Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 13 of 109
Found at i:2193507 original size:25 final size:25
Alignment explanation
Indices: 2193478--2193583 Score: 96
Period size: 25 Copynumber: 4.4 Consensus size: 25
2193468 AATTTTTTTT
2193478 TATTTTTGCATGATTTTTATTATGA
1 TATTTTTGCATGATTTTTATTATGA
* *
2193503 TATTTTTGCTTGATTTTTA-CA--A
1 TATTTTTGCATGATTTTTATTATGA
* * * *
2193525 TATTATTGCTTGATATTAATTATGA
1 TATTTTTGCATGATTTTTATTATGA
*
2193550 TATTTTTTTCATGA--TTTATTATGA
1 TA-TTTTTGCATGATTTTTATTATGA
*
2193574 TATTATTGCA
1 TATTTTTGCA
2193584 CAATATTCTT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
22 17 0.26
23 7 0.11
24 12 0.18
25 21 0.32
26 8 0.12
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (25 bp):
TATTTTTGCATGATTTTTATTATGA
Found at i:2193590 original size:49 final size:47
Alignment explanation
Indices: 2193496--2193590 Score: 109
Period size: 49 Copynumber: 2.0 Consensus size: 47
2193486 CATGATTTTT
* ***
2193496 ATTATGATATTTTTGCTTGATTTTTACAATATTATTGCTTGATATTA
1 ATTATGATATTTTTGCATGATTTTTACAATATTATTGCACAATATTA
* **
2193543 ATTATGATATTTTTTTCATGATTTATTATGATATTATTGCACAATATT
1 ATTATGATA-TTTTTGCATGATTT-TTACAATATTATTGCACAATATT
2193591 CTTATGGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 9 0.23
48 12 0.31
49 18 0.46
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.55
Consensus pattern (47 bp):
ATTATGATATTTTTGCATGATTTTTACAATATTATTGCACAATATTA
Found at i:2194810 original size:12 final size:13
Alignment explanation
Indices: 2194793--2194824 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2194783 CAGATTTATG
2194793 AAAATACAAAAA-
1 AAAATACAAAAAT
2194805 AAAATA-AAAAAT
1 AAAATACAAAAAT
2194817 AAAATACA
1 AAAATACA
2194825 GTATTTCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 12 0.67
13 1 0.06
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATACAAAAAT
Found at i:2195925 original size:13 final size:13
Alignment explanation
Indices: 2195889--2195913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2195879 ATTAAACCCC
2195889 TAAACCCTAAACT
1 TAAACCCTAAACT
2195902 TAAACCCTAAAC
1 TAAACCCTAAAC
2195914 CTTTACCCTA
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAACCCTAAACT
Found at i:2197908 original size:16 final size:17
Alignment explanation
Indices: 2197876--2197908 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2197866 GATATAAAAT
2197876 ATCATGCAAATTAATAA
1 ATCATGCAAATTAATAA
*
2197893 ATCATGTAAA-TAATAA
1 ATCATGCAAATTAATAA
2197909 TATAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (17 bp):
ATCATGCAAATTAATAA
Found at i:2198837 original size:58 final size:56
Alignment explanation
Indices: 2198775--2198908 Score: 155
Period size: 56 Copynumber: 2.4 Consensus size: 56
2198765 CTCTCTTTTT
* * *
2198775 TTAAATGACAAAAATACCTCTATTATAAATGTCAAATCACTATAATATCTCTTATGTC
1 TTAAATAACAAAAATACCTCT-TCATAAATGACAAATCACTATAATA-CTCTTATGTC
* * * *
2198833 TTAAATAACGAAAATACCTC-TCATAAATGACAAATTACTATGATACTTTTATGTC
1 TTAAATAACAAAAATACCTCTTCATAAATGACAAATCACTATAATACTCTTATGTC
* *
2198888 ATAATTAA-AAAAATACCTCTT
1 TTAAATAACAAAAATACCTCTT
2198909 ATCTCATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
54 10 0.15
55 16 0.25
56 21 0.32
58 18 0.28
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (56 bp):
TTAAATAACAAAAATACCTCTTCATAAATGACAAATCACTATAATACTCTTATGTC
Found at i:2199419 original size:57 final size:58
Alignment explanation
Indices: 2199345--2199454 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
2199335 ATGCATTTAC
* * * * *
2199345 TACCATAATTATGAAAATGCT-CTCTTATCAAAATTTGTCAAAATTACTATAATATAT
1 TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAATATAT
*
2199402 TACCATAATTATAAAAATACTCCTCTTACCATAATTAGTCAAAATTAATATAA
1 TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAA
2199455 ATTATGGCCC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 19 0.41
58 27 0.59
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (58 bp):
TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAATATAT
Found at i:2202463 original size:17 final size:18
Alignment explanation
Indices: 2202432--2202465 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2202422 AAAACCAAAA
*
2202432 TTTATTTTTTTAATTGTT
1 TTTATTTTTTAAATTGTT
2202450 TTTA-TTTTTAAATTGT
1 TTTATTTTTTAAATTGT
2202466 ATATTTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTAAATTGTT
Found at i:2203174 original size:24 final size:24
Alignment explanation
Indices: 2203129--2203176 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2203119 CTTTAAAATC
* **
2203129 TAAAAAAATTTGGAAATTTAAAAA
1 TAAAAAAATTTGAAAAAATAAAAA
*
2203153 TAAAAAATTTTGAAAAAATAAAAA
1 TAAAAAAATTTGAAAAAATAAAAA
2203177 AGGGAAACAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (24 bp):
TAAAAAAATTTGAAAAAATAAAAA
Found at i:2203224 original size:26 final size:25
Alignment explanation
Indices: 2203189--2203237 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
2203179 GGAAACATTC
* *
2203189 AAAAATTAAATAATCAAAAAAAATAG
1 AAAAACTAAAAAAT-AAAAAAAATAG
*
2203215 AAAAACTAAAAAATAAGAAAAAT
1 AAAAACTAAAAAATAAAAAAAAT
2203238 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAAACTAAAAAATAAAAAAAATAG
Found at i:2203243 original size:17 final size:17
Alignment explanation
Indices: 2203206--2203247 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2203196 AAATAATCAA
2203206 AAAAAAT-AGAAAAACT
1 AAAAAATAAGAAAAACT
*
2203222 AAAAAATAAGAAAAATT
1 AAAAAATAAGAAAAACT
*
2203239 TAAAAATAA
1 AAAAAATAA
2203248 TTCACACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAATAAGAAAAACT
Found at i:2203935 original size:15 final size:16
Alignment explanation
Indices: 2203910--2203939 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2203900 TGTGGTTGGA
2203910 ATTTTTAAAATTTTAT
1 ATTTTTAAAATTTTAT
2203926 ATTTTT-AAATTTTA
1 ATTTTTAAAATTTTA
2203940 GGATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTTAAAATTTTAT
Found at i:2203945 original size:16 final size:15
Alignment explanation
Indices: 2203910--2203948 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2203900 TGTGGTTGGA
*
2203910 ATTTTTAAAATTTTAT
1 ATTTTT-AAATTTTAG
2203926 ATTTTTAAATTTTAGG
1 ATTTTTAAATTTTA-G
2203942 ATTTTTA
1 ATTTTTA
2203949 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
ATTTTTAAATTTTAG
Found at i:2204069 original size:17 final size:17
Alignment explanation
Indices: 2204049--2204103 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
2204039 TCCTTTTTCC
2204049 AAAATTTTGGATTTTTA
1 AAAATTTTGGATTTTTA
*
2204066 AAAATTTCT--ATTTTTT
1 AAAATTT-TGGATTTTTA
*
2204082 TAAATTTTGGGA-TTTTA
1 AAAATTTT-GGATTTTTA
2204099 AAAAT
1 AAAAT
2204104 ATTTTAGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 1 0.03
16 12 0.40
17 15 0.50
18 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
AAAATTTTGGATTTTTA
Found at i:2205490 original size:18 final size:19
Alignment explanation
Indices: 2205458--2205493 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2205448 TTTATATTAA
2205458 TTTTTTATTGATTTGTTTT
1 TTTTTTATTGATTTGTTTT
*
2205477 TTTTTTTTTG-TTTGTTT
1 TTTTTTATTGATTTGTTT
2205494 ATTCACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (19 bp):
TTTTTTATTGATTTGTTTT
Found at i:2210766 original size:15 final size:14
Alignment explanation
Indices: 2210741--2210773 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
2210731 AGTGTTAAAT
2210741 ACAAAAATGACGAC
1 ACAAAAATGACGAC
2210755 ACAAACAATGACGAC
1 ACAAA-AATGACGAC
2210770 ACAA
1 ACAA
2210774 TCAAACTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (14 bp):
ACAAAAATGACGAC
Found at i:2213060 original size:14 final size:14
Alignment explanation
Indices: 2213043--2213120 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
2213033 TATTTTTTAT
2213043 TTTTTAATTTCTGC
1 TTTTTAATTTCTGC
*
2213057 TTTTTAATTCTTTG-
1 TTTTTAATT-TCTGC
*
2213071 TTTTTAA-TTC-CC
1 TTTTTAATTTCTGC
*
2213083 TTTTTTATTTCTGC
1 TTTTTAATTTCTGC
* *
2213097 -TTTTGATTACTG-
1 TTTTTAATTTCTGC
2213109 TTTTTAATTTCT
1 TTTTTAATTTCT
2213121 TTTTAAATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
12 7 0.14
13 23 0.46
14 17 0.34
15 3 0.06
ACGTcount: A:0.14, C:0.13, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTTAATTTCTGC
Found at i:2213177 original size:31 final size:30
Alignment explanation
Indices: 2213109--2213185 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 30
2213099 TTGATTACTG
2213109 TTTTTAATTTC--TTTTT-AAATTATGTTT
1 TTTTTAATTTCTATTTTTAAAATTATGTTT
* * *
2213136 TTTAT-GTTTCTATTTTTAAAATTTTTGTTT
1 TTTTTAATTTCTATTTTTAAAA-TTATGTTT
2213166 TTTTTAATTTCTATTTTTAA
1 TTTTTAATTTCTATTTTTAA
2213186 TTCTTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.10
27 4 0.10
28 5 0.12
29 3 0.08
30 11 0.28
31 13 0.32
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (30 bp):
TTTTTAATTTCTATTTTTAAAATTATGTTT
Found at i:2213184 original size:13 final size:13
Alignment explanation
Indices: 2213023--2213201 Score: 53
Period size: 14 Copynumber: 13.2 Consensus size: 13
2213013 TTTATTTAGC
*
2213023 TTCTATTTTTTATT
1 TTCTA-TTTTTAAT
*
2213037 TTTTATTTTTTAAT
1 TTCTA-TTTTTAAT
*
2213051 TTCTGCTTTTTAAT
1 TTCT-ATTTTTAAT
* *
2213065 TCTTTGTTTTTAAT
1 T-TCTATTTTTAAT
*
2213079 TCCCT-TTTTT-AT
1 T-TCTATTTTTAAT
** *
2213091 TTCTGCTTTTGAT
1 TTCTATTTTTAAT
* *
2213104 TACTGTTTTTAAT
1 TTCTATTTTTAAT
*
2213117 TTCT-TTTTAAAT
1 TTCTATTTTTAAT
* *
2213129 TATGT-TTTTTATGT
1 T-TCTATTTTTA-AT
2213143 TTCTATTTTTAAAATTT
1 TTCTATTTTT--AA--T
* *
2213160 TTGTTTTTTTTAAT
1 TT-CTATTTTTAAT
2213174 TTCTATTTTTAA-
1 TTCTATTTTTAAT
*
2213186 TTCTTGTTTTTAAT
1 TTC-TATTTTTAAT
2213200 TT
1 TT
2213202 TGTTTAAATA
Statistics
Matches: 126, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
11 2 0.02
12 18 0.14
13 45 0.36
14 47 0.37
15 2 0.02
16 3 0.02
17 3 0.02
18 6 0.05
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (13 bp):
TTCTATTTTTAAT
Found at i:2213204 original size:12 final size:12
Alignment explanation
Indices: 2213166--2213206 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
2213156 ATTTTTGTTT
*
2213166 TTTTTAATTTCTA
1 TTTTTAATTT-TG
2213179 TTTTTAATTCTTG
1 TTTTTAATT-TTG
2213192 TTTTTAATTTTG
1 TTTTTAATTTTG
2213204 TTT
1 TTT
2213207 AAATATTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.23
13 19 0.73
14 1 0.04
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTAATTTTG
Found at i:2213322 original size:25 final size:25
Alignment explanation
Indices: 2213294--2213399 Score: 105
Period size: 25 Copynumber: 4.4 Consensus size: 25
2213284 GAATTTTTTT
2213294 TATTTTTGCATGATTTTTATTATGA
1 TATTTTTGCATGATTTTTATTATGA
*
2213319 TATTTTTGCTTGATTTTTA-TA--A
1 TATTTTTGCATGATTTTTATTATGA
* * * *
2213341 TATTATTGCTTGATATTAATTATGA
1 TATTTTTGCATGATTTTTATTATGA
*
2213366 TATTTTTTTCATGA--TTTATTATGA
1 TA-TTTTTGCATGATTTTTATTATGA
*
2213390 TATTATTGCA
1 TATTTTTGCA
2213400 CAATATTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
22 17 0.25
23 8 0.12
24 13 0.19
25 21 0.31
26 8 0.12
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.58
Consensus pattern (25 bp):
TATTTTTGCATGATTTTTATTATGA
Found at i:2213369 original size:47 final size:49
Alignment explanation
Indices: 2213294--2213399 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 49
2213284 GAATTTTTTT
* * * *
2213294 TATTTTTGCATGATTTTTATTATGATA-TTTTTGCTTGATTT-TTATAA
1 TATTATTGCATGATATTAATTATGATATTTTTTGCATGATTTATTATAA
* * *
2213341 TATTATTGCTTGATATTAATTATGATATTTTTTTCATGATTTATTATGA
1 TATTATTGCATGATATTAATTATGATATTTTTTGCATGATTTATTATAA
2213390 TATTATTGCA
1 TATTATTGCA
2213400 CAATATTCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 23 0.47
48 12 0.24
49 14 0.29
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.58
Consensus pattern (49 bp):
TATTATTGCATGATATTAATTATGATATTTTTTGCATGATTTATTATAA
Found at i:2213406 original size:49 final size:47
Alignment explanation
Indices: 2213312--2213406 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 47
2213302 CATGATTTTT
* ***
2213312 ATTATGATATTTTTGCTTGATTTTTATAATATTATTGCTTGATATTA
1 ATTATGATATTTTTGCATGATTTTTATAATATTATTGCACAATATTA
* *
2213359 ATTATGATATTTTTTTCATGATTTATTATGATATTATTGCACAATATT
1 ATTATGATA-TTTTTGCATGATTT-TTATAATATTATTGCACAATATT
2213407 CTTATGGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 9 0.22
48 12 0.30
49 19 0.47
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.56
Consensus pattern (47 bp):
ATTATGATATTTTTGCATGATTTTTATAATATTATTGCACAATATTA
Found at i:2217693 original size:16 final size:17
Alignment explanation
Indices: 2217661--2217693 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2217651 GATATAAAAT
2217661 ATCATGCAAATTAATAA
1 ATCATGCAAATTAATAA
*
2217678 ATCATGTAAA-TAATAA
1 ATCATGCAAATTAATAA
2217694 TATAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (17 bp):
ATCATGCAAATTAATAA
Found at i:2218649 original size:58 final size:56
Alignment explanation
Indices: 2218576--2218709 Score: 146
Period size: 56 Copynumber: 2.4 Consensus size: 56
2218566 CTCTCTCTTT
* * * *
2218576 TTAAATGACAAAAATACCTCTATTATAAATGTCAAATCACTATAATATCTCTTATGTC
1 TTAAATAACGAAAATACCTCT-TCATAAATGACAAATCACTATAATA-CTCTTATGTC
* * *
2218634 TTAAATAACGAAAATACCTC-TCATAAATGACAAATTACTATGATACTTTTATGTC
1 TTAAATAACGAAAATACCTCTTCATAAATGACAAATCACTATAATACTCTTATGTC
* * *
2218689 ATAATTAA-GAAAATGCCTCTT
1 TTAAATAACGAAAATACCTCTT
2218710 ATGTCATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
54 10 0.15
55 16 0.25
56 21 0.32
58 18 0.28
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (56 bp):
TTAAATAACGAAAATACCTCTTCATAAATGACAAATCACTATAATACTCTTATGTC
Found at i:2219146 original size:34 final size:36
Alignment explanation
Indices: 2219107--2219179 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 36
2219097 TAAATTGGTT
*
2219107 AAAATTA-TGATGATGCCCCT-CTACCATAATT-TGA
1 AAAATTACTG-TGATGCACCTACTACCATAATTATGA
**
2219141 AAAATTACTGTGATGCATTTACTACCATAATTATGA
1 AAAATTACTGTGATGCACCTACTACCATAATTATGA
2219177 AAA
1 AAA
2219180 TGCTCTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 14 0.42
35 13 0.39
36 6 0.18
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (36 bp):
AAAATTACTGTGATGCACCTACTACCATAATTATGA
Found at i:2219237 original size:57 final size:58
Alignment explanation
Indices: 2219163--2219272 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
2219153 ATGCATTTAC
* * * * *
2219163 TACCATAATTATGAAAATGCT-CTCTTATCAAAATTTGTCAAAATTACTATAATATAT
1 TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAATATAT
*
2219220 TACCATAATTATAAAAATACTCCTCTTACCATAATTAGTCAAAATTAATATAA
1 TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAA
2219273 ATTATGGCCC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 19 0.41
58 27 0.59
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (58 bp):
TACCATAATTATAAAAATACTCCTCTTACCAAAATTAGTCAAAATTAATATAATATAT
Found at i:2222295 original size:17 final size:18
Alignment explanation
Indices: 2222264--2222297 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2222254 AAAACCAAAA
*
2222264 TTTATTTTTTTAATTGTT
1 TTTATTTTTTAAATTGTT
2222282 TTTA-TTTTTAAATTGT
1 TTTATTTTTTAAATTGT
2222298 ATATTTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTAAATTGTT
Found at i:2223015 original size:25 final size:25
Alignment explanation
Indices: 2222968--2223018 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2222958 TTTAAAATCT
* **
2222968 ATAAAAAATTTTGGAAATTTAAAAA
1 ATAAAAAATTTTGAAAAAATAAAAA
2222993 ATAAAAAATTTTGAAAAAATAAAAA
1 ATAAAAAATTTTGAAAAAATAAAAA
2223018 A
1 A
2223019 GGGAAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (25 bp):
ATAAAAAATTTTGAAAAAATAAAAA
Found at i:2223645 original size:18 final size:16
Alignment explanation
Indices: 2223615--2223648 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
2223605 TTTTAAAAAC
2223615 TTTTTTTAGTTTTTTA
1 TTTTTTTAGTTTTTTA
2223631 TTTTTTTATGATTTTTTA
1 TTTTTTTA-G-TTTTTTA
2223649 ATATCTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTTTAGTTTTTTA
Found at i:2223673 original size:53 final size:53
Alignment explanation
Indices: 2223616--2223747 Score: 124
Period size: 55 Copynumber: 2.4 Consensus size: 53
2223606 TTTAAAAACT
* * * * *
2223616 TTTTTTAGTTTTTTATTTTTTTATGATTTTT-TAATA-TCTCATATTGTTTTTTA
1 TTTTTTAGTTTTTAAATTTTTT-TGATTTTTAAAACATTCTCAGATT-TTTTTTA
* * *
2223669 TTTTTTTGAATTTTAAATTTTTTTGATTTTTAAAAACATTTTCAGATTTTTTTTA
1 TTTTTTAG-TTTTTAAATTTTTTTGATTTTT-AAAACATTCTCAGATTTTTTTTA
2223724 TTTTTTAGTTTTTCATAATTTTTT
1 TTTTTTAGTTTTT-A-AATTTTTT
2223748 GATGTGGTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
53 15 0.24
54 15 0.24
55 18 0.29
56 15 0.24
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (53 bp):
TTTTTTAGTTTTTAAATTTTTTTGATTTTTAAAACATTCTCAGATTTTTTTTA
Found at i:2223689 original size:16 final size:17
Alignment explanation
Indices: 2223668--2223702 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2223658 ATTGTTTTTT
2223668 ATTTTTTTGAATTTTAA
1 ATTTTTTTGAATTTTAA
*
2223685 ATTTTTTTGATTTTTAA
1 ATTTTTTTGAATTTTAA
2223702 A
1 A
2223703 AACATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
ATTTTTTTGAATTTTAA
Found at i:2223917 original size:35 final size:36
Alignment explanation
Indices: 2223878--2223959 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
2223868 TTAATTTCGA
* * * *
2223878 ATTTTTTATAATTTTC-CTTTTTCCAAAATTTTTGG
1 ATTTTTAAAAATTTTCTATTTTTCCAAAATTTTGGG
**
2223913 ATTTTTAAAAATTTTCTATTTTTTTAAAATTTTGGG
1 ATTTTTAAAAATTTTCTATTTTTCCAAAATTTTGGG
2223949 A-TTTTAAAAAT
1 ATTTTTAAAAAT
2223960 ATTTTAGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 24 0.60
36 16 0.40
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (36 bp):
ATTTTTAAAAATTTTCTATTTTTCCAAAATTTTGGG
Found at i:2223952 original size:19 final size:18
Alignment explanation
Indices: 2223902--2223953 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2223892 TCCTTTTTCC
*
2223902 AAAATTTTTGGA-TTTTT
1 AAAAATTTTGGATTTTTT
**
2223919 AAAAATTTTCTATTTTTT
1 AAAAATTTTGGATTTTTT
*
2223937 TAAAATTTTGGGATTTT
1 AAAAATTTT-GGATTTT
2223954 AAAAATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 9 0.33
18 13 0.48
19 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (18 bp):
AAAAATTTTGGATTTTTT
Found at i:2223953 original size:18 final size:17
Alignment explanation
Indices: 2223902--2223959 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2223892 TCCTTTTTCC
*
2223902 AAAATTTTTGGATTTTT
1 AAAAATTTTGGATTTTT
**
2223919 AAAAATTTTCTATTTTTT
1 AAAAATTTTGGA-TTTTT
*
2223937 TAAAATTTTGGGA-TTTT
1 AAAAATTTT-GGATTTTT
2223954 AAAAAT
1 AAAAAT
2223960 ATTTTAGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 18 0.56
18 13 0.41
19 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
AAAAATTTTGGATTTTT
Found at i:2225349 original size:17 final size:18
Alignment explanation
Indices: 2225318--2225352 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2225308 TTTATATTAA
2225318 TTTTTTATTGATTTGTTT
1 TTTTTTATTGATTTGTTT
*
2225336 TTTTTTTTTG-TTTGTTT
1 TTTTTTATTGATTTGTTT
2225353 ATTCACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (18 bp):
TTTTTTATTGATTTGTTT
Found at i:2225921 original size:19 final size:18
Alignment explanation
Indices: 2225869--2225922 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
2225859 AATTCATGAG
* * *
2225869 TTTTATCTATCTATATAA
1 TTTTATTTAACTATTTAA
*
2225887 TTTTATTTTACATATTTAA
1 TTTTATTTAAC-TATTTAA
2225906 TTTTCATTTAACTATTT
1 TTTT-ATTTAACTATTT
2225923 TCAATTGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 8 0.28
19 15 0.52
20 6 0.21
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATTTAACTATTTAA
Found at i:2227549 original size:28 final size:27
Alignment explanation
Indices: 2227500--2227567 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
2227490 ATAAAAAAAT
**
2227500 TAAATTAATTAAAATTTTATATTTTAAGTA
1 TAAATTAA--AAAATTAAATATTTT-AGTA
*
2227530 TAAATTAAAAAATTAAATATTTTATTA
1 TAAATTAAAAAATTAAATATTTTAGTA
*
2227557 TAATTTAAAAA
1 TAAATTAAAAA
2227568 TAATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.38
28 13 0.38
30 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TAAATTAAAAAATTAAATATTTTAGTA
Found at i:2227785 original size:12 final size:12
Alignment explanation
Indices: 2227768--2227833 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 12
2227758 CATCTTCACC
2227768 TATATATATTAT
1 TATATATATTAT
2227780 TATATATA-TAT
1 TATATATATTAT
2227791 T-TATAT-TTA-
1 TATATATATTAT
*
2227800 TATTTATA-T-T
1 TATATATATTAT
*
2227810 TATATTTATATAT
1 TATATATAT-TAT
2227823 ATATATATATT
1 -TATATATATT
2227834 TTTTCTTGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
9 1 0.02
10 18 0.43
11 4 0.10
12 9 0.21
13 2 0.05
14 8 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATATATTAT
Found at i:2227795 original size:6 final size:6
Alignment explanation
Indices: 2227779--2227834 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
2227769 ATATATATTA
* *
2227779 TTATAT ATATAT TTATAT TTATAT TTATAT TTATAT TTATAT ATATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
2227827 ATATAT TT
1 TTATAT TT
2227835 TTTCTTGTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTATAT
Found at i:2227800 original size:18 final size:18
Alignment explanation
Indices: 2227779--2227834 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
2227769 ATATATATTA
2227779 TTATATATATATTTATAT
1 TTATATATATATTTATAT
*
2227797 TTATATTTATATTTATAT
1 TTATATATATATTTATAT
*
2227815 TTATATATATATATATAT
1 TTATATATATATTTATAT
2227833 TT
1 TT
2227835 TTTCTTGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATATATATTTATAT
Found at i:2228123 original size:17 final size:17
Alignment explanation
Indices: 2228103--2228136 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2228093 TATAATTTTT
2228103 AAAATCATAAAATATAA
1 AAAATCATAAAATATAA
2228120 AAAATCATAAAATATAA
1 AAAATCATAAAATATAA
2228137 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATCATAAAATATAA
Found at i:2229998 original size:13 final size:14
Alignment explanation
Indices: 2229977--2230010 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2229967 TATATTTTTA
2229977 AAAAATTTGAGA-T
1 AAAAATTTGAGATT
*
2229990 AAAATTTTGAGATT
1 AAAAATTTGAGATT
2230004 AAAAATT
1 AAAAATT
2230011 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (14 bp):
AAAAATTTGAGATT
Found at i:2235587 original size:2 final size:2
Alignment explanation
Indices: 2235580--2235606 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2235570 GAGTAGCAAG
2235580 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 A
2235607 ATTGATGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2238250 original size:13 final size:13
Alignment explanation
Indices: 2238232--2238270 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2238222 TTTTATAGAG
2238232 AGAAAAAAAAAGA
1 AGAAAAAAAAAGA
2238245 AGAAAAAAGAAA-A
1 AGAAAAAA-AAAGA
*
2238258 AGAAAAAGAAAGA
1 AGAAAAAAAAAGA
2238271 GGGTGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAGA
Found at i:2239124 original size:41 final size:41
Alignment explanation
Indices: 2239000--2239133 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 41
2238990 ACAAACACAA
** * * * *
2239000 ACTAAAGCTTTAAATTCAACAATTAC-AGCATGGAAATACAA
1 ACTAAAGCTTTAAACACAACGATAACTA-CATGAAAATACAT
* * * *
2239041 ACGAAAACATTAAACACAACGATAACTATATGAAAATACAT
1 ACTAAAGCTTTAAACACAACGATAACTACATGAAAATACAT
** *
2239082 ACTAAAGCTTTAAACACATTGATAACTACATGAAAATGCAT
1 ACTAAAGCTTTAAACACAACGATAACTACATGAAAATACAT
2239123 ACTAAAGCTTT
1 ACTAAAGCTTT
2239134 TTAACTACAT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 74 0.99
42 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (41 bp):
ACTAAAGCTTTAAACACAACGATAACTACATGAAAATACAT
Found at i:2242539 original size:30 final size:31
Alignment explanation
Indices: 2242503--2242573 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
2242493 TATTGTATTG
*
2242503 TATAAAATATTATAT-TTATATTATATTTT-A
1 TATAAAATATTATATATTAAATT-TATTTTGA
* *
2242533 TATAAAA-AATATGTATTAAATTTATTTTGA
1 TATAAAATATTATATATTAAATTTATTTTGA
2242563 TATGAAAATAT
1 TAT-AAAATAT
2242574 AAAATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 11 0.33
30 17 0.52
31 4 0.12
32 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
TATAAAATATTATATATTAAATTTATTTTGA
Found at i:2242658 original size:11 final size:11
Alignment explanation
Indices: 2242632--2242690 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
2242622 ATTTTAAATC
2242632 ATATTATTTTT
1 ATATTATTTTT
*
2242643 ATATATTTTATTT
1 ATAT-TATT-TTT
2242656 ATATTATTTTT
1 ATATTATTTTT
*
2242667 ATATCATATTATT
1 ATAT--TATTTTT
2242680 ATATTATTTTT
1 ATATTATTTTT
2242691 TAAATTATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 17 0.43
12 6 0.15
13 17 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:2242664 original size:24 final size:24
Alignment explanation
Indices: 2242632--2242690 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
2242622 ATTTTAAATC
*
2242632 ATATTATTTTTATAT-ATTTTATTT
1 ATATTATTTTTATATCATATTA-TT
2242656 ATATTATTTTTATATCATATTATT
1 ATATTATTTTTATATCATATTATT
2242680 ATATTATTTTT
1 ATATTATTTTT
2242691 TAAATTATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATTATTTTTATATCATATTATT
Found at i:2249794 original size:26 final size:24
Alignment explanation
Indices: 2249765--2249823 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2249755 TTTCAATAAT
*
2249765 TTTAATAAGTTATCATTTGTACTATA
1 TTTAAT-A-TTATCATCTGTACTATA
* *
2249791 TTTAATATTTTCATCTGTATTATA
1 TTTAATATTATCATCTGTACTATA
*
2249815 TTTATTATT
1 TTTAATATT
2249824 TATTAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 22 0.76
25 1 0.03
26 6 0.21
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.58
Consensus pattern (24 bp):
TTTAATATTATCATCTGTACTATA
Found at i:2249809 original size:24 final size:24
Alignment explanation
Indices: 2249777--2249824 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2249767 TAATAAGTTA
*
2249777 TCATTTGTACTATATTTAATATTT
1 TCATCTGTACTATATTTAATATTT
* *
2249801 TCATCTGTATTATATTTATTATTT
1 TCATCTGTACTATATTTAATATTT
2249825 ATTAAACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.60
Consensus pattern (24 bp):
TCATCTGTACTATATTTAATATTT
Found at i:2249990 original size:16 final size:17
Alignment explanation
Indices: 2249948--2249992 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2249938 GGTTTTAGTC
2249948 ATTTCAATTTCAGATTG
1 ATTTCAATTTCAGATTG
**
2249965 ATTTGGATTT-AGATTG
1 ATTTCAATTTCAGATTG
*
2249981 TTTTCAATTTCA
1 ATTTCAATTTCA
2249993 AGTTAGGCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (17 bp):
ATTTCAATTTCAGATTG
Found at i:2250364 original size:21 final size:20
Alignment explanation
Indices: 2250339--2250390 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2250329 TAATTTAAGG
*
2250339 ATTTTAATTAGATTTATTTAT
1 ATTTTAATTAGA-TTACTTAT
*
2250360 ATTTTGATTCAGATTACTTAT
1 ATTTTAATT-AGATTACTTAT
*
2250381 TTTTTAATTA
1 ATTTTAATTA
2250391 TTTTTATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTTTAATTAGATTACTTAT
Found at i:2253585 original size:26 final size:26
Alignment explanation
Indices: 2253549--2253608 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
2253539 ATGTTTGTGA
*
2253549 CATTTGCATTTACATAAGGACATTGG
1 CATTTGCATTTACATAAAGACATTGG
2253575 CATTTGCATTTACATAAAGACATTGG
1 CATTTGCATTTACATAAAGACATTGG
2253601 CATTTGCA
1 CATTTGCA
2253609 CCTTTAGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (26 bp):
CATTTGCATTTACATAAAGACATTGG
Found at i:2254213 original size:33 final size:33
Alignment explanation
Indices: 2254174--2254236 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2254164 TATTTATTTG
*
2254174 AAGACATCTGCATTTACTT-GGTGGTGATATCTA
1 AAGACATCTGCATTTA-TTGGGTGCTGATATCTA
* *
2254207 AAGACATTTGTATTTATTGGGTGCTGATAT
1 AAGACATCTGCATTTATTGGGTGCTGATAT
2254237 TTGAGTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.08
33 24 0.92
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (33 bp):
AAGACATCTGCATTTATTGGGTGCTGATATCTA
Found at i:2254496 original size:49 final size:50
Alignment explanation
Indices: 2254389--2254504 Score: 148
Period size: 49 Copynumber: 2.3 Consensus size: 50
2254379 GAATATTTAA
2254389 AATCTTTAAAGTTTCAATGCCTCTAATTTAAAAGAGCTTTTTTCATATAAG
1 AATCTTTAAAGTTTCAATGCCTCTAATTTAAAAGAGCTTTTTT-ATATAAG
* * * **
2254440 AAT-TTTAAAATTTCAATGCCTCTAA-TTAGATGAGCTTTTTT-TATGTG
1 AATCTTTAAAGTTTCAATGCCTCTAATTTAAAAGAGCTTTTTTATATAAG
2254487 AACTCTTTAAAGTTTCAA
1 AA-TCTTTAAAGTTTCAA
2254505 AAACTCTGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
47 6 0.11
48 1 0.02
49 26 0.46
50 21 0.37
51 3 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (50 bp):
AATCTTTAAAGTTTCAATGCCTCTAATTTAAAAGAGCTTTTTTATATAAG
Found at i:2255059 original size:11 final size:11
Alignment explanation
Indices: 2255039--2255094 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
2255029 AAAATAAAAA
2255039 ATAAAGAAAATT
1 ATAAA-AAAATT
*
2255051 ATAAAAAAATG
1 ATAAAAAAATT
2255062 A-AACAAAAATT
1 ATAA-AAAAATT
*
2255073 AAAAAAAAAGTT
1 ATAAAAAAA-TT
2255085 -TAAAAAAATT
1 ATAAAAAAATT
2255095 CGAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 4 0.11
11 25 0.66
12 9 0.24
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (11 bp):
ATAAAAAAATT
Found at i:2255091 original size:22 final size:21
Alignment explanation
Indices: 2255040--2255106 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
2255030 AAATAAAAAA
*
2255040 TAAAGAAAATTATAAAAAAATG
1 TAAA-AAAATTAAAAAAAAATG
* *
2255062 AAACAAAAATTAAAAAAAAAGTT
1 TAA-AAAAATTAAAAAAAAA-TG
2255085 TAAAAAAATTCGAAAAAAAAAT
1 TAAAAAAATT--AAAAAAAAAT
2255107 CTTTTGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 23 0.62
23 5 0.14
24 9 0.24
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (21 bp):
TAAAAAAATTAAAAAAAAATG
Found at i:2256972 original size:23 final size:23
Alignment explanation
Indices: 2256942--2256987 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2256932 AATTTCAGTC
2256942 CCTGTCAATGAGAAACAATAGTT
1 CCTGTCAATGAGAAACAATAGTT
2256965 CCTGTCAATGAGAAACAATAGTT
1 CCTGTCAATGAGAAACAATAGTT
2256988 GAAAGCGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (23 bp):
CCTGTCAATGAGAAACAATAGTT
Found at i:2258380 original size:113 final size:115
Alignment explanation
Indices: 2258180--2258413 Score: 409
Period size: 113 Copynumber: 2.1 Consensus size: 115
2258170 AATATTTTTT
* * *
2258180 ATTTGGATCATCAATATATATACAATAATAATCATAAAATATATATATAGAAAATTAATTATCAA
1 ATTTGGATCACCAATATATATAAAATAATAATCATAAAATATATATATAGAAAATTAATTACCAA
2258245 TATTCCTTACATAATAAGTTATAAGTTATTACACAGGGTCCTACTTATCA
66 TATTCCTTACATAATAAGTTATAAGTTATTACACAGGGTCCTACTTATCA
2258295 ATTTGGATCACCAATATATATAAAATAATAATCAT-AAA-ATATATATAGAAAATTAATTACCAA
1 ATTTGGATCACCAATATATATAAAATAATAATCATAAAATATATATATAGAAAATTAATTACCAA
*
2258358 TATTCCTTACATGATAAGTTATAAGTTATTACACAGGGTCCTACTTATCA
66 TATTCCTTACATAATAAGTTATAAGTTATTACACAGGGTCCTACTTATCA
*
2258408 AATTGG
1 ATTTGG
2258414 CTTTATGTAA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 78 0.68
114 3 0.03
115 33 0.29
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (115 bp):
ATTTGGATCACCAATATATATAAAATAATAATCATAAAATATATATATAGAAAATTAATTACCAA
TATTCCTTACATAATAAGTTATAAGTTATTACACAGGGTCCTACTTATCA
Found at i:2259233 original size:21 final size:21
Alignment explanation
Indices: 2259203--2259259 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2259193 ATTAGATTGG
*
2259203 AATCGATAGAGATCATATTAT
1 AATCGTTAGAGATCATATTAT
2259224 AATCGTTAGAGATCATATTAT
1 AATCGTTAGAGATCATATTAT
*
2259245 AATCATTAGAGATCA
1 AATCGTTAGAGATCA
2259260 ATTTAAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (21 bp):
AATCGTTAGAGATCATATTAT
Found at i:2260342 original size:17 final size:17
Alignment explanation
Indices: 2260320--2260353 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2260310 CTAATCAATT
2260320 TTTTATATTTAAATATA
1 TTTTATATTTAAATATA
*
2260337 TTTTATATTTAATTATA
1 TTTTATATTTAAATATA
2260354 AAATATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATATTTAAATATA
Found at i:2261563 original size:18 final size:18
Alignment explanation
Indices: 2261540--2261578 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2261530 AAAAAATTTT
2261540 AATTATT-TTTATTAATAA
1 AATTATTATTTA-TAATAA
2261558 AATTATTATTTATAATAA
1 AATTATTATTTATAATAA
2261576 AAT
1 AAT
2261579 AGTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTATTATTTATAATAA
Found at i:2262309 original size:19 final size:18
Alignment explanation
Indices: 2262268--2262316 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2262258 AATAAAATTC
2262268 AATCGAGTTCAAGCTGAG
1 AATCGAGTTCAAGCTGAG
* * *
2262286 TATCGAGTTGCAAGTTGGG
1 AATCGAGTT-CAAGCTGAG
*
2262305 AATCGAGCTCAA
1 AATCGAGTTCAA
2262317 ATTTATCACT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (18 bp):
AATCGAGTTCAAGCTGAG
Found at i:2262933 original size:22 final size:24
Alignment explanation
Indices: 2262908--2262952 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
2262898 TAGATATAAA
*
2262908 TCTATTTAAATAA-AT-TAAAAAT
1 TCTATTAAAATAATATATAAAAAT
2262930 TCTATTAAAATAATATATAAAAA
1 TCTATTAAAATAATATATAAAAA
2262953 GAGAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TCTATTAAAATAATATATAAAAAT
Found at i:2263260 original size:20 final size:20
Alignment explanation
Indices: 2263221--2263261 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2263211 TTCATATTTT
*
2263221 AAATAATTATATTTGAACAA
1 AAATAATTATATATGAACAA
2263241 AAATAATTATCATATG-ACAA
1 AAATAATTAT-ATATGAACAA
2263261 A
1 A
2263262 TAGTCTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATAATTATATATGAACAA
Found at i:2264800 original size:20 final size:20
Alignment explanation
Indices: 2264764--2264802 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2264754 CATTACACAT
*
2264764 TTGATAGAAAAATTTAATTA
1 TTGATAGAAAAAATTAATTA
2264784 TTGAT-GAATAAAATTAATT
1 TTGATAGAA-AAAATTAATT
2264803 TTTGTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (20 bp):
TTGATAGAAAAAATTAATTA
Found at i:2265325 original size:15 final size:15
Alignment explanation
Indices: 2265305--2265334 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2265295 CACTAGGATT
2265305 CCACGAATTAGAATC
1 CCACGAATTAGAATC
2265320 CCACGAATTAGAATC
1 CCACGAATTAGAATC
2265335 TGGCAGTTAA
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:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
CCACGAATTAGAATC
Found at i:2267734 original size:2 final size:2
Alignment explanation
Indices: 2267727--2267756 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2267717 ATATTTTTCC
*
2267727 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2267757 CCTTCCCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2268926 original size:12 final size:12
Alignment explanation
Indices: 2268909--2268933 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2268899 TTACTATCTT
2268909 TACCATCACCTC
1 TACCATCACCTC
2268921 TACCATCACCTC
1 TACCATCACCTC
2268933 T
1 T
2268934 TCTCCAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (12 bp):
TACCATCACCTC
Found at i:2271604 original size:21 final size:22
Alignment explanation
Indices: 2271570--2271617 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2271560 TGCTAATATG
*
2271570 AAAAATATTGTATA-ACAACTTT
1 AAAAAAATTGTATACACAA-TTT
2271592 AAAAAAATT-TATATCACAATTT
1 AAAAAAATTGTATA-CACAATTT
2271614 AAAA
1 AAAA
2271618 GTCTTTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 15 0.65
23 4 0.17
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAAAATTGTATACACAATTT
Found at i:2271610 original size:23 final size:23
Alignment explanation
Indices: 2271570--2271617 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2271560 TGCTAATATG
*
2271570 AAAAATATTGTATAACAACTTTAA
1 AAAAATATTATATAACAA-TTTAA
*
2271594 AAAAAT-TTATATCACAATTTAA
1 AAAAATATTATATAACAATTTAA
2271616 AA
1 AA
2271618 GTCTTTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 9 0.41
24 6 0.27
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATATTATATAACAATTTAA
Found at i:2272813 original size:2 final size:2
Alignment explanation
Indices: 2272806--2272832 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2272796 GCCAGAATGA
2272806 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 A
2272833 AACATATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2273705 original size:43 final size:43
Alignment explanation
Indices: 2273627--2273708 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
2273617 CTAATATAAC
* * *
2273627 AAATATATAATTTTTTTTCCCATGCATAGAGTATGCATGATTG
1 AAATATATAATTTTTTTTACCATGCATACACTATGCATGATTG
*
2273670 AAATATATAATTTTTTTTACCATGCATACTCTATGCATG
1 AAATATATAATTTTTTTTACCATGCATACACTATGCATG
2273709 GTAGAACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (43 bp):
AAATATATAATTTTTTTTACCATGCATACACTATGCATGATTG
Found at i:2273727 original size:43 final size:43
Alignment explanation
Indices: 2273627--2273727 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 43
2273617 CTAATATAAC
* * * *
2273627 AAATATATAATTTTTTTTCCCATGCATAGAGTATGCATGATTG
1 AAATATATAATTTTTTTTACCATGCATACACTATGCATGATAG
* *
2273670 AAATATATAATTTTTTTTACCATGCATACTCTATGCATGGTAG
1 AAATATATAATTTTTTTTACCATGCATACACTATGCATGATAG
* *
2273713 AACTTTAT-ATTTTTT
1 AAATATATAATTTTTT
2273728 CATATATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
42 7 0.14
43 43 0.86
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (43 bp):
AAATATATAATTTTTTTTACCATGCATACACTATGCATGATAG
Found at i:2278282 original size:59 final size:58
Alignment explanation
Indices: 2278159--2278313 Score: 202
Period size: 59 Copynumber: 2.5 Consensus size: 58
2278149 GTAAGAAAAT
*
2278159 ATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTTGGAAACTTTGATTTTCAAGAAAAATTG
1 ATACTTTCAACTTTT-CCCAAAAATA-----TTTTTTGAAAACTTTGATTTTCAAGAAAAATTG
* *
2278223 ATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTGATTTTTAAGGAAAATTG
1 ATACTTTCAACTTTTCC-CAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAATTG
*
2278282 ATACTTTTAACTTTTTCCCAAAAATATTTTTT
1 ATACTTTCAAC-TTTTCCCAAAAATATTTTTT
2278314 TGATTTTTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
59 54 0.64
60 6 0.07
63 2 0.02
64 23 0.27
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (58 bp):
ATACTTTCAACTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAATTG
Found at i:2278343 original size:5 final size:5
Alignment explanation
Indices: 2278330--2278417 Score: 65
Period size: 5 Copynumber: 16.8 Consensus size: 5
2278320 TTATTTAAAG
*
2278330 AAAAT AAAAC AAAAT AAAAGT AAAA- ATAAAT AAAGAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT A-AAAT AAA-AT AAAAT AAAAT
* *
2278376 AAAGA- AAAGT AAAACA AAAAT AAAGAT AAAAT AAAGAT AAAA
1 AAA-AT AAAAT AAAA-T AAAAT AAA-AT AAAAT AAA-AT AAAA
2278418 ATTTTTTAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
4 5 0.07
5 36 0.54
6 26 0.39
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:2278359 original size:6 final size:6
Alignment explanation
Indices: 2278340--2278419 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
2278330 AAAATAAAAC
* * * * *
2278340 AAAATA AAAGTA AAAAT- -AAATA AAGATA AAAAAA ATAAAGA AAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A-AAATA AAAATA
* * *
2278386 AAAACA AAAATA AAGAT- AAAATA AAGATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
2278420 TTTTTAATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
4 4 0.07
5 7 0.13
6 38 0.70
7 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:2278360 original size:16 final size:16
Alignment explanation
Indices: 2278333--2278418 Score: 67
Period size: 16 Copynumber: 5.4 Consensus size: 16
2278323 TTTAAAGAAA
2278333 ATAAAACAAAATAAAAG
1 ATAAAA-AAAATAAAAG
2278350 -TAAAAATAAAT-AAAG
1 ATAAAAA-AAATAAAAG
2278365 ATAAAAAAAAT-AAAG
1 ATAAAAAAAATAAAAG
* *
2278380 A-AAAGTAAAACAAAA-
1 ATAAA-AAAAATAAAAG
2278395 ATAAAGATAAAAT-AAAG
1 ATAAA-A-AAAATAAAAG
2278412 ATAAAAA
1 ATAAAAA
2278419 TTTTTTAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.05
15 20 0.34
16 26 0.45
17 9 0.16
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (16 bp):
ATAAAAAAAATAAAAG
Found at i:2278406 original size:11 final size:10
Alignment explanation
Indices: 2278330--2278417 Score: 65
Period size: 11 Copynumber: 8.4 Consensus size: 10
2278320 TTATTTAAAG
*
2278330 AAAATAAAAC
1 AAAATAAAAT
2278340 AAAATAAAAGT
1 AAAATAAAA-T
2278351 AAAA-ATAAAT
1 AAAATA-AAAT
2278361 AAAGATAAAA-
1 AAA-ATAAAAT
2278371 AAAATAAAGA-
1 AAAATAAA-AT
* *
2278381 AAAGTAAAACA
1 AAAATAAAA-T
2278392 AAAATAAAGAT
1 AAAATAAA-AT
2278403 AAAATAAAGAT
1 AAAATAAA-AT
2278414 AAAA
1 AAAA
2278418 ATTTTTTAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
9 6 0.09
10 25 0.38
11 33 0.50
12 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:2278448 original size:4 final size:4
Alignment explanation
Indices: 2278439--2278485 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
2278429 AATCTAATCT
* * *
2278439 AATA AATA AAAA AATA AATAA AACA AATA AACA AATA AATA AA-A AAT
1 AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AAT
2278486 TTTCAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (4 bp):
AATA
Found at i:2278468 original size:21 final size:21
Alignment explanation
Indices: 2278442--2278482 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2278432 CTAATCTAAT
2278442 AAATAAAAAAATAAATAAAAC
1 AAATAAAAAAATAAATAAAAC
*
2278463 AAATAAACAAATAAATAAAA
1 AAATAAAAAAATAAATAAAA
2278483 AATTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (21 bp):
AAATAAAAAAATAAATAAAAC
Found at i:2279479 original size:5 final size:5
Alignment explanation
Indices: 2279433--2279558 Score: 127
Period size: 5 Copynumber: 24.8 Consensus size: 5
2279423 AGTAAATAGC
*
2279433 TAAAA TAAAA -AGAAA -AAAA GAAAA -AAAA TAATAA TAAAAA TAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAA-AA T-AAAA TAAAA
*
2279478 TAGAAA TAGAA TAAAAA TAAAA T-AAA -AAAA TAAAA TAAAA TAAAA TAAAAA
1 TA-AAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T-AAAA
*
2279529 CGAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 -TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
2279559 CATATACCTA
Statistics
Matches: 106, Mismatches: 4, Indels: 22
0.80 0.03 0.17
Matches are distributed among these distances:
4 14 0.13
5 67 0.63
6 23 0.22
7 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (5 bp):
TAAAA
Found at i:2279490 original size:22 final size:20
Alignment explanation
Indices: 2279433--2279558 Score: 120
Period size: 22 Copynumber: 6.2 Consensus size: 20
2279423 AGTAAATAGC
2279433 TAAAATAAAA-AGAA-AAAAA
1 TAAAATAAAATA-AATAAAAA
*
2279452 GAAAA-AAAATAATAATAAAAA
1 TAAAATAAAAT-A-AATAAAAA
2279473 TAAAATAGAAATAGAATAAAAA
1 TAAAATA-AAATA-AATAAAAA
2279495 TAAAATAAAA-AAAT-AAAA
1 TAAAATAAAATAAATAAAAA
*
2279513 TAAAATAAAATAAAAACGAAAA
1 TAAAATAAAATAAATA--AAAA
2279535 TAAAATAAAATAAA-ATAAAA
1 TAAAATAAAATAAATA-AAAA
2279555 TAAA
1 TAAA
2279559 CATATACCTA
Statistics
Matches: 92, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
18 18 0.20
19 10 0.11
20 12 0.13
21 13 0.14
22 35 0.38
23 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (20 bp):
TAAAATAAAATAAATAAAAA
Found at i:2279822 original size:41 final size:41
Alignment explanation
Indices: 2279730--2279851 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 41
2279720 TTTGACCAAA
* * *
2279730 GCTCCTTTAAGCAGAAGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGA-AAA-ATAAATG
*
2279773 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
* *
2279814 GCTCCTCTAAAT-AGAGGCACCACGACTTTGGAAAAATA
1 GCTCCTCT-AATCAGAGGCTCAACGACTTT-GAAAAATA
2279852 GAGGCACCAC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
41 29 0.41
42 14 0.20
43 28 0.39
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
Found at i:2279856 original size:25 final size:25
Alignment explanation
Indices: 2279822--2279872 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2279812 TTGCTCCTCT
2279822 AAATAGAGGCACCACGACTTTGGAA
1 AAATAGAGGCACCACGACTTTGGAA
2279847 AAATAGAGGCACCACGACTTTGGAA
1 AAATAGAGGCACCACGACTTTGGAA
2279872 A
1 A
2279873 GTAAATTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.16
Consensus pattern (25 bp):
AAATAGAGGCACCACGACTTTGGAA
Found at i:2280921 original size:18 final size:18
Alignment explanation
Indices: 2280898--2280932 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2280888 TCCTCTTTCA
2280898 TTCATTTTCTCTTTTTTT
1 TTCATTTTCTCTTTTTTT
*
2280916 TTCATTTTTTCTTTTTT
1 TTCATTTTCTCTTTTTT
2280933 CTTTTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCATTTTCTCTTTTTTT
Found at i:2280921 original size:22 final size:22
Alignment explanation
Indices: 2280893--2280955 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 22
2280883 AGTCCTCCTC
2280893 TTTCATTCATTTTCTCTTTTTT
1 TTTCATTCATTTTCTCTTTTTT
2280915 TTTCATT--TTTTCT-TTTTTCT
1 TTTCATTCATTTTCTCTTTTT-T
* *
2280935 TTT--TTCATTTTTTCATTTTT
1 TTTCATTCATTTTCTCTTTTTT
2280955 T
1 T
2280956 CATCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 17 0.49
21 4 0.11
22 7 0.20
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCATTCATTTTCTCTTTTTT
Found at i:2280923 original size:9 final size:8
Alignment explanation
Indices: 2280912--2281002 Score: 123
Period size: 8 Copynumber: 11.0 Consensus size: 8
2280902 TTTTCTCTTT
2280912 TTTTTTCA
1 TTTTTTCA
2280920 TTTTTTC-
1 TTTTTTCA
2280927 TTTTTTC-
1 TTTTTTCA
2280934 TTTTTTCA
1 TTTTTTCA
2280942 TTTTTTCA
1 TTTTTTCA
2280950 TTTTTTCATCA
1 -TTTTT--TCA
2280961 TTTTTTCA
1 TTTTTTCA
2280969 TTTTTTCA
1 TTTTTTCA
2280977 TTTTTTCCA
1 TTTTTT-CA
2280986 TTTTTTCCA
1 TTTTTT-CA
2280995 TTTTTTCA
1 TTTTTTCA
2281003 AGCATAGTAT
Statistics
Matches: 78, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.18
8 34 0.44
9 22 0.28
10 5 0.06
11 3 0.04
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:2280930 original size:16 final size:16
Alignment explanation
Indices: 2280911--2281002 Score: 98
Period size: 17 Copynumber: 5.6 Consensus size: 16
2280901 ATTTTCTCTT
2280911 TTTTTTTCATTTTTTC
1 TTTTTTTCATTTTTTC
2280927 -TTTTTTC-TTTTTTC
1 TTTTTTTCATTTTTTC
*
2280941 ATTTTTTCATTTTTTC
1 TTTTTTTCATTTTTTC
2280957 ATCATTTTTTCATTTTTTC
1 -T--TTTTTTCATTTTTTC
*
2280976 ATTTTTTCCATTTTTTCC
1 -TTTTTTTCATTTTTT-C
*
2280994 ATTTTTTCA
1 TTTTTTTCA
2281003 AGCATAGTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.11
15 14 0.21
16 7 0.11
17 20 0.30
18 1 0.02
19 17 0.26
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTCATTTTTTC
Found at i:2280931 original size:19 final size:20
Alignment explanation
Indices: 2280902--2280974 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 20
2280892 CTTTCATTCA
*
2280902 TTTTCTCTTTTTTTTTCATT
1 TTTTCTTTTTTTTTTTCATT
2280922 TTTTCTTTTTTCTTTTTTCATT
1 TTTTC-TTTTT-TTTTTTCATT
* **
2280944 TTTTC-ATTTTTTCATCATT
1 TTTTCTTTTTTTTTTTCATT
*
2280963 TTTTCATTTTTT
1 TTTTCTTTTTTT
2280975 CATTTTTTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 13 0.29
20 13 0.29
21 4 0.09
22 15 0.33
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTTTTTTTCATT
Found at i:2280934 original size:27 final size:26
Alignment explanation
Indices: 2280898--2281002 Score: 121
Period size: 27 Copynumber: 4.2 Consensus size: 26
2280888 TCCTCTTTCA
* *
2280898 TTCATTTTCTCTTTTTTTTTCATTTT
1 TTCATTTTTTCTCTTTTTTTCATTTT
2280924 TTC--TTTTT-TC-TTTTTTCATTTT
1 TTCATTTTTTCTCTTTTTTTCATTTT
*
2280946 TTCATTTTTTCATCATTTTTTCATTTT
1 TTCATTTTTTC-TCTTTTTTTCATTTT
*
2280973 TTCATTTTTTC-CATTTTTTCCATTTT
1 TTCATTTTTTCTC-TTTTTTTCATTTT
2280999 TTCA
1 TTCA
2281003 AGCATAGTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
22 15 0.22
23 1 0.01
24 9 0.13
25 1 0.01
26 20 0.29
27 23 0.33
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (26 bp):
TTCATTTTTTCTCTTTTTTTCATTTT
Found at i:2280936 original size:41 final size:42
Alignment explanation
Indices: 2280891--2281002 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 42
2280881 TAAGTCCTCC
**
2280891 TCTTTCATTCATTTTCTC-TTTTTTTTTCATTTTTTC-TTTTT
1 TCTTT-ATTCATTTTCTCATTTTTTCATCATTTTTTCATTTTT
* *
2280932 TCTTTTTTCATTTTTTCATTTTTTCATCATTTTTTCATTTTT
1 TCTTTATTCATTTTCTCATTTTTTCATCATTTTTTCATTTTT
* *
2280974 TCATTTTTTCCATTTTTTCCATTTTTTCA
1 TC-TTTATT-CATTTTCT-CATTTTTTCA
2281003 AGCATAGTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.16
41 21 0.34
42 7 0.11
43 6 0.10
44 8 0.13
45 10 0.16
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (42 bp):
TCTTTATTCATTTTCTCATTTTTTCATCATTTTTTCATTTTT
Found at i:2289449 original size:32 final size:32
Alignment explanation
Indices: 2289412--2289508 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
2289402 TTTTTTTGGA
2289412 AACTTTGATTTTCAAGGAAAATTGATACTTTC
1 AACTTTGATTTTCAAGGAAAATTGATACTTTC
* *
2289444 AACTTT--TTCTCAA--AAATATT--T--TTTGAA
1 AACTTTGATTTTCAAGGAAA-ATTGATACTTT--C
*
2289471 AACTTTGATTTTTAAGGAAAATTGATACTTTC
1 AACTTTGATTTTCAAGGAAAATTGATACTTTC
2289503 AACTTT
1 AACTTT
2289509 TCCTCAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 22
0.64 0.07 0.29
Matches are distributed among these distances:
25 3 0.06
27 7 0.14
28 3 0.06
29 8 0.16
30 9 0.18
31 3 0.06
32 13 0.27
34 3 0.06
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (32 bp):
AACTTTGATTTTCAAGGAAAATTGATACTTTC
Found at i:2289474 original size:59 final size:58
Alignment explanation
Indices: 2289358--2289763 Score: 464
Period size: 59 Copynumber: 6.8 Consensus size: 58
2289348 TGTTCTTGTG
* *
2289358 TAAGAAAAATTGATACTTTCAACTTTTCCCC-AAAAATTTTTTTTTTTTTTTGGAAACTTTGATT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAA-------TATTTTTT-GAAA-TTTGATT
2289422 TT
57 TT
* * *
2289424 CAAGGAAAATTGATACTTTCAACTTTTTCTC-AAAAATATTTTTTGAAAACTTTGATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAATATTTTTTG-AAA-TTTGATTTT
* * *
2289483 TAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAAACTCTTTTTTTGAAATTTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAA-T-ATTTTTTGAAATTTGATTTT
* *
2289542 TAAGGAAAATTGATACTTTCAACTTTT-CCCTAAGAATATTTTTTGAAAATTTTAATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAATATTTTTTG-AAA-TTTGATTTT
* * * *
2289601 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACACTTTTTTTTGAAATTTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAA-A-TATTTTTTGAAATTTGATTTT
*
2289661 TAAGGAAAATTGATACTTTCAACTTTT-CCCTAAAAATATTTTTTGGACATTTTGATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAATATTTTTT-GA-AATTTGATTTT
2289720 TAAGGAAAATTGATACTTTCAACTTTTCCCC-AAAAATATTTTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAATATTTTTT
2289764 TGATTTTTAT
Statistics
Matches: 305, Mismatches: 23, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
57 14 0.05
58 10 0.03
59 183 0.60
60 47 0.15
61 11 0.04
62 8 0.03
66 32 0.10
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (58 bp):
TAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAAATATTTTTTGAAATTTGATTTT
Found at i:2289559 original size:118 final size:118
Alignment explanation
Indices: 2289358--2289775 Score: 590
Period size: 119 Copynumber: 3.5 Consensus size: 118
2289348 TGTTCTTGTG
* * * *
2289358 TAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTTTTTTGGAAACTTTGATTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA-----CTCTTTTTTT-GAAA-TTTTATTT
* * *
2289423 TCAAGGAAAATTGATACTTTCAACTTTT-TCTCAAAAATATTTTTTGAAAACTTTGATTTT
59 TTAAGGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTGAAAATTTTGATTTT
*
2289483 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTCTTTTTTTGAAATTTTATTTTTAAGGA
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACTCTTTTTTTGAAATTTTATTTTTAAGGA
* *
2289548 AAATTGATACTTTCAACTTTTCCCTAAGAATATTTTTTGAAAATTTTAATTTT
66 AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTT
* *
2289601 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACACTTTTTTTTGAAATTTTATTTTTAAGG
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACTC-TTTTTTTGAAATTTTATTTTTAAGG
* *
2289666 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGACATTTTGATTTT
65 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTT
* *
2289720 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTG-ATTTTTATTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACTCTTTTTTTGAAATTTTATTT
2289776 AAAGAAAATA
Statistics
Matches: 272, Mismatches: 19, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
116 9 0.03
117 8 0.03
118 97 0.36
119 116 0.43
120 8 0.03
125 34 0.12
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (118 bp):
TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAACTCTTTTTTTGAAATTTTATTTTTAAGGA
AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTT
Found at i:2289793 original size:5 final size:5
Alignment explanation
Indices: 2289780--2289867 Score: 65
Period size: 5 Copynumber: 16.8 Consensus size: 5
2289770 TTATTTAAAG
*
2289780 AAAAT AAAAC AAAAT AAAAGT GAAAAT -AAAT AAAGAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAA-AT AAAAT AAAAT
* *
2289826 AAAGA- AAAGT AAAACA AAAAT AAAGAT AAAAT AAAGAT AAAA
1 AAA-AT AAAAT AAAA-T AAAAT AAA-AT AAAAT AAA-AT AAAA
2289868 AATTTTAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
4 8 0.12
5 33 0.49
6 22 0.33
7 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:2289846 original size:21 final size:22
Alignment explanation
Indices: 2289780--2289860 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 22
2289770 TTATTTAAAG
* **
2289780 AAAATAAA-ACAAAATAAAAGTG
1 AAAATAAAGATAAAATAAAA-CA
2289802 AAAAT-AA-ATAAAGAT-AAA-A
1 AAAATAAAGATAAA-ATAAAACA
*
2289821 AAAATAAAGA-AAAGTAAAACA
1 AAAATAAAGATAAAATAAAACA
2289842 AAAATAAAGATAAAATAAA
1 AAAATAAAGATAAAATAAA
2289861 GATAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
19 6 0.12
20 8 0.16
21 21 0.43
22 14 0.29
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAATAAAGATAAAATAAAACA
Found at i:2289856 original size:11 final size:10
Alignment explanation
Indices: 2289780--2289867 Score: 65
Period size: 11 Copynumber: 8.4 Consensus size: 10
2289770 TTATTTAAAG
*
2289780 AAAATAAAAC
1 AAAATAAAAT
2289790 AAAATAAAAGT
1 AAAATAAAA-T
2289801 GAAAAT-AAAT
1 -AAAATAAAAT
2289811 AAAGATAAAA-
1 AAA-ATAAAAT
2289821 AAAATAAAGA-
1 AAAATAAA-AT
* *
2289831 AAAGTAAAACA
1 AAAATAAAA-T
2289842 AAAATAAAGAT
1 AAAATAAA-AT
2289853 AAAATAAAGAT
1 AAAATAAA-AT
2289864 AAAA
1 AAAA
2289868 AATTTTAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
9 9 0.14
10 23 0.35
11 28 0.42
12 6 0.09
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:2289896 original size:4 final size:4
Alignment explanation
Indices: 2289889--2289931 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
2289879 AATCTAATCT
* *
2289889 AATA AATA AATA AATAA AACA AATA AACA AATA AATA AA-A AAT
1 AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AAT
2289932 TTCCAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:2289915 original size:21 final size:21
Alignment explanation
Indices: 2289889--2289928 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2289879 AATCTAATCT
*
2289889 AATAAATAAATAAATAAAACA
1 AATAAACAAATAAATAAAACA
2289910 AATAAACAAATAAATAAAA
1 AATAAACAAATAAATAAAA
2289929 AATTTCCAAA
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:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (21 bp):
AATAAACAAATAAATAAAACA
Found at i:2290409 original size:19 final size:19
Alignment explanation
Indices: 2290385--2290421 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2290375 TGGCTGGAAT
*
2290385 TTTCGTCGAAAAATTCAAG
1 TTTCGTCAAAAAATTCAAG
2290404 TTTCGTCAAAAAATTCAA
1 TTTCGTCAAAAAATTCAA
2290422 CTGAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (19 bp):
TTTCGTCAAAAAATTCAAG
Found at i:2290738 original size:17 final size:16
Alignment explanation
Indices: 2290716--2290753 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2290706 CAAGTCAGAT
2290716 AAATCAAAAAAGAAAAA
1 AAATC-AAAAAGAAAAA
*
2290733 AAATC-AAAAGAAAAT
1 AAATCAAAAAGAAAAA
2290748 AAATCA
1 AAATCA
2290754 GATAAATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 14 0.74
17 5 0.26
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (16 bp):
AAATCAAAAAGAAAAA
Found at i:2290743 original size:15 final size:15
Alignment explanation
Indices: 2290723--2290753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2290713 GATAAATCAA
2290723 AAAAGAAAAAAAATC
1 AAAAGAAAAAAAATC
*
2290738 AAAAGAAAATAAATC
1 AAAAGAAAAAAAATC
2290753 A
1 A
2290754 GATAAATCAG
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:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAGAAAAAAAATC
Found at i:2290887 original size:6 final size:6
Alignment explanation
Indices: 2290876--2290965 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
2290866 GTAAATAGCT
* * *
2290876 AAAATA AAAATA AAAA-A AGAA-A AAAATA ATAATA ATAATA ATAGAA-A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A-A-AATA
* *
2290923 GAAAT- AGAATA AAAATAAA AAAATA AAAA-A AAAAT- AAAATA AA
1 AAAATA AAAATA AAAAT--A AAAATA AAAATA AAAATA AAAATA AA
2290966 CATATACCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 23 0.34
6 35 0.52
7 1 0.01
8 8 0.12
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:2298068 original size:2 final size:2
Alignment explanation
Indices: 2298057--2298092 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2298047 ACAAAATGAC
2298057 AT AT -T 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 A
2298093 GACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2300077 original size:30 final size:30
Alignment explanation
Indices: 2300028--2300123 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
2300018 TATTGTATTT
* * * *
2300028 AAATAAACTCTTAATTTTTATTTTGTACTC
1 AAATAAATTTTTAATTTTTAATTTATACTC
* * *
2300058 AAATTAATTTTTAAATTTTAATTTATATTC
1 AAATAAATTTTTAATTTTTAATTTATACTC
* *
2300088 AAATAAATTTTTAATTTTTAATTTATATTT
1 AAATAAATTTTTAATTTTTAATTTATACTC
2300118 AAATAA
1 AAATAA
2300124 CCATTAACAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (30 bp):
AAATAAATTTTTAATTTTTAATTTATACTC
Found at i:2308929 original size:2 final size:2
Alignment explanation
Indices: 2308924--2308948 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2308914 TATATACGTG
2308924 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
2308949 TATCACCATT
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:2321924 original size:20 final size:20
Alignment explanation
Indices: 2321899--2321947 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
2321889 GAAATTTCCC
2321899 AAAAAAAAAAACTTTTTAAG
1 AAAAAAAAAAACTTTTTAAG
*
2321919 AAAAAAAAAAACTTTTTAAT
1 AAAAAAAAAAACTTTTTAAG
2321939 ACAAAAAAA
1 A-AAAAAAA
2321948 TTTTCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAAAAAAAACTTTTTAAG
Found at i:2329114 original size:3 final size:3
Alignment explanation
Indices: 2329106--2329131 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2329096 TGTTAAGTAA
2329106 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2329132 ATATTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2329561 original size:5 final size:5
Alignment explanation
Indices: 2329553--2329601 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
2329543 ATTAAATTAA
* * *
2329553 AAAAC AAAAC AAAAC AAATC AAAGC AAAAC AAAAC AAAAC AAAAT AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
2329602 GACTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.78, C:0.16, G:0.02, T:0.04
Consensus pattern (5 bp):
AAAAC
Found at i:2332653 original size:18 final size:18
Alignment explanation
Indices: 2332632--2332680 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2332622 CGAGCTCGAG
2332632 CTCGAACTCGACT-CACAA
1 CTCGAACTCGA-TACACAA
*
2332650 CTCGAAGCTCGATACTCAA
1 CTCGAA-CTCGATACACAA
*
2332669 CTCAAACTCGAT
1 CTCGAACTCGAT
2332681 CGAGTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (18 bp):
CTCGAACTCGATACACAA
Found at i:2332659 original size:25 final size:25
Alignment explanation
Indices: 2332626--2332679 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2332616 GAAGTTCGAG
*
2332626 CTCG-AGCTCGA-ACTCGACTCACAA
1 CTCGAAGCTCGATACTCAACTCA-AA
2332650 CTCGAAGCTCGATACTCAACTCAAA
1 CTCGAAGCTCGATACTCAACTCAAA
2332675 CTCGA
1 CTCGA
2332680 TCGAGTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 14 0.52
26 9 0.33
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (25 bp):
CTCGAAGCTCGATACTCAACTCAAA
Found at i:2334317 original size:24 final size:24
Alignment explanation
Indices: 2334263--2334321 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
2334253 TTTTGTTTTG
*
2334263 TATATTATTAAACATAAATATTTT
1 TATATTATTAAACATAAATATATT
2334287 TAGTATT-TTAATA-ATAAATAATATT
1 TA-TATTATTAA-ACATAAAT-ATATT
2334312 TATATTATTA
1 TATATTATTA
2334322 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATTATTAAACATAAATATATT
Found at i:2334341 original size:40 final size:40
Alignment explanation
Indices: 2334296--2334371 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2334286 TTAGTATTTT
2334296 AATAATAAATAAT-AT-TTATATTATTATTTTAATAATAAAC
1 AATAATAAATAATAATATT-T-TTATTATTTTAATAATAAAC
*
2334336 AATAATATATAATAATATTTTTATTATTTTAATAAT
1 AATAATAAATAATAATATTTTTATTATTTTAATAAT
2334372 TAATGTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
40 28 0.85
41 3 0.09
42 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
AATAATAAATAATAATATTTTTATTATTTTAATAATAAAC
Found at i:2334354 original size:37 final size:39
Alignment explanation
Indices: 2334299--2334409 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 39
2334289 GTATTTTAAT
*
2334299 AATAAATAATAT--TTATATTATTATTTTAATAATAAAC
1 AATAAATAATATAATAATATTATTATTTTAATAATAAAC
* *
2334336 AAT-AAT-ATATAATAATATTTTTATTATTTTAATAATTAAT
1 AATAAATAATATAATAATA---TTATTATTTTAATAATAAAC
**
2334376 GTTAAATAATATAATAATATTATT-TTCTTAATAA
1 AATAAATAATATAATAATATTATTATT-TTAATAA
2334410 GAATATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
35 4 0.07
36 3 0.05
37 7 0.11
38 2 0.03
39 12 0.20
40 19 0.31
41 3 0.05
42 11 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (39 bp):
AATAAATAATATAATAATATTATTATTTTAATAATAAAC
Found at i:2334590 original size:22 final size:23
Alignment explanation
Indices: 2334557--2334604 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
2334547 ATGATTTAAT
*
2334557 AATATATAT-TTTTAATA-TA-A
1 AATATAAATATTTTAATAGTATA
2334577 AATATAAATATTTTAATAGTATA
1 AATATAAATATTTTAATAGTATA
2334600 AATAT
1 AATAT
2334605 TTTAGTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 8 0.33
22 2 0.08
23 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATAAATATTTTAATAGTATA
Found at i:2334601 original size:17 final size:16
Alignment explanation
Indices: 2334578--2334620 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
2334568 TTAATATAAA
2334578 ATATAAATATTTTAAT
1 ATATAAATATTTTAAT
*
2334594 AGTATAAATATTTTAGT
1 A-TATAAATATTTTAAT
2334611 A-ATAAATATT
1 ATATAAATATT
2334621 ACTATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
ATATAAATATTTTAAT
Found at i:2334618 original size:38 final size:37
Alignment explanation
Indices: 2334551--2334632 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
2334541 TTTATTATGA
*
2334551 TTTAATAATATATATTTTTAATATAAAATATAAATAT
1 TTTAATAATATAAATTTTTAATATAAAATATAAATAT
* * * *
2334588 TTTAATAGTATAAATATTTTAGTA-ATAAATATTACTAT
1 TTTAATAATATAAAT-TTTTAATATA-AAATATAAATAT
2334626 TTTAATA
1 TTTAATA
2334633 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 14 0.37
38 24 0.63
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (37 bp):
TTTAATAATATAAATTTTTAATATAAAATATAAATAT
Found at i:2334788 original size:26 final size:26
Alignment explanation
Indices: 2334751--2334816 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
2334741 TTCTTAAATA
2334751 TTAATA-ATTTTAATAATAAATAA-TT
1 TTAATATA-TTTAATAATAAATAATTT
2334776 TTAATATACTTTAATAATAAATAATTT
1 TTAATATA-TTTAATAATAAATAATTT
2334803 TTAATAT-TTTAATA
1 TTAATATATTTAATA
2334817 GTTATATTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
25 13 0.34
26 16 0.42
27 9 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATATATTTAATAATAAATAATTT
Done.