Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 19 of 91
Found at i:3296052 original size:3 final size:3
Alignment explanation
Indices: 3296033--3296139 Score: 76
Period size: 3 Copynumber: 39.3 Consensus size: 3
3296023 AATCAGACCC
*
3296033 TAT T-T TAT TAT TTT TAT TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3296075 TA- TAT TA- TAT TA- TAT TAT TAT TAG TAT TAG TA- TAT TAT ATAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
3296117 TAT TA- TAT CA- TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3296140 TTTTTTTTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
2 23 0.28
3 57 0.70
4 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3296055 original size:5 final size:5
Alignment explanation
Indices: 3296033--3296138 Score: 112
Period size: 5 Copynumber: 21.2 Consensus size: 5
3296023 AATCAGACCC
* *
3296033 TATTT TATTA T-TTT TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* *
3296082 TATTA TATTA TTATTA GTA-T- TAGTA TATTA TA-TA GTATTA TATCA
1 TATTA TATTA -TATTA -TATTA TATTA TATTA TATTA -TATTA TATTA
3296127 TATTA TTATTA T
1 TATTA -TATTA T
3296139 TTTTTTTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
3 2 0.02
4 6 0.07
5 65 0.75
6 14 0.16
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:3301020 original size:102 final size:102
Alignment explanation
Indices: 3300844--3301048 Score: 392
Period size: 102 Copynumber: 2.0 Consensus size: 102
3300834 CCATATTATA
3300844 GCTAAAGTCCTCATCGACAATGGCTCTACTATTAACATCATACCAATGTCAACTTTGGCAAAGCT
1 GCTAAAGTCCTCATCGACAATGGCTCTACTATTAACATCATACCAATGTCAACTTTGGCAAAGCT
3300909 ACCTATTAATTATTCATATATGCAGAGTAGGCATATG
66 ACCTATTAATTATTCATATATGCAGAGTAGGCATATG
* *
3300946 GCTAAGGTCCTCATCGACAATGGCTCTACTATTAACATCATACCGATGTCAACTTTGGCAAAGCT
1 GCTAAAGTCCTCATCGACAATGGCTCTACTATTAACATCATACCAATGTCAACTTTGGCAAAGCT
3301011 ACCTATTAATTATTCATATATGCAGAGTAGGCATATG
66 ACCTATTAATTATTCATATATGCAGAGTAGGCATATG
3301048 G
1 G
3301049 TCATCCAAAG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (102 bp):
GCTAAAGTCCTCATCGACAATGGCTCTACTATTAACATCATACCAATGTCAACTTTGGCAAAGCT
ACCTATTAATTATTCATATATGCAGAGTAGGCATATG
Found at i:3305771 original size:33 final size:33
Alignment explanation
Indices: 3305710--3305774 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3305700 TTGACATTTG
* **
3305710 CATAGCATGCATTACATTTTTGAATGTTTAGTA
1 CATAGCATACATTACATTTAAGAATGTTTAGTA
* *
3305743 CATAGCATACATTGCATTTAAGAGTGTTTAGT
1 CATAGCATACATTACATTTAAGAATGTTTAGT
3305775 GCATGAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (33 bp):
CATAGCATACATTACATTTAAGAATGTTTAGTA
Found at i:3306132 original size:36 final size:40
Alignment explanation
Indices: 3306068--3306177 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 40
3306058 TAGCATTCTA
* * * * *
3306068 TATTTTTCAAAAGTCGTTAAACCACTATTTAGAA-AACC-
1 TATTATTCAAAAGTCATTGAGCCTCTATTTAGAAGAACCT
* *
3306106 T-TTA-TCAAAAGTCATTGAGCCTCTATTTGGAAGAGCCT
1 TATTATTCAAAAGTCATTGAGCCTCTATTTAGAAGAACCT
*
3306144 TAATTATTTCAAAAGTCATTGAGCCTCTGTTTAG
1 T-ATTA-TTCAAAAGTCATTGAGCCTCTATTTAG
3306178 GGGAATATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
36 23 0.40
37 5 0.09
38 2 0.04
40 3 0.05
42 24 0.42
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (40 bp):
TATTATTCAAAAGTCATTGAGCCTCTATTTAGAAGAACCT
Found at i:3306213 original size:43 final size:43
Alignment explanation
Indices: 3306113--3306268 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
3306103 ACCTTTATCA
* * * ** *
3306113 AAAGTCATTGAGCCTCTATTTGGAAGAGCCTTAATTA--TTTC
1 AAAGTCATTGAGCCTCTGTTTAGAGGAGATTTATTTATTTTTC
* *
3306154 AAAAGTCATTGAGCCTCTGTTTAGGGGA-ATATTTTTTATTTTTC
1 -AAAGTCATTGAGCCTCTGTTTAGAGGAGAT-TTATTTATTTTTC
* * *
3306198 AAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTC
1 AAAGTCATTGAGCCTCTGTTTAGAGGAGATTTATTTATTTTTC
*
3306241 AAAGTCACTGAGCCTCTGTTTAGAGGAG
1 AAAGTCATTGAGCCTCTGTTTAGAGGAG
3306269 TTTTTATGTT
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 28 0.30
43 61 0.65
44 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (43 bp):
AAAGTCATTGAGCCTCTGTTTAGAGGAGATTTATTTATTTTTC
Found at i:3306284 original size:85 final size:85
Alignment explanation
Indices: 3306113--3306285 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 85
3306103 ACCTTTATCA
* *
3306113 AAAGTCATTGAGCCTCTATTTGGAAGAGCCTTAATTATTTCAAAAGTCATTGAGCCTCTGTTTAG
1 AAAGTCATTGAGCCTCTATTTAGAAGAGCCTTAATTATTTCAAAAGTCACTGAGCCTCTGTTTAG
* * *
3306178 GGGAATATTTTTTATTTTTC
66 AGGAATATTTTATATTATTC
* * * *
3306198 AAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTC-AAAGTCACTGAGCCTCTGTTT
1 AAAGTCATTGAGCCTCTATTTAGAAGAGCCTTAATTA--TTTCAAAAGTCACTGAGCCTCTGTTT
* *
3306262 AGAGGAGT-TTTTATGTTATTC
64 AGAGGAATATTTTATATTATTC
3306283 AAA
1 AAA
3306286 AGGTTTGAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
85 45 0.60
86 26 0.35
87 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (85 bp):
AAAGTCATTGAGCCTCTATTTAGAAGAGCCTTAATTATTTCAAAAGTCACTGAGCCTCTGTTTAG
AGGAATATTTTATATTATTC
Found at i:3306464 original size:12 final size:12
Alignment explanation
Indices: 3306447--3306472 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3306437 TGTTTTTGTT
3306447 AATAAAAAATAA
1 AATAAAAAATAA
3306459 AATAAAAAATAA
1 AATAAAAAATAA
3306471 AA
1 AA
3306473 AAGGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:3307215 original size:17 final size:17
Alignment explanation
Indices: 3307195--3307228 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3307185 CCTATTTTGG
3307195 TATTT-TTTAATTTTATT
1 TATTTATTT-ATTTTATT
3307212 TATTTATTTATTTTATT
1 TATTTATTTATTTTATT
3307229 AAGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTATTTATTTTATT
Found at i:3310991 original size:19 final size:19
Alignment explanation
Indices: 3310946--3310994 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3310936 AAAATTTTTT
*
3310946 TAATTTTAAAATTCTAAAA
1 TAATTTCAAAATTCTAAAA
*
3310965 -ATTATTCAAAATTCTAAAA
1 TAAT-TTCAAAATTCTAAAA
3310984 TAATTTCAAAA
1 TAATTTCAAAA
3310995 AATGTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTTCAAAATTCTAAAA
Found at i:3311064 original size:11 final size:10
Alignment explanation
Indices: 3310853--3311099 Score: 101
Period size: 10 Copynumber: 25.5 Consensus size: 10
3310843 AAATACAAAA
*
3310853 TTAAAAATTT
1 TTAAAAAATT
*
3310863 TTAAGAAATT
1 TTAAAAAATT
3310873 CTT-AAAAA-T
1 -TTAAAAAATT
*
3310882 TTCAAAAATT
1 TTAAAAAATT
*
3310892 TTCTAAAAATT
1 TT-AAAAAATT
*
3310903 CTAAAAAATT
1 TTAAAAAATT
3310913 TTAAAAGAATT
1 TTAAAA-AATT
*
3310924 TCAAAAAA--
1 TTAAAAAATT
*
3310932 TTATAAAATT
1 TTAAAAAATT
***
3310942 TT-TTTAATT
1 TTAAAAAATT
3310951 TT--AAAATT
1 TTAAAAAATT
*
3310959 CT-AAAAATT
1 TTAAAAAATT
*
3310968 ATT-CAAAATT
1 -TTAAAAAATT
*
3310978 CTAAAATAATT
1 TTAAAA-AATT
*
3310989 TCAAAAAATGT
1 TTAAAAAAT-T
3311000 TT-AAAAA-T
1 TTAAAAAATT
**
3311008 TCCAAAAATT
1 TTAAAAAATT
*
3311018 TTTAAAAATT
1 TTAAAAAATT
** **
3311028 CCCAAAAAAAA
1 -TTAAAAAATT
3311039 TT-AAAAATT
1 TTAAAAAATT
* *
3311048 CTAAAAACTT
1 TTAAAAAATT
3311058 TTAAAAAATT
1 TTAAAAAATT
3311068 TT-AAAAA--
1 TTAAAAAATT
3311075 TTAAAAAATT
1 TTAAAAAATT
* *
3311085 CTAGAAAATT
1 TTAAAAAATT
3311095 TTAAA
1 TTAAA
3311100 TTTTCAAAAA
Statistics
Matches: 176, Mismatches: 42, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
7 2 0.01
8 20 0.11
9 36 0.20
10 84 0.48
11 34 0.19
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:3311079 original size:27 final size:29
Alignment explanation
Indices: 3310854--3311099 Score: 114
Period size: 30 Copynumber: 8.5 Consensus size: 29
3310844 AATACAAAAT
* *
3310854 TAAAAATTTTTAAGAAATTCTTAAAAATT-
1 TAAAAAATTTTAA-AAATTCTAAAAAATTC
* *
3310883 TCAAAAATTTTCTAAAAATTCTAAAAAATTT
1 T-AAAAAATTT-TAAAAATTCTAAAAAATTC
* * *
3310914 TAAAAGAATTTCAAAAAAT-TATAAAATT-
1 TAAAA-AATTTTAAAAATTCTAAAAAATTC
**** *
3310942 TTTTTAATTTT-AAAATTCT-AAAAATTA
1 TAAAAAATTTTAAAAATTCTAAAAAATTC
** *
3310969 TTCAAAATTCTAAAATAATT-TCAAAAAATGT-
1 TAAAAAATT-TTAAA-AATTCT-AAAAAAT-TC
* ** * *
3311000 TTAAAAATTCCAAAAATTTTTAAAAATTCC
1 TAAAAAATTTTAAAAATTCTAAAAAATT-C
* ** * *
3311030 CAAAAAAAATTAAAAATTCTAAAAACTTT
1 TAAAAAATTTTAAAAATTCTAAAAAATTC
3311059 TAAAAAATTTTAAAAA-T-TAAAAAATTC
1 TAAAAAATTTTAAAAATTCTAAAAAATTC
*
3311086 TAGAAAATTTTAAA
1 TAAAAAATTTTAAA
3311100 TTTTCAAAAA
Statistics
Matches: 166, Mismatches: 36, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
26 11 0.07
27 33 0.20
28 4 0.02
29 35 0.21
30 60 0.36
31 22 0.13
32 1 0.01
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAAAAATTTTAAAAATTCTAAAAAATTC
Found at i:3312646 original size:9 final size:9
Alignment explanation
Indices: 3312566--3312664 Score: 69
Period size: 9 Copynumber: 10.6 Consensus size: 9
3312556 AACAATTTTT
*
3312566 TAAAAATTGT
1 TAAAAATT-C
*
3312576 TAAAAAATC
1 TAAAAATTC
3312585 TAAAAA-TC
1 TAAAAATTC
3312593 TACAAAA-TC
1 TA-AAAATTC
*
3312602 TACAAAATTA
1 TA-AAAATTC
*
3312612 AAAAAATT-
1 TAAAAATTC
3312620 TAAGAAATTC
1 TAA-AAATTC
3312630 TAAAAAATTC
1 T-AAAAATTC
*
3312640 TAAAAATTTTT
1 TAAAAA--TTC
3312651 TAAAAATTC
1 TAAAAATTC
3312660 TAAAA
1 TAAAA
3312665 TATTTTTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
8 6 0.08
9 42 0.56
10 17 0.23
11 10 0.13
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTC
Found at i:3312654 original size:21 final size:22
Alignment explanation
Indices: 3312630--3312677 Score: 82
Period size: 20 Copynumber: 2.3 Consensus size: 22
3312620 TAAGAAATTC
3312630 TAAAAAATTCTAAAA-ATTTTT
1 TAAAAAATTCTAAAATATTTTT
3312651 T-AAAAATTCTAAAATATTTTT
1 TAAAAAATTCTAAAATATTTTT
3312672 TAAAAA
1 TAAAAA
3312678 TTCAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.52
21 8 0.32
22 4 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAAATTCTAAAATATTTTT
Found at i:3312655 original size:20 final size:21
Alignment explanation
Indices: 3312632--3312680 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3312622 AGAAATTCTA
3312632 AAAAATTCTAAAA-ATTTTTT
1 AAAAATTCTAAAATATTTTTT
3312652 AAAAATTCTAAAATATTTTTT
1 AAAAATTCTAAAATATTTTTT
3312673 AAAAATTC
1 AAAAATTC
3312681 AAATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAATTCTAAAATATTTTTT
Found at i:3312698 original size:18 final size:17
Alignment explanation
Indices: 3312671--3312705 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
3312661 AAAATATTTT
3312671 TTAAAAATTCAAATAAA
1 TTAAAAATTCAAATAAA
3312688 TTAATAAATTCAAATAAA
1 TTAA-AAATTCAAATAAA
3312706 AAATCTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAAAATTCAAATAAA
Found at i:3312750 original size:10 final size:10
Alignment explanation
Indices: 3312731--3312796 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
3312721 TAGAAAGTTC
3312731 TAAAAGAATTA
1 TAAAA-AATTA
*
3312742 CAAAAAATTA
1 TAAAAAATTA
*
3312752 TTAAAAATTA
1 TAAAAAATTA
*
3312762 TTAAAAATTTA
1 -TAAAAAATTA
* *
3312773 AAAAAAATCA
1 TAAAAAATTA
*
3312783 -AAAAAATTT
1 TAAAAAATTA
3312792 TAAAA
1 TAAAA
3312797 CTTTTTTTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
9 7 0.16
10 24 0.56
11 12 0.28
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:3312767 original size:9 final size:10
Alignment explanation
Indices: 3312744--3312770 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3312734 AAGAATTACA
3312744 AAAAATTATT
1 AAAAATTATT
3312754 AAAAATTATT
1 AAAAATTATT
3312764 AAAAATT
1 AAAAATT
3312771 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAAATTATT
Found at i:3312908 original size:19 final size:18
Alignment explanation
Indices: 3312866--3312919 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
3312856 AAATTTTACA
3312866 TTTAAAAATT-AAAAAAT
1 TTTAAAAATTCAAAAAAT
*
3312883 TTCTAAAAATTCCATAAAAT
1 TT-TAAAAATT-CAAAAAAT
3312903 TTTAAAAATTCAAAAAA
1 TTTAAAAATTCAAAAAA
3312920 GACTTATGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 2 0.06
18 14 0.44
19 8 0.25
20 8 0.25
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAATTCAAAAAAT
Found at i:3313109 original size:19 final size:20
Alignment explanation
Indices: 3313087--3313139 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3313077 AAATCAAATC
3313087 AAAAATAAAAAAAATTTT-A
1 AAAAATAAAAAAAATTTTAA
* * *
3313106 AAAAATATAATAATTTTTAA
1 AAAAATAAAAAAAATTTTAA
3313126 AAAAATTAAAAAAA
1 AAAAA-TAAAAAAA
3313140 CTTCTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 15 0.56
20 6 0.22
21 6 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAAAAAAAATTTTAA
Found at i:3313227 original size:20 final size:20
Alignment explanation
Indices: 3313204--3313273 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
3313194 ATTTTTTTAA
3313204 TTTTGAAATTTTT-TTAAATT
1 TTTTG-AATTTTTATTAAATT
*
3313224 TTTTGAGTTTTTATTAAA-T
1 TTTTGAATTTTTATTAAATT
* *
3313243 TTTT-AAGTTTTTTTTAGATT
1 TTTTGAA-TTTTTATTAAATT
*
3313263 TTTTTAATTTT
1 TTTTGAATTTT
3313274 AAAGAATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.02
19 20 0.48
20 19 0.45
21 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTGAATTTTTATTAAATT
Found at i:3313263 original size:19 final size:19
Alignment explanation
Indices: 3313195--3313265 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
3313185 TATATATATA
* *
3313195 TTTTTTT-AATTTTGAA-A
1 TTTTTTTAAATTTTTAAGT
*
3313212 TTTTTTTAAATTTTTTGAGT
1 TTTTTTTAAA-TTTTTAAGT
*
3313232 TTTTATTAAATTTTTAAGT
1 TTTTTTTAAATTTTTAAGT
*
3313251 TTTTTTTAGATTTTT
1 TTTTTTTAAATTTTT
3313266 TTAATTTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 7 0.16
18 2 0.05
19 26 0.59
20 9 0.20
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATTTTTAAGT
Found at i:3313326 original size:28 final size:26
Alignment explanation
Indices: 3313283--3313335 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
3313273 TAAAGAATGT
*
3313283 TTCAAAATTTTGAAATTATTTAATTG
1 TTCAAAATTTTAAAATTATTTAATTG
*
3313309 TTCAAAATTTTTTAAAATTTTTTAATT
1 TTCAAAA--TTTTAAAATTATTTAATT
3313336 TTTTCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
28 16 0.70
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TTCAAAATTTTAAAATTATTTAATTG
Found at i:3313355 original size:26 final size:26
Alignment explanation
Indices: 3313326--3313375 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3313316 TTTTTTAAAA
3313326 TTTTTTAA-TTTTTTCT-TATTTTAAG
1 TTTTTTAAGTTTTTT-TATATTTTAAG
3313351 TTTTTTAAGTTTTTTTATATTTTAA
1 TTTTTTAAGTTTTTTTATATTTTAA
3313376 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTTTAAGTTTTTTTATATTTTAAG
Found at i:3313472 original size:20 final size:20
Alignment explanation
Indices: 3313426--3313463 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3313416 ATTTTTTTAT
3313426 TTTTTAAAAAGTTTTCAAAG
1 TTTTTAAAAAGTTTTCAAAG
3313446 TTTTTAAAAA-TTTTCAAA
1 TTTTTAAAAAGTTTTCAAA
3313464 TTATGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAGTTTTCAAAG
Found at i:3313529 original size:19 final size:20
Alignment explanation
Indices: 3313507--3313553 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3313497 TTATTTTTTT
3313507 ATTTTTTTACAAATTTT-AA
1 ATTTTTTTACAAATTTTCAA
*
3313526 ATTTTTTT-TAAATTTTCAA
1 ATTTTTTTACAAATTTTCAA
*
3313545 AATTTTTTA
1 ATTTTTTTA
3313554 GAATGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTTACAAATTTTCAA
Found at i:3313530 original size:18 final size:19
Alignment explanation
Indices: 3313509--3313553 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3313499 ATTTTTTTAT
3313509 TTTTTTACAAATTTT-AAA
1 TTTTTTACAAATTTTAAAA
**
3313527 TTTTTTTTAAATTTTCAAAA
1 TTTTTTACAAATTTT-AAAA
3313547 TTTTTTA
1 TTTTTTA
3313554 GAATGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTACAAATTTTAAAA
Found at i:3313531 original size:20 final size:19
Alignment explanation
Indices: 3313507--3313552 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3313497 TTATTTTTTT
*
3313507 ATTTTTTTACAAATTTT-AA
1 ATTTTTTT-TAAATTTTAAA
3313526 ATTTTTTTTAAATTTTCAAA
1 ATTTTTTTTAAATTTT-AAA
3313546 ATTTTTT
1 ATTTTTT
3313553 AGAATGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 8 0.33
20 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTTTAAATTTTAAA
Found at i:3313533 original size:10 final size:9
Alignment explanation
Indices: 3313529--3313601 Score: 65
Period size: 10 Copynumber: 7.6 Consensus size: 9
3313519 ATTTTAAATT
3313529 TTTTTTAAA
1 TTTTTTAAA
**
3313538 TTTTCAAAA
1 TTTTTTAAA
3313547 TTTTTTAGAA
1 TTTTTTA-AA
*
3313557 TGTTTTAGAA
1 TTTTTTA-AA
*
3313567 TTGTTTTGAA
1 TT-TTTTAAA
3313577 TTTTTTAGAA
1 TTTTTTA-AA
3313587 TTTTTTAAA
1 TTTTTTAAA
3313596 TCTTTT
1 T-TTTT
3313602 GAGAAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 19 0.37
10 29 0.56
11 4 0.08
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:3313568 original size:20 final size:20
Alignment explanation
Indices: 3313545--3313611 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
3313535 AAATTTTCAA
*
3313545 AATTTTTTAGAATGTTTTAG
1 AATTTTTTAGAATCTTTTAG
*
3313565 AATTGTTTT-GAATTTTTTAG
1 AATT-TTTTAGAATCTTTTAG
3313585 AATTTTTTA-AATCTTTTGAG
1 AATTTTTTAGAATCTTTT-AG
3313605 AAATTTT
1 -AATTTT
3313612 AAAAACTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.27
20 20 0.49
21 10 0.24
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (20 bp):
AATTTTTTAGAATCTTTTAG
Found at i:3313620 original size:20 final size:20
Alignment explanation
Indices: 3313578--3313621 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3313568 TGTTTTGAAT
* * * *
3313578 TTTTTAGAATTTTTTAAATC
1 TTTTGAGAAATTTTAAAAAC
3313598 TTTTGAGAAATTTTAAAAAC
1 TTTTGAGAAATTTTAAAAAC
3313618 TTTT
1 TTTT
3313622 TCAATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTGAGAAATTTTAAAAAC
Found at i:3313702 original size:10 final size:10
Alignment explanation
Indices: 3313677--3313774 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 10
3313667 TGAAATTAAA
3313677 AATTTTTT-T
1 AATTTTTTAT
3313686 AAGTTTTTTCAT
1 AA-TTTTTT-AT
3313698 -ATTTTTTAT
1 AATTTTTTAT
*
3313707 AATTTTTTAG
1 AATTTTTTAT
*
3313717 AATAATTTTA-
1 AAT-TTTTTAT
*
3313727 AATTTTTTTT
1 AATTTTTTAT
*
3313737 AAAGTTTTTA-
1 -AATTTTTTAT
* *
3313747 AATGTTTTAG
1 AATTTTTTAT
* * *
3313757 AAATTTGTAA
1 AATTTTTTAT
3313767 AATTTTTT
1 AATTTTTT
3313775 GAATTTTCAA
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
9 15 0.22
10 38 0.57
11 13 0.19
12 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:3313774 original size:20 final size:19
Alignment explanation
Indices: 3313701--3313786 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 19
3313691 TTTTCATATT
*
3313701 TTTTATAATTTTTTAGAATAA
1 TTTTAAAATTTTTTAG-A-AA
* *
3313722 TTTTAAATTTTTTTTA-AAG
1 TTTTAAA-ATTTTTTAGAAA
* *
3313741 TTTTTAAATGTTTTAGAAA
1 TTTTAAAATTTTTTAGAAA
3313760 TTTGTAAAATTTTTT-G-AA
1 TTT-TAAAATTTTTTAGAAA
3313778 TTTTCAAAA
1 TTTT-AAAA
3313787 AAAAAATTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
17 1 0.02
18 15 0.29
19 13 0.25
20 10 0.19
21 6 0.12
22 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTAAAATTTTTTAGAAA
Found at i:3327581 original size:17 final size:18
Alignment explanation
Indices: 3327550--3327585 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3327540 GAGATAAAAA
3327550 TATTTTTATAATTTAATT
1 TATTTTTATAATTTAATT
*
3327568 TATTTTT-TATTTTAATT
1 TATTTTTATAATTTAATT
3327585 T
1 T
3327586 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTATAATTTAATT
Found at i:3328151 original size:47 final size:47
Alignment explanation
Indices: 3328082--3328176 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
3328072 TATGTGTAAG
3328082 TACTGTAAAATTGTGCCACTGTTTTTGCTATTTAAGACTCATTTGGA
1 TACTGTAAAATTGTGCCACTGTTTTTGCTATTTAAGACTCATTTGGA
*
3328129 TACTGTAAAATTGTGTCACTGTTTTTGCTATTTAAGACTCATTTGGA
1 TACTGTAAAATTGTGCCACTGTTTTTGCTATTTAAGACTCATTTGGA
3328176 T
1 T
3328177 TCAGACAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (47 bp):
TACTGTAAAATTGTGCCACTGTTTTTGCTATTTAAGACTCATTTGGA
Found at i:3331135 original size:2 final size:2
Alignment explanation
Indices: 3331128--3331152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3331118 CTGCAGATTA
3331128 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3331153 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3333512 original size:18 final size:18
Alignment explanation
Indices: 3333491--3333526 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3333481 TATTATAATA
*
3333491 ATTAATATTATTTTTATT
1 ATTAATATTAATTTTATT
*
3333509 ATTAATTTTAATTTTATT
1 ATTAATATTAATTTTATT
3333527 GAAACAAATC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTAATATTAATTTTATT
Found at i:3336883 original size:20 final size:18
Alignment explanation
Indices: 3336839--3336884 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
3336829 GTCATAATGC
3336839 AAATATT-ATTTTCTATA
1 AAATATTAATTTTCTATA
*
3336856 AAAAATTAATTTTCTATTCA
1 AAATATTAATTTTCTA-T-A
3336876 AAATATTAA
1 AAATATTAA
3336885 ATATATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 8 0.33
19 1 0.04
20 9 0.38
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATTAATTTTCTATA
Found at i:3337120 original size:22 final size:21
Alignment explanation
Indices: 3337078--3337127 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
3337068 AAAAATTAAG
*
3337078 TTAAAAATTCAAAATCCTTTT
1 TTAAAAATTCAAAATCATTTT
* *
3337099 TTAAAAAGTTCCATATCA--TT
1 TTAAAAA-TTCAAAATCATTTT
3337119 TTAAAAATT
1 TTAAAAATT
3337128 AAGTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 9 0.36
21 7 0.28
22 7 0.28
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAATTCAAAATCATTTT
Found at i:3337146 original size:31 final size:31
Alignment explanation
Indices: 3337100--3337208 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
3337090 AATCCTTTTT
* * *
3337100 TAAAAAGTTCCATATCATTTTAAAAATTAAG
1 TAAAAATTTTCATATCGTTTTAAAAATTAAG
* *
3337131 TAAAAATTTTTATATCGTTTTAAAAAATTAAA
1 TAAAAATTTTCATATCGTTTT-AAAAATTAAG
* * *
3337163 TAAAAATCTTCATATTGTTTTAAATATTAAG
1 TAAAAATTTTCATATCGTTTTAAAAATTAAG
* *
3337194 CAAATATTTTCATAT
1 TAAAAATTTTCATAT
3337209 TTAAAAAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 37 0.58
32 27 0.42
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
TAAAAATTTTCATATCGTTTTAAAAATTAAG
Found at i:3337209 original size:31 final size:31
Alignment explanation
Indices: 3337117--3337209 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 31
3337107 TTCCATATCA
* *
3337117 TTTTAAAAATTAAGTAAAAATTTTTATATCG
1 TTTTAAAAATTAAGTAAAAATTTTCATATTG
* *
3337148 TTTTAAAAAATTAAATAAAAATCTTCATATTG
1 TTTT-AAAAATTAAGTAAAAATTTTCATATTG
* * *
3337180 TTTTAAATATTAAGCAAATATTTTCATATT
1 TTTTAAAAATTAAGTAAAAATTTTCATATT
3337210 TAAAAAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 25 0.48
32 27 0.52
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (31 bp):
TTTTAAAAATTAAGTAAAAATTTTCATATTG
Found at i:3337329 original size:23 final size:24
Alignment explanation
Indices: 3337285--3337329 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3337275 TATTTTTTAT
* *
3337285 TAAAAATTTTATTTTTATACAAAA
1 TAAAAATATTATTTTCATACAAAA
3337309 TAAAAATATTATTTTCA-ACAA
1 TAAAAATATTATTTTCATACAA
3337330 TTCGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAATATTATTTTCATACAAAA
Found at i:3337826 original size:16 final size:16
Alignment explanation
Indices: 3337807--3337837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3337797 AAATTAGATA
*
3337807 TTTAATTAAAGATTTT
1 TTTAATTAAAAATTTT
3337823 TTTAATTAAAAATTT
1 TTTAATTAAAAATTT
3337838 AAATAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAATTAAAAATTTT
Found at i:3341692 original size:21 final size:21
Alignment explanation
Indices: 3341667--3341716 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
3341657 GGGTTTAGGA
3341667 TTTGGATTTTTTTGATGGAAT
1 TTTGGATTTTTTTGATGGAAT
*
3341688 TTTGGA-TTTTTTGATGGGAT
1 TTTGGATTTTTTTGATGGAAT
3341708 TTTGGATTT
1 TTTGGATTT
3341717 GTTGTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (21 bp):
TTTGGATTTTTTTGATGGAAT
Found at i:3344565 original size:2 final size:2
Alignment explanation
Indices: 3344558--3344599 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3344548 ATTTCGGTAC
* * *
3344558 AT AT AT AT AT AT AT AT AT GT AT AT AT AT GT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3344600 GTAGGTATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3348589 original size:22 final size:22
Alignment explanation
Indices: 3348564--3348610 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3348554 ATTAGTTTAA
3348564 GTTAGTTTGATATTTGAATTAG
1 GTTAGTTTGATATTTGAATTAG
*
3348586 GTTAGTTTTATATTTGAATTAG
1 GTTAGTTTGATATTTGAATTAG
3348608 GTT
1 GTT
3348611 CTTGGCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (22 bp):
GTTAGTTTGATATTTGAATTAG
Found at i:3355598 original size:85 final size:86
Alignment explanation
Indices: 3355454--3355622 Score: 259
Period size: 85 Copynumber: 2.0 Consensus size: 86
3355444 TGTACAATAC
* * * *
3355454 TTTTGTGTTTACGAGTTAAAGTTTTAACATAAAAAAATCGAAGTCAAAATTTTAACATAAGAAAG
1 TTTTGTATTTACGAGTCAAAATTTTAACAGAAAAAAATCGAAGTCAAAATTTTAACATAAGAAAG
* *
3355519 CCGAAGTATATATTTTATTAT
66 CAGAAGTATATATCTTATTAT
* *
3355540 TTTTGTATTTACGAGTCAAAATTTTAAC-GAAAAAAGTCGAAGTCAAAGTTTTAACATAAGAAAG
1 TTTTGTATTTACGAGTCAAAATTTTAACAGAAAAAAATCGAAGTCAAAATTTTAACATAAGAAAG
3355604 CAGAAGTATATATCTTATT
66 CAGAAGTATATATCTTATT
3355623 CGGTACAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 50 0.67
86 25 0.33
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.36
Consensus pattern (86 bp):
TTTTGTATTTACGAGTCAAAATTTTAACAGAAAAAAATCGAAGTCAAAATTTTAACATAAGAAAG
CAGAAGTATATATCTTATTAT
Found at i:3356511 original size:62 final size:62
Alignment explanation
Indices: 3356351--3356515 Score: 198
Period size: 62 Copynumber: 2.7 Consensus size: 62
3356341 TTTTGTGTAG
*
3356351 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATA----TTCTTTTGAAACTTTAATTTCAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTTTGAAACTTTAATTTCAA
* * * * *
3356409 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAACTCTTTTTTTTTTTTAAA-TTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCC-CAAAAA-TATTTTTTTTTTTGAAACTTTAATTTCAA
* *
3356471 GAAAAATTGATACTTTCAACTTTTTTCCAAAAATAGTTTTTTTTT
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTT
3356516 ATTTTATTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
57 6 0.07
58 25 0.28
59 1 0.01
61 10 0.11
62 34 0.38
63 14 0.16
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (62 bp):
GAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTTTGAAACTTTAATTTCAA
Found at i:3356562 original size:17 final size:16
Alignment explanation
Indices: 3356541--3356600 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
3356531 AGTAAAATAA
3356541 TAAAATAAAATAAAAG
1 TAAAATAAAATAAAAG
*
3356557 TGAAAATAAAAAAAAAG
1 T-AAAATAAAATAAAAG
*
3356574 TAAAAGAAAAATAAAA-
1 TAAAA-TAAAATAAAAG
3356590 TAAAGATAAAA
1 TAAA-ATAAAA
3356601 GAATATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 13 0.35
17 24 0.65
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (16 bp):
TAAAATAAAATAAAAG
Found at i:3356564 original size:22 final size:21
Alignment explanation
Indices: 3356539--3356603 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
3356529 AAAGTAAAAT
*
3356539 AATAAAATAAAATAAAAGTGAA
1 AATAAAATAAAATAAAAG-AAA
*
3356561 AATAAAAAAAAAGTAAAAGAAA
1 AATAAAATAAAA-TAAAAGAAA
3356583 AATAAAATAAAGATAAAAGAA
1 AATAAAATAAA-ATAAAAGAA
3356604 TATTAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 31 0.82
23 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (21 bp):
AATAAAATAAAATAAAAGAAA
Found at i:3356598 original size:6 final size:5
Alignment explanation
Indices: 3356539--3356614 Score: 62
Period size: 5 Copynumber: 14.2 Consensus size: 5
3356529 AAAGTAAAAT
* *
3356539 AATAA AATAA AATAA AAGTGAA AATAA AAAAA AAGTAA AAGAAA AATAA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA AA-TAA AA-TAA AATAA
* * *
3356588 AATAA AGATAA AAGAA TATTA AATAA A
1 AATAA A-ATAA AATAA AATAA AATAA A
3356615 CCTAATCTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 37 0.65
6 16 0.28
7 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:3357529 original size:21 final size:21
Alignment explanation
Indices: 3357496--3357554 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
3357486 AAAATAAATG
*
3357496 AAAATAAATCAGATAAATCAAA
1 AAAATTAA-CAGATAAATCAAA
*
3357518 AAAATTAACAGATAAATTAAA
1 AAAATTAACAGATAAATCAAA
3357539 ATTAAA-TAACAGATAA
1 A--AAATTAACAGATAA
3357555 TACATAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.39
22 17 0.52
23 3 0.09
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAATTAACAGATAAATCAAA
Found at i:3357551 original size:22 final size:21
Alignment explanation
Indices: 3357489--3357554 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
3357479 AAACAAAAAA
*
3357489 ATAAATGAAAATAAAT--CAG
1 ATAAATCAAAATAAATAACAG
3357508 ATAAATCAAAA-AAATTAACAG
1 ATAAATCAAAATAAA-TAACAG
*
3357529 ATAAATTAAAATTAAATAACAG
1 ATAAATCAAAA-TAAATAACAG
3357551 ATAA
1 ATAA
3357555 TACATAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
21 13 0.32
22 10 0.25
23 3 0.08
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (21 bp):
ATAAATCAAAATAAATAACAG
Found at i:3357677 original size:6 final size:5
Alignment explanation
Indices: 3357668--3357727 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 5
3357658 ATATATATAT
3357668 ATAACA ATAATA ATAATA A-AAA ATAAGA ATAAA ATAAAA ATAAA ATAAAA
1 ATAA-A ATAA-A ATAA-A ATAAA ATAA-A ATAAA AT-AAA ATAAA AT-AAA
3357718 ATAAA ATAAA
1 ATAAA ATAAA
3357728 GAAGAAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
4 2 0.04
5 20 0.41
6 27 0.55
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:3357692 original size:16 final size:15
Alignment explanation
Indices: 3357673--3357727 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 15
3357663 TATATATAAC
*
3357673 AATAATAATAATAAAA
1 AATAA-AATAAAAAAA
3357689 AATAAGAATAAAATAAA
1 AATAA-AATAAAA-AAA
3357706 AATAAAATAAAAATAA
1 AATAAAATAAAAA-AA
3357722 AATAAA
1 AATAAA
3357728 GAAGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 1 0.03
16 26 0.74
17 8 0.23
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AATAAAATAAAAAAA
Found at i:3357703 original size:11 final size:11
Alignment explanation
Indices: 3357645--3357740 Score: 79
Period size: 11 Copynumber: 8.5 Consensus size: 11
3357635 CCTAAGATAA
*
3357645 AAAAATAAAAG
1 AAAAATAAAAT
*
3357656 AAATATATATATAT
1 AAA-A-ATA-AAAT
*
3357670 AACAATAATAAT
1 AAAAATAA-AAT
*
3357682 AATAA-AAAAT
1 AAAAATAAAAT
*
3357692 AAGAATAAAAT
1 AAAAATAAAAT
3357703 AAAAATAAAAT
1 AAAAATAAAAT
3357714 AAAAATAAAAT
1 AAAAATAAAAT
*
3357725 AAAGAAGAAAA-
1 AAA-AATAAAAT
3357736 AAAAA
1 AAAAA
3357741 AGAACATAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
10 9 0.13
11 38 0.54
12 16 0.23
13 4 0.06
14 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3357863 original size:40 final size:40
Alignment explanation
Indices: 3357808--3357905 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
3357798 GGGTGTCTAC
*
3357808 AACATTAATAAAAGAAAAGAATTTACATTATATTT-GAATA
1 AACATTAATAAAAGAAAAGAACTTACATTATATTTAG-ATA
* ** *
3357848 AACATTAGTAAAAGAAAAGAACTTATGTTATGTTTAGATA
1 AACATTAATAAAAGAAAAGAACTTACATTATATTTAGATA
*
3357888 AAAATTAATAAAAGAAAA
1 AACATTAATAAAAGAAAA
3357906 TAAAGTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 49 0.98
41 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.30
Consensus pattern (40 bp):
AACATTAATAAAAGAAAAGAACTTACATTATATTTAGATA
Found at i:3358212 original size:22 final size:23
Alignment explanation
Indices: 3358184--3358228 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3358174 AAATGTTTAT
3358184 AAATATTAATTAAAGATA-ATAA
1 AAATATTAATTAAAGATATATAA
* *
3358206 AAATATTATTTAAATATATATAA
1 AAATATTAATTAAAGATATATAA
3358229 TGTATTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTAATTAAAGATATATAA
Found at i:3363361 original size:19 final size:20
Alignment explanation
Indices: 3363316--3363354 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3363306 CCGTTCAACC
3363316 AACTCTCCCTTCTCATTTTT
1 AACTCTCCCTTCTCATTTTT
3363336 AACTCTCCCTTCTC-TTTTT
1 AACTCTCCCTTCTCATTTTT
3363355 CTCTCTCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.13, C:0.36, G:0.00, T:0.51
Consensus pattern (20 bp):
AACTCTCCCTTCTCATTTTT
Found at i:3364972 original size:20 final size:21
Alignment explanation
Indices: 3364938--3364992 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
3364928 AAATAAAATA
3364938 ATAATAATAATAATAATAGTAA-
1 ATAA-AATAA-AATAATAGTAAG
* *
3364960 ATGAGATAAAAT-ATAGTAAG
1 ATAAAATAAAATAATAGTAAG
3364980 ATAAAATAAAATA
1 ATAAAATAAAATA
3364993 CTAATTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.26
20 13 0.48
21 4 0.15
22 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (21 bp):
ATAAAATAAAATAATAGTAAG
Found at i:3368702 original size:20 final size:20
Alignment explanation
Indices: 3368670--3368711 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3368660 TTAAAATTCA
3368670 AATATTAATATAA-AATATTT
1 AATATTAATATAATAA-ATTT
3368690 AATATTTAA-ATAATAAATTT
1 AATA-TTAATATAATAAATTT
3368710 AA
1 AA
3368712 AATACACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATTAATATAATAAATTT
Found at i:3369082 original size:19 final size:19
Alignment explanation
Indices: 3369058--3369100 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3369048 TATTTATATG
*
3369058 TATTTAATAA-ATTAATTTT
1 TATTTAATAATA-TAAATTT
3369077 TATTTAATAATATAAATTT
1 TATTTAATAATATAAATTT
3369096 TATTT
1 TATTT
3369101 TTGATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTAATAATATAAATTT
Found at i:3369931 original size:19 final size:19
Alignment explanation
Indices: 3369907--3369952 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3369897 CATTTCAACA
*
3369907 AAGAAAGTAGTGACAAAAG
1 AAGAAAGTAGTGACAAAAC
3369926 AAGAAAGTAGTGACAAAAC
1 AAGAAAGTAGTGACAAAAC
3369945 AAGAAAGT
1 AAGAAAGT
3369953 CAAGCTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.59, C:0.07, G:0.24, T:0.11
Consensus pattern (19 bp):
AAGAAAGTAGTGACAAAAC
Found at i:3372040 original size:2 final size:2
Alignment explanation
Indices: 3371991--3372025 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3371981 ACTTTTGTTA
*
3371991 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3372026 ATAGTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3372458 original size:13 final size:15
Alignment explanation
Indices: 3372412--3372459 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 15
3372402 AATTTTTAAA
*
3372412 ATTTAAATAT-TACT
1 ATTTAAATATATAAT
*
3372426 A-TAAAATATATAAT
1 ATTTAAATATATAAT
3372440 ATTTAAATA-ATAA-
1 ATTTAAATATATAAT
3372453 ATTTAAA
1 ATTTAAA
3372460 ATACACTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 14 0.48
14 9 0.31
15 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTAAATATATAAT
Found at i:3372461 original size:14 final size:16
Alignment explanation
Indices: 3372427--3372462 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
3372417 AATATTACTA
3372427 TAAAATATATAATATT
1 TAAAATATATAATATT
3372443 T-AAATA-ATAA-ATT
1 TAAAATATATAATATT
3372456 TAAAATA
1 TAAAATA
3372463 CACTTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 5 0.26
16 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATATATAATATT
Found at i:3373749 original size:24 final size:24
Alignment explanation
Indices: 3373703--3373749 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3373693 GTTAGAACCC
* **
3373703 AAGTGAAGGAGGAGCCTTTTTTGA
1 AAGTGAAGGAAGAGCCTGATTTGA
3373727 AAGTGAAGGAAGAGCCTGATTTG
1 AAGTGAAGGAAGAGCCTGATTTG
3373750 GGGATTGAAA
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:0.32, C:0.09, G:0.34, T:0.26
Consensus pattern (24 bp):
AAGTGAAGGAAGAGCCTGATTTGA
Found at i:3373872 original size:66 final size:65
Alignment explanation
Indices: 3373726--3373876 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 65
3373716 GCCTTTTTTG
* ** * *
3373726 AAAGTGAAGGAAGAGCCTGATTTGGGGATTGAAAGCACTGTTTTGATGAAAGAAAATAAGGAGAT
1 AAAGTGAA-GAAGAGCCTGATTTAGGGATTGAAAGCAAAGTTTTCATGAAAGAAAATAAAGAGAT
3373791 T
65 T
* *
3373792 AAACTGAAGAAAGAGCTTGATTTAGGGATTGAAAGCAAAGTTTTCATGAAAGAAAATAAAGAGAT
1 AAAGTGAAG-AAGAGCCTGATTTAGGGATTGAAAGCAAAGTTTTCATGAAAGAAAATAAAGAGAT
3373857 T
65 T
*
3373858 AAAGTAAATGAAGAGCCTG
1 AAAGTGAA-GAAGAGCCTG
3373877 GTTTGGGGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 71 0.97
67 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.23
Consensus pattern (65 bp):
AAAGTGAAGAAGAGCCTGATTTAGGGATTGAAAGCAAAGTTTTCATGAAAGAAAATAAAGAGATT
Found at i:3380919 original size:14 final size:14
Alignment explanation
Indices: 3380896--3380926 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3380886 ACTCACAAAC
*
3380896 AAAATGATAATAAT
1 AAAATAATAATAAT
3380910 AAAATAATAATAAT
1 AAAATAATAATAAT
3380924 AAA
1 AAA
3380927 TAAGATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:3380934 original size:26 final size:27
Alignment explanation
Indices: 3380905--3380978 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
3380895 CAAAATGATA
3380905 ATAATAA-AATAATAATAATAAATAAG
1 ATAATAACAATAATAATAATAAATAAG
* * * *
3380931 ATAA-AATATTAATTATAGTAAATAAG
1 ATAATAACAATAATAATAATAAATAAG
*
3380957 ATACATAACAATAATAAAAATA
1 ATA-ATAACAATAATAATAATA
3380979 TAACACTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 2 0.05
26 23 0.62
27 1 0.03
28 11 0.30
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (27 bp):
ATAATAACAATAATAATAATAAATAAG
Found at i:3383527 original size:21 final size:23
Alignment explanation
Indices: 3383503--3383554 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3383493 AAATACAAAT
*
3383503 AATAAAATTTAAAATAA-T-AAA
1 AATAAAATTTAAAAAAAGTAAAA
*
3383524 AATAATATTTTAAAAAAAGTAAAA
1 AATAA-AATTTAAAAAAAGTAAAA
3383548 AATAAAA
1 AATAAAA
3383555 AAATTTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 5 0.20
22 10 0.40
23 2 0.08
24 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAAATTTAAAAAAAGTAAAA
Found at i:3383815 original size:9 final size:9
Alignment explanation
Indices: 3383801--3383834 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3383791 CCAAATTAGA
3383801 TTTTTTTAT
1 TTTTTTTAT
3383810 TTTTTTTAT
1 TTTTTTTAT
**
3383819 TTTTTTCCT
1 TTTTTTTAT
3383828 TTTTTTT
1 TTTTTTT
3383835 CTCTTTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3384497 original size:9 final size:9
Alignment explanation
Indices: 3384470--3384504 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3384460 AGGTGCTAAT
*
3384470 AAAAGAAAG
1 AAAAAAAAG
3384479 AAAGAAAAAG
1 AAA-AAAAAG
3384489 AAAAAAAAG
1 AAAAAAAAG
3384498 AAAAAAA
1 AAAAAAA
3384505 TAATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3384880 original size:49 final size:49
Alignment explanation
Indices: 3384811--3385157 Score: 319
Period size: 49 Copynumber: 7.1 Consensus size: 49
3384801 TAACTTTTTA
* *
3384811 AAAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTTAACAACTTA
1 AAAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT
* *
3384860 AAAAAAATCATCTTGAAAAAGCT-TCTCTAAG-TGAAGGCTCAACAACTTT
1 AAAAAATTCATCTTGAAAAAGCTCT-TCTAAGCAG-AGGCTCAACAACTTT
* * * * * * * *
3384909 TAAAATTTCATCTTAAAAAAAACTCCTCTTAGCAGAAGCTCAATAACTTT
1 AAAAAATTCATCTT-GAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT
* * *
3384959 -AAAAATTCATCTTGAAAATGGCTCTTTTAAGCAGAGGTTCAACAACTTT
1 AAAAAATTCATCTTGAAAA-AGCTCTTCTAAGCAGAGGCTCAACAACTTT
* * *
3385008 AAATATTTCATCTTGAGAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTT
1 AAAAAATTCATCTTGA-AAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT
* * * * * * *
3385058 TAAGATTTCATCCTGAAAAAGCTCCTT-TGAGCAAAGGCTTAACAAC-TT
1 AAAAAATTCATCTTGAAAAAGCT-CTTCTAAGCAGAGGCTCAACAACTTT
* * * * *
3385106 AAAAAATTCATCTTGAATAAGGTTCCTCTAAGTAG-GGCTCAACAATTTT
1 AAAAAATTCATCTTGAA-AAAGCTCTTCTAAGCAGAGGCTCAACAACTTT
3385155 AAA
1 AAA
3385158 GATTCTCATT
Statistics
Matches: 237, Mismatches: 49, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
48 32 0.14
49 121 0.51
50 80 0.34
51 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (49 bp):
AAAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAACTTT
Found at i:3384957 original size:99 final size:98
Alignment explanation
Indices: 3384775--3385056 Score: 284
Period size: 99 Copynumber: 2.8 Consensus size: 98
3384765 TCTTGATAAT
* * * * *
3384775 AAAT-GCTCATCTAAGTAAAGGCTTAATAACTTTTTAAAAAAATTCATCTTGAAAAAGCTCTTCT
1 AAATAGCTCTTCTAAGTAAAGGCTCAACAAC-TTTT--AAAATTTCATCTTAAAAAAGCTCTTCT
* *
3384839 AAGCAGAGGCTTAACAACTTAAAAAAAATCATCTTGA
63 AAGCAGAGGCTCAATAACTT-AAAAAAATCATCTTGA
* * * *
3384876 AAA-AGCT-TCTCTAAGTGAAGGCTCAACAACTTTTAAAATTTCATCTTAAAAAAAACTCCTCTT
1 AAATAGCTCT-TCTAAGTAAAGGCTCAACAACTTTTAAAATTTCATCTT-AAAAAAGCTCTTCTA
* * *
3384939 AGCAGAAGCTCAATAACTTTAAAAATTCATCTTGA
64 AGCAGAGGCTCAATAACTTAAAAAAATCATCTTGA
* * * * * *
3384974 AAATGGCTCTTTTAAGCAGAGGTTCAACAAC-TTTAAATATTTCATCTTGAGAAAAGCTCTTCTA
1 AAATAGCTCTTCTAAGTAAAGGCTCAACAACTTTTAAA-ATTTCATCTT-AAAAAAGCTCTTCTA
3385038 AGCAGAGGCTCAATAACTT
64 AGCAGAGGCTCAATAACTT
3385057 TTAAGATTTC
Statistics
Matches: 149, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
98 35 0.23
99 85 0.57
100 5 0.03
101 24 0.16
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (98 bp):
AAATAGCTCTTCTAAGTAAAGGCTCAACAACTTTTAAAATTTCATCTTAAAAAAGCTCTTCTAAG
CAGAGGCTCAATAACTTAAAAAAATCATCTTGA
Found at i:3385057 original size:99 final size:96
Alignment explanation
Indices: 3384812--3385162 Score: 314
Period size: 99 Copynumber: 3.6 Consensus size: 96
3384802 AACTTTTTAA
* * * * *
3384812 AAAAATTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTTAACAACTTAAAAAAAATCATCTTGAA
1 AAAATTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAACTT-TAAAAATTCATCTTGAA
* * *
3384877 AAAGCT-TCTCTAAG-TGAAGGCTCAACAACTTTT
65 AAAGCTCT-TTTAAGCAG-AGGTTCAACAAC-TTT
* * * * *
3384910 AAAATTTCATCTTAAAAAAAACTCCTCTTAGCAGAAGCTCAATAACTTTAAAAATTCATCTTGAA
1 AAAATTTCATCTT-GAAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTTAAAAATTCATCTTGAA
*
3384975 AATGGCTCTTTTAAGCAGAGGTTCAACAACTTT
65 AA-AGCTCTTTTAAGCAGAGGTTCAACAACTTT
* * *
3385008 AAATATTTCATCTTGAGAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTTTAAGATTTCATCCTG
1 AAA-ATTTCATCTTGA-AAAAGCTCTTCTAAGCAGAGGCTCAATAAC-TTTAAAAATTCATCTTG
* * * *
3385073 AAAAAGCTCCTTTGAGCAAAGGCTT-AACAACTTA
63 AAAAAGCTCTTTTAAGCAGAGG-TTCAACAACTTT
* * * * * * * *
3385107 AAAAATTCATCTTGAATAAGGTTCCTCTAAGTAG-GGCTCAACAATTTTAAAGATTC
1 AAAATTTCATCTTGAA-AAAGCTCTTCTAAGCAGAGGCTCAATAACTTTAAAAATTC
3385163 TCATTTTTTC
Statistics
Matches: 207, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
96 8 0.04
97 10 0.05
98 60 0.29
99 107 0.52
100 22 0.11
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (96 bp):
AAAATTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAACTTTAAAAATTCATCTTGAAA
AAGCTCTTTTAAGCAGAGGTTCAACAACTTT
Found at i:3397611 original size:21 final size:21
Alignment explanation
Indices: 3397577--3397630 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
3397567 TAACATGCAT
* * **
3397577 AAATACTAATAATAAATTTTG
1 AAATAATAAAAATAAATTTAA
3397598 AAATAATAAAAAT-AATTTAA
1 AAATAATAAAAATAAATTTAA
3397618 AAATAA-AAAAATA
1 AAATAATAAAAATA
3397631 TTTATCTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
21 11 0.39
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAATAAAAATAAATTTAA
Found at i:3397633 original size:18 final size:20
Alignment explanation
Indices: 3397598--3397634 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3397588 ATAAATTTTG
3397598 AAATAATAAAAATAATTTAA
1 AAATAATAAAAATAATTTAA
3397618 AAATAA-AAAAAT-ATTTA
1 AAATAATAAAAATAATTTA
3397635 TCTGAATCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAATAAAAATAATTTAA
Found at i:3400449 original size:32 final size:32
Alignment explanation
Indices: 3400412--3400479 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3400402 CAAATTTAAA
*
3400412 TAAAATTATGAATTATTTAGAATCCTATCCTT
1 TAAAATTATGAATTATTTAGAATCCCATCCTT
3400444 TAAAATTATGAATTATTTAGAATCCCATCCTT
1 TAAAATTATGAATTATTTAGAATCCCATCCTT
3400476 TAAA
1 TAAA
3400480 TAAAATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (32 bp):
TAAAATTATGAATTATTTAGAATCCCATCCTT
Found at i:3400657 original size:41 final size:41
Alignment explanation
Indices: 3400581--3400663 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
3400571 AGTTCCGTAT
*
3400581 TTTAATTATATTTGAATAAATATTAATAGAAGAAAA-AAAA
1 TTTAATTATATTTGAATAAACATTAATAGAAGAAAAGAAAA
*
3400621 TTTACATTATATTTGAATAAACATTAGTA-AATGAAAAGAAAA
1 TTTA-ATTATATTTGAATAAACATTAATAGAA-GAAAAGAAAA
3400663 T
1 T
3400664 AAGTAAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 6 0.16
41 27 0.71
42 5 0.13
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (41 bp):
TTTAATTATATTTGAATAAACATTAATAGAAGAAAAGAAAA
Found at i:3404866 original size:10 final size:10
Alignment explanation
Indices: 3404838--3404869 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3404828 ATTTCGGTAC
*
3404838 ATATATATAT
1 ATATATATGT
3404848 ATATATATGT
1 ATATATATGT
3404858 ATATATATGT
1 ATATATATGT
3404868 AT
1 AT
3404870 GTATGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:3404870 original size:14 final size:14
Alignment explanation
Indices: 3404838--3404873 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3404828 ATTTCGGTAC
*
3404838 ATATATATATATAT
1 ATATGTATATATAT
3404852 ATATGTATATATAT
1 ATATGTATATATAT
*
3404866 GTATGTAT
1 ATATGTAT
3404874 GTGTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:3404944 original size:19 final size:18
Alignment explanation
Indices: 3404917--3404954 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3404907 TCAAACTAAA
*
3404917 TTTTTTAATTTTATTTAT
1 TTTTTTAATTTTATATAT
3404935 TTTTTATAATTTTATATAT
1 TTTTT-TAATTTTATATAT
3404954 T
1 T
3404955 ACAATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAATTTTATATAT
Found at i:3412488 original size:2 final size:2
Alignment explanation
Indices: 3412481--3412516 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3412471 GAGGTTGGTT
3412481 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3412517 CCCAATTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3414932 original size:36 final size:35
Alignment explanation
Indices: 3414867--3414940 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
3414857 CGACTCACAA
3414867 ATAAAATGATAATAATAATAATAATAGTAAATAAG
1 ATAAAATGATAATAATAATAATAATAGTAAATAAG
* *
3414902 ATAAAAT-ATAATAAAATATTAATTATAGTAAATAAG
1 ATAAAATGATAAT--AATAATAATAATAGTAAATAAG
3414938 ATA
1 ATA
3414941 CATAACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 5 0.14
35 7 0.20
36 23 0.66
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (35 bp):
ATAAAATGATAATAATAATAATAATAGTAAATAAG
Found at i:3414951 original size:36 final size:37
Alignment explanation
Indices: 3414875--3414959 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
3414865 AAATAAAATG
*
3414875 ATAATAATAATAATAATAGTAAATAAGATAAAATATA
1 ATAATAATAATAATAATAGTAAATAAGATAAAATACA
* * *
3414912 ATAA-AATATTAATTATAGTAAATAAGAT-ACATAACA
1 ATAATAATAATAATAATAGTAAATAAGATAAAAT-ACA
*
3414948 ATAATAAAAATA
1 ATAATAATAATA
3414960 TAACACTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.08
36 28 0.70
37 9 0.22
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (37 bp):
ATAATAATAATAATAATAGTAAATAAGATAAAATACA
Found at i:3417508 original size:21 final size:21
Alignment explanation
Indices: 3417484--3417524 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3417474 AAATACAAAT
*
3417484 AATAAAATTTAAAATAATAAA
1 AATAAAATTTAAAAAAATAAA
**
3417505 AATAGTATTTAAAAAAATAA
1 AATAAAATTTAAAAAAATAA
3417525 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAAAATTTAAAAAAATAAA
Found at i:3418894 original size:50 final size:50
Alignment explanation
Indices: 3418769--3419062 Score: 260
Period size: 49 Copynumber: 6.0 Consensus size: 50
3418759 TAACTTTTAA
* * *
3418769 AAAAAAATTCATCTTG-AAAAAGCTCTTCTAAGCAAAGGCTTAACAATTT
1 AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
* * * *
3418818 TAAAAATTTTATC-TAAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
1 AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
* * *
3418867 AAAAAAAATCATCTTGAAAAAAACTCATCTAAGCAGAGGCTCAACAACTT
1 AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
* ** * * * *
3418917 -TAAAAATTCATCTTGAAAATGGCTCTTCTAAGTAGAGGCTCAATAACTT
1 AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
* * * * * * *
3418966 TAAAGATTTCATCCTG--AAAAGCTCATCTGAGTAGAGACTTAACAACTT
1 AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
* * * ** *
3419014 -AAAAAATTCATATTGAATAAGGCTTC-TCTAAATAGAGGCTCAACAACTT
1 AAAAAAATTCATCTTGAAAAAAGC-TCATCTAAGCAGAGGCTTAACAACTT
3419063 TAAAGATTCT
Statistics
Matches: 196, Mismatches: 43, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
47 11 0.06
48 26 0.13
49 113 0.58
50 46 0.23
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (50 bp):
AAAAAAATTCATCTTGAAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
Found at i:3418947 original size:99 final size:97
Alignment explanation
Indices: 3418768--3419062 Score: 306
Period size: 99 Copynumber: 3.0 Consensus size: 97
3418758 ATAACTTTTA
* * * * *
3418768 AAAAAAAATTCATCTTGAAAAAGCTCTTCTAAGCAAAGGCTTAACAATTTTAAAAATTTTATCTA
1 AAAAAAAA-TCATCTTGAAAAAGCTCATCTAAGCAGAGGCTTAACAACTTTAAAAA-TTCATCTT
* * * * *
3418833 AAAAAAGCTCATCTAAGCAGAGGCTTAACAACTT
64 GAAAAGGCTCTTCTAAGTAGAGGCTCAACAACTT
* *
3418867 AAAAAAAATCATCTTGAAAAAAACTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTG
1 AAAAAAAATCATCTTG-AAAAAGCTCATCTAAGCAGAGGCTTAACAACTTTAAAAATTCATCTTG
*
3418932 AAAATGGCTCTTCTAAGTAGAGGCTCAATAACTT
65 AAAA-GGCTCTTCTAAGTAGAGGCTCAACAACTT
* * ** * * * * * *
3418966 TAAAGATTTCATCCTG-AAAAGCTCATCTGAGTAGAGACTTAACAACTTAAAAAATTCATATTGA
1 AAAAAAAATCATCTTGAAAAAGCTCATCTAAGCAGAGGCTTAACAACTTTAAAAATTCATCTTGA
*
3419030 ATAAGGCT-TCTCTAAATAGAGGCTCAACAACTT
66 A-AAGGCTCT-TCTAAGTAGAGGCTCAACAACTT
3419063 TAAAGATTCT
Statistics
Matches: 165, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
96 1 0.01
97 67 0.41
98 20 0.12
99 77 0.47
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (97 bp):
AAAAAAAATCATCTTGAAAAAGCTCATCTAAGCAGAGGCTTAACAACTTTAAAAATTCATCTTGA
AAAGGCTCTTCTAAGTAGAGGCTCAACAACTT
Found at i:3419030 original size:97 final size:98
Alignment explanation
Indices: 3418885--3419075 Score: 262
Period size: 97 Copynumber: 2.0 Consensus size: 98
3418875 TCATCTTGAA
* * *
3418885 AAAAACTCATCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAA-AATGGC-TCTTCTAA
1 AAAAACTCATCTAAGCAGAGACTCAACAACTTAAAAAATTCATATTGAATAA-GGCTTC-TCTAA
* *
3418948 GTAGAGGCTCAATAACTTTAAAGATT-TCATCCTG
64 ATAGAGGCTCAACAACTTTAAAGATTCTCATCCTG
* * * *
3418982 AAAAGCTCATCTGAGTAGAGACTTAACAACTTAAAAAATTCATATTGAATAAGGCTTCTCTAAAT
1 AAAAACTCATCTAAGCAGAGACTCAACAACTTAAAAAATTCATATTGAATAAGGCTTCTCTAAAT
3419047 AGAGGCTCAACAACTTTAAAGATTCTCAT
66 AGAGGCTCAACAACTTTAAAGATTCTCAT
3419076 TTTTTCTTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
97 74 0.90
98 8 0.10
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (98 bp):
AAAAACTCATCTAAGCAGAGACTCAACAACTTAAAAAATTCATATTGAATAAGGCTTCTCTAAAT
AGAGGCTCAACAACTTTAAAGATTCTCATCCTG
Found at i:3423405 original size:25 final size:26
Alignment explanation
Indices: 3423360--3423411 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
3423350 ATAACAATGG
* *
3423360 AATGGCAAGAAAATGATAAAA-GAAA
1 AATGGAAAGAAAATAATAAAATGAAA
3423385 AATGGAAAGAAAA-AATGAAAATGAAA
1 AATGGAAAGAAAATAAT-AAAATGAAA
3423411 A
1 A
3423412 CAATAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 16 0.70
26 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (26 bp):
AATGGAAAGAAAATAATAAAATGAAA
Found at i:3423423 original size:13 final size:13
Alignment explanation
Indices: 3423377--3423423 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
3423367 AGAAAATGAT
3423377 AAAAG-AAAAATG
1 AAAAGAAAAAATG
*
3423389 GAAAGAAAAAATG
1 AAAAGAAAAAATG
3423402 AAAATGAAAACAAT-
1 AAAA-GAAAA-AATG
3423416 AAAAGAAA
1 AAAAGAAA
3423424 TGCGGATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 4 0.13
13 14 0.47
14 9 0.30
15 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAGAAAAAATG
Found at i:3423423 original size:19 final size:19
Alignment explanation
Indices: 3423375--3423423 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3423365 CAAGAAAATG
* *
3423375 ATAAAAGAAAAATGGAAAGA
1 ATAAAAG-AAAATGAAAACA
3423395 A-AAAATGAAAATGAAAACA
1 ATAAAA-GAAAATGAAAACA
3423414 ATAAAAGAAA
1 ATAAAAGAAA
3423424 TGCGGATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.10
Consensus pattern (19 bp):
ATAAAAGAAAATGAAAACA
Found at i:3432156 original size:21 final size:21
Alignment explanation
Indices: 3432132--3432179 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3432122 TTTACAAAAA
*
3432132 TTTTTTTT-AGCA-GAGTTTT
1 TTTTTTTTGAACATGAGTTTT
*
3432151 TTTTTTTTGAATATGAGTTTT
1 TTTTTTTTGAACATGAGTTTT
3432172 TTTTTTTT
1 TTTTTTTT
3432180 TGCAGGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 15 0.60
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (21 bp):
TTTTTTTTGAACATGAGTTTT
Found at i:3434837 original size:20 final size:20
Alignment explanation
Indices: 3434805--3434846 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3434795 TTAAAATTCA
3434805 AATATTAATATAA-AATATTT
1 AATATTAATATAATAA-ATTT
3434825 AATATGTAA-ATAATAAATTT
1 AATAT-TAATATAATAAATTT
3434845 AA
1 AA
3434847 AATACACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATTAATATAATAAATTT
Found at i:3435202 original size:22 final size:23
Alignment explanation
Indices: 3435160--3435206 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3435150 TACCGATCCC
*
3435160 TATACATTTATATTATTTAATAA
1 TATAAATTTATATTATTTAATAA
3435183 TATAAATTT-TATT-TTATAATAA
1 TATAAATTTATATTATT-TAATAA
3435205 TA
1 TA
3435207 CGAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 12 0.55
23 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATAAATTTATATTATTTAATAA
Found at i:3436501 original size:33 final size:29
Alignment explanation
Indices: 3436461--3436522 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 29
3436451 AAATTTATTT
*
3436461 AATATAATTTATTTTATAAATCATCAAAAAATA
1 AATATAATTT-TATTA-AAAT-AT-AAAAAATA
3436494 AATATAATTTTATTAAAATATAAAAAATA
1 AATATAATTTTATTAAAATATAAAAAATA
3436523 GCATGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.29
30 2 0.07
31 4 0.14
32 4 0.14
33 10 0.36
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
AATATAATTTTATTAAAATATAAAAAATA
Found at i:3437609 original size:24 final size:24
Alignment explanation
Indices: 3437563--3437609 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3437553 GTTAAAACCC
* **
3437563 AAGTGAAGGAGGAGCCTTTTTTGA
1 AAGTGAAGGAAGAGCCTGGTTTGA
3437587 AAGTGAAGGAAGAGCCTGGTTTG
1 AAGTGAAGGAAGAGCCTGGTTTG
3437610 GGGATAGAAA
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:0.36, T:0.26
Consensus pattern (24 bp):
AAGTGAAGGAAGAGCCTGGTTTGA
Found at i:3437696 original size:66 final size:66
Alignment explanation
Indices: 3437590--3437744 Score: 211
Period size: 66 Copynumber: 2.3 Consensus size: 66
3437580 TTTTTGAAAG
* **
3437590 TGAAGGAAGAGCCTGGTTTGGGGATAGAAAGCACCGTTTTGATGAAAGAAAATAAGAAGATTAAA
1 TGAAGGAAGAGCCTGATTTGGGGATAGAAAGCAAAGTTTTGATGAAAGAAAATAAGAAGATTAAA
3437655 C
66 C
* * *
3437656 TGAAGGAAGAGTCTGATTTGGGGATTGAAAGCAAAGTTTTGATGAAAGAAAATAAGGAGATTAAA
1 TGAAGGAAGAGCCTGATTTGGGGATAGAAAGCAAAGTTTTGATGAAAGAAAATAAGAAGATTAAA
*
3437721 G
66 C
* * * *
3437722 TAAAGCAGGAGCCTGGTTTGGGG
1 TGAAGGAAGAGCCTGATTTGGGG
3437745 TTTGAGAGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.23
Consensus pattern (66 bp):
TGAAGGAAGAGCCTGATTTGGGGATAGAAAGCAAAGTTTTGATGAAAGAAAATAAGAAGATTAAA
C
Found at i:3439536 original size:19 final size:19
Alignment explanation
Indices: 3439509--3439573 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
3439499 CTATCTTTCA
*
3439509 GTTTTGGAAATCTAAGATG
1 GTTTGGGAAATCTAAGATG
***
3439528 GTTTGGGAATATCT-TTCT-
1 GTTTGGGAA-ATCTAAGATG
**
3439546 GTTTTCGAAATCTAAGATG
1 GTTTGGGAAATCTAAGATG
3439565 GTTTGGGAA
1 GTTTGGGAA
3439574 CTTATTAACA
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
17 4 0.12
18 8 0.25
19 16 0.50
20 4 0.12
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (19 bp):
GTTTGGGAAATCTAAGATG
Found at i:3439542 original size:37 final size:37
Alignment explanation
Indices: 3439500--3439573 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
3439490 TTTAAGCATC
*
3439500 TATCTTTCAGTTTTGGAAATCTAAGATGGTTTGGGAA
1 TATCTTTCAGTTTTCGAAATCTAAGATGGTTTGGGAA
*
3439537 TATCTTTCTGTTTTCGAAATCTAAGATGGTTTGGGAA
1 TATCTTTCAGTTTTCGAAATCTAAGATGGTTTGGGAA
3439574 CTTATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (37 bp):
TATCTTTCAGTTTTCGAAATCTAAGATGGTTTGGGAA
Found at i:3456419 original size:3 final size:3
Alignment explanation
Indices: 3456411--3456463 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3456401 GGTAATGAGC
3456411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3456459 TTA TT
1 TTA TT
3456464 TTGAAGGCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3457885 original size:2 final size:2
Alignment explanation
Indices: 3457878--3457907 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3457868 TATTTGTCTG
3457878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3457908 AAATCTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3468865 original size:15 final size:15
Alignment explanation
Indices: 3468845--3468878 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3468835 ATTCATTGGT
3468845 TAAATCA-ACAAAATA
1 TAAATCATA-AAAATA
3468860 TAAATCATAAAAATA
1 TAAATCATAAAAATA
3468875 TAAA
1 TAAA
3468879 ATAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAATCATAAAAATA
Found at i:3469960 original size:2 final size:2
Alignment explanation
Indices: 3469955--3469981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3469945 TTGTGGGTTT
3469955 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 T
3469982 TAGTGACATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3471981 original size:31 final size:31
Alignment explanation
Indices: 3471946--3472021 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
3471936 TACTCATACA
** *
3471946 AAATTTGAAATTTAATCATTGTACTGGCATG
1 AAATTTGAAATTTAATCATTACACTCGCATG
*
3471977 AAATTTGAAATTTAATCTTTACACTCGCATG
1 AAATTTGAAATTTAATCATTACACTCGCATG
*
3472008 CAATTTGAAATTTA
1 AAATTTGAAATTTA
3472022 CTCTCTCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
AAATTTGAAATTTAATCATTACACTCGCATG
Found at i:3472811 original size:19 final size:19
Alignment explanation
Indices: 3472787--3472823 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3472777 TATTCATTTA
*
3472787 TTGTTTATCTTTGATTTTT
1 TTGTTTATATTTGATTTTT
*
3472806 TTGTTTTTATTTGATTTT
1 TTGTTTATATTTGATTTT
3472824 ATCTTTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.03, G:0.11, T:0.76
Consensus pattern (19 bp):
TTGTTTATATTTGATTTTT
Found at i:3474547 original size:21 final size:21
Alignment explanation
Indices: 3474506--3474547 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3474496 TAGTCATATT
* *
3474506 ATTAATATGATATTATTAATA
1 ATTAATATGATATAATAAATA
3474527 ATTAATTAT-ATATAATAAATA
1 ATTAA-TATGATATAATAAATA
3474548 CTAATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAATATGATATAATAAATA
Found at i:3482585 original size:21 final size:21
Alignment explanation
Indices: 3482561--3482602 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3482551 TTTAATTGAA
*
3482561 TTTTTGCTTTAATTAAATGTG
1 TTTTTACTTTAATTAAATGTG
3482582 TTTTTACTTTAATTAAATGTG
1 TTTTTACTTTAATTAAATGTG
3482603 GACCATCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTTTACTTTAATTAAATGTG
Found at i:3483542 original size:31 final size:31
Alignment explanation
Indices: 3483500--3483561 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3483490 AAGCTAGCTA
3483500 GATTCACCCCCTTCCTTTCTTATCAAATAAT
1 GATTCACCCCCTTCCTTTCTTATCAAATAAT
*
3483531 GATTCAGCCCCTTCCTTTCTTATCAAATAAT
1 GATTCACCCCCTTCCTTTCTTATCAAATAAT
3483562 TGACAAGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.39
Consensus pattern (31 bp):
GATTCACCCCCTTCCTTTCTTATCAAATAAT
Found at i:3484439 original size:2 final size:2
Alignment explanation
Indices: 3484391--3484424 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3484381 TAGACATGTC
* *
3484391 AT AT AT AT AA AT AT CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3484425 CATCTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3486581 original size:31 final size:30
Alignment explanation
Indices: 3486497--3486581 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 30
3486487 AGATTAATAT
3486497 AATTATATAAAAAATAAAA-ATATTTTAGTAAA
1 AATTAT-T-AAAAATAAAATATATTTTA-TAAA
*
3486529 AATTATTAGAAAAT-AATTATATTTT-TACAA
1 AATTATTA-AAAATAAAATATATTTTATA-AA
*
3486559 ATTTATTAAAATATAAAATATAT
1 AATTATTAAAA-ATAAAATATAT
3486582 AGTATGGGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 5 0.11
30 14 0.31
31 20 0.44
32 6 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (30 bp):
AATTATTAAAAATAAAATATATTTTATAAA
Found at i:3487426 original size:4 final size:4
Alignment explanation
Indices: 3487405--3487466 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
3487395 CATAATTGTC
* * * * *
3487405 TATT TATT TTTT TGTT TATT TATT TGTT TATTT TATT TATT TGA-C TATG
1 TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT T-ATT TATT
3487454 TATT TATT TATT T
1 TATT TATT TATT T
3487467 GTAAATATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 1 0.02
4 41 0.87
5 5 0.11
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:3487439 original size:29 final size:29
Alignment explanation
Indices: 3487407--3487466 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
3487397 TAATTGTCTA
* ** * *
3487407 TTTATTTTTTTGTTTATTTATTTGTTTAT
1 TTTATTTATTTGACTATGTATTTATTTAT
3487436 TTTATTTATTTGACTATGTATTTATTTAT
1 TTTATTTATTTGACTATGTATTTATTTAT
3487465 TT
1 TT
3487467 GTAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (29 bp):
TTTATTTATTTGACTATGTATTTATTTAT
Found at i:3487441 original size:17 final size:17
Alignment explanation
Indices: 3487400--3487447 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3487390 TTTATCATAA
*
3487400 TTGTCTATTTATTT-TT
1 TTGTTTATTTATTTGTT
3487416 TTGTTTATTTATTTGTT
1 TTGTTTATTTATTTGTT
3487433 TAT-TTTATTTATTTG
1 T-TGTTTATTTATTTG
3487448 ACTATGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 13 0.45
17 15 0.52
18 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (17 bp):
TTGTTTATTTATTTGTT
Found at i:3487842 original size:43 final size:41
Alignment explanation
Indices: 3487755--3487850 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 41
3487745 AAAAAAATAG
* *
3487755 TTTTCAATAAAGCTTTATCAACATATTGAAAAGCAATTTGAT
1 TTTTAAATAAAGCTTTATCAACATATTGAAAA-CAATTTAAT
* *
3487797 TTTTAAGATAAAGTTTTATCAACATATTGAAAA-ATCTTATAAT
1 TTTTAA-ATAAAGCTTTATCAACATATTGAAAACA-ATT-TAAT
3487840 TTTTAAATAAA
1 TTTTAAATAAA
3487851 AATTAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.02
42 12 0.26
43 34 0.72
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (41 bp):
TTTTAAATAAAGCTTTATCAACATATTGAAAACAATTTAAT
Found at i:3487894 original size:35 final size:35
Alignment explanation
Indices: 3487854--3487939 Score: 86
Period size: 38 Copynumber: 2.4 Consensus size: 35
3487844 AAATAAAAAT
*
3487854 TAATTTTTAGAAAATCCTACCAACATATTGGAGAA
1 TAATTTTTAGAAAATCCTACCAACATATTGAAGAA
* * * *
3487889 TAATTTCTAATAAAAAATCTTACTAACATATTGAAGGA
1 TAATTT-T--TAGAAAATCCTACCAACATATTGAAGAA
3487927 T-ATTTTT-GAAAAT
1 TAATTTTTAGAAAAT
3487940 AAAGAGTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
33 5 0.12
34 1 0.02
35 6 0.14
36 2 0.05
37 4 0.10
38 24 0.57
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (35 bp):
TAATTTTTAGAAAATCCTACCAACATATTGAAGAA
Found at i:3489165 original size:3 final size:3
Alignment explanation
Indices: 3489153--3489203 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
3489143 CTACTACTAC
*
3489153 TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3489201 TAT
1 TAT
3489204 ATTTAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3493170 original size:18 final size:18
Alignment explanation
Indices: 3493147--3493185 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3493137 AATTAAAATT
* *
3493147 AATATATTTTTATTAAAA
1 AATATATATTTATAAAAA
3493165 AATATATATTTATAAAAA
1 AATATATATTTATAAAAA
3493183 AAT
1 AAT
3493186 TACTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATATATTTATAAAAA
Found at i:3494199 original size:21 final size:23
Alignment explanation
Indices: 3494169--3494211 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3494159 ATGTAATATG
*
3494169 TATTTTTAA-TTTTA-TAAAATC
1 TATTTATAATTTTTATTAAAATC
3494190 TATTTATAATTTTTATTAAAAT
1 TATTTATAATTTTTATTAAAAT
3494212 TTTAAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTATAATTTTTATTAAAATC
Done.