTACCTAATAGGGA-TCAATAGTGAAAAGCTTTC-AAGGGTTTTCTTCTTTTCTTAG-AATTA
* * * *
39851846 GTGGTTTGATTGAAGAAAAAAGTAACGATGAGCATTTTTAAATTATGTTTAATATATATTAATTA
126 GTGGTTCGATTGAAGAAAAAAGAAAAGATGAGCA-TTTTAAATTATGTTTAATAGATA-T-A--A
39851911 ATTCATTAATCATTAAATTAATC-TTTAATTAATTAACCTTAATCTCAATTAACAAAATTTAATG
186 ATT-ATT-A--ATT-AATTAATCATTTAATTAA-T---CTTAATCTCAA-TAA-AAAA-TTAATG
39851975 GATGATAACATCATCCTCCACTAATTGATG-AA-AAAATAGTTTAATTACCATTTTGAACCTTTT
239 GATGATAACATCATCCTCCACTAATTGATGAAACAAAATAGTTTAATTACCATTTTGAACCTTTT
39852038 CCTAATTAAAAATATACAGCGATAAAA
304 CCTAATTAAAAATATACAGCGATAAAA
39852065 TATTTATAAT
Statistics
Matches: 301, Mismatches: 24, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
400 72 0.24
401 18 0.06
402 51 0.17
403 23 0.08
404 1 0.00
405 1 0.00
407 3 0.01
408 3 0.01
409 1 0.00
411 12 0.04
412 8 0.03
415 11 0.04
416 56 0.19
417 6 0.02
418 35 0.12
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (399 bp):
GCTAGCTAAATCAAGCTCCCGGACCTCAAAAACATAAAAATTACAAGAAAATGACTTGAAATTAC
TTACCTAATAGGGATCAATAGTGAAAAGCTTTCAAGGGTTTTCTTCTTTTCTTAGAATTAGTGGT
TCGATTGAAGAAAAAAGAAAAGATGAGCATTTTAAATTATGTTTAATAGATATAAATTATTAATT
AATTAATCATTTAATTAATCTTAATCTCAATAAAAAATTAATGGATGATAACATCATCCTCCACT
AATTGATGAAACAAAATAGTTTAATTACCATTTTGAACCTTTTCCTAATTAAAAATATACAGCGA
TAAAAAATTACAATTTAATCATTGTGCTTTAATTAAACAATTAATAAGACCAAACTTTAACAAAC
TTTTATATG
Found at i:39854790 original size:14 final size:14
Alignment explanation
Indices: 39854771--39854815 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
39854761 AAAATTAGGA
39854771 AAATAACAAAACAT
1 AAATAACAAAACAT
*
39854785 AAATAACAAAGCAT
1 AAATAACAAAACAT
*
39854799 AAATAAAAAAACAT
1 AAATAACAAAACAT
39854813 AAA
1 AAA
39854816 GAAACCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.13
Consensus pattern (14 bp):
AAATAACAAAACAT
Found at i:39856504 original size:71 final size:71
Alignment explanation
Indices: 39856404--39856549 Score: 247
Period size: 71 Copynumber: 2.1 Consensus size: 71
39856394 CCATCAGAGT
* * *
39856404 ATCGATAAAAGTGCAGGGGATGTTGAACTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
39856469 CAAGGA
66 CAAGGA
*
39856475 ATCGATAAAAGTACAGGAGATGTTGAACTTTTGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
1 ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
*
39856540 CAAGGT
66 CAAGGA
39856546 ATCG
1 ATCG
39856550 GTAGCACTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (71 bp):
ATCGATAAAAGTACAGGAGATGTTGAACTTTGGCTACTAACTTGACTTGTTTCAGTAGAAGTCCT
CAAGGA
Found at i:39857131 original size:22 final size:22
Alignment explanation
Indices: 39857106--39857153 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
39857096 TATTTTGATT
39857106 CAAAGAAAATTGATATTAGGTG
1 CAAAGAAAATTGATATTAGGTG
39857128 CAAAGAAAATTGATATTAGGTG
1 CAAAGAAAATTGATATTAGGTG
39857150 CAAA
1 CAAA
39857154 TGTTGTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (22 bp):
CAAAGAAAATTGATATTAGGTG
Found at i:39860187 original size:9 final size:9
Alignment explanation
Indices: 39860173--39860198 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39860163 TTAAGTTTAA
39860173 ATTTTATTT
1 ATTTTATTT
39860182 ATTTTATTT
1 ATTTTATTT
39860191 ATTTTATT
1 ATTTTATT
39860199 AGAGTGATTG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTATTT
Found at i:39860736 original size:22 final size:22
Alignment explanation
Indices: 39860697--39860740 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39860687 GGACTAGATA
* *
39860697 TAAAAACATTGAAGACTAAATT
1 TAAAAAAATTGAACACTAAATT
*
39860719 TAAAAAAATTTAACACTAAATT
1 TAAAAAAATTGAACACTAAATT
39860741 GAATAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (22 bp):
TAAAAAAATTGAACACTAAATT
Found at i:39862137 original size:33 final size:34
Alignment explanation
Indices: 39862073--39862138 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
39862063 GCCCCCCAAA
*
39862073 AAAACCTAACCCAAAAAAAAGAAGAAGAAAAAAG
1 AAAACCTAACCCAAAAAAAAGAAAAAGAAAAAAG
* *
39862107 AAAACTTAA-CCAAAAAATAA-AAAAATAAAAAA
1 AAAACCTAACCCAAAAAA-AAGAAAAAGAAAAAA
39862139 ACCTAGCCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.08
Consensus pattern (34 bp):
AAAACCTAACCCAAAAAAAAGAAAAAGAAAAAAG
Found at i:39862452 original size:13 final size:13
Alignment explanation
Indices: 39862426--39862479 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
39862416 TATATACATC
39862426 ATAATAAAAA-AT
1 ATAATAAAAATAT
39862438 ATAATAAAAATAT
1 ATAATAAAAATAT
* *
39862451 ATATACAAAACAAAT
1 ATA-ATAAAA-ATAT
39862466 ATAA-AAAAAT-T
1 ATAATAAAAATAT
39862477 ATA
1 ATA
39862480 TTTTTCGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.11
12 11 0.31
13 9 0.25
14 6 0.17
15 6 0.17
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:39862647 original size:29 final size:29
Alignment explanation
Indices: 39862591--39862647 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
39862581 TCTCTTCTTT
* *
39862591 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
39862620 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
39862648 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:39862908 original size:11 final size:11
Alignment explanation
Indices: 39862890--39862919 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39862880 GTGTATATTG
39862890 TATATATTATA
1 TATATATTATA
*
39862901 TTTATATTATA
1 TATATATTATA
39862912 TATATATT
1 TATATATT
39862920 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:39864797 original size:17 final size:19
Alignment explanation
Indices: 39864755--39864798 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39864745 ATGAAATTTT
*
39864755 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
39864774 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
39864792 AA-TATTA
1 AATTATTA
39864799 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:39866439 original size:28 final size:28
Alignment explanation
Indices: 39866393--39866460 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
39866383 GCGTAGATCA
39866393 CGAAATTA-CCCTAAAGAGTAAAATTAC
1 CGAAATTACCCCTAAAGAGTAAAATTAC
*
39866420 CGAAATTACCCCTAAAGAGTAAAATTAT
1 CGAAATTACCCCTAAAGAGTAAAATTAC
*
39866448 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39866461 GGGTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGTAAAATTAC
Found at i:39868875 original size:17 final size:19
Alignment explanation
Indices: 39868833--39868876 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39868823 ATGAAATTTT
*
39868833 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
39868852 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
39868870 AA-TATTA
1 AATTATTA
39868877 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:39870549 original size:27 final size:28
Alignment explanation
Indices: 39870472--39870540 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
39870462 GCGTAGATCA
*
39870472 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGTAAAATTAC
39870500 CGAAATTACCCCTAAAGAGTAAAATTAC
1 CGAAATTACCCCTAAAGAGTAAAATTAC
*
39870528 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39870541 GGGTTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGTAAAATTAC
Found at i:39874177 original size:16 final size:15
Alignment explanation
Indices: 39874113--39874181 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
39874103 AAAAATTATG
*
39874113 TTTTCCATCATTCTAA
1 TTTTCCATCCTTC-AA
* *
39874129 TTTTCTATCCGTTTAA
1 TTTTCCATCC-TTCAA
39874145 TTTTCCATCCCTTCAA
1 TTTTCCAT-CCTTCAA
39874161 TTTTCCATCCTTCCAA
1 TTTTCCATCCTT-CAA
39874177 TTTTC
1 TTTTC
39874182 TTTCCACTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.09
16 37 0.82
17 4 0.09
ACGTcount: A:0.19, C:0.29, G:0.01, T:0.51
Consensus pattern (15 bp):
TTTTCCATCCTTCAA
Found at i:39874999 original size:21 final size:20
Alignment explanation
Indices: 39874971--39875010 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
39874961 GTCAATAACC
39874971 AAAAGTTCACACAAACAGAA
1 AAAAGTTCACACAAACAGAA
**
39874991 AAAATGTTCTGACAAACAGA
1 AAAA-GTTCACACAAACAGA
39875011 CGTATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAAGTTCACACAAACAGAA
Found at i:39875849 original size:15 final size:16
Alignment explanation
Indices: 39875812--39875852 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
39875802 TTGCACATGG
39875812 CCGTGTGG-ACACAGC
1 CCGTGTGGCACACAGC
39875827 CCATGTGTGGCACAC-GC
1 CC--GTGTGGCACACAGC
39875844 CCGTGTGGC
1 CCGTGTGGC
39875853 CACTCGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.17
Consensus pattern (16 bp):
CCGTGTGGCACACAGC
Found at i:39877308 original size:27 final size:28
Alignment explanation
Indices: 39877271--39877410 Score: 184
Period size: 27 Copynumber: 5.2 Consensus size: 28
39877261 AGCATGGCTG
* *
39877271 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
39877297 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
39877325 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
39877352 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
39877379 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
39877406 CCAGA
1 CCAGA
39877411 ACGCTTCCTC
Statistics
Matches: 106, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.05
27 84 0.79
28 17 0.16
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:39879039 original size:26 final size:26
Alignment explanation
Indices: 39879003--39879112 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
39878993 CATTAAATTC
39879003 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39879029 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39879055 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
39879081 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
39879107 TTATCA
1 TTATCA
39879113 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39881135 original size:16 final size:18
Alignment explanation
Indices: 39881106--39881146 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
39881096 TATTCTTTAG
*
39881106 AATTTTTTAATAAATTAT-
1 AATTTTTT-ATAAAATATC
39881124 AATTTTTT-TAAAATATC
1 AATTTTTTATAAAATATC
39881141 AATTTT
1 AATTTT
39881147 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
17 6 0.29
18 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTTTATAAAATATC
Found at i:39881137 original size:17 final size:18
Alignment explanation
Indices: 39881106--39881146 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
39881096 TATTCTTTAG
39881106 AATTTTTTAATAAATTAT-
1 AATTTTTTAATAAA-TATC
*
39881124 AATTTTTTTA-AAATATC
1 AATTTTTTAATAAATATC
39881141 AATTTT
1 AATTTT
39881147 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 9 0.43
18 9 0.43
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTTTAATAAATATC
Done.