Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 15 of 25
Found at i:2419923 original size:13 final size:13
Alignment explanation
Indices: 2419905--2419938 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2419895 TTTTGATTTT
2419905 TTTATTATTAATA
1 TTTATTATTAATA
*
2419918 TTTATTATTTATA
1 TTTATTATTAATA
2419931 TTTATTAT
1 TTTATTAT
2419939 AATTTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:2422113 original size:13 final size:15
Alignment explanation
Indices: 2422084--2422130 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
2422074 TAAAAATAAA
2422084 AAAATTATAAATATT
1 AAAATTATAAATATT
2422099 AAAATTA-AAAT-TT
1 AAAATTATAAATATT
2422112 AAAATTTATTAAATATT
1 AAAA-TTA-TAAATATT
2422129 AA
1 AA
2422131 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.21
14 7 0.25
15 7 0.25
16 4 0.14
17 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:2422163 original size:21 final size:21
Alignment explanation
Indices: 2422148--2422199 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2422138 TAAATTATTA
2422148 TATAAATCAATTAAATTAAAT
1 TATAAATCAATTAAATTAAAT
*
2422169 TATAAATCAATT-AAGTAGAAT
1 TATAAATCAATTAAATTA-AAT
2422190 TATAAATCAA
1 TATAAATCAA
2422200 GTTTGTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (21 bp):
TATAAATCAATTAAATTAAAT
Found at i:2437257 original size:20 final size:21
Alignment explanation
Indices: 2437225--2437263 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2437215 ATTTTAATAT
2437225 TTATAATTTATTTAATAATTA
1 TTATAATTTATTTAATAATTA
*
2437246 TTATAA-TTATTTATTAAT
1 TTATAATTTATTTAATAAT
2437264 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATAATTTATTTAATAATTA
Found at i:2438004 original size:17 final size:18
Alignment explanation
Indices: 2437970--2438008 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2437960 AAATGATATT
**
2437970 TAAAAAATTATTTTTTTA
1 TAAAAAATTATTAATTTA
2437988 TAAAAAATTA-TAATTTA
1 TAAAAAATTATTAATTTA
2438005 TAAA
1 TAAA
2438009 TAAAATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAAATTATTAATTTA
Found at i:2439392 original size:29 final size:27
Alignment explanation
Indices: 2439356--2439414 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
2439346 ATTAAAATAT
* *
2439356 TAAAAATTATTTTTATATATAAATTTAAA
1 TAAAAATTATTTTT-T-TAAAAAATTAAA
2439385 TAAAAATTATTTTTTTAAAAAATTAAA
1 TAAAAATTATTTTTTTAAAAAATTAAA
2439412 TAA
1 TAA
2439415 TGATTCACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.46
28 1 0.04
29 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATTATTTTTTTAAAAAATTAAA
Found at i:2441068 original size:16 final size:17
Alignment explanation
Indices: 2441034--2441069 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2441024 TAATAGAGAC
2441034 ATATTTATTTTCAAATTA
1 ATATTTATTTT-AAATTA
2441052 ATATTTATTTT-AATTA
1 ATATTTATTTTAAATTA
2441068 AT
1 AT
2441070 TTTTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTATTTTAAATTA
Found at i:2444043 original size:14 final size:14
Alignment explanation
Indices: 2444020--2444053 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2444010 GAATTGAATT
2444020 AATTTAAATTTTAA
1 AATTTAAATTTTAA
*
2444034 AATTTTAATTTT-A
1 AATTTAAATTTTAA
2444047 AATTTAA
1 AATTTAA
2444054 TCTGATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTAAATTTTAA
Found at i:2445715 original size:2 final size:2
Alignment explanation
Indices: 2445708--2445742 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2445698 TAGATTAAGA
2445708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2445743 AACAATTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2448255 original size:2 final size:2
Alignment explanation
Indices: 2448248--2448292 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2448238 ACGATACTTT
2448248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2448290 TA T
1 TA T
2448293 CCTTATTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2448838 original size:17 final size:18
Alignment explanation
Indices: 2448810--2448847 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2448800 TTTAATTATA
2448810 AAATATATAAAAAAATTT
1 AAATATATAAAAAAATTT
*
2448828 AAATA-ATAAAATAATTT
1 AAATATATAAAAAAATTT
2448845 AAA
1 AAA
2448848 CTCAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATAAAAAAATTT
Found at i:2449801 original size:13 final size:13
Alignment explanation
Indices: 2449783--2449807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2449773 TTCACTTTTT
2449783 TTTAATATTTATG
1 TTTAATATTTATG
2449796 TTTAATATTTAT
1 TTTAATATTTAT
2449808 AATTAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTAATATTTATG
Found at i:2449869 original size:11 final size:11
Alignment explanation
Indices: 2449853--2449877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2449843 TCTTTTAAAT
2449853 ATTTAAAATAA
1 ATTTAAAATAA
2449864 ATTTAAAATAA
1 ATTTAAAATAA
2449875 ATT
1 ATT
2449878 AAACATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAAAATAA
Found at i:2450420 original size:3 final size:3
Alignment explanation
Indices: 2450412--2450444 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2450402 AAAATATACA
2450412 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2450445 TTACAAAAGA
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:2450785 original size:14 final size:15
Alignment explanation
Indices: 2450754--2450817 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 15
2450744 TTTTAATTCT
2450754 TAAATTTATTAAATA
1 TAAATTTATTAAATA
2450769 TAAATTT-TT-AATA
1 TAAATTTATTAAATA
2450782 -ATAA-TTATATAAAT-
1 TA-AATTTAT-TAAATA
**
2450796 TAAATAAATTAAAT-
1 TAAATTTATTAAATA
2450810 TAAATTTA
1 TAAATTTA
2450818 AAATTCAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
12 3 0.08
13 7 0.18
14 16 0.41
15 13 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTTATTAAATA
Found at i:2450821 original size:17 final size:16
Alignment explanation
Indices: 2450801--2450834 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2450791 TAAATTAAAT
2450801 AAATTAAATTAAATTTA
1 AAATTAAATT-AATTTA
*
2450818 AAATTCAATTAATTTA
1 AAATTAAATTAATTTA
2450834 A
1 A
2450835 TAGTTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTAAATTAATTTA
Found at i:2454829 original size:21 final size:21
Alignment explanation
Indices: 2454804--2454845 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2454794 CCAATATTAA
*
2454804 ATATAAATATAAATTTAATAT
1 ATATAAATATAAACTTAATAT
* *
2454825 ATATATATATATACTTAATAT
1 ATATAAATATAAACTTAATAT
2454846 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAAATATAAACTTAATAT
Found at i:2455439 original size:2 final size:2
Alignment explanation
Indices: 2455432--2455465 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2455422 TAGATATAGA
2455432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2455466 GGCTCTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2456404 original size:8 final size:7
Alignment explanation
Indices: 2456357--2456414 Score: 91
Period size: 7 Copynumber: 8.1 Consensus size: 7
2456347 TAATATGTAA
2456357 TAAA-TT
1 TAAATTT
2456363 TAAATTT
1 TAAATTT
2456370 TAAATTT
1 TAAATTT
2456377 TAAATTT
1 TAAATTT
2456384 TAAATTT
1 TAAATTT
2456391 TAAATTT
1 TAAATTT
2456398 ATAAATTT
1 -TAAATTT
2456406 ATAAATTT
1 -TAAATTT
2456414 T
1 T
2456415 TATTATTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 4 0.08
7 31 0.62
8 15 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TAAATTT
Found at i:2456552 original size:21 final size:21
Alignment explanation
Indices: 2456528--2456570 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2456518 TTGTAAGCAA
2456528 AGGAACTCCAAAAGTATATAT
1 AGGAACTCCAAAAGTATATAT
*
2456549 AGGAACTCCAAAAGTATGTAT
1 AGGAACTCCAAAAGTATATAT
2456570 A
1 A
2456571 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (21 bp):
AGGAACTCCAAAAGTATATAT
Found at i:2457815 original size:36 final size:36
Alignment explanation
Indices: 2457774--2457850 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
2457764 TATAGCGATT
* *
2457774 ATATAAGCATAACATAAATTATTAAATAT-T-TTAAAA
1 ATATAAACATAA-ATAAA-TATTAAATATATCATAAAA
* *
2457810 ATATAAATATAAATATATATTAAATATATCATAAAA
1 ATATAAACATAAATAAATATTAAATATATCATAAAA
2457846 ATATA
1 ATATA
2457851 TTTAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 10 0.29
35 5 0.14
36 20 0.57
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (36 bp):
ATATAAACATAAATAAATATTAAATATATCATAAAA
Found at i:2457834 original size:23 final size:23
Alignment explanation
Indices: 2457797--2457859 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
2457787 ATAAATTATT
* *
2457797 AAATAT-TTTAAAAATATAAATAT
1 AAATATATTTAAATATAT-AATAA
*
2457820 AAATATATATTAAATATATCATAA
1 AAATATAT-TTAAATATATAATAA
2457844 AAATATATTTAAATAT
1 AAATATATTTAAATAT
2457860 TTTATATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.40
24 12 0.34
25 9 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATATTTAAATATATAATAA
Found at i:2457857 original size:34 final size:33
Alignment explanation
Indices: 2457793--2457859 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
2457783 TAACATAAAT
*
2457793 TATTAAATATTTTAAAAATATAAATATAAATATA
1 TATTAAATATTATAAAAATAT-AATATAAATATA
*
2457827 TATTAAATATATCATAAAAATAT-ATTTAAATAT
1 TATTAAATAT-T-ATAAAAATATAATATAAATAT
2457860 TTTATATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 19 0.66
35 1 0.03
36 9 0.31
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
TATTAAATATTATAAAAATATAATATAAATATA
Found at i:2458163 original size:16 final size:16
Alignment explanation
Indices: 2458138--2458197 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
2458128 AACATGATAC
*
2458138 TATAAAATAAAATAAA
1 TATAATATAAAATAAA
2458154 TATAATATAAATATATAA
1 TATAATATAAA-ATA-AA
* * **
2458172 -ATATTTTAAAATTTA
1 TATAATATAAAATAAA
2458187 TATAATATAAA
1 TATAATATAAA
2458198 TTATTAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.03
16 20 0.59
17 11 0.32
18 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAATATAAAATAAA
Found at i:2458174 original size:14 final size:14
Alignment explanation
Indices: 2458138--2458286 Score: 51
Period size: 14 Copynumber: 10.1 Consensus size: 14
2458128 AACATGATAC
2458138 TATA-AAATA-AAA
1 TATATAAATATAAA
*
2458150 TAAATATAATATAAA
1 TATATA-AATATAAA
2458165 TATATAAATATTTTAAAA
1 TATATAAATA---T-AAA
*
2458183 TTTATATAATATAAA
1 TATATA-AATATAAA
2458198 T-TATTAATATATCAAAA
1 TATA-TAA-ATAT--AAA
2458215 TTTATATAAATATAACA
1 --TATATAAATATAA-A
**
2458232 T-TATAAATATATT
1 TATATAAATATAAA
* * *
2458245 TTTAATATATAAAAA
1 TAT-ATAAATATAAA
2458260 TATATAAATA-AAA
1 TATATAAATATAAA
2458273 TA-A-AAGATATAAA
1 TATATAA-ATATAAA
2458286 T
1 T
2458287 TACCGCATCT
Statistics
Matches: 106, Mismatches: 11, Indels: 39
0.68 0.07 0.25
Matches are distributed among these distances:
11 2 0.02
12 7 0.07
13 11 0.10
14 28 0.26
15 28 0.26
16 3 0.03
17 5 0.05
18 12 0.11
19 8 0.08
20 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (14 bp):
TATATAAATATAAA
Found at i:2458215 original size:32 final size:32
Alignment explanation
Indices: 2458153--2458243 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
2458143 AATAAAATAA
* *
2458153 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAAT-TATAAATATATCAAAATTT
*
2458186 ATATAATATAAATTATTAATATATCAAAATTT
1 ATATAATATAAATTATAAATATATCAAAATTT
2458218 ATATAAATATAACATTATAAATATAT
1 ATAT-AATATAA-ATTATAAATATAT
2458244 TTTTAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
32 20 0.38
33 20 0.38
34 12 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATCAAAATTT
Found at i:2458226 original size:20 final size:18
Alignment explanation
Indices: 2458178--2458243 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 18
2458168 ATAAATATTT
2458178 TAAAATTTATAT-A-ATA
1 TAAAATTTATATAATATA
2458194 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAATATA
2458209 TCAAAATTTATATAA-ATA
1 T-AAAATTTATATAATATA
*
2458227 TAACA-TTATA-AATATA
1 TAAAATTTATATAATATA
2458243 T
1 T
2458244 TTTTAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 9 0.21
16 10 0.24
17 6 0.14
18 8 0.19
19 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTATATAATATA
Found at i:2458539 original size:18 final size:18
Alignment explanation
Indices: 2458497--2458542 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2458487 AGATGTAATT
2458497 TAATTAAAT-TTTTTAAA
1 TAATTAAATATTTTTAAA
*
2458514 TAAATAAATAATTTTTAAA
1 TAATTAAAT-ATTTTTAAA
2458533 -AATTAAATAT
1 TAATTAAATAT
2458543 ATATTCGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTAAATATTTTTAAA
Found at i:2458730 original size:21 final size:21
Alignment explanation
Indices: 2458704--2458746 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2458694 ACAATCACTT
2458704 ATTTAATTTAACATAATATTA
1 ATTTAATTTAACATAATATTA
*
2458725 ATTTAATTTAACATGATATTA
1 ATTTAATTTAACATAATATTA
2458746 A
1 A
2458747 AACTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTAATTTAACATAATATTA
Found at i:2460389 original size:2 final size:2
Alignment explanation
Indices: 2460351--2460376 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2460341 AAGCAATACC
2460351 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
2460377 TTCTTAAATA
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:2461609 original size:16 final size:17
Alignment explanation
Indices: 2461579--2461611 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2461569 TATATTTACA
2461579 TTAAAGATAATAAAAAT
1 TTAAAGATAATAAAAAT
2461596 TTAAAGAT-ATAAAAAT
1 TTAAAGATAATAAAAAT
2461612 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TTAAAGATAATAAAAAT
Found at i:2461617 original size:17 final size:17
Alignment explanation
Indices: 2461580--2461617 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2461570 ATATTTACAT
*
2461580 TAAAGATAATAAAAATT
1 TAAAGATAATAAAAATA
2461597 TAAAGAT-ATAAAAATAA
1 TAAAGATAATAAAAAT-A
2461614 TAAA
1 TAAA
2461618 ATTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAGATAATAAAAATA
Found at i:2465113 original size:16 final size:16
Alignment explanation
Indices: 2465094--2465157 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
2465084 ATATATTTTT
2465094 TAAAATTTAAATAATA
1 TAAAATTTAAATAATA
2465110 T-AAATTATAAAT-ATA
1 TAAAATT-TAAATAATA
* *
2465125 TCTAAATTTATATAAATA
1 T-AAAATTTAAAT-AATA
2465143 TAAATATTTTAAATA
1 TAAA-A-TTTAAATA
2465158 CGATTATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
15 9 0.24
16 10 0.26
17 7 0.18
18 6 0.16
19 6 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTTAAATAATA
Found at i:2465212 original size:20 final size:19
Alignment explanation
Indices: 2465174--2465212 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2465164 TAATAAAATA
*
2465174 AAATACATAAATATGATAT
1 AAATACATAAATATCATAT
*
2465193 AAATACCTAAATTATCATAT
1 AAATACATAAA-TATCATAT
2465213 CTATTCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATACATAAATATCATAT
Found at i:2469655 original size:21 final size:22
Alignment explanation
Indices: 2469630--2469676 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2469620 TATTAATAGG
* *
2469630 TTTAATTTTGTATTAGTAG-AT
1 TTTAAATTTATATTAGTAGAAT
*
2469651 TTTAAATTTATATTATTAGAAT
1 TTTAAATTTATATTAGTAGAAT
2469673 TTTA
1 TTTA
2469677 TATTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTAAATTTATATTAGTAGAAT
Found at i:2470466 original size:11 final size:11
Alignment explanation
Indices: 2470452--2470477 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2470442 AGATATATAA
2470452 ATTTAATATTT
1 ATTTAATATTT
2470463 ATTTAATATTT
1 ATTTAATATTT
2470474 ATTT
1 ATTT
2470478 TTTAAAATTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATATTT
Found at i:2470542 original size:46 final size:45
Alignment explanation
Indices: 2470435--2470542 Score: 114
Period size: 46 Copynumber: 2.4 Consensus size: 45
2470425 ATATGATCAA
* * *
2470435 TAAATT-TAGATATATAAATTTAATATTTATTTAATATTTATTTTT
1 TAAATTATA-ATAAATAAATTTAATATTTAATAAATATTTATTTTT
* *
2470480 TAAAATTA-ATTTAATAAATTTAAATATTTAATAAATA-TTATTTTT
1 T-AAATTATAATAAATAAATTT-AATATTTAATAAATATTTATTTTT
2470525 TAAATTATACATAAATAA
1 TAAATTATA-ATAAATAA
2470543 TAATAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
44 6 0.12
45 20 0.39
46 25 0.49
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (45 bp):
TAAATTATAATAAATAAATTTAATATTTAATAAATATTTATTTTT
Found at i:2471139 original size:21 final size:22
Alignment explanation
Indices: 2471115--2471161 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2471105 TATAACAAAC
2471115 AAAAAAATAATT-AATAATATT
1 AAAAAAATAATTAAATAATATT
* * *
2471136 AAAAAATTATTTAAATATTATT
1 AAAAAAATAATTAAATAATATT
2471158 AAAA
1 AAAA
2471162 TATTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAAATAATTAAATAATATT
Found at i:2471152 original size:19 final size:20
Alignment explanation
Indices: 2471116--2471169 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2471106 ATAACAAACA
2471116 AAAAAATAATTAATAATATT
1 AAAAAATAATTAATAATATT
* *
2471136 AAAAAATTATTTA-AATATT
1 AAAAAATAATTAATAATATT
*
2471155 ATTAAAAT-ATTAATA
1 A-AAAAATAATTAATA
2471170 TATCATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATTAATAATATT
Found at i:2471155 original size:11 final size:11
Alignment explanation
Indices: 2471127--2471166 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2471117 AAAAATAATT
*
2471127 AATAATATTAA
1 AATATTATTAA
* *
2471138 AAAATTATTTA
1 AATATTATTAA
2471149 AATATTATTAA
1 AATATTATTAA
2471160 AATATTA
1 AATATTA
2471167 ATATATCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATATTATTAA
Found at i:2471172 original size:19 final size:18
Alignment explanation
Indices: 2471116--2471172 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
2471106 ATAACAAACA
2471116 AAAAAATAATTAATAATATT
1 AAAAAAT-ATTAAT-ATATT
2471136 AAAAAATTATTTAA-ATATT
1 AAAAAA-TA-TTAATATATT
*
2471155 ATTAAAATATTAATATAT
1 A-AAAAATATTAATATAT
2471173 CATGTGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 4 0.12
19 12 0.38
20 11 0.34
21 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAAATATTAATATATT
Found at i:2471363 original size:14 final size:14
Alignment explanation
Indices: 2471346--2471396 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
2471336 CTATAATTTA
2471346 TAAAATATAAAAAT
1 TAAAATATAAAAAT
* *
2471360 TAAAATATTAAATT
1 TAAAATATAAAAAT
2471374 TAATAATATAAAAAT
1 TAA-AATATAAAAAT
2471389 TAAAATAT
1 TAAAATAT
2471397 TTTTTCGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATATAAAAAT
Found at i:2471369 original size:8 final size:8
Alignment explanation
Indices: 2471346--2471397 Score: 53
Period size: 7 Copynumber: 7.1 Consensus size: 8
2471336 CTATAATTTA
2471346 TAAAATA-
1 TAAAATAT
2471353 TAAAA-AT
1 TAAAATAT
2471360 TAAAATAT
1 TAAAATAT
2471368 T-AAAT-T
1 TAAAATAT
2471374 TAATAATA-
1 TAA-AATAT
2471382 TAAAA-AT
1 TAAAATAT
2471389 TAAAATAT
1 TAAAATAT
2471397 T
1 T
2471398 TTTTCGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 4 0.11
7 22 0.58
8 12 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATAT
Found at i:2471383 original size:29 final size:30
Alignment explanation
Indices: 2471340--2471397 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
2471330 TATTTACTAT
2471340 AATTTATAAAATATAAAAATTAAAATATTA
1 AATTTATAAAATATAAAAATTAAAATATTA
*
2471370 AATTTA-ATAATATAAAAATTAAAATATT
1 AATTTATAAAATATAAAAATTAAAATATT
2471398 TTTTCGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTTATAAAATATAAAAATTAAAATATTA
Found at i:2471473 original size:2 final size:2
Alignment explanation
Indices: 2471466--2471491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2471456 ATTAAAGTTA
2471466 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
2471492 GCATTTACGC
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:2471763 original size:17 final size:18
Alignment explanation
Indices: 2471735--2471768 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2471725 TATCATTTAA
*
2471735 TTTATATTTAAATAAATC
1 TTTATATTTAAAAAAATC
2471753 TTTAT-TTTAAAAAAAT
1 TTTATATTTAAAAAAAT
2471769 TTTGAGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTTAAAAAAATC
Found at i:2474682 original size:19 final size:18
Alignment explanation
Indices: 2474645--2474696 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
2474635 ATTTTTTATT
2474645 ATTAATTAAAAATAAAAA
1 ATTAATTAAAAATAAAAA
** *
2474663 ACTTAATTAAACTTATAAA
1 A-TTAATTAAAAATAAAAA
*
2474682 ATT-ATTTAAAATAAA
1 ATTAATTAAAAATAAA
2474697 TATTTAAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 15 0.58
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTAATTAAAAATAAAAA
Found at i:2474720 original size:22 final size:24
Alignment explanation
Indices: 2474695--2474754 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
2474685 ATTTAAAATA
2474695 AATATTTAAATTTAATTT-A-CTC
1 AATATTTAAATTTAATTTGAGCTC
*
2474717 AATAATTAAATTT-ATTTGAGCTC
1 AATATTTAAATTTAATTTGAGCTC
2474740 AAT-TTTAAA-TTAATT
1 AATATTTAAATTTAATT
2474755 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.18
22 21 0.64
23 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (24 bp):
AATATTTAAATTTAATTTGAGCTC
Found at i:2475090 original size:10 final size:10
Alignment explanation
Indices: 2475024--2475193 Score: 63
Period size: 10 Copynumber: 18.4 Consensus size: 10
2475014 AGATTTAAAA
2475024 AAATAT-TAT
1 AAATATATAT
2475033 AAA-AT-TA-
1 AAATATATAT
* *
2475040 AAAAATATAA
1 AAATATATAT
2475050 AAATATAT-T
1 AAATATATAT
*
2475059 AAACATA-AT
1 AAATATATAT
2475068 --ATA-ATAT
1 AAATATATAT
*
2475075 ACATATATAT
1 AAATATATAT
* *
2475085 AAATATTTTT
1 AAATATATAT
*
2475095 AAATTTATAT
1 AAATATATAT
*
2475105 AATATAAATAT
1 AA-ATATATAT
*
2475116 TAAT-TAT-T
1 AAATATATAT
*
2475124 AAA-ATTTAT
1 AAATATATAT
2475133 ATAA-ATATA-
1 A-AATATATAT
2475142 AAATACT-T-T
1 AAATA-TATAT
2475151 AAATATA-ATT
1 AAATATATA-T
*
2475161 AAATTTA-AT
1 AAATATATAT
2475170 AAA-ATATAT
1 AAATATATAT
2475179 AAATATAATAT
1 AAATAT-ATAT
2475190 AAAT
1 AAAT
2475194 TTAATTAAAT
Statistics
Matches: 121, Mismatches: 19, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
6 1 0.01
7 7 0.06
8 16 0.13
9 36 0.30
10 46 0.38
11 15 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATATATAT
Found at i:2475111 original size:25 final size:29
Alignment explanation
Indices: 2475077--2475143 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
2475067 TATAATATAC
2475077 ATAT-ATATAAATA-T-TT-TT-AAATTT
1 ATATAATATAAATATTATTATTAAAATTT
2475101 ATATAATATAAATATTAATTATTAAAATTT
1 ATATAATATAAATATT-ATTATTAAAATTT
2475131 ATATAAATATAAA
1 ATAT-AATATAAA
2475144 ATACTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.11
25 9 0.25
26 1 0.03
28 2 0.06
29 2 0.06
30 10 0.28
31 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATAATATAAATATTATTATTAAAATTT
Found at i:2475216 original size:29 final size:28
Alignment explanation
Indices: 2475139--2475205 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 28
2475129 TTATATAAAT
*
2475139 ATAAAATACTTTAAATATAATTAAATTTA
1 ATAAAATA-TATAAATATAATTAAATTTA
2475168 ATAAAATATATAAATATAATATAAATTTA
1 ATAAAATATATAAATATAAT-TAAATTTA
*
2475197 ATTAAATAT
1 ATAAAATAT
2475206 TAATAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAAAATATATAAATATAATTAAATTTA
Found at i:2475632 original size:23 final size:24
Alignment explanation
Indices: 2475606--2475655 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2475596 ATTAATTTTG
* *
2475606 TTTTA-ATGTATAATATATAATAAT
1 TTTTATATGAATAATATA-AAAAAT
2475630 TTTTATATGAATAATATAAAAAAT
1 TTTTATATGAATAATATAAAAAAT
2475654 TT
1 TT
2475656 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTTATATGAATAATATAAAAAAT
Found at i:2475737 original size:14 final size:14
Alignment explanation
Indices: 2475678--2475742 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
2475668 ATTAAAATTG
* *
2475678 ATTAAATTAATTGA
1 ATTAATTTAATTTA
* *
2475692 TTTAAGTTAATTTTA
1 ATTAATTTAA-TTTA
*
2475707 ATT--TTTTATTT-
1 ATTAATTTAATTTA
2475718 ATTAATTTAATTTA
1 ATTAATTTAATTTA
2475732 ATTAATTTAAT
1 ATTAATTTAAT
2475743 CAATTATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 10 0.25
14 19 0.47
15 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTAATTTAATTTA
Found at i:2478935 original size:2 final size:2
Alignment explanation
Indices: 2478928--2478968 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2478918 GAGCCTCCAA
2478928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2478969 AATAAACTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2480526 original size:14 final size:14
Alignment explanation
Indices: 2480507--2480565 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2480497 TTGTTTATTA
2480507 TATTATTAATATAT
1 TATTATTAATATAT
*
2480521 TATTATT--TTTAT
1 TATTATTAATATAT
* *
2480533 TAATATTTATATATT
1 TATTATTAATATA-T
2480548 TATTATTAA-ATAAT
1 TATTATTAATAT-AT
2480562 TATT
1 TATT
2480566 TGAGTTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 10 0.28
14 17 0.47
15 9 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTAATATAT
Found at i:2486013 original size:29 final size:29
Alignment explanation
Indices: 2485980--2486038 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
2485970 GAATTATTAT
2485980 TTTAAGTAATAAA-A-AAATATATATTTAAA
1 TTTAA-TAATAAATATAAATATAT-TTTAAA
* *
2486009 TTTAATTATAAATATTAATATATTTTAAA
1 TTTAATAATAAATATAAATATATTTTAAA
2486038 T
1 T
2486039 AATAAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 6 0.23
29 13 0.50
30 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TTTAATAATAAATATAAATATATTTTAAA
Found at i:2491779 original size:18 final size:17
Alignment explanation
Indices: 2491752--2491806 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
2491742 TATTTAGAAT
2491752 ATTTTATATTTTTATAA
1 ATTTTATATTTTTATAA
*
2491769 ATTTTATTATTTTAAT-A
1 ATTTTA-TATTTTTATAA
*
2491786 A-TTTAT-TTTATATAA
1 ATTTTATATTTTTATAA
2491801 ATTTTA
1 ATTTTA
2491807 AAATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 3 0.09
16 8 0.25
17 8 0.25
18 8 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTATATTTTTATAA
Found at i:2500325 original size:20 final size:20
Alignment explanation
Indices: 2500297--2500344 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2500287 ATATAATTTT
2500297 TATAATATAAAAATTAAATA
1 TATAATATAAAAATTAAATA
* * *
2500317 TATATTATAAATATTAAAAAA
1 TATAATATAAAAATT-AAATA
2500338 TATAATA
1 TATAATA
2500345 AATTATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATAATATAAAAATTAAATA
Found at i:2500644 original size:2 final size:2
Alignment explanation
Indices: 2500637--2500677 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2500627 ATTACTTATT
2500637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2500678 GTATTCGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2505198 original size:2 final size:2
Alignment explanation
Indices: 2505193--2505230 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2505183 CTTTTGTGTG
*
2505193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2505231 ACCTTATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2509164 original size:31 final size:33
Alignment explanation
Indices: 2509100--2509172 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
2509090 TTTAATTAAA
2509100 ATATAATACGAATATATAAATATATAAAAATTT
1 ATATAATACGAATATATAAATATATAAAAATTT
* *
2509133 ATATAATACGAATAT-TAACT-TATCAAAATTT
1 ATATAATACGAATATATAAATATATAAAAATTT
2509164 ATATGAATA
1 ATAT-AATA
2509173 TATAATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 14 0.38
32 8 0.22
33 15 0.41
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.37
Consensus pattern (33 bp):
ATATAATACGAATATATAAATATATAAAAATTT
Found at i:2509751 original size:29 final size:30
Alignment explanation
Indices: 2509710--2509766 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
2509700 ATAATTTTTT
*
2509710 AAATAAATCAAAATTTAA-TTAAATTTATAA
1 AAATAAATCAAAA-ATAATTTAAATTTATAA
2509740 AAATAAAT-AAAAATAATTTAAATTTAT
1 AAATAAATCAAAAATAATTTAAATTTAT
2509767 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 14 0.56
30 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATAAATCAAAAATAATTTAAATTTATAA
Found at i:2510210 original size:16 final size:15
Alignment explanation
Indices: 2510189--2510224 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2510179 TAAATATGAT
2510189 ATAAAAAATAACATAA
1 ATAAAAAATAACAT-A
*
2510205 ATAAAAAATAATATA
1 ATAAAAAATAACATA
2510220 ATAAA
1 ATAAA
2510225 TAAGGCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAACATA
Found at i:2510624 original size:21 final size:22
Alignment explanation
Indices: 2510600--2510640 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2510590 AATATTAAAA
*
2510600 TATTTTTAT-ATTAATTTTATT
1 TATTTTTATAATTAAATTTATT
2510621 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
2510641 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATT
Found at i:2512157 original size:15 final size:15
Alignment explanation
Indices: 2512134--2512171 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2512124 TAAGACACGT
2512134 TTAATATTTATCA-AA
1 TTAATATTTA-CATAA
*
2512149 TTTATATTTACATAA
1 TTAATATTTACATAA
2512164 TTAATATT
1 TTAATATT
2512172 AATAAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATTTACATAA
Found at i:2512192 original size:2 final size:2
Alignment explanation
Indices: 2512185--2512216 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2512175 AAAATACAAA
*
2512185 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2512217 GCATGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2512698 original size:20 final size:20
Alignment explanation
Indices: 2512664--2512701 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2512654 ATAAATTATT
**
2512664 ATATTAAATTCATAATTTTG
1 ATATTAAATAAATAATTTTG
2512684 ATATTAAATAAATAATTT
1 ATATTAAATAAATAATTT
2512702 AATATTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
ATATTAAATAAATAATTTTG
Found at i:2513950 original size:7 final size:7
Alignment explanation
Indices: 2513916--2513952 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2513906 AATTTAAAAA
*
2513916 TAAATTA
1 TAAATTT
*
2513923 TAAATAT
1 TAAATTT
2513930 TAAATTT
1 TAAATTT
2513937 TAAATTT
1 TAAATTT
2513944 TAAATTT
1 TAAATTT
2513951 TA
1 TA
2513953 CTTTTTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TAAATTT
Found at i:2515524 original size:24 final size:24
Alignment explanation
Indices: 2515497--2515566 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
2515487 ATATTTAAAA
2515497 TTATTTTTATATTAATAAGTAATT
1 TTATTTTTATATTAATAAGTAATT
* * * *
2515521 TTATTATTAAATAAATAA--AAAT
1 TTATTTTTATATTAATAAGTAATT
*
2515543 AT-TTTTTATATTAA-AGAGTAATT
1 TTATTTTTATATTAATA-AGTAATT
2515566 T
1 T
2515567 GAATTAGGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 7
0.66 0.20 0.14
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 4 0.12
23 3 0.09
24 15 0.45
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATTTTTATATTAATAAGTAATT
Found at i:2515595 original size:2 final size:2
Alignment explanation
Indices: 2515588--2515632 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2515578 ATCTAAACTA
2515588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2515630 AT A
1 AT A
2515633 AGGACTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2516236 original size:25 final size:23
Alignment explanation
Indices: 2516169--2516249 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 23
2516159 TTAAACCCGG
* *
2516169 ATCATATTTAAATTTATCTATTAT
1 ATCATATTTATATTTATTTA-TAT
* *
2516193 ATTATATTTTATTTTTATTTAATAT
1 ATCATA-TTTATATTTATTT-ATAT
2516218 ATCATATTTATATTATATTT-TA-
1 ATCATATTTATATT-TATTTATAT
2516240 ATCATATTTA
1 ATCATATTTA
2516250 AAATTATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 2 0.04
24 12 0.25
25 23 0.48
26 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (23 bp):
ATCATATTTATATTTATTTATAT
Found at i:2516248 original size:36 final size:34
Alignment explanation
Indices: 2516169--2516250 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 34
2516159 TTAAACCCGG
*
2516169 ATCATATTTAAATTTATCTATTATATTATATTTTA
1 ATCATATTT-AATATATCTATTATATTATATTTTA
* **
2516204 TTTTTATTTAATATATCATATTTATATTATATTTTA
1 ATCATATTTAATATATC-TA-TTATATTATATTTTA
2516240 ATCATATTTAA
1 ATCATATTTAA
2516251 AATTATTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
34 7 0.18
35 8 0.21
36 23 0.61
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (34 bp):
ATCATATTTAATATATCTATTATATTATATTTTA
Found at i:2516405 original size:23 final size:23
Alignment explanation
Indices: 2516360--2516408 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2516350 TGTATTTTTA
*
2516360 AATATTTATAAACATATTCATTT
1 AATATTTATAAACAAATTCATTT
* * *
2516383 AATATTTATTAATAAATTTATTT
1 AATATTTATAAACAAATTCATTT
2516406 AAT
1 AAT
2516409 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTATAAACAAATTCATTT
Found at i:2518006 original size:28 final size:29
Alignment explanation
Indices: 2517974--2518031 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
2517964 AATAATTATC
*
2517974 TTTTA-AATATAAAAAA-ATATCTTAAAAA
1 TTTTAGAA-ATAAAAAATAGATCTTAAAAA
*
2518002 TTTTAGAAATAAAAAATAGATTTTAAAAA
1 TTTTAGAAATAAAAAATAGATCTTAAAAA
2518031 T
1 T
2518032 GTTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTTAGAAATAAAAAATAGATCTTAAAAA
Found at i:2518986 original size:17 final size:17
Alignment explanation
Indices: 2518956--2518988 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2518946 AAATCATCAA
2518956 TAAAGAAATTAATTAAT
1 TAAAGAAATTAATTAAT
2518973 TAAA-AAATTAAATTAA
1 TAAAGAAATT-AATTAA
2518989 ACTCATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAGAAATTAATTAAT
Found at i:2519997 original size:22 final size:20
Alignment explanation
Indices: 2519947--2520000 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 20
2519937 TAAATTATTT
*
2519947 TATATTTTATTTATTTTTAAA
1 TATATTTT-TTAATTTTTAAA
2519968 T-TACTTTTTTAATTTTTACATA
1 TATA-TTTTTTAATTTTTA-A-A
2519990 TATATTTTTTA
1 TATATTTTTTA
2520001 TTAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 9 0.32
23 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTTTTTAATTTTTAAA
Found at i:2520512 original size:19 final size:20
Alignment explanation
Indices: 2520476--2520513 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2520466 TCAATTTAGT
**
2520476 ACATCTAAAATTTTATTTTC
1 ACATCTAAAATTAAATTTTC
2520496 ACAT-TAAAATTAAATTTT
1 ACATCTAAAATTAAATTTT
2520514 AATAAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
ACATCTAAAATTAAATTTTC
Found at i:2524548 original size:82 final size:83
Alignment explanation
Indices: 2524460--2524624 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
2524450 TGTTTATGTC
2524460 AGAATATATATTGAGTATGACTGTAATATTCTAAATACTTGAAAATAAAAAGTTA-AAAATAAAA
1 AGAATATATATTGAGTATGACTGTAATATTCTAAATACTTGAAAATAAAAAGTTAGAAAATAAAA
2524524 AGTAGAAGCACAATAAAA
66 AGTAGAAGCACAATAAAA
2524542 AGAATATATATTGAGTATGACTGTAATATTCTAAATACTTGAAAATAAAAAGTTAGAAAATAAAA
1 AGAATATATATTGAGTATGACTGTAATATTCTAAATACTTGAAAATAAAAAGTTAGAAAATAAAA
2524607 AGTAGAAGCACAATAAAA
66 AGTAGAAGCACAATAAAA
2524625 GTTGCGGCTG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 55 0.67
83 27 0.33
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.27
Consensus pattern (83 bp):
AGAATATATATTGAGTATGACTGTAATATTCTAAATACTTGAAAATAAAAAGTTAGAAAATAAAA
AGTAGAAGCACAATAAAA
Found at i:2524612 original size:14 final size:15
Alignment explanation
Indices: 2524582--2524613 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2524572 CTAAATACTT
2524582 GAAAATAAAAAGTTA
1 GAAAATAAAAAGTTA
2524597 GAAAATAAAAAG-TA
1 GAAAATAAAAAGTTA
2524611 GAA
1 GAA
2524614 GCACAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
GAAAATAAAAAGTTA
Found at i:2529148 original size:18 final size:19
Alignment explanation
Indices: 2529125--2529161 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2529115 TTTAATAAGT
2529125 AAATATTCA-TAATAAAAA
1 AAATATTCATTAATAAAAA
*
2529143 AAATATTGATTAATAAAAA
1 AAATATTCATTAATAAAAA
2529162 TTTTTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATATTCATTAATAAAAA
Found at i:2530895 original size:18 final size:17
Alignment explanation
Indices: 2530870--2530903 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2530860 TAAAAACATT
2530870 AAAAATATAAATTAAAA
1 AAAAATATAAATTAAAA
*
2530887 AAAATATATACATTAAA
1 AAAA-ATATAAATTAAA
2530904 CATGCTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATATAAATTAAAA
Found at i:2531674 original size:21 final size:21
Alignment explanation
Indices: 2531650--2531689 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2531640 GACTACTGAA
2531650 TGGATCAGGCTTAAAAAAAAC
1 TGGATCAGGCTTAAAAAAAAC
*
2531671 TGGATTAGGCTTAAAAAAA
1 TGGATCAGGCTTAAAAAAA
2531690 TTGTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (21 bp):
TGGATCAGGCTTAAAAAAAAC
Found at i:2531869 original size:34 final size:34
Alignment explanation
Indices: 2531826--2531894 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2531816 TACTTTGAAC
2531826 CTTAGCTTGTATATAATACATGAATAAGCTTATA
1 CTTAGCTTGTATATAATACATGAATAAGCTTATA
*
2531860 CTTAGCTTGTATATAATACATGAATAAGTTTATA
1 CTTAGCTTGTATATAATACATGAATAAGCTTATA
2531894 C
1 C
2531895 ATTTTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (34 bp):
CTTAGCTTGTATATAATACATGAATAAGCTTATA
Found at i:2534174 original size:13 final size:13
Alignment explanation
Indices: 2534139--2534177 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2534129 GATAAGTTGC
*
2534139 ATATATATATATAT
1 ATATATATAT-TCT
2534153 ATATATATATTCT
1 ATATATATATTCT
*
2534166 ATATTTATATTC
1 ATATATATATTC
2534178 GAATCCAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATTCT
Found at i:2540521 original size:15 final size:15
Alignment explanation
Indices: 2540501--2540532 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2540491 ATCTGATGCA
2540501 TTAATAACATCAACT
1 TTAATAACATCAACT
2540516 TTAATAACATCAACT
1 TTAATAACATCAACT
2540531 TT
1 TT
2540533 GCACATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATAACATCAACT
Found at i:2541188 original size:45 final size:45
Alignment explanation
Indices: 2541110--2541226 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 45
2541100 TTTTTTGGCT
* **
2541110 ACGACCTCCCTTTTGATGAGCTCTCCATCGACGAGATCTCTTCTA
1 ACGAGCTCCCTTTCAATGAGCTCTCCATCGACGAGATCTCTTCTA
** * * * * * *
2541155 ACGAGCTTTCTTTTAGTGAGCTCTCCATTGACGAGCTTTTTTCTA
1 ACGAGCTCCCTTTCAATGAGCTCTCCATCGACGAGATCTCTTCTA
2541200 ACGAGCTCCCTTTCAATGAGCTCTCCA
1 ACGAGCTCCCTTTCAATGAGCTCTCCA
2541227 CCGATAAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (45 bp):
ACGAGCTCCCTTTCAATGAGCTCTCCATCGACGAGATCTCTTCTA
Found at i:2541339 original size:15 final size:15
Alignment explanation
Indices: 2541328--2541358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2541318 CGACGAGGTT
2541328 TCCATTGACGAGCTC
1 TCCATTGACGAGCTC
*
2541343 TCCATTGACAAGCTC
1 TCCATTGACGAGCTC
2541358 T
1 T
2541359 TTTTTGACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (15 bp):
TCCATTGACGAGCTC
Found at i:2541457 original size:30 final size:30
Alignment explanation
Indices: 2541403--2541479 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
2541393 TGACGAGTTT
* * *
2541403 CTTTTT-ATAAGCTTCCTATCGATGAGCTC
1 CTTTTTAACAAGCTCCCTATAGATGAGCTC
* * *
2541432 TTTTTTAACGAGCTCCCTATAGATGAGTTC
1 CTTTTTAACAAGCTCCCTATAGATGAGCTC
*
2541462 CTTTTTGACAAGCTCCCT
1 CTTTTTAACAAGCTCCCT
2541480 TTTGACAAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (30 bp):
CTTTTTAACAAGCTCCCTATAGATGAGCTC
Found at i:2541607 original size:45 final size:45
Alignment explanation
Indices: 2541548--2541700 Score: 139
Period size: 45 Copynumber: 3.4 Consensus size: 45
2541538 CTATTGAAGA
* * *
2541548 GCTCTTTATCGATGAGCTCCTTCCTGATGAGTTCCCTTTTAATAG
1 GCTCCTTATCGATGAGCTCCTTCTTGATGAGTTCCATTTTAATAG
* * * * *
2541593 GCTCCTTATTGATGAGCTTCC--CATTAATGAGTTCCTTTTTGATAA
1 GCTCCTTATCGATGAGC-TCCTTC-TTGATGAGTTCCATTTTAATAG
* * * * *
2541638 GTTCTTTATCGATGAGCTCCTTCTTGACGAGCTCCATTTTAACAG
1 GCTCCTTATCGATGAGCTCCTTCTTGATGAGTTCCATTTTAATAG
* *
2541683 GCTCCCTATTGATGAGCT
1 GCTCCTTATCGATGAGCT
2541701 TCCCATTAAT
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
44 4 0.05
45 75 0.90
46 4 0.05
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.39
Consensus pattern (45 bp):
GCTCCTTATCGATGAGCTCCTTCTTGATGAGTTCCATTTTAATAG
Found at i:2541620 original size:30 final size:30
Alignment explanation
Indices: 2541559--2541713 Score: 88
Period size: 30 Copynumber: 5.2 Consensus size: 30
2541549 CTCTTTATCG
** *
2541559 ATGAGCTCCTTCCTGATGAG-TTCCCTTTTA
1 ATGAGCTCCTTATTGATGAGCTTCCC-ATTA
2541589 AT-AGGCTCCTTATTGATGAGCTTCCCATTA
1 ATGA-GCTCCTTATTGATGAGCTTCCCATTA
* * * ** **
2541619 ATGAGTTCCTTTTTGATAAG-TTCTTTATCG
1 ATGAGCTCCTTATTGATGAGCTTC-CCATTA
* *
2541649 ATGAGCTCCTTCTTGACGAGC-T-CCATTTTA
1 ATGAGCTCCTTATTGATGAGCTTCCCA--TTA
* *
2541679 A-CAGGCTCCCTATTGATGAGCTTCCCATTA
1 ATGA-GCTCCTTATTGATGAGCTTCCCATTA
2541709 ATGAG
1 ATGAG
2541714 TTCCCTTTTG
Statistics
Matches: 91, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
28 1 0.01
29 5 0.05
30 74 0.81
31 8 0.09
32 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (30 bp):
ATGAGCTCCTTATTGATGAGCTTCCCATTA
Found at i:2541685 original size:90 final size:90
Alignment explanation
Indices: 2541550--2541729 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 90
2541540 ATTGAAGAGC
* * * * *
2541550 TCTTTATCGATGAGCTCCTTCCTGATGAGTTCCCTTTTAATAGGCTCCTTATTGATGAGCTTCCC
1 TCTTTATCGATGAGCTCCTTCCTGACGAGCTCCATTTTAACAGGCTCCCTATTGATGAGCTTCCC
*
2541615 ATTAATGAGTTCCTTTTTGATAAGT
66 ATTAATGAGTTCCCTTTTGATAAGT
*
2541640 TCTTTATCGATGAGCTCCTTCTTGACGAGCTCCATTTTAACAGGCTCCCTATTGATGAGCTTCCC
1 TCTTTATCGATGAGCTCCTTCCTGACGAGCTCCATTTTAACAGGCTCCCTATTGATGAGCTTCCC
2541705 ATTAATGAGTTCCCTTTTGATAAGT
66 ATTAATGAGTTCCCTTTTGATAAGT
2541730 CGACAAGTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (90 bp):
TCTTTATCGATGAGCTCCTTCCTGACGAGCTCCATTTTAACAGGCTCCCTATTGATGAGCTTCCC
ATTAATGAGTTCCCTTTTGATAAGT
Found at i:2542188 original size:27 final size:27
Alignment explanation
Indices: 2542144--2542197 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2542134 TTCCTTTTGT
*
2542144 AGCATCACCTTGCCAAAAACCTCTTTA
1 AGCATCACCTTACCAAAAACCTCTTTA
* * * *
2542171 AGCATCATCTTACTAAAAGCCTTTTTA
1 AGCATCACCTTACCAAAAACCTCTTTA
2542198 GGCTCCGACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.31
Consensus pattern (27 bp):
AGCATCACCTTACCAAAAACCTCTTTA
Found at i:2542233 original size:45 final size:45
Alignment explanation
Indices: 2542162--2542269 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
2542152 CTTGCCAAAA
* * *
2542162 ACCTCTTTAAGCATCATCTTACTAAAAGCCTTTTTAGGCTCCGAC
1 ACCTCTTTAAGCATCACCTCACTAAAAGCCTTTTTAGGCTCCAAC
* * *
2542207 ATCTCTTTAAGCATCACCTCATTAAAATCCTTTTTAGGCTCCAAC
1 ACCTCTTTAAGCATCACCTCACTAAAAGCCTTTTTAGGCTCCAAC
* *
2542252 ACCTCTTCAAGGATCACC
1 ACCTCTTTAAGCATCACC
2542270 AGGCCAAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (45 bp):
ACCTCTTTAAGCATCACCTCACTAAAAGCCTTTTTAGGCTCCAAC
Found at i:2542284 original size:45 final size:45
Alignment explanation
Indices: 2542162--2542310 Score: 120
Period size: 45 Copynumber: 3.3 Consensus size: 45
2542152 CTTGCCAAAA
* * ** * *
2542162 ACCTCTTTAAGCATCATCTTACTAAAAGCCTTTTTAGGCTCCGAC
1 ACCTCTTCAAGCATCACCACACCAAAAGCCTTTTTAGGCTCCAAC
* * * ** *
2542207 ATCTCTTTAAGCATCACCTCATTAAAATCCTTTTTAGGCTCCAAC
1 ACCTCTTCAAGCATCACCACACCAAAAGCCTTTTTAGGCTCCAAC
* ** * *
2542252 ACCTCTTCAAGGATCACCAGGCCAAAAGCCTTTTCAGGCTTCAA-
1 ACCTCTTCAAGCATCACCACACCAAAAGCCTTTTTAGGCTCCAAC
**
2542296 TGCTCTTCAAGCATC
1 ACCTCTTCAAGCATC
2542311 GTTTCGCCAA
Statistics
Matches: 84, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 12 0.14
45 72 0.86
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (45 bp):
ACCTCTTCAAGCATCACCACACCAAAAGCCTTTTTAGGCTCCAAC
Found at i:2543988 original size:26 final size:26
Alignment explanation
Indices: 2543956--2544005 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2543946 GATTTAACTC
2543956 AATTAATTTATATAATTATAATGATG
1 AATTAATTTATATAATTATAATGATG
2543982 AATTAATTTATATAATTATAATGA
1 AATTAATTTATATAATTATAATGA
2544006 CGTATAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
AATTAATTTATATAATTATAATGATG
Found at i:2554581 original size:24 final size:24
Alignment explanation
Indices: 2554543--2554617 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
2554533 AAAATATTTA
*
2554543 TATTAAATATATAAATT-TATATAT
1 TATTAAAAAT-TAAATTATATATAT
*
2554567 TATTAATAAATTAAATTATAATATTT
1 TATTAA-AAATTAAATTAT-ATATAT
* *
2554593 TATTAAAAATAAAATTATTTATAT
1 TATTAAAAATTAAATTATATATAT
2554617 T
1 T
2554618 TATTTTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 17 0.40
25 15 0.35
26 11 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTAAAAATTAAATTATATATAT
Found at i:2554619 original size:25 final size:26
Alignment explanation
Indices: 2554557--2554646 Score: 80
Period size: 26 Copynumber: 3.4 Consensus size: 26
2554547 AAATATATAA
*
2554557 ATTTATATATTATTAATAAATTAAATT
1 ATTTATAT-TTATTAATAAATAAAATT
*
2554584 A-TAATATTTTATTAA-AAATAAAATT
1 ATTTATA-TTTATTAATAAATAAAATT
*
2554609 ATTTATATTTATTTTAATAAA-AAATATC
1 ATTTATATTTA--TTAATAAATAAA-ATT
2554637 ATTTA-ATTTA
1 ATTTATATTTA
2554647 AGTAAATCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
25 14 0.26
26 15 0.28
27 14 0.26
28 10 0.19
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTATATTTATTAATAAATAAAATT
Found at i:2554706 original size:20 final size:21
Alignment explanation
Indices: 2554673--2554721 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
2554663 TTTTTTAAAA
*
2554673 ATAATAAT-AAAAATAAATAT
1 ATAATATTAAAAAATAAATAT
2554693 AT-ATATTAAAAAATAAATAT
1 ATAATATTAAAAAATAAATAT
2554713 ATAATATTA
1 ATAATATTA
2554722 TCTTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATATTAAAAAATAAATAT
Found at i:2555462 original size:21 final size:21
Alignment explanation
Indices: 2555438--2555480 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2555428 TATTCACAAC
2555438 AAAAAAAAA-TCTTTAATTAAT
1 AAAAAAAAATTC-TTAATTAAT
*
2555459 AAAAAATAATTCTTAATTAAT
1 AAAAAAAAATTCTTAATTAAT
2555480 A
1 A
2555481 TTTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAAAAATTCTTAATTAAT
Found at i:2557080 original size:20 final size:19
Alignment explanation
Indices: 2557055--2557092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2557045 ATTTAAAAAT
*
2557055 TAATAATATTAAAAGTATAA
1 TAATAAAATTAAAA-TATAA
2557075 TAATAAAATTAAAATATA
1 TAATAAAATTAAAATATA
2557093 CAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TAATAAAATTAAAATATAA
Found at i:2557682 original size:2 final size:2
Alignment explanation
Indices: 2557675--2557707 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2557665 GTTTTGGTGC
2557675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2557708 GTAAGAGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2558126 original size:6 final size:6
Alignment explanation
Indices: 2558117--2558169 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
2558107 TAATTTAAAT
* * * *
2558117 TATTTA TATTTA TTATTTA TAATTA TAAATTA TTTTTA TATTAA TATTTA
1 TATTTA TATTTA -TATTTA TATTTA T-ATTTA TATTTA TATTTA TATTTA
2558167 TAT
1 TAT
2558170 ATTTTATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 27 0.69
7 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATTTA
Found at i:2558133 original size:13 final size:13
Alignment explanation
Indices: 2558115--2558173 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
2558105 ATTAATTTAA
2558115 ATTATTTATATTT
1 ATTATTTATATTT
*
2558128 ATTATTTATAATT
1 ATTATTTATATTT
* * *
2558141 ATAAATTATTTTT
1 ATTATTTATATTT
*
2558154 A-TATTAATATTT
1 ATTATTTATATTT
2558166 ATATATTT
1 AT-TATTT
2558174 TATAATTAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
12 8 0.24
13 22 0.65
14 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTTATATTT
Found at i:2558146 original size:40 final size:40
Alignment explanation
Indices: 2558102--2558181 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
2558092 TAATTTTAAC
*
2558102 TAAATTAATTTAAATTATTTATATTTAT-TA-TTTATAATTA
1 TAAATT-ATTTAAA-TATTAATATTTATATATTTTATAATTA
**
2558142 TAAATTATTTTTATATTAATATTTATATATTTTATAATTA
1 TAAATTATTTAAATATTAATATTTATATATTTTATAATTA
2558182 AATTTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 12 0.34
39 7 0.20
40 16 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (40 bp):
TAAATTATTTAAATATTAATATTTATATATTTTATAATTA
Found at i:2558897 original size:2 final size:2
Alignment explanation
Indices: 2558892--2558916 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2558882 TGATAATTGT
2558892 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2558917 GCTTAATTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2559074 original size:2 final size:2
Alignment explanation
Indices: 2559067--2559092 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2559057 TTGTAACCAA
2559067 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
2559093 GCTTTAATTT
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:2560002 original size:15 final size:15
Alignment explanation
Indices: 2559982--2560018 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
2559972 ACTTAACTTA
2559982 AATCTAATAAATAAT
1 AATCTAATAAATAAT
2559997 AATCTAATAAATAAT
1 AATCTAATAAATAAT
2560012 AAT-TAAT
1 AATCTAAT
2560019 TTTTACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTAATAAATAAT
Found at i:2560346 original size:36 final size:36
Alignment explanation
Indices: 2560275--2560349 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2560265 AAAGTTTGAT
* * *
2560275 TTAATTTAAAATATAAATTTTAAATTTTGTCCAAAC
1 TTAATTTAAAATAGAAATTTTAAAATTTCTCCAAAC
2560311 TTAATTTATAAATAGATAA-TTTAAAATTTCT-CAAAC
1 TTAATTTA-AAATAGA-AATTTTAAAATTTCTCCAAAC
2560347 TTA
1 TTA
2560350 TCTATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 16 0.47
37 16 0.47
38 2 0.06
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
TTAATTTAAAATAGAAATTTTAAAATTTCTCCAAAC
Found at i:2560809 original size:6 final size:6
Alignment explanation
Indices: 2560798--2560834 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
2560788 TTTATTAATT
2560798 ATATAA ATATAA ATATTAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATA-TAA ATATAA ATATAA ATATAA
2560835 CATGTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:2562638 original size:5 final size:5
Alignment explanation
Indices: 2562631--2562665 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2562621 ATTATATAGC
*
2562631 AAATC AAATT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
2562666 TCATCTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:2563310 original size:13 final size:13
Alignment explanation
Indices: 2563282--2563318 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2563272 ATAATATTTA
2563282 ATAAATTTATATAT
1 ATAAATTTA-ATAT
2563296 ATAAATTTAATAT
1 ATAAATTTAATAT
2563309 ATAAATTTAA
1 ATAAATTTAA
2563319 GTAAAATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAATTTAATAT
Found at i:2563410 original size:11 final size:11
Alignment explanation
Indices: 2563389--2563431 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
2563379 TTTTATCACA
2563389 TATTAAATTTTT
1 TATT-AATTTTT
2563401 TATTAATTTTT
1 TATTAATTTTT
*
2563412 TA-AAATTTTT
1 TATTAATTTTT
2563422 TATATAATTT
1 TAT-TAATTT
2563432 AAAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTAATTTTT
Found at i:2563436 original size:20 final size:20
Alignment explanation
Indices: 2563393--2563456 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
2563383 ATCACATATT
*
2563393 AAATTTTTTATTAATTTTTTA
1 AAATTTTTTATTAA-TTTTAA
*
2563414 AAATTTTTTATATAATTTAAAA
1 AAATTTTTTAT-TAATTT-TAA
2563436 AATATTTTTTTATTAATTTTA
1 AA-A-TTTTTTATTAATTTTA
2563457 CTTATAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 14 0.39
22 7 0.19
23 7 0.19
24 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTTTTTATTAATTTTAA
Found at i:2563442 original size:23 final size:22
Alignment explanation
Indices: 2563393--2563454 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
2563383 ATCACATATT
***
2563393 AAATTTTTTAT-TAATTTTTTA
1 AAATTTTTTATATAATTTAAAA
2563414 AAATTTTTTATATAATTTAAAA
1 AAATTTTTTATATAATTTAAAA
2563436 AATATTTTTT-TATTAATTT
1 AA-ATTTTTTATA-TAATTT
2563455 TACTTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.31
22 11 0.31
23 13 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATTTTTTATATAATTTAAAA
Found at i:2565115 original size:10 final size:9
Alignment explanation
Indices: 2565088--2565240 Score: 51
Period size: 9 Copynumber: 16.0 Consensus size: 9
2565078 TTTAAATTAA
*
2565088 ATTTAATAT
1 ATTTTATAT
2565097 -TTTTATAT
1 ATTTTATAT
2565105 ATTTTATTAT
1 ATTTTA-TAT
* *
2565115 ATTATAATTAA
1 ATT-TTA-TAT
* *
2565126 ATTTAAAAT
1 ATTTTATAT
2565135 ATTTTATAT
1 ATTTTATAT
* *
2565144 -TTATATAA
1 ATTTTATAT
2565152 ATTTTAATAAT
1 ATTTT-AT-AT
** * *
2565163 AAATAATTT
1 ATTTTATAT
2565172 ATTTTATAAT
1 ATTTTAT-AT
*
2565182 TTTTTAAATAT
1 ATTTT--ATAT
*
2565193 ATTCATATCAT
1 ATT-TTAT-AT
*
2565204 ATTATATTAT
1 ATTTTA-TAT
2565214 ATTTT-TATT
1 ATTTTATA-T
2565223 ATTTTATAT
1 ATTTTATAT
2565232 ATTTTATAT
1 ATTTTATAT
2565241 TTATATAATA
Statistics
Matches: 107, Mismatches: 23, Indels: 28
0.68 0.15 0.18
Matches are distributed among these distances:
8 15 0.14
9 37 0.35
10 31 0.29
11 21 0.20
12 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTTATAT
Found at i:2565126 original size:38 final size:36
Alignment explanation
Indices: 2565069--2565143 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 36
2565059 AGATTCGAAT
*
2565069 TATTTTTTATTTAAATTAAATTTAATAT-TTTTATA
1 TATTTTTTATTTAAATTAAATTTAAAATATTTTATA
2565104 TATTTTATTATATTATAATTAAATTTAAAATATTTTATA
1 TATTTT-TTAT-TTA-AATTAAATTTAAAATATTTTATA
2565143 T
1 T
2565144 TTATATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 6 0.17
36 4 0.11
37 3 0.09
38 14 0.40
39 8 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
TATTTTTTATTTAAATTAAATTTAAAATATTTTATA
Found at i:2565222 original size:16 final size:16
Alignment explanation
Indices: 2565203--2565247 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
2565193 ATTCATATCA
2565203 TATTATATTATAT-TTT
1 TATTAT-TTATATATTT
2565219 TATTATTTTATATATTT
1 TATTA-TTTATATATTT
2565236 TA-TATTTATATA
1 TATTATTTATATA
2565248 ATAACGTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.30
16 13 0.48
17 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTATATATTT
Found at i:2565852 original size:34 final size:34
Alignment explanation
Indices: 2565787--2565970 Score: 262
Period size: 34 Copynumber: 5.4 Consensus size: 34
2565777 AATGTAAGTT
* *
2565787 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* *
2565820 TTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2565854 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2565888 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
2565922 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2565956 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2565971 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 12 0.09
34 121 0.91
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2566331 original size:19 final size:19
Alignment explanation
Indices: 2566275--2566337 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2566265 TGGTTGTCGA
**
2566275 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2566294 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2566313 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2566332 GTTACT
1 GGTACT
2566338 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2570469 original size:34 final size:34
Alignment explanation
Indices: 2570403--2570587 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
2570393 AAGTGGGAGA
* *
2570403 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2570436 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2570470 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2570504 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2570538 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2570572 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2570588 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Done.