Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 109 of 130
Found at i:21214812 original size:23 final size:23
Alignment explanation
Indices: 21214760--21214813 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
21214750 AAAATTAATA
*
21214760 TTAATATT-TTATTATCAATATT
1 TTAATATTATTATTATCAATAGT
**
21214782 TTTCTATTATTATTAAT-AATAGT
1 TTAATATTATTATT-ATCAATAGT
21214805 TTAATATTA
1 TTAATATTA
21214814 ATAAGTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.24
23 17 0.68
24 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATTATTATTATCAATAGT
Found at i:21215333 original size:18 final size:18
Alignment explanation
Indices: 21215299--21215333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21215289 TTAATTATGA
* *
21215299 TTATAATTTTATTAAATC
1 TTATAATTTCATAAAATC
21215317 TTATAATTTCATAAAAT
1 TTATAATTTCATAAAAT
21215334 AAAAAGAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATAATTTCATAAAATC
Found at i:21215616 original size:2 final size:2
Alignment explanation
Indices: 21215609--21215634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21215599 TCAAAAAGTA
21215609 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
21215635 CAACGACAAG
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:21221598 original size:19 final size:20
Alignment explanation
Indices: 21221561--21221605 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
21221551 TCTCACATTA
*
21221561 AATTTGTTATTTATTAATTT
1 AATTTTTTATTTATTAATTT
*
21221581 TATTTTTTATTT-TTAATTT
1 AATTTTTTATTTATTAATTT
21221600 AATTTT
1 AATTTT
21221606 AAACATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
AATTTTTTATTTATTAATTT
Found at i:21222538 original size:16 final size:15
Alignment explanation
Indices: 21222517--21222558 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
21222507 AATAAGTGAC
21222517 ATTTAATAATTTTAAA
1 ATTT-ATAATTTTAAA
*
21222533 ATTTA-AATTTTAAC
1 ATTTATAATTTTAAA
*
21222547 ACTTATAATTTT
1 ATTTATAATTTT
21222559 TTTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATAATTTTAAA
Found at i:21227740 original size:23 final size:23
Alignment explanation
Indices: 21227705--21227759 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
21227695 TTTACCTTTT
*
21227705 ATATAAGAT-AAATTATATAATAC
1 ATATAA-ATAAAATTATATAATAA
21227728 ATATAAATAAAATTATATAATAA
1 ATATAAATAAAATTATATAATAA
21227751 ATA-AAATAA
1 ATATAAATAA
21227760 TGAGAAGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATAAATAAAATTATATAATAA
Found at i:21240380 original size:22 final size:22
Alignment explanation
Indices: 21240355--21240399 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
21240345 TTAAATTGTT
21240355 AGATCTAATTAACA-TTGGTCAA
1 AGATCTAATTAA-AGTTGGTCAA
* *
21240377 AGATGTACTTAAAGTTGGTCAA
1 AGATCTAATTAAAGTTGGTCAA
21240399 A
1 A
21240400 TGATTGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
AGATCTAATTAAAGTTGGTCAA
Found at i:21246490 original size:22 final size:22
Alignment explanation
Indices: 21246462--21246521 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
21246452 TGGTAATAAA
21246462 TAGGAGAAGAGAAAGTTGGTTT
1 TAGGAGAAGAGAAAGTTGGTTT
21246484 TAGGAGAAGAGAAAGTTGGTTT
1 TAGGAGAAGAGAAAGTTGGTTT
*
21246506 TAGGAGAAAAGAAAGT
1 TAGGAGAAGAGAAAGT
21246522 GAGAAAGCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (22 bp):
TAGGAGAAGAGAAAGTTGGTTT
Found at i:21246950 original size:70 final size:70
Alignment explanation
Indices: 21246873--21247009 Score: 220
Period size: 70 Copynumber: 2.0 Consensus size: 70
21246863 CTATAATTCT
* * * * *
21246873 TCTTATATCGAAGAAATTAAAATTGTAAGTTACTATTTTTTTTTATTTTATATTCTTGTTTTAAG
1 TCTTATATCGAAGAAATTAAAATTATAAGTTACCATTCTTTTCTAGTTTATATTCTTGTTTTAAG
21246938 TTTTA
66 TTTTA
*
21246943 TCTTATATCGAAGTAATTAAAATTATAAGTTACCATTCTTTTCTAGTTTATATTCTTGTTTTAAG
1 TCTTATATCGAAGAAATTAAAATTATAAGTTACCATTCTTTTCTAGTTTATATTCTTGTTTTAAG
21247008 TT
66 TT
21247010 ATGAAAATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (70 bp):
TCTTATATCGAAGAAATTAAAATTATAAGTTACCATTCTTTTCTAGTTTATATTCTTGTTTTAAG
TTTTA
Found at i:21255398 original size:16 final size:16
Alignment explanation
Indices: 21255377--21255414 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
21255367 GTCACCTTTT
*
21255377 TTATTTCGGTATTTGA
1 TTATTTCAGTATTTGA
21255393 TTATTTCAGTATTTGA
1 TTATTTCAGTATTTGA
21255409 TTATTT
1 TTATTT
21255415 GAGGCATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.61
Consensus pattern (16 bp):
TTATTTCAGTATTTGA
Found at i:21257632 original size:22 final size:22
Alignment explanation
Indices: 21257584--21257632 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
21257574 TTGTTTTCAC
*
21257584 AAACTTTGAAAAATTAACCTGA
1 AAACTTTGAAAAATTAACATGA
* *
21257606 CAACTTTGAAAAATTAATATGA
1 AAACTTTGAAAAATTAACATGA
21257628 AAACT
1 AAACT
21257633 CTTCACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (22 bp):
AAACTTTGAAAAATTAACATGA
Found at i:21257965 original size:23 final size:23
Alignment explanation
Indices: 21257937--21257994 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 23
21257927 GCTTCTAAAG
21257937 ATTTTCCTTTTTATT-CTTTC-TT
1 ATTTTCCTTTTTATTGC-TTCATT
*
21257959 ATCTTT-CTCTTTATTGCTTCATTT
1 AT-TTTCCTTTTTATTGCTTCA-TT
21257983 ATTTTCCTTTTT
1 ATTTTCCTTTTT
21257995 GTTTCACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 13 0.45
23 7 0.24
24 9 0.31
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTTCCTTTTTATTGCTTCATT
Found at i:21258000 original size:21 final size:24
Alignment explanation
Indices: 21257957--21258000 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 24
21257947 TTATTCTTTC
21257957 TTATCTTTCTCTTTATTGCTTCAT
1 TTATCTTTCTCTTTATTGCTTCAT
*
21257981 TTAT-TTTC-CTTT-TTGTTTCA
1 TTATCTTTCTCTTTATTGCTTCA
21258001 CAATTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 4 0.21
24 4 0.21
ACGTcount: A:0.11, C:0.18, G:0.05, T:0.66
Consensus pattern (24 bp):
TTATCTTTCTCTTTATTGCTTCAT
Found at i:21260479 original size:18 final size:18
Alignment explanation
Indices: 21260458--21260493 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21260448 ATACGAATAT
* *
21260458 AAATGTCGATGTGAATGC
1 AAATGTCAATGCGAATGC
21260476 AAATGTCAATGCGAATGC
1 AAATGTCAATGCGAATGC
21260494 TTGATACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (18 bp):
AAATGTCAATGCGAATGC
Found at i:21260841 original size:22 final size:21
Alignment explanation
Indices: 21260810--21260850 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21260800 GTATACAATG
* *
21260810 CTAAACTAATCTCTAAAATTTT
1 CTAAAATAATCAC-AAAATTTT
21260832 CTAAAATAATCACAAAATT
1 CTAAAATAATCACAAAATT
21260851 GGCCCAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (21 bp):
CTAAAATAATCACAAAATTTT
Found at i:21261964 original size:140 final size:139
Alignment explanation
Indices: 21261705--21261988 Score: 315
Period size: 140 Copynumber: 2.0 Consensus size: 139
21261695 CTTTACTATT
* *
21261705 TTTTTTTGGAAACATTTGATTTCATCTTTAGCATTCTACTTTCTTGAATTCTTAAGATTCAAACT
1 TTTTTTT-GAAACATTTGACTTCATCTTTAGCAATCTACTTTCTTGAATTCTTAAGATTCAAACT
* * * * *
21261770 GAAACTTTATTCACTTTTTACCTTATATTCTTATCTCTGAAGTACATATCTTTCTTTTCTTTGCT
65 GAAACCTTATTCACTTTTTACCTTAGACTCTCATCTCTGAAGTACATATATTTC-TTTCTTTGCT
21261835 CTTTTCTTTTTG
129 -TTTTCTTTTTG
* * * *
21261847 TTTTTTT-AAACATTTGACTTCATCTTTGGCAATCTACTTTCTTGAATTCTTAGGATTCTAA-TT
1 TTTTTTTGAAACATTTGACTTCATCTTTAGCAATCTACTTTCTTGAATTCTTAAGATTCAAACTG
* * * * ** *
21261910 AAAGCCTTATTCACTTTTT-GCTCTGGACTCTCAT-TTTCGAGGTGTATGTATTTCTTTCTTTGC
66 AAA-CCTTATTCACTTTTTACCT-TAGACTCTCATCTCT-GAAGTACATATATTTCTTTCTTTGC
*
21261973 TTTTTTTTTTTG
128 TTTTTCTTTTTG
21261985 TTTT
1 TTTT
21261989 GTTTTGTGTT
Statistics
Matches: 120, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
138 14 0.12
139 18 0.15
140 81 0.68
142 7 0.06
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (139 bp):
TTTTTTTGAAACATTTGACTTCATCTTTAGCAATCTACTTTCTTGAATTCTTAAGATTCAAACTG
AAACCTTATTCACTTTTTACCTTAGACTCTCATCTCTGAAGTACATATATTTCTTTCTTTGCTTT
TTCTTTTTG
Found at i:21265832 original size:8 final size:8
Alignment explanation
Indices: 21265819--21265862 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
21265809 TTTTTATCAA
21265819 TTTTTCTT
1 TTTTTCTT
21265827 TTTTTCTT
1 TTTTTCTT
*
21265835 CTTTTCATT
1 TTTTTC-TT
21265844 TTTTTCTT
1 TTTTTCTT
*
21265852 TTATTCTT
1 TTTTTCTT
21265860 TTT
1 TTT
21265863 CTACCTGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 24 0.77
9 7 0.23
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:21265839 original size:17 final size:16
Alignment explanation
Indices: 21265819--21265862 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
21265809 TTTTTATCAA
21265819 TTTTTCTTTTTTTCTT
1 TTTTTCTTTTTTTCTT
*
21265835 CTTTTCATTTTTTTCTT
1 TTTTTC-TTTTTTTCTT
*
21265852 TTATTCTTTTT
1 TTTTTCTTTTT
21265863 CTACCTGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTT
Found at i:21265850 original size:14 final size:13
Alignment explanation
Indices: 21265819--21265864 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
21265809 TTTTTATCAA
21265819 TTTTTC-TTT-TT
1 TTTTTCTTTTATT
*
21265830 TTCTTCTTTTCATT
1 TTTTTCTTTT-ATT
21265844 TTTTTCTTTTATT
1 TTTTTCTTTTATT
21265857 CTTTTTCT
1 -TTTTTCT
21265865 ACCTGCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 5 0.17
12 3 0.10
13 3 0.10
14 18 0.62
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:21267692 original size:21 final size:20
Alignment explanation
Indices: 21267655--21267693 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21267645 TTTGATATTT
*
21267655 AAAAATTAATTTTTTATTGA
1 AAAAAATAATTTTTTATTGA
*
21267675 AAAAAATATTTTTATTATT
1 AAAAAATAATTTT-TTATT
21267694 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
AAAAAATAATTTTTTATTGA
Found at i:21269230 original size:30 final size:30
Alignment explanation
Indices: 21269196--21269338 Score: 138
Period size: 30 Copynumber: 4.9 Consensus size: 30
21269186 GGAAAGTTAG
*
21269196 GGGTTTAGGGTTTTAGTTTTAGAGTTTGAA
1 GGGTTTAGGGTTTTAGTTTTAGGGTTTGAA
*
21269226 GGGTTTAGGGTTTTTA-TCTTA-GGTTTG-A
1 GGGTTTAGGG-TTTTAGTTTTAGGGTTTGAA
** * *
21269254 -GGTTT-GAAATTTT-GATTTTAAGGTTTAAA
1 GGGTTTAG-GGTTTTAG-TTTTAGGGTTTGAA
* *
21269283 GGGTTTAGGGTTTTAATTTTAGGGTTTGGA
1 GGGTTTAGGGTTTTAGTTTTAGGGTTTGAA
21269313 GGGTTTAGGG-TTTAGTTTTAGGGTTT
1 GGGTTTAGGGTTTTAGTTTTAGGGTTT
21269339 TGATGATTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
26 5 0.05
27 9 0.10
28 6 0.07
29 21 0.23
30 44 0.48
31 6 0.07
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (30 bp):
GGGTTTAGGGTTTTAGTTTTAGGGTTTGAA
Found at i:21269294 original size:16 final size:16
Alignment explanation
Indices: 21269270--21269326 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
21269260 AAATTTTGAT
*
21269270 TTTAAGGTTTAAAGGG
1 TTTAGGGTTTAAAGGG
* *
21269286 TTTAGGGTTTTAA--T
1 TTTAGGGTTTAAAGGG
**
21269300 TTTAGGGTTTGGAGGG
1 TTTAGGGTTTAAAGGG
21269316 TTTAGGGTTTA
1 TTTAGGGTTTA
21269327 GTTTTAGGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 11 0.34
16 21 0.66
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (16 bp):
TTTAGGGTTTAAAGGG
Found at i:21269348 original size:29 final size:28
Alignment explanation
Indices: 21269285--21269377 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
21269275 GGTTTAAAGG
* * *
21269285 GTTTAGGGTTTTAATTTTAGGGTTTGGAGG
1 GTTTAGGG-TTTAGTTTTAGGGTTTTGA-T
21269315 GTTTAGGGTTTAGTTTTAGGGTTTTGAT
1 GTTTAGGGTTTAGTTTTAGGGTTTTGAT
*
21269343 GATTTA-AGTTTAG---TAGGGTTTTGAT
1 G-TTTAGGGTTTAGTTTTAGGGTTTTGAT
21269368 -TTTAGGGTTT
1 GTTTAGGGTTT
21269378 GAAAGGTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 4 0.07
24 4 0.07
25 12 0.21
28 7 0.12
29 21 0.38
30 8 0.14
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (28 bp):
GTTTAGGGTTTAGTTTTAGGGTTTTGAT
Found at i:21269419 original size:59 final size:58
Alignment explanation
Indices: 21269356--21269667 Score: 272
Period size: 59 Copynumber: 5.3 Consensus size: 58
21269346 TTAAGTTTAG
21269356 TAGGGTTTTGATTTTAGGGTTTGAAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTT
1 TAGGGTTTTGATTTTAGGGTTT-AAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTT
* * * ** *
21269415 TAGGGTTTAG-TTTTAGGGTTTAAAGGATTTAGGATTTTGATTTTAAGGGCTAGCGGGTT
1 TAGGGTTTTGATTTTAGGGTTTAAAGG-TTTAGGGTTTAG-TTTTAAGGTTTAGAGGGTT
* * ** * *
21269474 TAGGGTTTTGATTTTAAGGTTTAGAGGGTTTAGCATTTAGTTTTAGGGTTT-GAAGGATT
1 TAGGGTTTTGATTTTAGGGTTTA-AAGGTTTAGGGTTTAGTTTTAAGGTTTAG-AGGGTT
* * * * * * *
21269533 TATGGTTTT-AGTTTTAGGGTTTGGAAGGTTTAGAGTTTAGTTTGAGGGTTT-GAAAGATT
1 TAGGGTTTTGA-TTTTAGGGTTT-AAAGGTTTAGGGTTTAGTTTTAAGGTTTAG-AGGGTT
* * * * * *
21269592 GAGAGTTTTGATTTTAGGGGTTAGAAGGTTTAAGGTTTTGATTTTATGGTTTAGAGGGTT
1 TAGGGTTTTGATTTTAGGGTTTA-AAGGTTTAGGGTTTAG-TTTTAAGGTTTAGAGGGTT
*
21269652 TAGGATTTTGATTTTA
1 TAGGGTTTTGATTTTA
21269668 TGGCTTAGAG
Statistics
Matches: 203, Mismatches: 39, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
57 5 0.02
58 23 0.11
59 123 0.61
60 48 0.24
61 4 0.02
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.46
Consensus pattern (58 bp):
TAGGGTTTTGATTTTAGGGTTTAAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTT
Found at i:21269421 original size:16 final size:14
Alignment explanation
Indices: 21269284--21269585 Score: 83
Period size: 16 Copynumber: 21.0 Consensus size: 14
21269274 AGGTTTAAAG
*
21269284 GGTTTAGGGTTTTA
1 GGTTTAGGGTTTGA
**
21269298 ATTTTAGGGTTTGGA
1 GGTTTAGGGTTT-GA
21269313 GGGTTTAGGGTTT-A
1 -GGTTTAGGGTTTGA
*
21269327 GTTTTAGGGTTTTGA
1 GGTTTAGGG-TTTGA
* *
21269342 TGATTTA-AGTTT-A
1 -GGTTTAGGGTTTGA
21269355 -G--TAGGGTTTTGA
1 GGTTTAGGG-TTTGA
*
21269367 -TTTTAGGGTTTGAAA
1 GGTTTAGGGTTTG--A
21269382 GGTTTAGGGTTT-A
1 GGTTTAGGGTTTGA
* *
21269395 GTTTTAAGGTTTAGA
1 GGTTTAGGGTTT-GA
21269410 GGGTTTAGGGTTT-A
1 -GGTTTAGGGTTTGA
* *
21269424 GTTTTAGGGTTTAAA
1 GGTTTAGGGTTT-GA
*
21269439 GGATTTAGGATTTTGA
1 GG-TTTAGG-GTTTGA
* * * *
21269455 -TTTTAAGGGCTAGCG
1 GGTTT-AGGGTTTG-A
21269470 GGTTTAGGGTTTTGA
1 GGTTTAGGG-TTTGA
* *
21269485 -TTTTAAGGTTTAGA
1 GGTTTAGGGTTT-GA
**
21269499 GGGTTTAGCATTT-A
1 -GGTTTAGGGTTTGA
*
21269513 GTTTTAGGGTTTGAA
1 GGTTTAGGGTTTG-A
* *
21269528 GGATTTATGGTTTTA
1 GG-TTTAGGGTTTGA
*
21269543 GTTTTAGGGTTTGGAA
1 GGTTTAGGGTTT-G-A
*
21269559 GGTTTAGAGTTT-A
1 GGTTTAGGGTTTGA
21269572 -GTTTGAGGGTTTGA
1 GGTTT-AGGGTTTGA
21269586 AAGATTGAGA
Statistics
Matches: 207, Mismatches: 47, Indels: 68
0.64 0.15 0.21
Matches are distributed among these distances:
9 2 0.01
10 1 0.00
11 3 0.01
12 5 0.02
13 54 0.26
14 47 0.23
15 18 0.09
16 74 0.36
17 3 0.01
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTGA
Found at i:21269563 original size:89 final size:86
Alignment explanation
Indices: 21269359--21269694 Score: 304
Period size: 89 Copynumber: 3.8 Consensus size: 86
21269349 AGTTTAGTAG
* *
21269359 GGTTTTGATTTTAGGGTTTGAAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTTTAGGGTTTA
1 GGTTTTGATTTTAGGGTTTGGAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTTTA-GATTTA
*
21269424 GTTTTAGGGTTTAAAGGATTTA
65 GTTTTAGGGTTTGAAGGATTTA
* * *
21269446 GGATTTTGATTTTAAGGGCTAGCG--GGTTTAGGGTTTTGATTTTAAGGTTTAGAGGGTTTAGCA
1 GG-TTTTGATTTT-AGGGTTTG-GAAGGTTTAGGGTTTAG-TTTTAAGGTTTAGAGGGTTTAG-A
21269509 TTTAGTTTTAGGGTTTGAAGGATTTA
61 TTTAGTTTTAGGGTTTGAAGGATTTA
* * * * * *
21269535 TGGTTTT-AGTTTTAGGGTTTGGAAGGTTTAGAGTTTAGTTTGAGGGTTT-GAAAGATTGAGAGT
1 -GGTTTTGA-TTTTAGGGTTTGGAAGGTTTAGGGTTTAGTTTTAAGGTTTAG-AGGGTTTAGA-T
* *
21269598 TTTGATTTTAGGGGTTAGAAGG-TTTAA
62 TTAG-TTTTA-GGGTTTGAAGGATTT-A
* * * * * * * *
21269625 GGTTTTGATTTTATGGTTTAGAGGGTTTAGGATTTTGATTTTATGGCTTAGAGGGTTTAGAGTTA
1 GGTTTTGATTTTAGGGTTTGGAAGGTTTAGGGTTTAG-TTTTAAGGTTTAGAGGGTTTAGATTTA
*
21269690 TTTTT
65 GTTTT
21269695 TAAAAAAATA
Statistics
Matches: 200, Mismatches: 32, Indels: 33
0.75 0.12 0.12
Matches are distributed among these distances:
87 5 0.03
88 54 0.27
89 111 0.56
90 29 0.14
91 1 0.00
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (86 bp):
GGTTTTGATTTTAGGGTTTGGAAGGTTTAGGGTTTAGTTTTAAGGTTTAGAGGGTTTAGATTTAG
TTTTAGGGTTTGAAGGATTTA
Found at i:21269668 original size:30 final size:30
Alignment explanation
Indices: 21269356--21269684 Score: 234
Period size: 30 Copynumber: 11.1 Consensus size: 30
21269346 TTAAGTTTAG
* *
21269356 TAGGGTTTTGATTTTAGGGTTT-GAAAGGTT
1 TAGGATTTTGATTTTAGGGTTTAG-AGGGTT
* * *
21269386 TAGGGTTTAG-TTTTAAGGTTTAGAGGGTT
1 TAGGATTTTGATTTTAGGGTTTAGAGGGTT
* * * *
21269415 TAGGGTTTAG-TTTTAGGGTTTAAAGGATT
1 TAGGATTTTGATTTTAGGGTTTAGAGGGTT
* *
21269444 TAGGATTTTGATTTTAAGGG-CTAGCGGGTT
1 TAGGATTTTGATTTT-AGGGTTTAGAGGGTT
* *
21269474 TAGGGTTTTGATTTTAAGGTTTAGAGGGTT
1 TAGGATTTTGATTTTAGGGTTTAGAGGGTT
* * *
21269504 TAGCATTTAG-TTTTAGGGTTT-GAAGGATT
1 TAGGATTTTGATTTTAGGGTTTAG-AGGGTT
* *
21269533 TATGG-TTTT-AGTTTTAGGGTTTGGAAGGTT
1 TA-GGATTTTGA-TTTTAGGGTTTAGAGGGTT
* * ** *
21269563 TA-GAGTTT-AGTTTGAGGGTTT-GAAAGAT
1 TAGGATTTTGA-TTTTAGGGTTTAGAGGGTT
* *
21269591 T-GAGAGTTTTGATTTTAGGGGTTAGAAGGTT
1 TAG-GA-TTTTGATTTTAGGGTTTAGAGGGTT
*
21269622 TAAGG-TTTTGATTTTATGGTTTAGAGGGTT
1 T-AGGATTTTGATTTTAGGGTTTAGAGGGTT
* *
21269652 TAGGATTTTGATTTTATGGCTTAGAGGGTT
1 TAGGATTTTGATTTTAGGGTTTAGAGGGTT
21269682 TAG
1 TAG
21269685 AGTTATTTTT
Statistics
Matches: 243, Mismatches: 38, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
28 8 0.03
29 92 0.38
30 129 0.53
31 12 0.05
32 1 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.45
Consensus pattern (30 bp):
TAGGATTTTGATTTTAGGGTTTAGAGGGTT
Found at i:21270176 original size:12 final size:12
Alignment explanation
Indices: 21270157--21270187 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21270147 AAATAAAACT
21270157 AAAATAATATAA
1 AAAATAATATAA
*
21270169 ATAATAATATAA
1 AAAATAATATAA
21270181 AAAATAA
1 AAAATAA
21270188 AAAAAATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:21272054 original size:29 final size:30
Alignment explanation
Indices: 21272020--21272091 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
21272010 ATTTTTTTAA
*
21272020 AAATAAATTTTTATACTTTT-A-TTATATTT
1 AAATAAATTTTTATA-TTTTAATTTATATTC
* *
21272049 AAATAAATTATTGTATTTTAATTTATATTC
1 AAATAAATTTTTATATTTTAATTTATATTC
21272079 AAATAAAATTTTT
1 AAAT-AAATTTTT
21272092 TTCAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 14 0.39
30 11 0.31
31 7 0.19
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTAATTTATATTC
Found at i:21272245 original size:29 final size:30
Alignment explanation
Indices: 21272134--21272269 Score: 86
Period size: 30 Copynumber: 4.6 Consensus size: 30
21272124 ATTTCGAAAC
*
21272134 AAATTAAAAAT-TAAAAATTTCATTTGAACAT-
1 AAATTAAAAATATAAAAACTT-ATTT-AA-ATA
* * * * * *
21272165 AAATT-AAATTTTAAAGATTTATTTGAGTAA
1 AAATTAAAAATATAAAAACTTATTTAAAT-A
* * *
21272195 AAATTAAAAAT-TAAGAACTTATTTCAATT
1 AAATTAAAAATATAAAAACTTATTTAAATA
* *
21272224 TAA-TAAAAATATAAAAATTTATTTAAATA
1 AAATTAAAAATATAAAAACTTATTTAAATA
21272253 AAATTAAAAA-ATAAAAA
1 AAATTAAAAATATAAAAA
21272270 AATTTTATTA
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 8 0.10
29 26 0.32
30 31 0.38
31 17 0.21
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTAAAAATATAAAAACTTATTTAAATA
Found at i:21272263 original size:23 final size:23
Alignment explanation
Indices: 21272221--21272264 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21272211 ACTTATTTCA
21272221 ATTTAATAAAAATATAAAAATTT
1 ATTTAATAAAAATATAAAAATTT
*
21272244 ATTTAAATAAAATTA-AAAAAT
1 ATTT-AATAAAAATATAAAAAT
21272265 AAAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTAATAAAAATATAAAAATTT
Found at i:21272735 original size:20 final size:20
Alignment explanation
Indices: 21272700--21272754 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 20
21272690 TTCAATCCAA
21272700 TTTTAAATTAATAAAATATTAT
1 TTTTAAA-T-ATAAAATATTAT
21272722 TTTTAAATATAAAATATTAT
1 TTTTAAATATAAAATATTAT
21272742 TTTTAAATATAAA
1 TTTTAAATATAAA
21272755 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 25 0.76
21 1 0.03
22 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAATATAAAATATTAT
Found at i:21273559 original size:17 final size:17
Alignment explanation
Indices: 21273523--21273573 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
21273513 ATTCAATAAA
***
21273523 AAATATTTTAAAAACAT
1 AAATATTTTAAAATTTT
21273540 AAATATTTTAAAATTTT
1 AAATATTTTAAAATTTT
21273557 AAA-ATTTT-AAATTTT
1 AAATATTTTAAAATTTT
21273572 AA
1 AA
21273574 CTACAGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTTAAAATTTT
Found at i:21273570 original size:7 final size:8
Alignment explanation
Indices: 21273539--21273573 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
21273529 TTTAAAAACA
21273539 TAAATATTT
1 TAAA-ATTT
21273548 TAAAATTT
1 TAAAATTT
21273556 TAAAATTT
1 TAAAATTT
21273564 T-AAATTT
1 TAAAATTT
21273571 TAA
1 TAA
21273574 CTACAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 14 0.56
9 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TAAAATTT
Found at i:21273775 original size:27 final size:27
Alignment explanation
Indices: 21273718--21273776 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
21273708 AAATCATATT
** *
21273718 TTATATTTTAATAGTTAGAAATAATAT
1 TTATATTTTAATAAATAGAAATAATAA
* * *
21273745 TTATATTTTAATAAATATAATTAGTAA
1 TTATATTTTAATAAATAGAAATAATAA
21273772 TTATA
1 TTATA
21273777 AATAATTGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
TTATATTTTAATAAATAGAAATAATAA
Found at i:21273780 original size:23 final size:23
Alignment explanation
Indices: 21273754--21273798 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21273744 TTTATATTTT
*
21273754 AATAAATATAATTAGTAATTATA
1 AATAAATATAAATAGTAATTATA
* *
21273777 AATAATTGTAAATAGTAATTAT
1 AATAAATATAAATAGTAATTAT
21273799 TGTATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (23 bp):
AATAAATATAAATAGTAATTATA
Found at i:21274069 original size:16 final size:16
Alignment explanation
Indices: 21274039--21274087 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
21274029 TAATTAATCA
21274039 TTTTTATTTACATTTTAT
1 TTTTTA-TTA-ATTTTAT
21274057 TTTTTATTAATTTTAT
1 TTTTTATTAATTTTAT
* *
21274073 ATATTATT-ATTTTAT
1 TTTTTATTAATTTTAT
21274088 AATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 13 0.45
17 3 0.10
18 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTATTAATTTTAT
Found at i:21284126 original size:22 final size:21
Alignment explanation
Indices: 21284096--21284137 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
21284086 TTGGAAAAGA
* *
21284096 AACAGACAATACATTCCAGAAG
1 AACAAACAATA-ATACCAGAAG
21284118 AACAAACAATAATACCAGAA
1 AACAAACAATAATACCAGAA
21284138 CAGCAAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.21, G:0.10, T:0.12
Consensus pattern (21 bp):
AACAAACAATAATACCAGAAG
Found at i:21289714 original size:46 final size:46
Alignment explanation
Indices: 21289627--21289714 Score: 104
Period size: 46 Copynumber: 1.9 Consensus size: 46
21289617 TGCAAGTGTG
* * ***
21289627 ATTAAGAGATCCATTTCATTACATTCTCTTAATCTGGTATCAAGTT
1 ATTAAGAGATCCACTTCATTACATTATCTTAATCAAATATCAAGTT
** *
21289673 ATTAAGAGATCCACTTCATTTGATTATCTTAGTCAAATATCA
1 ATTAAGAGATCCACTTCATTACATTATCTTAATCAAATATCA
21289715 TCCATGTACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (46 bp):
ATTAAGAGATCCACTTCATTACATTATCTTAATCAAATATCAAGTT
Found at i:21290340 original size:3 final size:3
Alignment explanation
Indices: 21290332--21290378 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
21290322 TGAAACCAGA
21290332 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21290379 AACCCTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21291146 original size:37 final size:38
Alignment explanation
Indices: 21291102--21291181 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
21291092 ATATCTCTCA
21291102 AATTTATGTAATTGTCAA-TTTTAAACTT-AAAATAATG
1 AATTTATGTAATTGT-AAGTTTTAAACTTAAAAATAATG
* *
21291139 AATTTATGTGATTGTAAGTTTTAAAGTTAAAAATAATG
1 AATTTATGTAATTGTAAGTTTTAAACTTAAAAATAATG
*
21291177 CATTT
1 AATTT
21291182 GGTTTAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 2 0.05
37 23 0.61
38 13 0.34
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (38 bp):
AATTTATGTAATTGTAAGTTTTAAACTTAAAAATAATG
Found at i:21292682 original size:44 final size:45
Alignment explanation
Indices: 21292634--21292722 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
21292624 TAAACTCTAA
* *
21292634 TGTCTTTTAAGCAATTGACATGAT-AAAATTACTAAGAAAAATGT
1 TGTCTTTTAAGCAACTGACATGATAAAAATTAATAAGAAAAATGT
* *
21292678 TGTCTTTTAAGCAACTGAGATGTTAAAAATTAATAAGAAAAATGT
1 TGTCTTTTAAGCAACTGACATGATAAAAATTAATAAGAAAAATGT
21292723 AAACTCTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 21 0.52
45 19 0.47
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.34
Consensus pattern (45 bp):
TGTCTTTTAAGCAACTGACATGATAAAAATTAATAAGAAAAATGT
Found at i:21295867 original size:51 final size:52
Alignment explanation
Indices: 21295806--21295908 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 52
21295796 TACTGTTTAA
* *
21295806 TTTTACAAGTTTCATTGCTAAATCTTCCACCATTTGGGTT-TATTTAGAAAT
1 TTTTACAAGTTTCATTGCTAAATCTTCCACCATTTGAGTTAAATTTAGAAAT
* * * *
21295857 TTTTTCAAGTTTCATTTCTAAGTTTTCCACCATTTGAGTTAAATTTAGAAAT
1 TTTTACAAGTTTCATTGCTAAATCTTCCACCATTTGAGTTAAATTTAGAAAT
21295909 ATCTTTCCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
51 35 0.78
52 10 0.22
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (52 bp):
TTTTACAAGTTTCATTGCTAAATCTTCCACCATTTGAGTTAAATTTAGAAAT
Found at i:21299792 original size:25 final size:26
Alignment explanation
Indices: 21299742--21299792 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
21299732 ATTCTTAATC
*
21299742 TAAAATTTCTCAAAAAATTTACCATT
1 TAAAATTTCTCAAAAAATTCACCATT
*
21299768 TAAAATTT-T-AAAAAATCTCATCATT
1 TAAAATTTCTCAAAAAAT-TCACCATT
21299793 GGATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAATTTCTCAAAAAATTCACCATT
Found at i:21302607 original size:52 final size:53
Alignment explanation
Indices: 21302546--21302649 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
21302536 TTTAATTTTA
* *
21302546 CAAGTTTCATTTCTAAATTTTTCACTATTTGGATT-TATTTAAAAATATCTTG
1 CAAGTTTCATTTCTAAATTTTTCACCATTTGGATTAAATTTAAAAATATCTTG
* * * * *
21302598 CAAGTTTCATTTTTAAGTTTTTTACCATTTGGGTTAAATTTAGAAATATCTT
1 CAAGTTTCATTTCTAAATTTTTCACCATTTGGATTAAATTTAAAAATATCTT
21302650 TTCTAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 30 0.68
53 14 0.32
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (53 bp):
CAAGTTTCATTTCTAAATTTTTCACCATTTGGATTAAATTTAAAAATATCTTG
Found at i:21305366 original size:239 final size:239
Alignment explanation
Indices: 21304940--21305407 Score: 660
Period size: 239 Copynumber: 2.0 Consensus size: 239
21304930 TTTAACTTTC
* * * * *
21304940 ATACAAAAAATTTATATTACCCATCCAAAACCCCAAAATAAAAAAAATAGTATTTACAAAAATGC
1 ATACAAAAAACTTATATCACCCATCCAAAACCCCAAAAGAAAAAAAATAATATTTACAAAAATAC
* *
21305005 ATGCTTAATATAAGTTAAACATCATCAATAAATCCTATTCTCAACATTTCATCTACCTCATCAAA
66 ATGCCTAATATAAGTTAAACATCATCAATAAATCCTAATCTCAACATTTCATCTACCTCATCAAA
*
21305070 AATTTTAAAATTTTAATGAGCCTAAGTGAATATTCCCCCTCTCTATGTGATCCAGCATCATTTGC
131 AATTTTAAAATTTTAATGAGCCTAAGTGAATATTCCCCCTCTCTATGTGAACCAGCATCATTTGC
*
21305135 AATAGATCATCATCAAATATCATCAATTAATAAATGTATTTTTG
196 AATAGATCATCATCAAATATCATCAAGTAATAAATGTATTTTTG
* *
21305179 ATACAAAAAACTTATATCACCCATCCAACACCTCAAAAGAAAAAAAAGTAATATTTA-ACAAAAT
1 ATACAAAAAACTTATATCACCCATCCAAAACCCCAAAAGAAAAAAAA-TAATATTTACA-AAAAT
* * * * ** *
21305243 ACATGCCTAATATAAGTTCAACATCGTCAATAAATCGTAATCTCAACATTTCATTTGTCTCAT-T
64 ACATGCCTAATATAAGTTAAACATCATCAATAAATCCTAATCTCAACATTTCATCTACCTCATCA
*
21305307 AAAA-TTTCAAATTTTCAATGAAG-CTAAGTGAATATTCCCCCTCT-TAATGAT-AACCAGCATC
129 AAAATTTTAAAATTTT-AATG-AGCCTAAGTGAATATTCCCCCTCTCT-ATG-TGAACCAGCATC
*
21305368 ATTTGCAATAGATCGTCATCAAATATCATCAAGTAATAAA
190 ATTTGCAATAGATCATCATCAAATATCATCAAGTAATAAA
21305408 AGCATTCCAA
Statistics
Matches: 203, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
238 11 0.05
239 122 0.60
240 70 0.34
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (239 bp):
ATACAAAAAACTTATATCACCCATCCAAAACCCCAAAAGAAAAAAAATAATATTTACAAAAATAC
ATGCCTAATATAAGTTAAACATCATCAATAAATCCTAATCTCAACATTTCATCTACCTCATCAAA
AATTTTAAAATTTTAATGAGCCTAAGTGAATATTCCCCCTCTCTATGTGAACCAGCATCATTTGC
AATAGATCATCATCAAATATCATCAAGTAATAAATGTATTTTTG
Found at i:21306113 original size:164 final size:161
Alignment explanation
Indices: 21305924--21306237 Score: 445
Period size: 164 Copynumber: 1.9 Consensus size: 161
21305914 AATTGCAATG
*
21305924 TAGATTATATCCAAAATTGTTAATAAGAGACAAAGATGAAATTTTAATTTTTAGATACATATA-T
1 TAGATTATATCCAAAATTGTTAATAAGAGACAAAGATGAAATTTTAATATTTAGATACATATATT
**
21305988 TTGAAAATAATTTTAAATTTATATTTAAATTTTTTTAAAAATCTAATTTTTTATGATATTTTAAA
66 TTGAAAATAATTTTAAATTTATATTTAAA-TTTTAAAAAAATCT-A--TTTTATGATATTTTAAA
*
21306053 CT-TGATAACTTCCATAATTTTAAAATCTAATCTTT
127 -TGTGATAACTTCCATAATATTAAAATCTAATCTTT
** *
21306088 TAGATTATATTTAAAA-TGTTTAATAAGAGACAGAGATGAAATTTTAATATTTAGATACATATAT
1 TAGATTATATCCAAAATTG-TTAATAAGAGACAAAGATGAAATTTTAATATTTAGATACATATAT
* * *
21306152 TTTTAAAATAGTTTTAAATTTATATTTTAATTTTAAAAAAATCTATTTTATGATATTTTAAATGT
65 TTTGAAAATAATTTTAAATTTATATTTAAATTTTAAAAAAATCTATTTTATGATATTTTAAATGT
* *
21306217 GGTAACTTGCATAATATTAAA
130 GATAACTTCCATAATATTAAA
21306238 CATTTTTTAA
Statistics
Matches: 135, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
160 1 0.01
161 36 0.27
163 3 0.02
164 68 0.50
165 27 0.20
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (161 bp):
TAGATTATATCCAAAATTGTTAATAAGAGACAAAGATGAAATTTTAATATTTAGATACATATATT
TTGAAAATAATTTTAAATTTATATTTAAATTTTAAAAAAATCTATTTTATGATATTTTAAATGTG
ATAACTTCCATAATATTAAAATCTAATCTTT
Found at i:21306945 original size:22 final size:22
Alignment explanation
Indices: 21306920--21306961 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
21306910 AAATTTTATT
21306920 TAATATATAGAAAA-TAAAAACA
1 TAATATATA-AAAATTAAAAACA
21306942 TAATATATAAAAATTAAAAA
1 TAATATATAAAAATTAAAAA
21306962 AATATTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TAATATATAAAAATTAAAAACA
Found at i:21317350 original size:2 final size:2
Alignment explanation
Indices: 21317343--21317369 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21317333 CTCAGACAAC
21317343 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
21317370 ATGTAAGGTG
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:21319571 original size:13 final size:13
Alignment explanation
Indices: 21319555--21319585 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21319545 CGAATTTAGG
21319555 TATTTTTTTTACT
1 TATTTTTTTTACT
*
21319568 TATTTTTTTTATT
1 TATTTTTTTTACT
21319581 TATTT
1 TATTT
21319586 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TATTTTTTTTACT
Found at i:21319593 original size:16 final size:16
Alignment explanation
Indices: 21319574--21319604 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21319564 TACTTATTTT
21319574 TTTTATTTATTTATTC
1 TTTTATTTATTTATTC
21319590 TTTTATTTATTTATT
1 TTTTATTTATTTATT
21319605 TTCATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTATTC
Found at i:21323758 original size:22 final size:22
Alignment explanation
Indices: 21323718--21323759 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21323708 ATCATTTAAA
* *
21323718 ATATGTACATATTGTTTATAGG
1 ATATGTACATAGTGCTTATAGG
*
21323740 ATATGTATATAGTGCTTATA
1 ATATGTACATAGTGCTTATA
21323760 ACTAATACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (22 bp):
ATATGTACATAGTGCTTATAGG
Found at i:21323807 original size:22 final size:22
Alignment explanation
Indices: 21323782--21323824 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21323772 GGATACATAT
*
21323782 ATAGTGTTTATAGAATATGTAA
1 ATAGTGCTTATAGAATATGTAA
*
21323804 ATAGTGCTTATAGTATATGTA
1 ATAGTGCTTATAGAATATGTA
21323825 CATAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (22 bp):
ATAGTGCTTATAGAATATGTAA
Found at i:21323891 original size:22 final size:22
Alignment explanation
Indices: 21323863--21323916 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
21323853 GGAACTCATT
21323863 TGAGATATGTACATATTACTTA
1 TGAGATATGTACATATTACTTA
*
21323885 TGAGATATGTATATATTACTTA
1 TGAGATATGTACATATTACTTA
*
21323907 TAAGATATGT
1 TGAGATATGT
21323917 GCATGTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.43
Consensus pattern (22 bp):
TGAGATATGTACATATTACTTA
Found at i:21324652 original size:104 final size:105
Alignment explanation
Indices: 21324513--21324790 Score: 355
Period size: 104 Copynumber: 2.6 Consensus size: 105
21324503 TTCTAATTAG
* * * * *
21324513 TTTGATAAGATTTAATTTTGATATTTAAATACTCCAATAATTTGGTATGATTAAAAAATTTTATT
1 TTTGATAAAATTTAATTTTAATATTTAAATCCTCCAATAATTTGGTAAGATTAAAAAATTATATT
* *
21324578 TTCAATTATTTTTTTTTAAAAAGATCATTAGATC-TTC-CAA
66 TTCAATTA--ATTTTTTAAAAAGATCATTAAATCTTTCACAA
* * * *
21324618 -TTGGTAAATTTTAATTTTAAGATTTAAATCCTCCAATAATTTGGTAAGATTAAAAAAATATATT
1 TTTGATAAAATTTAATTTTAATATTTAAATCCTCCAATAATTTGGTAAGATTAAAAAATTATATT
* * *
21324682 TTTAATTAATTTTTTAAAAAGATTATTAAATCTTTCAATAA
66 TTCAATTAATTTTTTAAAAAGATCATTAAATCTTTC-ACAA
* *
21324723 TTTGATAAAATTTAATTTCAATATTTAAATCCTTCCAATAATTTGGTAAGATTAAAAAATTATTT
1 TTTGATAAAATTTAATTTTAATATTTAAATCC-TCCAATAATTTGGTAAGATTAAAAAATTATAT
21324788 TTT
65 TTT
21324791 AAAAATTTAT
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
102 21 0.14
103 3 0.02
104 62 0.42
105 2 0.01
106 27 0.18
107 33 0.22
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (105 bp):
TTTGATAAAATTTAATTTTAATATTTAAATCCTCCAATAATTTGGTAAGATTAAAAAATTATATT
TTCAATTAATTTTTTAAAAAGATCATTAAATCTTTCACAA
Found at i:21325933 original size:24 final size:25
Alignment explanation
Indices: 21325901--21325948 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
21325891 ATGGGGTGTT
*
21325901 TATAGTACATAGTGCTTATAAGATA
1 TATAGTACATAATGCTTATAAGATA
*
21325926 TATA-TACATAATGTTTATAAGAT
1 TATAGTACATAATGCTTATAAGAT
21325949 CAATTCATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (25 bp):
TATAGTACATAATGCTTATAAGATA
Found at i:21332935 original size:12 final size:13
Alignment explanation
Indices: 21332910--21332939 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21332900 TTCGATTTTT
21332910 AAATAAAAATTAA
1 AAATAAAAATTAA
21332923 AAATAAAAA-TAA
1 AAATAAAAATTAA
21332935 AAATA
1 AAATA
21332940 TTTAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAAATTAA
Found at i:21332936 original size:5 final size:6
Alignment explanation
Indices: 21332910--21332939 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
21332900 TTCGATTTTT
21332910 AAATAA AAATTAA AAATAA AAATAA AAATA
1 AAATAA AAA-TAA AAATAA AAATAA AAATA
21332940 TTTAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:21335086 original size:38 final size:38
Alignment explanation
Indices: 21335044--21335116 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
21335034 ATATTCGTAC
* *
21335044 ACATTTAGAAAAACTTTTAGAATTTCATATTGTCATAT
1 ACATTTAGAAAAACTTTGAGAATTTCATAATGTCATAT
*
21335082 ACATTTAGAATAACTTTGAGAATTTCATAATGTCA
1 ACATTTAGAAAAACTTTGAGAATTTCATAATGTCA
21335117 GCTTGCAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (38 bp):
ACATTTAGAAAAACTTTGAGAATTTCATAATGTCATAT
Found at i:21343369 original size:7 final size:8
Alignment explanation
Indices: 21343352--21343376 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21343342 ATGTAGTATT
21343352 AAAATTAA
1 AAAATTAA
21343360 AAAATTAA
1 AAAATTAA
21343368 AAAATTAA
1 AAAATTAA
21343376 A
1 A
21343377 TTTTTATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:21345809 original size:3 final size:3
Alignment explanation
Indices: 21345801--21345845 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
21345791 CTTTAATGCT
21345801 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
21345846 TTGCAACAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:21347632 original size:2 final size:2
Alignment explanation
Indices: 21347627--21347659 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21347617 CCCGTTCATT
21347627 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
21347660 GTATGCTTTA
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:21350152 original size:16 final size:16
Alignment explanation
Indices: 21350131--21350162 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21350121 TTTTAAACGT
21350131 ATTTTTTCAAACAAAA
1 ATTTTTTCAAACAAAA
*
21350147 ATTTTTTTAAACAAAA
1 ATTTTTTCAAACAAAA
21350163 CATCAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTTTTCAAACAAAA
Found at i:21352586 original size:25 final size:25
Alignment explanation
Indices: 21352558--21352613 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
21352548 AAAAAAGGGC
* * *
21352558 AAAAAAGAAAGG-GAAAACCCACAG
1 AAAAAAAAAAGGTGAAAACCAACAA
21352582 AAAAAAAAAAGGTGAAAACCAACAA
1 AAAAAAAAAAGGTGAAAACCAACAA
21352607 AAAAAAA
1 AAAAAAA
21352614 TAGACGTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.71, C:0.12, G:0.14, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAGGTGAAAACCAACAA
Found at i:21354097 original size:13 final size:13
Alignment explanation
Indices: 21354074--21354133 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 13
21354064 TAATTTTTTG
* *
21354074 AAACTCTAAAATG
1 AAACCCTAAAATA
*
21354087 TAACCCTAAAATA
1 AAACCCTAAAATA
* *
21354100 AAACCTTAAAGTA
1 AAACCCTAAAATA
*
21354113 AAACCCTAAAATG
1 AAACCCTAAAATA
21354126 AAACCCTA
1 AAACCCTA
21354134 GAACTTATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.53, C:0.22, G:0.05, T:0.20
Consensus pattern (13 bp):
AAACCCTAAAATA
Found at i:21356969 original size:43 final size:43
Alignment explanation
Indices: 21356921--21357023 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
21356911 CTCAGTGGCA
* * * *
21356921 ATATCTGAGTGTTTAAATTCTAATTTTTCAAATCTTGATGGTG
1 ATATCTAAGTGTTCAAAGTCTAAGTTTTCAAATCTTGATGGTG
* *
21356964 ATATCTAAGTGTTCAAAGTCTAAGTTTTCAAATCTTGATGATA
1 ATATCTAAGTGTTCAAAGTCTAAGTTTTCAAATCTTGATGGTG
*
21357007 ATATTTAAGTGTTCAAA
1 ATATCTAAGTGTTCAAA
21357024 AGTCCAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (43 bp):
ATATCTAAGTGTTCAAAGTCTAAGTTTTCAAATCTTGATGGTG
Found at i:21357042 original size:44 final size:43
Alignment explanation
Indices: 21356920--21357042 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
21356910 TCTCAGTGGC
* * * * * *
21356920 AATATCTGAGTGTTTAAATTCTAATTTTTCAAATCTTGATGGT
1 AATATCTAAGTGTTCAAAGTCAAAATTTTCAAATCTTGATGAT
* * *
21356963 GATATCTAAGTGTTCAAAGTCTAAGTTTTCAAATCTTGATGAT
1 AATATCTAAGTGTTCAAAGTCAAAATTTTCAAATCTTGATGAT
*
21357006 AATATTTAAGTGTTCAAAAGTCCAAAATTTT-AAATCT
1 AATATCTAAGTGTTC-AAAGT-CAAAATTTTCAAATCT
21357043 AATAGTGATA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 50 0.74
44 11 0.16
45 7 0.10
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (43 bp):
AATATCTAAGTGTTCAAAGTCAAAATTTTCAAATCTTGATGAT
Found at i:21357223 original size:35 final size:34
Alignment explanation
Indices: 21357158--21357226 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
21357148 AGCATTCTAG
*
21357158 TATGAACTTTATTAAAAAAATTTTTTGTGGTGATA
1 TATGAACTTTATT-AAAAAATTTTTAGTGGTGATA
*
21357193 TATGAACTTTCATT-AAAACTTTCTTAGTGGTGAT
1 TATGAACTTT-ATTAAAAAATTT-TTAGTGGTGAT
21357227 GTTTTTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.23
35 20 0.67
36 3 0.10
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (34 bp):
TATGAACTTTATTAAAAAATTTTTAGTGGTGATA
Found at i:21357943 original size:31 final size:31
Alignment explanation
Indices: 21357908--21358009 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
21357898 TAAACTCTAG
* *
21357908 CCTAAACTTTAAACCTTAACATAAATC-TATC
1 CCTAAACTTTAAACC-TAACCTAAATCATAAC
* * *
21357939 CCTAAGCCTTAAACCATAACCTAAA-CTTAAC
1 CCTAAACTTTAAACC-TAACCTAAATCATAAC
*
21357970 CCTAAACTCT-AACCTAACCTAAATCATAAAC
1 CCTAAACTTTAAACCTAACCTAAATCAT-AAC
21358001 CCTAAACTT
1 CCTAAACTT
21358010 ACCTTAAATC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 9 0.16
30 7 0.12
31 42 0.72
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.26
Consensus pattern (31 bp):
CCTAAACTTTAAACCTAACCTAAATCATAAC
Found at i:21357999 original size:24 final size:25
Alignment explanation
Indices: 21357972--21358026 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
21357962 AACTTAACCC
* *
21357972 TAAACTCTAACCTAACC-TAAATCA
1 TAAACCCTAAACTAACCTTAAATCA
* *
21357996 TAAACCCTAAACTTACCTTAAATCT
1 TAAACCCTAAACTAACCTTAAATCA
21358021 TAAACC
1 TAAACC
21358027 AAACCTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAACCCTAAACTAACCTTAAATCA
Found at i:21358034 original size:24 final size:25
Alignment explanation
Indices: 21357972--21358034 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
21357962 AACTTAACCC
* *
21357972 TAAACTCT-AACCTAACCTAAATCA
1 TAAACCCTAAACCTTACCTAAATCA
*
21357996 TAAACCCTAAA-CTTACCTTAAATCT
1 TAAACCCTAAACCTTACC-TAAATCA
21358021 TAAA-CC-AAACCTTA
1 TAAACCCTAAACCTTA
21358035 AACCCTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 18 0.55
25 12 0.36
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAACCCTAAACCTTACCTAAATCA
Found at i:21358553 original size:42 final size:42
Alignment explanation
Indices: 21358491--21358570 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
21358481 TATTTAGAGG
*
21358491 AGCATTTTATTTTTCAAAAGTTGTTAAGCCTCTGTTTAAAGA
1 AGCATTTTATTTTTCAAAAGTTCTTAAGCCTCTGTTTAAAGA
* *
21358533 AGCA-TTTATTTTTCTTAAAGTTCTTAAGCCTTTGTTTA
1 AGCATTTTATTTTTC-AAAAGTTCTTAAGCCTCTGTTTA
21358571 GAGGAACTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 10 0.29
42 24 0.71
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (42 bp):
AGCATTTTATTTTTCAAAAGTTCTTAAGCCTCTGTTTAAAGA
Found at i:21359678 original size:7 final size:8
Alignment explanation
Indices: 21359658--21359687 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
21359648 TTTTCAAACC
21359658 AAAAAAATT
1 AAAAAAA-T
21359667 AAAAAAAT
1 AAAAAAAT
21359675 AAAAAAAT
1 AAAAAAAT
21359683 AAAAA
1 AAAAA
21359688 TACAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:21359987 original size:170 final size:170
Alignment explanation
Indices: 21359704--21360153 Score: 652
Period size: 170 Copynumber: 2.7 Consensus size: 170
21359694 TTACCCAAGG
* * *
21359704 ATGAGATTCTTAAAAATTTTAAATGATAAATTCTTAAGAAATCTCTAGGTAAAAAATTTTCTCTA
1 ATGAGATTCTTAAAAATTTTAAATGATAAATTCCTAAGAAATCTCTAGGTGAGAAATTTTCTCTA
* * *
21359769 AATTTATCCCAAATGGTGGAATCATTTAGATGAAATTTCAATAAAAGTAATTGTATTATTTTTCA
66 AATTTGTCCCAAATGGTGGAATAATTTAGATGAAATTTCAATAAAAGTAATTGTATTATTTTCCA
* *
21359834 AATAAAA-CTTTGGTTGAAAATATGTGATAATTATCCGATG
131 AA-AAAATCTTTGGTTGAAAATATGTGATAATTATCCAATA
* * *
21359874 TTGAGATTCTTAAAAATTTTAAATGATAAATTCCTAATAAATCTTTAGGTGAGAAATTTTCTCTA
1 ATGAGATTCTTAAAAATTTTAAATGATAAATTCCTAAGAAATCTCTAGGTGAGAAATTTTCTCTA
* * *
21359939 AATTTGTCCCAAATGATGGAATAATTTAGATAAAATTTCAATAAAAGTAATTGTATTCTTTTCCA
66 AATTTGTCCCAAATGGTGGAATAATTTAGATGAAATTTCAATAAAAGTAATTGTATTATTTTCCA
* *
21360004 AAAAAATTTTTGGTTGAAAATATGTGATAATTATCTAATA
131 AAAAAATCTTTGGTTGAAAATATGTGATAATTATCCAATA
* * * * *
21360044 ATGAGATTTTTAAAAATTTCAAATTATAAATTCCTAAGAAATCTCTAAGTGAGAAA-TTTCTTTA
1 ATGAGATTCTTAAAAATTTTAAATGATAAATTCCTAAGAAATCTCTAGGTGAGAAATTTTCTCTA
* * * *
21360108 AATTTGTCCTAAATGGTGGAAGAATTTAAATGAAATTTCAACAAAA
66 AATTTGTCCCAAATGGTGGAATAATTTAGATGAAATTTCAATAAAA
21360154 AATAATTATC
Statistics
Matches: 249, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
169 51 0.20
170 198 0.80
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (170 bp):
ATGAGATTCTTAAAAATTTTAAATGATAAATTCCTAAGAAATCTCTAGGTGAGAAATTTTCTCTA
AATTTGTCCCAAATGGTGGAATAATTTAGATGAAATTTCAATAAAAGTAATTGTATTATTTTCCA
AAAAAATCTTTGGTTGAAAATATGTGATAATTATCCAATA
Found at i:21360308 original size:10 final size:10
Alignment explanation
Indices: 21360278--21360302 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21360268 AAATTGACTC
21360278 AAATTATGAA
1 AAATTATGAA
21360288 AAATTATGAA
1 AAATTATGAA
21360298 AAATT
1 AAATT
21360303 TAGAAATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AAATTATGAA
Found at i:21360341 original size:123 final size:124
Alignment explanation
Indices: 21360189--21360417 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 124
21360179 CGAAAGCAAA
* * * *
21360189 AAAAAAAAAAAAGAACAAGAATTTTTAAATATGCACAAATGGT-GAAAATGTTAAAAATTTCAAA
1 AAAAAAAAAAAAGAAAAAAAATTTCTAAATAGGCACAAATGGTAGAAAAT-TTAAAAA-TTCAAA
*
21360253 A-AAGCAAATATTTCTAAATTGACTCAAATTATGAAA-AATTATGAAAAATTTAGAAATCC
64 ACAAGAAAATATTTCTAAATTGACTCAAATTATGAAATAATTATGAAAAATTTAGAAATCC
* * * *
21360312 AAAAAAAATAAATAAAAAAAATTTCTAAATAGGCCCAAGTGGTAGAAAATTTAAAAATTCAAAAC
1 AAAAAAAAAAAAGAAAAAAAATTTCTAAATAGGCACAAATGGTAGAAAATTTAAAAATTCAAAAC
* *
21360377 AAGAAAATATTTTTAATTTGACTCAAATTATGAAATAATTA
66 AAGAAAATATTTCTAAATTGACTCAAATTATGAAATAATTA
21360418 GATATATTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
122 7 0.08
123 74 0.80
124 11 0.12
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (124 bp):
AAAAAAAAAAAAGAAAAAAAATTTCTAAATAGGCACAAATGGTAGAAAATTTAAAAATTCAAAAC
AAGAAAATATTTCTAAATTGACTCAAATTATGAAATAATTATGAAAAATTTAGAAATCC
Found at i:21360439 original size:123 final size:122
Alignment explanation
Indices: 21360185--21360449 Score: 297
Period size: 123 Copynumber: 2.2 Consensus size: 122
21360175 TTTTCGAAAG
* * * * * *
21360185 CAAAAAAAAAAAAAAAGAACAAGAATTTTTAAATATGCACAAATGGTGAAAATGTTAAAAATTTC
1 CAAAAAAAAAAATAAATAAAAAAAATTTCTAAATAGGCACAAATGGTGAAAATGTTAAAAATTTC
*
21360250 AAAAAAGCAAATATTTCTAAATTGACTCAAATTATGAAAAATTATGAAAAATTTAGA
66 AAAAAAGAAAATATTTCTAAATTGACTCAAATTATGAAAAATTATGAAAAATTTAGA
* * *
21360307 -AATCCAAAAAAAATAAATAAAAAAAATTTCTAAATAGGCCCAAGTGGTAGAAAAT-TTAAAAA-
1 CAA--AAAAAAAAATAAATAAAAAAAATTTCTAAATAGGCACAAATGGT-GAAAATGTTAAAAAT
* * * * *
21360369 TTCAAAACAAGAAAATATTTTTAATTTGACTCAAATTATGAAATAATTA-GATATATTTTTGA
63 TTCAAAA-AAGAAAATATTTCTAAATTGACTCAAATTATGAAA-AATTATGA-AAAATTTAGA
*
21360431 CAAAAAAAAGAAT-AATAAA
1 CAAAAAAAAAAATAAATAAA
21360450 TAACATTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
121 2 0.02
122 13 0.11
123 84 0.71
124 18 0.15
125 2 0.02
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.27
Consensus pattern (122 bp):
CAAAAAAAAAAATAAATAAAAAAAATTTCTAAATAGGCACAAATGGTGAAAATGTTAAAAATTTC
AAAAAAGAAAATATTTCTAAATTGACTCAAATTATGAAAAATTATGAAAAATTTAGA
Found at i:21361110 original size:20 final size:21
Alignment explanation
Indices: 21361066--21361118 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
21361056 TTGTTTTAAA
* *
21361066 TATT-TAATTATGATACATAT
1 TATTATAATTATTATACAAAT
21361086 T-TTATAATTATTATA-AAAT
1 TATTATAATTATTATACAAAT
*
21361105 TATTATTATTATTA
1 TATTATAATTATTA
21361119 ATAATATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATAATTATTATACAAAT
Found at i:21361283 original size:15 final size:14
Alignment explanation
Indices: 21361252--21361286 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21361242 TAGTAAATGC
21361252 ATATATTAAAATAT
1 ATATATTAAAATAT
*
21361266 ATATATTAAATTTAT
1 ATATATTAAA-ATAT
21361281 ATATAT
1 ATATAT
21361287 ATATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTAAAATAT
Found at i:21362598 original size:20 final size:21
Alignment explanation
Indices: 21362559--21362599 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
21362549 AACCCGTTTC
*
21362559 AACTTTCAAGGCTGATTTTTA
1 AACTTTCAAGGCTAATTTTTA
21362580 AACTTTCAA-GCTAATTTTTA
1 AACTTTCAAGGCTAATTTTTA
21362600 TTACCTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (21 bp):
AACTTTCAAGGCTAATTTTTA
Found at i:21363749 original size:30 final size:30
Alignment explanation
Indices: 21363715--21363772 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
21363705 TGATACAATC
*
21363715 TATTTAAATATTAATTTATATCTTAATAAA
1 TATTTAAATATTAATCTATATCTTAATAAA
*
21363745 TATTTAAATATTAGTCTATATCTTAATA
1 TATTTAAATATTAATCTATATCTTAATA
21363773 CACCATGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
TATTTAAATATTAATCTATATCTTAATAAA
Found at i:21363924 original size:30 final size:30
Alignment explanation
Indices: 21363888--21363948 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
21363878 TGATGCAATC
**
21363888 TATTTAAATATTAATTTATATCTTAATAAA
1 TATTTAAATATTAACCTATATCTTAATAAA
21363918 TATTTAAATATTAACCTATATCTTAATAAA
1 TATTTAAATATTAACCTATATCTTAATAAA
21363948 T
1 T
21363949 CACGGAGGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTTAAATATTAACCTATATCTTAATAAA
Found at i:21363976 original size:173 final size:172
Alignment explanation
Indices: 21363688--21364013 Score: 521
Period size: 173 Copynumber: 1.9 Consensus size: 172
21363678 AAGACTTGAA
*
21363688 ATATATATATATCAAGTTGATACAATCTATTTAAATATTAATTTATATCTTAATAAATATTTAAA
1 ATATAGATATATCAAGTTGATACAATCTATTTAAATATTAATTTATATCTTAATAAATATTTAAA
** * * * *
21363753 TATTAGTCTATATCTTAATACACCATGTAGGTCCAACTACTTAACAATTGCCATGCAAATCTTTT
66 TATTAACCTATATCTTAATAAACCACGGAGGCCCAACTACTTAACAATTGCCATGCAAATCTTTT
21363818 TGAGTAATCTAAAGAGATTTGGATGACATATATATATATATATAC
131 T--G-AATCTAAAGAGATTTGGATGACATATATATATATATATAC
*
21363863 ATATAGATATAT-AA-TTGATGCAATCTATTTAAATATTAATTTATATCTTAATAAATATTTAAA
1 ATATAGATATATCAAGTTGATACAATCTATTTAAATATTAATTTATATCTTAATAAATATTTAAA
* *
21363926 TATTAACCTATATCTTAATAAATCACGGAGGCCCAACTACTTAGCAATTGCCATGCAAATCTTTT
66 TATTAACCTATATCTTAATAAACCACGGAGGCCCAACTACTTAACAATTGCCATGCAAATCTTTT
21363991 TGAATCTAAAGAGATTTGGATGA
131 TGAATCTAAAGAGATTTGGATGA
21364014 GTTATAAATC
Statistics
Matches: 141, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
170 21 0.15
171 1 0.01
173 106 0.75
174 2 0.01
175 11 0.08
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (172 bp):
ATATAGATATATCAAGTTGATACAATCTATTTAAATATTAATTTATATCTTAATAAATATTTAAA
TATTAACCTATATCTTAATAAACCACGGAGGCCCAACTACTTAACAATTGCCATGCAAATCTTTT
TGAATCTAAAGAGATTTGGATGACATATATATATATATATAC
Found at i:21364750 original size:22 final size:24
Alignment explanation
Indices: 21364724--21364827 Score: 76
Period size: 22 Copynumber: 4.4 Consensus size: 24
21364714 TCTAAAAGTA
*
21364724 ATAATTATATAAATT-AT-TTAAT
1 ATAATAATATAAATTAATATTAAT
* * *
21364746 ATAATTATTTAATATTAAATTTTAAT
1 ATAATAATATAA-ATT-AATATTAAT
* *
21364772 ACATAATAATATGAATTAATATAAAT
1 --ATAATAATATAAATTAATATTAAT
21364798 AT-A-AATATAAATT-ATATTAA-
1 ATAATAATATAAATTAATATTAAT
21364818 ATAATAATAT
1 ATAATAATAT
21364828 GCATTTATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.03
21 7 0.11
22 25 0.38
23 4 0.06
24 2 0.03
25 2 0.03
26 12 0.18
27 3 0.05
28 9 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
ATAATAATATAAATTAATATTAAT
Found at i:21364753 original size:13 final size:14
Alignment explanation
Indices: 21364730--21364821 Score: 59
Period size: 13 Copynumber: 6.4 Consensus size: 14
21364720 AGTAATAATT
21364730 ATATAAATTATTTA
1 ATATAAATTATTTA
21364744 ATAT-AATTATTTA
1 ATATAAATTATTTA
21364757 ATATTAAATT-TTAATA
1 ATA-TAAATTATT--TA
* *
21364773 CATAATAATATGAATTA
1 -AT-ATAA-ATTATTTA
*
21364790 ATATAAA-TA-TAA
1 ATATAAATTATTTA
21364802 ATATAAATTATATTA
1 ATATAAATTAT-TTA
21364817 A-ATAA
1 ATATAA
21364822 TAATATGCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
12 9 0.15
13 15 0.24
14 12 0.19
15 11 0.18
16 4 0.06
17 7 0.11
18 3 0.05
19 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (14 bp):
ATATAAATTATTTA
Found at i:21364822 original size:44 final size:46
Alignment explanation
Indices: 21364741--21364849 Score: 123
Period size: 44 Copynumber: 2.4 Consensus size: 46
21364731 TATAAATTAT
* * * * *
21364741 TTAATATAATTATTTAATATTAAATTTTAATACATAATAATATGAA
1 TTAATATAAATACTAAATATTAAATTATAATAAATAATAATATGAA
* *
21364787 TTAATATAAATA-TAAATA-TAAATTATATTAAATAATAATATGCA
1 TTAATATAAATACTAAATATTAAATTATAATAAATAATAATATGAA
*
21364831 TTTATATATAATACTAAAT
1 TTAATATA-AATACTAAAT
21364850 TTTTACACTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 29 0.54
45 9 0.17
46 16 0.30
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (46 bp):
TTAATATAAATACTAAATATTAAATTATAATAAATAATAATATGAA
Found at i:21367071 original size:7 final size:7
Alignment explanation
Indices: 21367061--21367086 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21367051 ATGAAATTGT
21367061 GGTTTAA
1 GGTTTAA
21367068 GGTTTAA
1 GGTTTAA
21367075 GGTTTAA
1 GGTTTAA
21367082 GGTTT
1 GGTTT
21367087 GAGAGGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
GGTTTAA
Found at i:21368647 original size:21 final size:23
Alignment explanation
Indices: 21368610--21368652 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
21368600 TTATTACATA
21368610 AAGCATGAAAGTGTAA-CTAGTG
1 AAGCATGAAAGTGTAACCTAGTG
21368632 AAGCATGAAA-TGTAACCTAGT
1 AAGCATGAAAGTGTAACCTAGT
21368653 TTAAATGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (23 bp):
AAGCATGAAAGTGTAACCTAGTG
Found at i:21371682 original size:178 final size:178
Alignment explanation
Indices: 21371382--21371727 Score: 586
Period size: 178 Copynumber: 1.9 Consensus size: 178
21371372 TCTCTCAATA
* * *
21371382 GCAATGATCCTCGCGTAGCTAGATGCCAAAATTGCTGTTGTGGGTGGGGTATCTAAGATTGCTTT
1 GCAATGATCCACGCATAGCTAGATGCCAAAATTGCTGTTATGGGTGGGGTATCTAAGATTGCTTT
*
21371447 CATGCATCTATGGAAGTATGCTTTGCACTGGCGGTGGTTTTTGCTGTTATTTTTGCTATTTTGGG
66 CATGCATCTATGGAAGTATGCTTTGCACTGGCGGTGGTTTTTGCTGTTATCTTTGCTATTTTGGG
21371512 GATAGCTTATGGTTTCCTTGCTGCCACAATGGCAATACAGTCTCGATG
131 GATAGCTTATGGTTTCCTTGCTGCCACAATGGCAATACAGTCTCGATG
* * *
21371560 GCAATGATCCACGCATGGCTGGATGCCAAAATTGCTGTTATGGGTGGGGTATCTTAGATTGCTTT
1 GCAATGATCCACGCATAGCTAGATGCCAAAATTGCTGTTATGGGTGGGGTATCTAAGATTGCTTT
* * *
21371625 CTTGCATCTATTGAAGTATGCTTTGCACT-GCTGGTGGTTTTTGTTGTTATCTTTGCTATTTTGG
66 CATGCATCTATGGAAGTATGCTTTGCACTGGC-GGTGGTTTTTGCTGTTATCTTTGCTATTTTGG
21371689 GGATAGCTTATGGTTTCCTTGCTGCCACAATGGCAATAC
130 GGATAGCTTATGGTTTCCTTGCTGCCACAATGGCAATAC
21371728 GGCGAATTTG
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
177 2 0.01
178 155 0.99
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (178 bp):
GCAATGATCCACGCATAGCTAGATGCCAAAATTGCTGTTATGGGTGGGGTATCTAAGATTGCTTT
CATGCATCTATGGAAGTATGCTTTGCACTGGCGGTGGTTTTTGCTGTTATCTTTGCTATTTTGGG
GATAGCTTATGGTTTCCTTGCTGCCACAATGGCAATACAGTCTCGATG
Found at i:21378949 original size:2 final size:2
Alignment explanation
Indices: 21378942--21378967 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21378932 AAGTATTTCC
21378942 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
21378968 TACCTATAAT
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:21380915 original size:16 final size:17
Alignment explanation
Indices: 21380883--21380915 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21380873 ATTTTAATAT
21380883 AATATTATATTTATAAA
1 AATATTATATTTATAAA
*
21380900 AATATTA-ATTTTTAAA
1 AATATTATATTTATAAA
21380916 TTAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATTATATTTATAAA
Found at i:21380974 original size:13 final size:13
Alignment explanation
Indices: 21380956--21380997 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
21380946 AATAATTTTA
21380956 TTAAATTAATATT
1 TTAAATTAATATT
* *
21380969 TTAAATTAAAATA
1 TTAAATTAATATT
21380982 TTAAA-TAATAATT
1 TTAAATTAAT-ATT
21380995 TTA
1 TTA
21380998 TTAATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTAATATT
Found at i:21381008 original size:26 final size:25
Alignment explanation
Indices: 21380954--21381006 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
21380944 ATAATAATTT
21380954 TATTAAATTAATATTTTAAATTAAAA
1 TATTAAATTAATATTTT-AATTAAAA
*
21380980 TATTAAA-TAATAATTTT-ATTAATA
1 TATTAAATTAAT-ATTTTAATTAAAA
21381004 TAT
1 TAT
21381007 ATACATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
26 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTAAATTAATATTTTAATTAAAA
Found at i:21381032 original size:45 final size:42
Alignment explanation
Indices: 21380944--21381034 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 42
21380934 ATATATAAAT
* *
21380944 ATAATAATTTTATTAAATTAATATTTTAAATTAAAATATTAA
1 ATAATAATTTTATTAAATTAACATTATAAATTAAAATATTAA
21380986 ATAATAATTTTATTAATATATATACATATATAAA-TATAAA-ATTAA
1 ATAATAATTTTATTAA-AT-TA-ACAT-TATAAATTA-AAATATTAA
21381031 ATAA
1 ATAA
21381035 ATAACAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
42 16 0.38
43 2 0.05
44 2 0.05
45 14 0.33
46 8 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (42 bp):
ATAATAATTTTATTAAATTAACATTATAAATTAAAATATTAA
Found at i:21387390 original size:21 final size:19
Alignment explanation
Indices: 21387364--21387402 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
21387354 AAAAAAACAA
21387364 AAGACAAAAGAGAGGAAAAAG
1 AAGACAAAA-A-AGGAAAAAG
21387385 AAGACAAAAAAGGAAAAA
1 AAGACAAAAAAGGAAAAA
21387403 TGAAAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (19 bp):
AAGACAAAAAAGGAAAAAG
Found at i:21387668 original size:25 final size:23
Alignment explanation
Indices: 21387640--21387723 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 23
21387630 GGGAAAAGCC
21387640 AAAAAATGAAAGAAGAGGAAAAAAT
1 AAAAAA-GAAA-AAGAGGAAAAAAT
*
21387665 AAAAGAAAAAGAAAAAGAGAGAAAAATT
1 ---A-AAAAAGAAAAAGAG-GAAAAAAT
*
21387693 AAATAAAGAAAAAGAAGAAAAAATT
1 AAA-AAAGAAAAAGAGGAAAAAA-T
21387718 AAAAAA
1 AAAAAA
21387724 AAATTTTGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
24 11 0.22
25 16 0.33
27 5 0.10
28 12 0.24
29 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (23 bp):
AAAAAAGAAAAAGAGGAAAAAAT
Found at i:21387678 original size:18 final size:18
Alignment explanation
Indices: 21387640--21387680 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21387630 GGGAAAAGCC
* * *
21387640 AAAAAATGAAAGAAGAGG
1 AAAAAATAAAAGAAAAAG
21387658 AAAAAATAAAAGAAAAAG
1 AAAAAATAAAAGAAAAAG
21387676 AAAAA
1 AAAAA
21387681 GAGAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAAATAAAAGAAAAAG
Found at i:21393100 original size:11 final size:11
Alignment explanation
Indices: 21393092--21393121 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
21393082 ATATAATATC
21393092 AAAATAATAAA
1 AAAATAATAAA
21393103 AAAAT-ATAAA
1 AAAATAATAAA
21393113 AAAATAATA
1 AAAATAATA
21393122 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:21394236 original size:8 final size:8
Alignment explanation
Indices: 21394225--21394253 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
21394215 TAAATATTTA
21394225 AATAAATT
1 AATAAATT
21394233 AATAAATT
1 AATAAATT
21394241 AATAAATT
1 AATAAATT
21394249 -ATAAA
1 AATAAA
21394254 AAAACACGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAAATT
Found at i:21394468 original size:17 final size:17
Alignment explanation
Indices: 21394437--21394479 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
21394427 AAACTCTTTT
21394437 TAAAAATGTAAAAAAAAA
1 TAAAAAT-TAAAAAAAAA
* *
21394455 TAAAAATTATAAAAATA
1 TAAAAATTAAAAAAAAA
21394472 TAAAAATT
1 TAAAAATT
21394480 GACATATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAAAATTAAAAAAAAA
Found at i:21394607 original size:15 final size:14
Alignment explanation
Indices: 21394574--21394621 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
21394564 TACAAAACAT
**
21394574 TTTAAAAAATGCAA
1 TTTAAAAAATAAAA
21394588 TTTAAAAAATAAAA
1 TTTAAAAAATAAAA
21394602 TATTAAAAAA-ATAAA
1 T-TTAAAAAATA-AAA
21394617 TTTAA
1 TTTAA
21394622 TATTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
TTTAAAAAATAAAA
Found at i:21394646 original size:18 final size:17
Alignment explanation
Indices: 21394623--21394670 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
21394613 TAAATTTAAT
21394623 ATTTTTAAAAAATCAAGAA
1 ATTTTTAAAAAATC-A-AA
21394642 ATTTTCTAAAAAAATCAAA
1 ATTTT-T-AAAAAATCAAA
21394661 A-TTTTAAAAA
1 ATTTTTAAAAA
21394671 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.19
17 1 0.04
18 3 0.11
19 8 0.30
20 2 0.07
21 8 0.30
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTTTTAAAAAATCAAA
Found at i:21394809 original size:25 final size:24
Alignment explanation
Indices: 21394781--21394830 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
21394771 TCTAAAATTG
21394781 ATATATTAATTTTT-ATTAAAAAATA
1 ATATATT--TTTTTAATTAAAAAATA
21394806 ATATATTTTTTTAAATTAAAAAATA
1 ATATATTTTTTT-AATTAAAAAATA
21394831 TGATTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
25 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTTTTTTAATTAAAAAATA
Found at i:21395878 original size:22 final size:22
Alignment explanation
Indices: 21395853--21395894 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21395843 TTAATATAAT
*
21395853 TTATATAAATTCGATGATCTTA
1 TTATATAAATTCGATAATCTTA
* *
21395875 TTATATTAATTTGATAATCT
1 TTATATAAATTCGATAATCT
21395895 CAATCAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
TTATATAAATTCGATAATCTTA
Found at i:21397137 original size:24 final size:25
Alignment explanation
Indices: 21397110--21397180 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
21397100 GAAAAGGTTT
21397110 TTAAATATATTTTATAAAAT-TTAA
1 TTAAATATATTTTATAAAATATTAA
* *
21397134 TTAAATAAAATGTT-TAAAATATTAA
1 TTAAAT-ATATTTTATAAAATATTAA
*
21397159 TTATCAATAT-TTTTAAAAAATA
1 TTA--AATATATTTTATAAAATA
21397181 AACCCACATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
24 12 0.32
25 15 0.41
26 7 0.19
27 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
TTAAATATATTTTATAAAATATTAA
Found at i:21402998 original size:12 final size:11
Alignment explanation
Indices: 21402981--21403027 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 11
21402971 TCAGACATAC
21402981 CATTCAGTAAAT
1 CATTCAG-AAAT
21402993 CATTCAGAAAT
1 CATTCAGAAAT
21403004 ACTATTCAGCAAAT
1 -C-ATTCAG-AAAT
21403018 CATTCAGAAA
1 CATTCAGAAA
21403028 ACCATTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.22
12 14 0.44
13 7 0.22
14 4 0.12
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (11 bp):
CATTCAGAAAT
Found at i:21402999 original size:25 final size:24
Alignment explanation
Indices: 21402971--21403033 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
21402961 AGCAATGTGC
*
21402971 TCAGACATACCATTCAGTAAATCAT
1 TCAGA-ATACCATTCAGCAAATCAT
*
21402996 TCAGAAATACTATTCAGCAAATCAT
1 TCAG-AATACCATTCAGCAAATCAT
*
21403021 TCAGAAAACCATT
1 TCAGAATACCATT
21403034 TAACATACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 7 0.21
25 25 0.76
26 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (24 bp):
TCAGAATACCATTCAGCAAATCAT
Found at i:21403033 original size:12 final size:12
Alignment explanation
Indices: 21402979--21403033 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
21402969 GCTCAGACAT
*
21402979 ACCATTCAGTAA
1 ACCATTCAGAAA
*
21402991 ATCATTCAGAAA
1 ACCATTCAGAAA
* *
21403003 TACTATTCAGCAA
1 -ACCATTCAGAAA
*
21403016 ATCATTCAGAAA
1 ACCATTCAGAAA
21403028 ACCATT
1 ACCATT
21403034 TAACATACGA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (12 bp):
ACCATTCAGAAA
Found at i:21404142 original size:187 final size:185
Alignment explanation
Indices: 21403804--21404720 Score: 1113
Period size: 187 Copynumber: 4.9 Consensus size: 185
21403794 AAAAGACACT
* **
21403804 TTTAATAATC-CTAAATATTTTTAAAAGAAAATTATTGAAGGCATTTGTTCTCAAAAAACGCCTT
1 TTTAATAATCTC-AAATATTTTTAAAA-AAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTT
* * * *
21403868 TAATAATTATGTAAAAAAAATTAAAATG-AATTAGTGAAGGTATTTTTCTAGAATAAAAGCCTTC
64 CAATAATTATGT--ACAAAATT-AAATGAAATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTC
* * * ** * *
21403932 ATTAACCATCTTAAAATTTGAGTAATGAAATATTTAAGGCGTTTTTCA-TTAGAAAATGTC
126 ACTAACCATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGA-AAAATGCC
* * *
21403992 TTTAATAATCTCAAATGTTTTTAAAAAGAAATTATTGAAGGTATTTATTCTAAAAAAATACCTTC
1 TTTAATAATCTCAAATATTTTTAAAAA-AAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTC
* * * * *
21404057 AATAATTATATACATAAATTAAATGAAATCAGTAAAGGCATTTTTCTAGAATAAACGCATTTACT
65 AATAATTATGTACA-AAATTAAATGAAATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTCACT
* * **
21404122 AACTATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAAAGTT
129 AACCATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATGCC
21404179 TTTAATAATCTCAAATATTTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTC
1 TTTAATAATCTCAAATA-TTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTC
* * ** * *
21404244 AATAATTATATATAAAATTTAAAAAAAATCAGTGAAGGTATTTTTTTAGAATAAATGCCTTCACT
65 AATAATTATGTACAAAA-TTAAATGAAATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTCACT
* * *
21404309 AACCATCTTAAAATTTGA--A-T--AGTA--GAAGATATTTTTCACTGAAAGATGCC
129 AACCATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATGCC
*
21404359 TTTAATAATCTCAAATATTTTTAAAAAAAATTATTGAAGGCGTTTGTTCTAAAAAAATACCTTCA
1 TTTAATAATCTCAAATATTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTCA
* **
21404424 ATAATTATGTACAAAATTTAAA--AAGAACAGTGAAGCCATTTTTCTAGAATAAACGCCTTCACT
66 ATAATTATGTACAAAA-TTAAATGAA-ATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTCACT
* *
21404487 AACTATCTTAAAATTTAAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATGCC
129 AACCATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATGCC
* * * * *
21404544 TTTAATAATCTTAAATTTTTTTTTAAAAAAATTATTTAATGCATTTGTTCTAAAAAAATACCTTC
1 TTTAATAATCTCAAA-TATTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTC
* * * * * * *
21404609 AATAATTATGTACATATATTAAATGGAATCAATGAAGGTATTTTTTTAAAATAAACACATTCACT
65 AATAATTATGTACA-AAATTAAATGAAATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTCACT
* *
21404674 AACCAT-TTAAAAATTTGAGTAGTGGAATATTGAAGGTATTTTACACT
129 AACCATCTT-AAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACT
21404721 TTTAATAAAT
Statistics
Matches: 633, Mismatches: 76, Indels: 41
0.84 0.10 0.05
Matches are distributed among these distances:
177 2 0.00
178 49 0.08
179 67 0.11
180 39 0.06
181 1 0.00
182 3 0.00
183 3 0.00
184 1 0.00
185 39 0.06
186 75 0.12
187 276 0.44
188 77 0.12
189 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (185 bp):
TTTAATAATCTCAAATATTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTCA
ATAATTATGTACAAAATTAAATGAAATCAGTGAAGGTATTTTTCTAGAATAAACGCCTTCACTAA
CCATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATGCC
Found at i:21404265 original size:62 final size:62
Alignment explanation
Indices: 21403823--21404617 Score: 173
Period size: 62 Copynumber: 12.9 Consensus size: 62
21403813 CCTAAATATT
* * * *
21403823 TTTAAAAGAAAATTATTGAAGGCATTTGTTCT-CAAAAAACGCCTTTAATAATTATGTAAAAAAA
1 TTTAAAA-AAAATTATTGAAGGCATTT-TTCTACAAAAAATGCCTTCAATAATTATAT-ATAAAA
* ** * * * * ** *
21403887 ATTAAAATGAATTAGTGAAGGTATTTTTCTAGAATAAAA-GCCTTCATTAACCATCT-TAAAA
1 TTTAAAAAAAATTATTGAAGGCATTTTTCTACAA-AAAATGCCTTCAATAATTATATATAAAA
** * * * * * *
21403948 TTTGAGTAATGAAA-TATTTAAGGCGTTTTTC-ATTAGAAAATGTCTTTAATAATCTCA-A-AT-
1 TTT-A--AAAAAAATTATTGAAGGCATTTTTCTA-CAAAAAATGCCTTCAATAAT-T-ATATATA
***
21404008 GTT
60 AAA
* * *
21404011 TTTAAAAAGAAATTATTGAAGGTATTTATTCTA-AAAAAATACCTTCAATAATTATATACATAAA
1 TTTAAAAA-AAATTATTGAAGGCATTT-TTCTACAAAAAATGCCTTCAATAATTATATATA-AAA
** * * * * * * * * * * *
21404075 -TTAAATGAAATCAGTAAAGGCATTTTTCTAGAATAAACGCATTTACTAACTATCT-TAAAA
1 TTTAAAAAAAATTATTGAAGGCATTTTTCTACAAAAAATGCCTTCAATAATTATATATAAAA
*** * ** *
21404135 TTTGAGTAGTGAAA-TATTGAAGGTATTTTTC-ACTGAAAAAA-GTTTTTAATAATCTCA-A-AT
1 TTT-A--AAAAAAATTATTGAAGGCATTTTTCTAC--AAAAAATGCCTTCAATAAT-T-ATATAT
***
21404195 ATTT
59 AAAA
*
21404199 TTTAAAAAAAATTATTGAAGGCATTTGTTCTA-AAAAAATACCTTCAATAATTATATATAAAA
1 TTTAAAAAAAATTATTGAAGGCATTT-TTCTACAAAAAATGCCTTCAATAATTATATATAAAA
* * * * * * * ** *
21404261 TTTAAAAAAAATCAGTGAAGGTATTTTTTTAGAATAAATGCCTTCACTAACCATCT-TAAAA
1 TTTAAAAAAAATTATTGAAGGCATTTTTCTACAAAAAATGCCTTCAATAATTATATATAAAA
* * * ** * * * **
21404322 TTT---GAATAGTA--GAAGATATTTTTC-ACTGAAAGATGCCTTTAATAATCTCA-A-AT-ATT
1 TTTAAAAAAAATTATTGAAGGCATTTTTCTAC-AAAAAATGCCTTCAATAAT-T-ATATATAAAA
* * * *
21404378 TTTAAAAAAAATTATTGAAGGCGTTTGTTCTA-AAAAAATACCTTCAATAATTATGTACAAAA
1 TTTAAAAAAAATTATTGAAGGCATTT-TTCTACAAAAAATGCCTTCAATAATTATATATAAAA
* * * * * * * * * *
21404440 TTTAAAAAGAA-CAGTGAAGCCATTTTTCTAGAATAAACGCCTTCACTAACTATCT-TAAAA
1 TTTAAAAAAAATTATTGAAGGCATTTTTCTACAAAAAATGCCTTCAATAATTATATATAAAA
** * * * * **
21404500 TTTAAGTAGTGAAA-TATTGAAGGTATTTTTC-ACTGAAAAATGCCTTTAATAATCT-TAAATTT
1 TTTAA--A-AAAAATTATTGAAGGCATTTTTCTAC-AAAAAATGCCTTCAATAAT-TATATATAA
**
21404562 TT
61 AA
* * * *
21404564 TTTTAAAAAAATTATTTAATGCATTTGTTCTA-AAAAAATACCTTCAATAATTAT
1 TTTAAAAAAAATTATTGAAGGCATTT-TTCTACAAAAAATGCCTTCAATAATTAT
21404618 GTACATATAT
Statistics
Matches: 504, Mismatches: 167, Indels: 122
0.64 0.21 0.15
Matches are distributed among these distances:
55 1 0.00
56 28 0.06
57 1 0.00
58 5 0.01
59 6 0.01
60 22 0.04
61 98 0.19
62 180 0.36
63 120 0.24
64 41 0.08
65 2 0.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (62 bp):
TTTAAAAAAAATTATTGAAGGCATTTTTCTACAAAAAATGCCTTCAATAATTATATATAAAA
Found at i:21404527 original size:365 final size:368
Alignment explanation
Indices: 21403802--21404697 Score: 1168
Period size: 365 Copynumber: 2.4 Consensus size: 368
21403792 TTAAAAGACA
* **
21403802 CTTTTAATAATC-CTAAATA-TTTTTAAAAGAAAATTATTGAAGGCATTTGTTCTCAAAAAACGC
1 CTTTTAATAATCTC-AAATATTTTTTAAAA-AAAATTATTGAAGGCATTTGTTCTAAAAAAATAC
* * * * *
21403865 CTTTAATAATTATGTAAAAAAAATTAAAATGAATTAGTGAAGGTATTTTTCTAGAATAAAAGCCT
64 CTTCAATAATTATGT--AAAAATTTAAAAAGAATCAGTGAAGGTATTTTTTTAGAATAAAAGCCT
* * * * *
21403930 TCATTAACCATCTTAAAATTTGAGTAATGAAATATTTAAGGCGTTTTTCATTAGAAAATGTCTTT
127 TCACTAACCATCTTAAAATTTGAGTAGTGAAAGA-TTAA---GTTTTTCACTAGAAAATGCCTTT
* *
21403995 AATAATCTCAAATGTTTTTAAAAAGAAATTATTGAAGGTATTTATTCTAAAAAAATACCTTCAAT
188 AATAATCTCAAATATTTTTAAAAAGAAATTATTGAAGGCATTTATTCTAAAAAAATACCTTCAAT
* * *
21404060 AATTATATACATAAATTAAATGAAATCAGTAAAGGCATTTTTCTAGAATAAACGCATTTACTAAC
253 AATTATATACATAAATTAAA-GAAAACAGTAAAGCCATTTTTCTAGAATAAACGCATTCACTAAC
*
21404125 TATCTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAAAG
317 TATCTTAAAATTTAAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAAAG
*
21404177 TTTTTAATAATCTCAAATATTTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCT
1 CTTTTAATAATCTCAAATATTTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCT
* * *
21404242 TCAATAATTATATATAAAATTTAAAAAAAATCAGTGAAGGTATTTTTTTAGAATAAATGCCTTCA
66 TCAATAATTATGTA-AAAATTTAAAAAGAATCAGTGAAGGTATTTTTTTAGAATAAAAGCCTTCA
*
21404307 CTAACCATCTTAAAATTTGAATAGT-AGAAGA-T-A-TTTTTCACT-GAAAGATGCCTTTAATAA
130 CTAACCATCTTAAAATTTGAGTAGTGA-AAGATTAAGTTTTTCACTAGAAA-ATGCCTTTAATAA
* *
21404367 TCTCAAATATTTTTAAAAA-AAATTATTGAAGGCGTTTGTTCTAAAAAAATACCTTCAATAATTA
193 TCTCAAATATTTTTAAAAAGAAATTATTGAAGGCATTTATTCTAAAAAAATACCTTCAATAATTA
* * *
21404431 TGTACA-AAATTTAAA-AAGAACAGTGAAGCCATTTTTCTAGAATAAACGCCTTCACTAACTATC
258 TATACATAAA-TTAAAGAA-AACAGTAAAGCCATTTTTCTAGAATAAACGCATTCACTAACTATC
*
21404494 TTAAAATTTAAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAATG
321 TTAAAATTTAAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAAAG
* * * * * *
21404542 CCTTTAATAATCTTAAATTTTTTTTTAAAAAAATTATTTAATGCATTTGTTCTAAAAAAATACCT
1 CTTTTAATAATCTCAAATATTTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCT
* * ** * * *
21404607 TCAATAATTATGTACATATATTAAATGGAATCAATGAAGGTATTTTTTTAAAATAAACA-CATTC
66 TCAATAATTATGTAAAAAT-TTAAAAAGAATCAGTGAAGGTATTTTTTTAGAATAAA-AGCCTTC
21404671 ACTAACCAT-TTAAAAATTTGAGTAGTG
129 ACTAACCATCTT-AAAATTTGAGTAGTG
21404698 GAATATTGAA
Statistics
Matches: 462, Mismatches: 48, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
364 7 0.02
365 218 0.47
366 56 0.12
367 38 0.08
371 1 0.00
372 1 0.00
373 2 0.00
374 69 0.15
375 60 0.13
376 10 0.02
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (368 bp):
CTTTTAATAATCTCAAATATTTTTTAAAAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCT
TCAATAATTATGTAAAAATTTAAAAAGAATCAGTGAAGGTATTTTTTTAGAATAAAAGCCTTCAC
TAACCATCTTAAAATTTGAGTAGTGAAAGATTAAGTTTTTCACTAGAAAATGCCTTTAATAATCT
CAAATATTTTTAAAAAGAAATTATTGAAGGCATTTATTCTAAAAAAATACCTTCAATAATTATAT
ACATAAATTAAAGAAAACAGTAAAGCCATTTTTCTAGAATAAACGCATTCACTAACTATCTTAAA
ATTTAAGTAGTGAAATATTGAAGGTATTTTTCACTGAAAAAAG
Found at i:21422913 original size:21 final size:21
Alignment explanation
Indices: 21422858--21422901 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
21422848 GTTAACTTCT
*
21422858 AAAATCAAGTAAATATAATTG
1 AAAATCAAATAAATATAATTG
21422879 AAAATCAAATAAATATAATTG
1 AAAATCAAATAAATATAATTG
21422900 AA
1 AA
21422902 TTATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAATCAAATAAATATAATTG
Found at i:21423929 original size:16 final size:16
Alignment explanation
Indices: 21423853--21423939 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
21423843 TCATGTCATA
*
21423853 AGTTTGAATTAATTTG
1 AGTTTGAATCAATTTG
* *
21423869 AATTTGGATCAATTTG
1 AGTTTGAATCAATTTG
* *
21423885 A-TTTAAATCAATTTT
1 AGTTTGAATCAATTTG
* * * *
21423900 AGTTGGAGTTAATTTC
1 AGTTTGAATCAATTTG
21423916 AGTTTGAATCAATTTG
1 AGTTTGAATCAATTTG
21423932 A-TTTGAAT
1 AGTTTGAAT
21423940 GAGGTTAGGT
Statistics
Matches: 55, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
15 19 0.35
16 36 0.65
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (16 bp):
AGTTTGAATCAATTTG
Found at i:21427152 original size:2 final size:2
Alignment explanation
Indices: 21427141--21427191 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
21427131 GGATGGGTTG
21427141 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
21427182 CT GT CT CT CT
1 CT CT CT CT CT
21427192 GTCAAAATCT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
CT
Found at i:21429982 original size:62 final size:62
Alignment explanation
Indices: 21429908--21430028 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 62
21429898 AAAAAGAAAA
* *
21429908 GAAAAAATCTGTAAGGGTTTCTATGCTTGAAGTATTACCCACTTCTTGGAAATCTACGGCTT
1 GAAAAAACCTGTAAGGGTTTCTATGCTTGAAATATTACCCACTTCTTGGAAATCTACGGCTT
*
21429970 GAAAAAACCTGTAAGGGTTTCTATGCTTGAAATATTACCCACTTGTTGGAAATCTACGG
1 GAAAAAACCTGTAAGGGTTTCTATGCTTGAAATATTACCCACTTCTTGGAAATCTACGG
21430029 GCTTTCTCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (62 bp):
GAAAAAACCTGTAAGGGTTTCTATGCTTGAAATATTACCCACTTCTTGGAAATCTACGGCTT
Found at i:21446514 original size:23 final size:25
Alignment explanation
Indices: 21446483--21446530 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21446473 GTGATGTTTA
21446483 TTTAAAATA-TAT-TAAAAATTATT
1 TTTAAAATATTATATAAAAATTATT
* *
21446506 TTTATAATATTTTATAAAAATTATT
1 TTTAAAATATTATATAAAAATTATT
21446531 ATATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 2 0.10
25 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAAAATATTATATAAAAATTATT
Found at i:21447921 original size:25 final size:23
Alignment explanation
Indices: 21447893--21447951 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
21447883 GAAATTAACA
21447893 TAAATATAACAAAAATTTATAATAT
1 TAAATA-AACAAAAATTTA-AATAT
* *
21447918 TAAATGCATCAAAAATTTAAATAT
1 TAAAT-AAACAAAAATTTAAATAT
*
21447942 CAAATAAACA
1 TAAATAAACA
21447952 CAAACACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 3 0.11
24 9 0.32
25 16 0.57
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAATAAACAAAAATTTAAATAT
Found at i:21447955 original size:25 final size:24
Alignment explanation
Indices: 21447901--21447947 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21447891 CATAAATATA
* *
21447901 ACAAAAATTTATAATATTAAATGC
1 ACAAAAATTTATAATATCAAATAC
21447925 ATCAAAAATTTA-AATATCAAATA
1 A-CAAAAATTTATAATATCAAATA
21447948 AACACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
ACAAAAATTTATAATATCAAATAC
Found at i:21448319 original size:24 final size:24
Alignment explanation
Indices: 21448292--21448338 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
21448282 CTAATTTTTA
*
21448292 AATTTTATTATATTATATCTCTAT
1 AATTTTATTAGATTATATCTCTAT
* *
21448316 AATTTTGTTAGGTTATATCTCTA
1 AATTTTATTAGATTATATCTCTA
21448339 CAACATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (24 bp):
AATTTTATTAGATTATATCTCTAT
Found at i:21449211 original size:10 final size:9
Alignment explanation
Indices: 21449173--21449243 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
21449163 TTAATATAAC
21449173 TATTAAAA-
1 TATTAAAAT
21449181 TATTAAAAAT
1 TATT-AAAAT
*
21449191 TATT--TAT
1 TATTAAAAT
21449198 TATTAAAAT
1 TATTAAAAT
*
21449207 ATATTTAAAT
1 -TATTAAAAT
*
21449217 TATT--TAT
1 TATTAAAAT
21449224 TATTAAAAT
1 TATTAAAAT
*
21449233 TATTAATAT
1 TATTAAAAT
21449242 TA
1 TA
21449244 AAAAATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
7 12 0.24
8 4 0.08
9 22 0.44
10 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TATTAAAAT
Done.