Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 123 of 129
Found at i:22338711 original size:22 final size:22
Alignment explanation
Indices: 22338665--22338757 Score: 82
Period size: 26 Copynumber: 4.0 Consensus size: 22
22338655 GAATATTAAC
*
22338665 AGATAAATTA-AAAATA-ATAAT
1 AGATAAATTATAATATATA-AAT
22338686 AGATAAATTATAATATATAAAT
1 AGATAAATTATAATATATAAAT
*
22338708 AGATAAATAATAATAAATATATAACT
1 AGATAAAT--T-AT-AATATATAAAT
* *
22338734 AGATAAATAAAATATATATAAAT
1 AGATAAATTATA-ATATATAAAT
22338757 A
1 A
22338758 TTAACAGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
21 10 0.17
22 17 0.28
23 12 0.20
24 1 0.02
25 2 0.03
26 18 0.30
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (22 bp):
AGATAAATTATAATATATAAAT
Found at i:22338726 original size:7 final size:7
Alignment explanation
Indices: 22338667--22338895 Score: 53
Period size: 7 Copynumber: 32.7 Consensus size: 7
22338657 ATATTAACAG
22338667 ATAAATTA
1 ATAAA-TA
22338675 A-AAATA
1 ATAAATA
22338681 AT-AATA
1 ATAAATA
*
22338687 GATAAATT
1 -ATAAATA
22338695 AT-AATA
1 ATAAATA
22338701 TATAAATA
1 -ATAAATA
22338709 GATAAATA
1 -ATAAATA
22338717 AT-AATA
1 ATAAATA
*
22338723 A-ATAT-
1 ATAAATA
*
22338728 ATAACTA
1 ATAAATA
22338735 GATAAATA
1 -ATAAATA
22338743 A-AATATA
1 ATAA-ATA
22338750 TATAAATA
1 -ATAAATA
* *
22338758 TTAACAGA
1 ATAA-ATA
22338766 A-AAGA-A
1 ATAA-ATA
*
22338772 AGAAA-A
1 ATAAATA
*
22338778 AGAAA-A
1 ATAAATA
22338784 A-AAATA
1 ATAAATA
*
22338790 A-AGATA
1 ATAAATA
*
22338796 TATATATTA
1 -ATA-AATA
22338805 ATAAATA
1 ATAAATA
*
22338812 GT-AATA
1 ATAAATA
22338818 ATAAATAA
1 ATAAAT-A
22338826 ATAAATA
1 ATAAATA
22338833 ATAAATA
1 ATAAATA
22338840 CAT-AATA
1 -ATAAATA
*
22338847 TACAAAT-
1 -ATAAATA
22338854 ATAAAATA
1 AT-AAATA
*
22338862 ATAATAAA
1 ATAA-ATA
22338870 ATATAA-A
1 ATA-AATA
22338877 ATACAA-A
1 ATA-AATA
*
22338884 ATAAAAA
1 ATAAATA
22338891 ATAAA
1 ATAAA
22338896 AATGGGCCTA
Statistics
Matches: 172, Mismatches: 22, Indels: 55
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.02
6 46 0.27
7 66 0.38
8 51 0.30
9 5 0.03
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (7 bp):
ATAAATA
Found at i:22338865 original size:32 final size:31
Alignment explanation
Indices: 22338820--22338898 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
22338810 TAGTAATAAT
*
22338820 AAAT-AAATAAATAATAAATACATAATATACA
1 AAATAAAAT-AATAATAAATACATAAAATACA
*
22338851 AATATAAAATAATAATAAA-ATATAAAATACA
1 AA-ATAAAATAATAATAAATACATAAAATACA
22338882 AAATAAAA-AATAA-AAAT
1 AAATAAAATAATAATAAAT
22338899 GGGCCTACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 6 0.14
31 14 0.33
32 11 0.26
33 4 0.09
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (31 bp):
AAATAAAATAATAATAAATACATAAAATACA
Found at i:22338896 original size:7 final size:7
Alignment explanation
Indices: 22338814--22338897 Score: 60
Period size: 7 Copynumber: 11.1 Consensus size: 7
22338804 AATAAATAGT
*
22338814 AATAATA
1 AATAAAA
22338821 AATAAATA
1 AATAAA-A
*
22338829 AATAATA
1 AATAAAA
22338836 AATACATAA
1 AATA-A-AA
*
22338845 TATACAAA
1 AATA-AAA
*
22338853 TATAAAA
1 AATAAAA
22338860 TAATAATAA
1 -AATAA-AA
*
22338869 AATATAA
1 AATAAAA
*
22338876 AATACAA
1 AATAAAA
22338883 AATAAAA
1 AATAAAA
22338890 AATAAAA
1 AATAAAA
22338897 A
1 A
22338898 TGGGCCTACC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
7 35 0.55
8 21 0.33
9 8 0.12
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAA
Found at i:22339185 original size:43 final size:43
Alignment explanation
Indices: 22339080--22339291 Score: 293
Period size: 43 Copynumber: 4.9 Consensus size: 43
22339070 TGATCAAGGT
* *
22339080 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAACATAAACAATA-C
1 TCCTCTAATCAGAGGCTCAACGACTTTG-AAAA-ATAAATAA-AGC
*
22339125 TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATGAATAAAGC
1 TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGC
* *
22339168 TCCTCTAATCAGAGGCTCAAGGACTTTG-AAAATGAATAAAGC
1 TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGC
*
22339210 TCATCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGC
1 TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGC
* * *
22339253 TCATCTAATCAGAGGCTCGACGACTTTTGAAAAGTAAAT
1 TCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAAT
22339292 GACTCATTGA
Statistics
Matches: 155, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
42 41 0.26
43 70 0.45
44 17 0.11
45 27 0.17
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (43 bp):
TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGC
Found at i:22339242 original size:85 final size:85
Alignment explanation
Indices: 22339080--22339290 Score: 289
Period size: 85 Copynumber: 2.4 Consensus size: 85
22339070 TGATCAAGGT
* *
22339080 TCCTCTAAACAGAGGCTCAACGACTTTGAAAAACATAAACAATACTCCTCTAATCAGAGGCTCAA
1 TCCTCTAATCAGAGGCTCAACGACTTTG--AAA-ATAAACAATACTCATCTAATCAGAGGCTCAA
*
22339145 CGACTTTGAAAAATGAATAAAGC
63 CGACTTTGAAAAATAAATAAAGC
* * *
22339168 TCCTCTAATCAGAGGCTCAAGGACTTTGAAAATGAATAA-AGCTCATCTAATCAGAGGCTCAACG
1 TCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAACAATA-CTCATCTAATCAGAGGCTCAACG
22339232 ACTTTGAAAAATAAATAAAGC
65 ACTTTGAAAAATAAATAAAGC
* *
22339253 TCATCTAATCAGAGGCTCGACGACTTTTGAAAAGTAAA
1 TCCTCTAATCAGAGGCTCAACGAC-TTTGAAAA-TAAA
22339291 TGACTCATTG
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
84 1 0.01
85 69 0.63
86 11 0.10
87 3 0.03
88 26 0.24
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (85 bp):
TCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAACAATACTCATCTAATCAGAGGCTCAACGA
CTTTGAAAAATAAATAAAGC
Found at i:22340061 original size:13 final size:13
Alignment explanation
Indices: 22340043--22340071 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22340033 TTACAAGGAT
22340043 AAGTATGGGGACA
1 AAGTATGGGGACA
22340056 AAGTATGGGGACA
1 AAGTATGGGGACA
22340069 AAG
1 AAG
22340072 CCCAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.38, T:0.14
Consensus pattern (13 bp):
AAGTATGGGGACA
Found at i:22340343 original size:19 final size:19
Alignment explanation
Indices: 22340321--22340372 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
22340311 TTTCATTCAC
*
22340321 TTTTTCTTTTTTTTTT-CT
1 TTTTTCTTTTTTTTTTAAT
*
22340339 TTTTTTTAATTTTTTTTTAAT
1 TTTTTCT--TTTTTTTTTAAT
22340360 TTTTTCATTTTTT
1 TTTTTC-TTTTTT
22340373 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.22
20 14 0.52
21 6 0.22
22 1 0.04
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTTAAT
Found at i:22340370 original size:15 final size:15
Alignment explanation
Indices: 22340351--22340385 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22340341 TTTTTAATTT
22340351 TTTTTTAATTTTTTCA
1 TTTTTTAA-TTTTTCA
*
22340367 TTTTTTCATTTTTCA
1 TTTTTTAATTTTTCA
22340382 TTTT
1 TTTT
22340386 CACTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTAATTTTTCA
Found at i:22350867 original size:58 final size:55
Alignment explanation
Indices: 22350739--22351184 Score: 423
Period size: 58 Copynumber: 7.7 Consensus size: 55
22350729 TTTATACAGA
* **
22350739 AAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTAGAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTAAAAACTTT--TTTTAAG
*
22350796 GAAAATTGATACTTTCAACTTTTTCTCAAAAATCCATTTTTAAAAACTTCTTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAAT--ATTTTTAAAAACTT-TTTTTAAG
* * * *
22350854 AAAAATTGATACTTTCAATTTTTTCCCAAAAATATTTTTTAAAACTTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTAAAAACTTTT--TTT-AAG
* * * * * *
22350912 AAAAATTGATATTTTTAACTTTTCCTCAAAAATTCACTTTTGAAAA-TTTATTTCTAAA
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAA-T-ATTTTTAAAAACTTT-TTT-TAAG
* *
22350970 AAAAATTGATACTTTCAACTTTTTCTCAAAAATCCATTTTTGAAAACTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAAT--ATTTTTAAAAACTT-TTTTTAAG
* * * *
22351028 GAAAATTGATACTTTTAAC-TTTTCTTCAAAAATATTTTTTTTAGAAAGCTTATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTTC-TCAAAAATA---TTTTTA-AAAACTT-TTTTTAAG
* * *
22351088 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTCTTAGAAAGTTTATTTTCAA-
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT-TTAAAAACTTT-TTTT-AAG
22351145 AGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
1 A-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
22351185 TTGAATTTTA
Statistics
Matches: 329, Mismatches: 36, Indels: 48
0.80 0.09 0.12
Matches are distributed among these distances:
55 2 0.01
56 15 0.05
57 48 0.15
58 179 0.54
59 27 0.08
60 54 0.16
61 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (55 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTAAAAACTTTTTTTAAG
Found at i:22351110 original size:118 final size:116
Alignment explanation
Indices: 22350739--22351178 Score: 525
Period size: 116 Copynumber: 3.8 Consensus size: 116
22350729 TTTATACAGA
* *
22350739 AAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTAGAAACTTTAATTTCGAGGAAAATT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTGA-AAACTTTAATTTCAAGGAAAATT
* * *
22350803 GATACTTTCAACTTTTTCTCAAAAATCCATTTTTA-AAAACTTCTTTTTAAG
65 GATACTTTCAACTTTTTCTCAAAAATTCATTTTTAGAAAACTTATTTTCAAG
* * * * *
22350854 AAAAATTGATACTTTCAATTTTTTCCCAAAAATATTTTTTAAAACTTTTAATTTCGAGAAAAATT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTGAAAAC-TTTAATTTCAAGGAAAATT
* * * * * *
22350919 GATATTTTTAACTTTTCCTCAAAAATTCACTTTT-GAAAATTTA-TTTCTAAA
65 GATACTTTCAACTTTTTCTCAAAAATTCATTTTTAGAAAACTTATTTTC-AAG
*
22350970 AAAAATTGATACTTTCAACTTTTTCTCAAAAATCCATTTTTGAAAAC-TTATTTTCAAGGAAAAT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAAT--ATTTTTGAAAACTTTAATTTCAAGGAAAAT
* ** *
22351034 TGATACTTTTAAC-TTTTCTTCAAAAATATTTTTTTTAGAAAGCTTATTTTCAAG
64 TGATACTTTCAACTTTTTC-TCAAAAAT-TCATTTTTAGAAAACTTATTTTCAAG
* * * *
22351088 AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTCTT-AGAAAGTTTATTTTCAAAGAAAAT
1 AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT-TTGA-AAACTTTAATTTCAAGGAAAAT
22351152 TGATACTTTCAACTTTTTCTCAAAAAT
64 TGATACTTTCAACTTTTTCTCAAAAAT
22351179 ATTTTTTTGA
Statistics
Matches: 281, Mismatches: 30, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
115 36 0.13
116 138 0.49
117 10 0.04
118 88 0.31
119 9 0.03
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (116 bp):
AAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTG
ATACTTTCAACTTTTTCTCAAAAATTCATTTTTAGAAAACTTATTTTCAAG
Found at i:22351210 original size:5 final size:5
Alignment explanation
Indices: 22351202--22351273 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
22351192 TTATTTAAAG
*
22351202 AAAAT AAAAT --AAT AAAAT AAAAT GAAAAT GAAAGT GAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT -AAAAT
22351249 AAAGA- AAAAT AAAAT AAAAAT AAAA
1 AAA-AT AAAAT AAAAT -AAAAT AAAA
22351274 AAATATTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 28 0.48
6 26 0.45
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:22351241 original size:12 final size:11
Alignment explanation
Indices: 22351201--22351267 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 11
22351191 TTTATTTAAA
22351201 GAAAATAAAAT
1 GAAAATAAAAT
*
22351212 AATAAAATAAAAT
1 --GAAAATAAAAT
*
22351225 GAAAATGAAAGT
1 GAAAAT-AAAAT
22351237 GAAAATAAAAAT
1 GAAAAT-AAAAT
22351249 -AAAGA-AAAAT
1 GAAA-ATAAAAT
22351259 -AAAATAAAA
1 GAAAATAAAA
22351268 ATAAAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
9 1 0.02
10 12 0.26
11 8 0.17
12 15 0.33
13 10 0.22
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (11 bp):
GAAAATAAAAT
Found at i:22351262 original size:21 final size:20
Alignment explanation
Indices: 22351202--22351276 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
22351192 TTATTTAAAG
*
22351202 AAAAT-AAAATAATAAAAT-
1 AAAATAAAAAAAATAAAATA
*
22351220 AAAATGAAAATGAAAGTGAAAATA
1 AAAAT-AAAA--AAAAT-AAAATA
22351244 AAAATAAAGAAAAATAAAATA
1 AAAATAAA-AAAAATAAAATA
22351265 AAAATAAAAAAA
1 AAAATAAAAAAA
22351277 TATTAAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.11
20 7 0.15
21 14 0.30
22 7 0.15
23 8 0.17
24 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (20 bp):
AAAATAAAAAAAATAAAATA
Found at i:22351267 original size:11 final size:11
Alignment explanation
Indices: 22351202--22351273 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
22351192 TTATTTAAAG
22351202 AAAATAAAATAAT
1 AAAAT-AAA-AAT
22351215 AAAAT-AAAAT
1 AAAATAAAAAT
* *
22351225 GAAAATGAAAGT
1 -AAAATAAAAAT
22351237 GAAAATAAAAAT
1 -AAAATAAAAAT
*
22351249 -AAAGAAAAAT
1 AAAATAAAAAT
22351259 AAAATAAAAAT
1 AAAATAAAAAT
22351270 AAAA
1 AAAA
22351274 AAATATTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 12 0.24
11 20 0.39
12 14 0.27
13 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:22351303 original size:3 final size:3
Alignment explanation
Indices: 22351295--22351321 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22351285 AATTCTAATC
22351295 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
22351322 ATAAAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:22352128 original size:31 final size:31
Alignment explanation
Indices: 22352085--22352247 Score: 84
Period size: 32 Copynumber: 5.0 Consensus size: 31
22352075 AAAAAAAAAA
22352085 TAAAA-ATCAAATAAAAAATATTAATAGATAAT
1 TAAAAGAT-AAATAAAAAATA-TAATAGATAAT
*
22352117 TAAAAGA-AAATAATAAGATA-AATCAGA-ATAT
1 TAAAAGATAAATAA-AAAATATAAT-AGATA-AT
* *
22352148 TAACAGATAAATTAAAAATAATAATAGATAAAT
1 TAAAAGATAAATAAAAAAT-ATAATAGAT-AAT
* * *
22352181 TATAATATATAAATAGATAAATAATAATAAAT-AT
1 TA-AA-AGATAAATA-AAAAAT-ATAATAGATAAT
* * *
22352215 ATAACTAGATAAATAAAATATATATATATATAA
1 -TAA-AAGATAAATAAAAAATATA-ATAGATAA
22352248 ATATTAACAG
Statistics
Matches: 101, Mismatches: 14, Indels: 30
0.70 0.10 0.21
Matches are distributed among these distances:
30 4 0.04
31 21 0.21
32 22 0.22
33 17 0.17
34 14 0.14
35 9 0.09
36 14 0.14
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (31 bp):
TAAAAGATAAATAAAAAATATAATAGATAAT
Found at i:22352180 original size:14 final size:14
Alignment explanation
Indices: 22352163--22352234 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 14
22352153 GATAAATTAA
22352163 AAATAATAATAGAT
1 AAATAATAATAGAT
* *
22352177 AAATTATAATATAT
1 AAATAATAATAGAT
*
22352191 AAATAGATAAATAATAAT
1 AAATA-AT-AAT-A-GAT
22352209 AAATATATAACTAGAT
1 AAATA-ATAA-TAGAT
22352225 AAATAA-AATA
1 AAATAATAATA
22352235 TATATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
13 2 0.04
14 18 0.38
15 3 0.06
16 10 0.21
17 4 0.09
18 10 0.21
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAATAATAGAT
Found at i:22352210 original size:42 final size:42
Alignment explanation
Indices: 22352101--22352250 Score: 119
Period size: 42 Copynumber: 3.5 Consensus size: 42
22352091 TCAAATAAAA
* *
22352101 AATAT-TAATAGATAATTAAAAGAAAATAATAAGATAAATCAG
1 AATATATAATAGATAAATAAAA-ATAATAATAAGATAAATCAG
* * *
22352143 AATAT-TAACAGATAAATTAAAAATAATAAT-AGATAAATTAT
1 AATATATAATAGATAAA-TAAAAATAATAATAAGATAAATCAG
* *
22352184 AATATATAAATAGATAAATAATAATAAATATATAACTAGATAAAT-AA
1 AATATAT-AATAGATAAATAAAAAT-AATA-AT-A--AGATAAATCAG
*
22352231 AATATATATATATATAAATA
1 AATATATA-ATAGATAAATA
22352251 TTAACAGAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
41 14 0.16
42 28 0.31
43 18 0.20
44 2 0.02
46 1 0.01
47 18 0.20
48 8 0.09
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (42 bp):
AATATATAATAGATAAATAAAAATAATAATAAGATAAATCAG
Found at i:22352295 original size:6 final size:6
Alignment explanation
Indices: 22352273--22352390 Score: 51
Period size: 6 Copynumber: 18.7 Consensus size: 6
22352263 AAAGAAAAAG
* * * * ** *
22352273 AAAAGA AAAA-A ATAATA AAAATA AAAATA TATATA TTAATA AATAGTA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA
* * * *
22352321 ATAATA AATACATA AGACACA AATATA -AAATA AAAATA AAAATAA TAAAATA
1 AAAATA AA-A-ATA A-AAATA AAAATA AAAATA AAAATA AAAAT-A -AAAATA
22352373 TAAAATA CAAAATA AAAA
1 -AAAATA -AAAATA AAAA
22352391 GCAAAAATGA
Statistics
Matches: 86, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
5 8 0.09
6 45 0.52
7 23 0.27
8 9 0.10
9 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:22352362 original size:7 final size:7
Alignment explanation
Indices: 22352341--22352390 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
22352331 CATAAGACAC
*
22352341 AAATATA
1 AAATAAA
22352348 AAAT-AA
1 AAATAAA
22352354 AAAT-AA
1 AAATAAA
22352360 AAATAATA
1 AAATAA-A
*
22352368 AAATATA
1 AAATAAA
*
22352375 AAATACA
1 AAATAAA
22352382 AAATAAA
1 AAATAAA
22352389 AA
1 AA
22352391 GCAAAAATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 11 0.30
7 20 0.54
8 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (7 bp):
AAATAAA
Found at i:22352367 original size:22 final size:23
Alignment explanation
Indices: 22352345--22352388 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
22352335 AGACACAAAT
22352345 ATAAAATA-AAAATA-AAAAT-A
1 ATAAAATATAAAATACAAAATAA
22352365 ATAAAATATAAAATACAAAATAA
1 ATAAAATATAAAATACAAAATAA
22352388 A
1 A
22352389 AAGCAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 5 0.24
23 2 0.10
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
ATAAAATATAAAATACAAAATAA
Found at i:22352678 original size:3 final size:3
Alignment explanation
Indices: 22352670--22352709 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
22352660 CAATCAAATA
22352670 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22352710 TAATGTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22353173 original size:20 final size:19
Alignment explanation
Indices: 22353137--22353176 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22353127 GTAAATGAAT
* *
22353137 TGAAAAAAATAATTTTTTA
1 TGAAAAAAAAAAATTTTTA
22353156 TGAAAAAAAAAAGATTTTTA
1 TGAAAAAAAAAA-ATTTTTA
22353176 T
1 T
22353177 AGTTCTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
TGAAAAAAAAAAATTTTTA
Found at i:22361946 original size:22 final size:24
Alignment explanation
Indices: 22361894--22361946 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
22361884 TACATTTTTT
*
22361894 TTATTTTAATAAATTTATTTATGA
1 TTATTTTAATAAATTTAATTATGA
*
22361918 TT-TTTTTA-AAATTTAAATTAT-A
1 TTATTTTAATAAATTT-AATTATGA
22361940 TTATTTT
1 TTATTTT
22361947 CATATCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 9 0.36
23 14 0.56
24 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTTTAATAAATTTAATTATGA
Found at i:22361987 original size:13 final size:13
Alignment explanation
Indices: 22361969--22361993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22361959 TCATATAATT
22361969 ATCATATCGTATC
1 ATCATATCGTATC
22361982 ATCATATCGTAT
1 ATCATATCGTAT
22361994 TTGATTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
ATCATATCGTATC
Found at i:22362355 original size:9 final size:9
Alignment explanation
Indices: 22362337--22362366 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22362327 ATCTCTAATC
22362337 ATAT-ATAT
1 ATATAATAT
22362345 ATATAATAT
1 ATATAATAT
22362354 ATATAATAT
1 ATATAATAT
22362363 ATAT
1 ATAT
22362367 TACAACATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATAATAT
Found at i:22364689 original size:25 final size:25
Alignment explanation
Indices: 22364647--22364698 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 25
22364637 GTATAATTCA
22364647 TTATTTTTTTCATACTCTATTTCTTTTT
1 TTATTTTTTTC--ACTCTATTT-TTTTT
22364675 TTATTTTTTTC-CTCTATTTTTTTT
1 TTATTTTTTTCACTCTATTTTTTTT
22364699 CTTCAGACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.21
25 8 0.33
28 11 0.46
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (25 bp):
TTATTTTTTTCACTCTATTTTTTTT
Found at i:22364790 original size:2 final size:2
Alignment explanation
Indices: 22364783--22364808 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22364773 TTCATATGTT
22364783 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
22364809 GGCTTAATAA
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):
TA
Found at i:22365237 original size:15 final size:15
Alignment explanation
Indices: 22365213--22365244 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22365203 TATACCTTCA
22365213 TTATTCTTTTATTTT
1 TTATTCTTTTATTTT
*
22365228 TTATTTTTTTATTTT
1 TTATTCTTTTATTTT
22365243 TT
1 TT
22365245 TAGTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTCTTTTATTTT
Found at i:22365243 original size:9 final size:8
Alignment explanation
Indices: 22365213--22365246 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
22365203 TATACCTTCA
*
22365213 TTATTCTT
1 TTATTTTT
22365221 TTA-TTTT
1 TTATTTTT
22365228 TTATTTTT
1 TTATTTTT
22365236 TTATTTTT
1 TTATTTTT
22365244 TTA
1 TTA
22365247 GTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:22365745 original size:3 final size:3
Alignment explanation
Indices: 22365737--22365796 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
22365727 CAATCAAATA
22365737 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
22365784 TAT TAT TAG TAT T
1 TAT TAT TAT TAT T
22365797 TAATGTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:22375837 original size:41 final size:41
Alignment explanation
Indices: 22375751--22375828 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
22375741 TAAAATTATA
22375751 GGTTTATGGTTGAATTTCTTGACTGTGCAATATGTAGACGC
1 GGTTTATGGTTGAATTTCTTGACTGTGCAATATGTAGACGC
*
22375792 GGTTTA-GGATTGAGTTTCTTGACTGTGCAATATGTAG
1 GGTTTATGG-TTGAATTTCTTGACTGTGCAATATGTAG
22375829 GTGTGGTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 2 0.06
41 33 0.94
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (41 bp):
GGTTTATGGTTGAATTTCTTGACTGTGCAATATGTAGACGC
Found at i:22382419 original size:22 final size:22
Alignment explanation
Indices: 22382391--22382452 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
22382381 AATCAATACG
*
22382391 AATTTAATTTAATTAATTTTTA
1 AATTTAATTTAATTAATTTTCA
*
22382413 AATTTAATTTAATT-ATTATCA
1 AATTTAATTTAATTAATTTTCA
* *
22382434 AATTAAATTTAAATAATTT
1 AATTTAATTTAATTAATTT
22382453 AATTTATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTAATTTAATTAATTTTCA
Found at i:22386852 original size:16 final size:16
Alignment explanation
Indices: 22386833--22386863 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22386823 TTAAATTATA
22386833 TTTTAAATTTTAAATT
1 TTTTAAATTTTAAATT
*
22386849 TTTTATATTTTAAAT
1 TTTTAAATTTTAAAT
22386864 AAATTAAATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAAATTTTAAATT
Found at i:22387096 original size:22 final size:23
Alignment explanation
Indices: 22387053--22387096 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
22387043 AAATTCTTTT
* *
22387053 AAAATTATTTTCGTTAACCAATC
1 AAAATTATATTCGATAACCAATC
*
22387076 AAAATTA-ATTCGATAATCAAT
1 AAAATTATATTCGATAACCAAT
22387097 TAATTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAATTATATTCGATAACCAATC
Found at i:22387117 original size:14 final size:14
Alignment explanation
Indices: 22387092--22387127 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22387082 AATTCGATAA
22387092 TCAATT-AATTAAT
1 TCAATTAAATTAAT
*
22387105 TGAATTAAATTAAT
1 TCAATTAAATTAAT
22387119 TCAATTAAA
1 TCAATTAAA
22387128 ATCGAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
TCAATTAAATTAAT
Found at i:22387218 original size:21 final size:22
Alignment explanation
Indices: 22387183--22387223 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
22387173 ATGAATTTAC
*
22387183 TATAATTAAACAATTATAAGAT
1 TATAATTAAAAAATTATAAGAT
22387205 TATAA-TAAAAAATTATAAG
1 TATAATTAAAAAATTATAAG
22387224 TAAAATGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
TATAATTAAAAAATTATAAGAT
Found at i:22391821 original size:14 final size:14
Alignment explanation
Indices: 22391802--22391831 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
22391792 TTAATTCGAT
22391802 TTTAATTGAATTAA
1 TTTAATTGAATTAA
22391816 TTTAATTGAATTAA
1 TTTAATTGAATTAA
22391830 TT
1 TT
22391832 ATTTTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAATTGAATTAA
Found at i:22393119 original size:16 final size:16
Alignment explanation
Indices: 22393088--22393134 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
22393078 TTTTTTAAAA
* *
22393088 ATATAAATATATAATT
1 ATATAAATAAAAAATT
22393104 ATATAAATAAAAAATT
1 ATATAAATAAAAAATT
*
22393120 A-ATTAATTAAAAAAT
1 ATA-TAAATAAAAAAT
22393135 AAAATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 1 0.04
16 26 0.96
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAAATAAAAAATT
Found at i:22393586 original size:7 final size:7
Alignment explanation
Indices: 22393574--22393625 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
22393564 ATGATAATAA
22393574 AAATTTT
1 AAATTTT
22393581 AAATTTT
1 AAATTTT
22393588 AAATTTT
1 AAATTTT
22393595 AAATTTT
1 AAATTTT
22393602 -AATTTT
1 AAATTTT
*
22393608 AATTTTT
1 AAATTTT
22393615 AAATTTT
1 AAATTTT
22393622 AAAT
1 AAAT
22393626 ATGTTTAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 6 0.14
7 36 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AAATTTT
Found at i:22393607 original size:20 final size:20
Alignment explanation
Indices: 22393574--22393623 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
22393564 ATGATAATAA
22393574 AAATTTTAAATTTTAAATTTT
1 AAATTTT-AATTTTAAATTTT
*
22393595 AAATTTTAATTTTAATTTTT
1 AAATTTTAATTTTAAATTTT
22393615 AAATTTTAA
1 AAATTTTAA
22393624 ATATGTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATTTTAATTTTAAATTTT
Found at i:22394926 original size:22 final size:21
Alignment explanation
Indices: 22394884--22394955 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
22394874 CCTGAAATTA
22394884 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
22394905 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTT-AAAT
* * *
22394927 ATAAATATATAATTATATAAAT
1 ATAAA-ATATTATTTTTTAAAT
*
22394949 AAAAAAT
1 ATAAAAT
22394956 TAATTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.42
22 17 0.38
23 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:22394956 original size:16 final size:16
Alignment explanation
Indices: 22394925--22394971 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
22394915 ATTTTTTAAA
* *
22394925 ATATAAATATATAATT
1 ATATAAATAAAAAATT
22394941 ATATAAATAAAAAATT
1 ATATAAATAAAAAATT
*
22394957 A-ATTAATTAAAAAAT
1 ATA-TAAATAAAAAAT
22394972 AATTTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 1 0.04
16 26 0.96
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAAATAAAAAATT
Found at i:22395427 original size:22 final size:21
Alignment explanation
Indices: 22395402--22395450 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
22395392 AAAAAATCCT
*
22395402 AATATGATAATAAAAAATTATA
1 AATATGAAAATAAAAAATT-TA
* **
22395424 AATATTAAAATTTAAAATTTA
1 AATATGAAAATAAAAAATTTA
22395445 AATATG
1 AATATG
22395451 TTTAATATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AATATGAAAATAAAAAATTTA
Found at i:22395907 original size:14 final size:13
Alignment explanation
Indices: 22395881--22395905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22395871 TTATTTGTGA
22395881 TTTTTATTAAAAT
1 TTTTTATTAAAAT
22395894 TTTTTATTAAAA
1 TTTTTATTAAAA
22395906 ATGAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTATTAAAAT
Found at i:22395923 original size:21 final size:21
Alignment explanation
Indices: 22395899--22395941 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
22395889 AAAATTTTTT
22395899 ATTAAAAATGA-ATAATTAAAA
1 ATTAAAAATGATA-AATTAAAA
*
22395920 ATTAAAATTGATAAATTAAAA
1 ATTAAAAATGATAAATTAAAA
22395941 A
1 A
22395942 ATTTTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATTAAAAATGATAAATTAAAA
Found at i:22395987 original size:11 final size:11
Alignment explanation
Indices: 22395971--22396026 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
22395961 ACGTATAAAA
22395971 TTTAATAAATT
1 TTTAATAAATT
22395982 TTTAATAAA-T
1 TTTAATAAATT
* *
22395992 TTTGATATATT
1 TTTAATAAATT
22396003 TATTAAATAAATATT
1 T-TT-AAT-AA-ATT
22396018 TTTAATAAA
1 TTTAATAAA
22396027 AATATTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 8 0.22
11 12 0.33
12 4 0.11
13 5 0.14
14 3 0.08
15 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAATAAATT
Found at i:22396003 original size:21 final size:23
Alignment explanation
Indices: 22395965--22396014 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
22395955 AATCAAACGT
*
22395965 ATAAAATTTAATAAATTT-TT-A
1 ATAAATTTTAATAAATTTATTAA
* *
22395986 ATAAATTTTGATATATTTATTAA
1 ATAAATTTTAATAAATTTATTAA
22396009 ATAAAT
1 ATAAAT
22396015 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATAAATTTTAATAAATTTATTAA
Found at i:22397844 original size:49 final size:47
Alignment explanation
Indices: 22397748--22397844 Score: 106
Period size: 47 Copynumber: 2.0 Consensus size: 47
22397738 ATAATACGAT
* *
22397748 ATAAAAATAATATAAAAAATATATAAATTATATATTTTTAATTTTTA
1 ATAAAAATAATATAAAAAATATATAAAATATATATTTTTAATGTTTA
* * * *
22397795 ATAAAAATTATAT-ATAAATTTAATAAAATATATTAATTTTTTATGTTTA
1 ATAAAAATAATATAAAAAATAT-ATAAAATATA-T-ATTTTTAATGTTTA
22397844 A
1 A
22397845 CTTACTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
46 6 0.15
47 21 0.51
48 1 0.02
49 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (47 bp):
ATAAAAATAATATAAAAAATATATAAAATATATATTTTTAATGTTTA
Found at i:22398491 original size:12 final size:12
Alignment explanation
Indices: 22398474--22398501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22398464 AATCTATTGA
22398474 ATTAAATTTTTT
1 ATTAAATTTTTT
22398486 ATTAAATTTTTT
1 ATTAAATTTTTT
22398498 ATTA
1 ATTA
22398502 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTAAATTTTTT
Found at i:22407704 original size:13 final size:12
Alignment explanation
Indices: 22407685--22407721 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
22407675 AAGAAACTCC
22407685 CAAAAAAAAAAA
1 CAAAAAAAAAAA
*
22407697 CTAAAAAAAAAAG
1 C-AAAAAAAAAAA
22407710 CAAAAAAAAAAA
1 CAAAAAAAAAAA
22407722 AATTCAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:22413566 original size:28 final size:25
Alignment explanation
Indices: 22413514--22413578 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
22413504 TTAATATAAA
**
22413514 TATTAAAATATTAAAATTTATTTAT
1 TATTAAAATATTAAAAAATATTTAT
22413539 TATTAAAATATAATAAAAAATA-TT-T
1 TATTAAAATAT--TAAAAAATATTTAT
22413564 TATTAAAATTATTAA
1 TATTAAAA-TATTAA
22413579 TATTCAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
24 3 0.09
25 20 0.57
26 5 0.14
27 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTAAAATATTAAAAAATATTTAT
Found at i:22413830 original size:75 final size:77
Alignment explanation
Indices: 22413717--22414035 Score: 216
Period size: 77 Copynumber: 4.2 Consensus size: 77
22413707 GCTAATAGTA
* * * *
22413717 TATTCTTTATTAATAATATATTATTTACTCATATATTATTATAATATTTATTAAT-TAATTTAAT
1 TATTATTTATTAATAATATATTATTTACTAATACATTATAATAATATTTATTAATATAATTTAAT
22413781 AAT-TATTATAT
66 AATATATTATAT
* * * * *
22413792 TATTATTTATTAAT-ATAATATTATTTAGTAATACATTATAATATTATTTCTTAATATTATTTAT
1 TATTATTTATTAATAAT-ATATTATTTACTAATACATTATAATAATATTTATTAATATAATTTAA
22413856 TAATATATTATAT
65 TAATATATTATAT
* * * * * * * * *
22413869 TAATAGTATATTATTTAT-TAATATATTA-TAATA-TTTTTAATAGTATATTATTTAT-TAATAT
1 TATTA-TTTATTAATAATATATTAT-TTACTAATACATTATAATAATAT-TTATTAATATAAT-T
*
22413930 TAAT-ATATCAGTATA-
62 TAATAATAT-ATTATAT
* * * * *
22413945 TATTTATTTA-TAATAATATTTTATTAATA-TTATACTATT-TATTAATATATA-TAATATTATT
1 TA-TTATTTATTAATAATATATTATT--TACTAATAC-ATTATAATAATATTTATTAATATAATT
* *
22414006 TATTAATATATTATAA
62 TAATAATATATTATAT
22414022 TATT-TTTATTAATA
1 TATTATTTATTAATA
22414036 TGTTTTATTC
Statistics
Matches: 189, Mismatches: 36, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
74 2 0.01
75 55 0.29
76 55 0.29
77 56 0.30
78 17 0.09
79 4 0.02
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (77 bp):
TATTATTTATTAATAATATATTATTTACTAATACATTATAATAATATTTATTAATATAATTTAAT
AATATATTATAT
Found at i:22413862 original size:111 final size:104
Alignment explanation
Indices: 22413734--22414019 Score: 245
Period size: 100 Copynumber: 2.7 Consensus size: 104
22413724 TATTAATAAT
* *
22413734 ATATTATTTACTCATATATTAT-TATAATATTTATTAATTAATTTAATAAT-TATTATATTATTA
1 ATATTATTTACTAATATATTATAT-TAATA-GTA-T-ATT-ATTTAATAATATATTATA--A-TA
22413797 TTTATTAATA-TAATATTATTTAGTAATACATTATAATATTATTTCTTA
58 TTT-TTAATAGT-ATATTATTTAGTAATACATTATAATATTATTTCTTA
* *
22413845 ATATTATTTATTAATATATTATATTAATAGTATATTATTTATTAATATATTATAATATTTTTAAT
1 ATATTATTTACTAATATATTATATTAATAGTATATTATTTAATAATATATTATAATATTTTTAAT
* *
22413910 AGTATATTATTTATTAAT--A-T-TAATA-TA--TCAGTA
66 AGTATATTATTTAGTAATACATTATAATATTATTTC-TTA
* * * *
22413943 TATATTTATTTA-TAATAATATTTTATTAATATTATACTATTTATTAATATA-TATAATATTATT
1 -ATA-TTATTTACTAAT-ATATTATATTAATAGTATATTATTTAATAATATATTATAATATT-TT
* *
22414006 TATTAATATATTAT
62 TAATAGTATATTAT
22414020 AATATTTTTA
Statistics
Matches: 156, Mismatches: 11, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
97 2 0.01
98 2 0.01
99 18 0.12
100 57 0.37
101 1 0.01
102 1 0.01
104 20 0.13
105 6 0.04
106 1 0.01
107 9 0.06
108 10 0.06
109 1 0.01
110 2 0.01
111 25 0.16
112 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (104 bp):
ATATTATTTACTAATATATTATATTAATAGTATATTATTTAATAATATATTATAATATTTTTAAT
AGTATATTATTTAGTAATACATTATAATATTATTTCTTA
Found at i:22413866 original size:188 final size:184
Alignment explanation
Indices: 22413671--22414071 Score: 412
Period size: 189 Copynumber: 2.1 Consensus size: 184
22413661 TTTTATTTTG
*
22413671 TATATTATTTATTAATAATATTTATT-A-ATA-TAT-TA-TGCTAATAGTATATTCTTTATTAAT
1 TATATTATTTATTAATAATATTTATTAATATATTATATATTGCTAATAGTATATTATTTATTAAT
* * *
22413731 AATATATTATTTACTCA-TATATTATTATAATATT-TATTAATTAATTTAATAATTATTATATTA
66 -AT-TA--ATATA-TCAGTATA-TATT-T-AT-TTATAATAA-TAATTTAATAA-TATTATACTA
* *
22413794 -TTATTTAT-TAATATAATATTATTTAGTAATACATTATAATATTATTTCTTAATAT-TATTTAT
120 TTTATTAATAT-ATATAATATTATTTAGTAATACATTATAATATT-TTTATTAATATGT-TTTAT
22413856 TAA
182 TAA
* * **
22413859 TATATTATATTAATAGTATATTATTTATTAATATATTATAATATTTTTAATAGTATATTATTTAT
1 TATATTAT-TTATTA--ATAATATTTATTAATATATTAT-ATATTGCTAATAGTATATTATTTAT
* *
22413924 TAATATTAATATATCAGTATATATTTATTTATAATAATATTTTATTAATATTATACTATTTATTA
62 TAATATTAATATATCAGTATATATTTATTTATAATAATAATTTAATAATATTATACTATTTATTA
* * *
22413989 ATATATATAATATTATTTATTAATATATTATAATATTTTTATTAATATGTTTTATTCA
127 ATATATATAATATTATTTAGTAATACATTATAATATTTTTATTAATATGTTTTATTAA
22414047 TATATTA--TATTAATAATATATTATT
1 TATATTATTTATTAATAATAT-TTATT
22414072 TATTCATATA
Statistics
Matches: 181, Mismatches: 17, Indels: 34
0.78 0.07 0.15
Matches are distributed among these distances:
183 6 0.03
184 5 0.03
185 4 0.02
188 41 0.23
189 55 0.30
190 8 0.04
191 12 0.07
192 8 0.04
193 11 0.06
194 3 0.02
195 2 0.01
196 4 0.02
197 22 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (184 bp):
TATATTATTTATTAATAATATTTATTAATATATTATATATTGCTAATAGTATATTATTTATTAAT
ATTAATATATCAGTATATATTTATTTATAATAATAATTTAATAATATTATACTATTTATTAATAT
ATATAATATTATTTAGTAATACATTATAATATTTTTATTAATATGTTTTATTAA
Found at i:22414005 original size:122 final size:121
Alignment explanation
Indices: 22413722--22414155 Score: 351
Period size: 122 Copynumber: 3.5 Consensus size: 121
22413712 TAGTATATTC
* * * * * *
22413722 TTTATTAATAATATATTATTTACTCATATATTATTATAATATTTATTAATTAATT-TAATAATTA
1 TTTATTAATATTATATTATTTATTAATATATTATAATATTATTTATTAATT-ATTATAAT-ATTT
* *
22413786 TT-ATAT-TATTATTTATTAATA-TAATATTATTTAGTA-ATA--CA-TTATAATATTA-
64 TTAATATATATTATTTATTAATATTAATATTA--TAGTATATATTTATTTATAATAATAT
* * *
22413838 TTTCTTAATATTAT-TTATTAATATATTATATTAATAGTATATTATTTATTAATATATTATAATA
1 TTTATTAATATTATATTATTTAT-TAATATATT-ATA--ATATTATTTATTAAT-TATTATAATA
22413902 TTTTTAATAGTATATTATTTATTAATATTAATA-TATCAGTATATATTTATTTATAATAATAT
61 TTTTTAATA-TATATTATTTATTAATATTAATATTAT-AGTATATATTTATTTATAATAATAT
*
22413964 TTTATTAATATTATACTATTTATTAATATA-TATAATATTATTTATTAATATATTATAATATTTT
1 TTTATTAATATTATATTATTTATTAATATATTATAATATTATTTATTAAT-TATTATAATATTTT
* * *
22414028 TATTA-ATATGT-TTTATTCATATATT-ATATTAATAATATATTATTTATTCAT-ATAATATT
65 TAATATATAT-TATTTATT-A-ATATTAATATT-ATAGTATA-TATTTATTTATAATAATA-T
* * * * *
22414087 ATTTATTAATATATTGTAATATATTATTATCTATTAATATAATATTATTTTATTAATTAATATAA
1 -TTTATT-A-ATATTATATTAT-TTATTA-ATA-TATTATAATATTA-TTTATTAATTATTATAA
22414152 TATT
59 TATT
22414156 ATTCATAAGT
Statistics
Matches: 264, Mismatches: 22, Indels: 50
0.79 0.07 0.15
Matches are distributed among these distances:
115 6 0.02
116 19 0.07
117 2 0.01
119 22 0.08
120 19 0.07
121 10 0.04
122 71 0.27
123 18 0.07
124 10 0.04
125 12 0.05
126 29 0.11
127 12 0.05
128 2 0.01
129 2 0.01
130 21 0.08
131 9 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (121 bp):
TTTATTAATATTATATTATTTATTAATATATTATAATATTATTTATTAATTATTATAATATTTTT
AATATATATTATTTATTAATATTAATATTATAGTATATATTTATTTATAATAATAT
Found at i:22414098 original size:18 final size:18
Alignment explanation
Indices: 22413716--22414158 Score: 182
Period size: 18 Copynumber: 25.4 Consensus size: 18
22413706 TGCTAATAGT
*
22413716 ATATTCTTTATTAATA-A
1 ATATTATTTATTAATATA
*
22413733 TATATTATTTACTCATATATTATT
1 -ATATTATTTA-T--TA-A-TATA
*
22413757 ATAATATTTATTAAT-TA
1 ATATTATTTATTAATATA
* * *
22413774 AT-TTAATAATTATTATA
1 ATATTATTTATTAATATA
*
22413791 TTATTATTTATTAATATA
1 ATATTATTTATTAATATA
* *
22413809 ATATTATTTAGTAATACA
1 ATATTATTTATTAATATA
* * **
22413827 TTATAATATTATTTCT-TA
1 ATATTAT-TTATTAATATA
22413845 ATATTATTTATT-A-AT-
1 ATATTATTTATTAATATA
22413860 ATATTA--TATTAATAGT-
1 ATATTATTTATTAATA-TA
22413876 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
*
22413894 TTATAATATTT-TTAATAGT-
1 --ATATTATTTATTAATA-TA
22413913 ATATTATTTATTAATATTA
1 ATATTATTTATTAATA-TA
* *
22413932 ATA-TA-TCAGT-ATAT-
1 ATATTATTTATTAATATA
22413946 AT-TTATTTA-T-A-ATA
1 ATATTATTTATTAATATA
*
22413960 ATA-T-TTTATTAATATT
1 ATATTATTTATTAATATA
*
22413976 ATACTATTTATTAATATATATA
1 ATATTATTTA-T--TA-ATATA
22413998 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
*
22414016 TTATAATATTT-TT-AT-TA
1 --ATATTATTTATTAATATA
*
22414033 ATATGT-TTTATT--CAT-
1 ATAT-TATTTATTAATATA
22414048 ATATTA--TATTAATA-A
1 ATATTATTTATTAATATA
*
22414063 TATATTATTTATTCATATA
1 -ATATTATTTATTAATATA
22414082 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
* * * * *
22414100 TTGTAATATATTATTAT-
1 ATATTATTTATTAATATA
* * *
22414117 CTATTA-ATA-TAATATT
1 ATATTATTTATTAATATA
* *
22414133 ATTTTATTAATTAATATA
1 ATATTATTTATTAATATA
22414151 ATATTATT
1 ATATTATT
22414159 CATAAGTAAA
Statistics
Matches: 321, Mismatches: 54, Indels: 100
0.68 0.11 0.21
Matches are distributed among these distances:
13 14 0.04
14 12 0.04
15 27 0.08
16 41 0.13
17 30 0.09
18 125 0.39
19 22 0.07
20 19 0.06
21 5 0.02
22 15 0.05
23 11 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (18 bp):
ATATTATTTATTAATATA
Found at i:22414154 original size:23 final size:23
Alignment explanation
Indices: 22414057--22414158 Score: 102
Period size: 23 Copynumber: 4.4 Consensus size: 23
22414047 TATATTATAT
* * * *
22414057 TAATAATATATTATTTATTCATA
1 TAATATTATTTTATTAATTAATA
* *
22414080 TAATATTA-TTTATTAATATATTG
1 TAATATTATTTTATTAAT-TAATA
22414103 TAATA-TATTATTATCT-ATTAATA
1 TAATATTATT-TTAT-TAATTAATA
22414126 TAATATTATTTTATTAATTAATA
1 TAATATTATTTTATTAATTAATA
22414149 TAATATTATT
1 TAATATTATT
22414159 CATAAGTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
22 10 0.15
23 44 0.68
24 10 0.15
25 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (23 bp):
TAATATTATTTTATTAATTAATA
Found at i:22414723 original size:28 final size:28
Alignment explanation
Indices: 22414676--22414730 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
22414666 TTATTAAACA
*
22414676 AATTTAATCGAAAGAGTTCGAATAATTT
1 AATTTAATCGAAAGAATTCGAATAATTT
*
22414704 AATTTAATCGAATA-AATTCGAGTAATT
1 AATTTAATCGAA-AGAATTCGAATAATT
22414731 CGATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (28 bp):
AATTTAATCGAAAGAATTCGAATAATTT
Found at i:22415442 original size:26 final size:27
Alignment explanation
Indices: 22415395--22415455 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
22415385 AAATAGTAAT
22415395 AAAAAA-TATTGTAATTACGATT-AAA
1 AAAAAATTATTGTAATTACGATTGAAA
* **
22415420 AAAAAATTATTGTAGTTGTGATTGAAA
1 AAAAAATTATTGTAATTACGATTGAAA
22415447 AAAACAATT
1 AAAA-AATT
22415456 TTAATGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 6 0.20
26 13 0.43
27 7 0.23
28 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAAAATTATTGTAATTACGATTGAAA
Found at i:22417114 original size:18 final size:18
Alignment explanation
Indices: 22417091--22417134 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
22417081 CAGGCTTAAA
22417091 AAAAATTTAAAAAAATTC
1 AAAAATTTAAAAAAATTC
** *
22417109 AAAAATTTTTAAAAATTT
1 AAAAATTTAAAAAAATTC
22417127 AAAAATTT
1 AAAAATTT
22417135 CTTTAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATTTAAAAAAATTC
Found at i:22427092 original size:199 final size:198
Alignment explanation
Indices: 22426791--22427148 Score: 599
Period size: 199 Copynumber: 1.8 Consensus size: 198
22426781 TTGAAATATG
* * * *
22426791 AAACCTGAAGGTCGACAATAATATTCATAAAACAATAACCAAGTCATGCCATTGGAACAAAAAGC
1 AAACCTGAAAGACGAAAATAATATTCATAAAACAATAACCAAATCATGCCATTGGAACAAAAAGC
* *
22426856 AAACCAAGTTGAAACATATTGAATGTCTCACTGTTATTAGTTATCTGACCAACACCTCAACCATC
66 AAACCAAGTTGAAACATATTGAATGTCTCAATGTTATTAGTCATCTGACCAACACCTCAACCATC
*
22426921 CTAAACTCCCAACGGCACAGCTACCAATAAGTATCTTCACAAAATCAAATGAGACAGGTTGAACT
131 CTAAACTCCCAACGCCACAGCTACCAATAAGTATCTTCACAAAATCAAATGAGACAGGTTGAACT
22426986 ACC
196 ACC
*
22426989 AAACCTGAAAGACGAAAATAATCATTCATAAAACAATAACTAAATCATGCCATTGGAACAAAAAG
1 AAACCTGAAAGACGAAAATAAT-ATTCATAAAACAATAACCAAATCATGCCATTGGAACAAAAAG
* * *
22427054 CAGACCAAGTTGAAACATATTGGATGTCTCAATGTTATTAGTCATCTGACTAACACCTCAACCAT
65 CAAACCAAGTTGAAACATATTGAATGTCTCAATGTTATTAGTCATCTGACCAACACCTCAACCAT
*
22427119 CCTAAACTCCCAATGCCACAGCTACCAATA
130 CCTAAACTCCCAACGCCACAGCTACCAATA
22427149 GAGAGATACA
Statistics
Matches: 147, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
198 19 0.13
199 128 0.87
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (198 bp):
AAACCTGAAAGACGAAAATAATATTCATAAAACAATAACCAAATCATGCCATTGGAACAAAAAGC
AAACCAAGTTGAAACATATTGAATGTCTCAATGTTATTAGTCATCTGACCAACACCTCAACCATC
CTAAACTCCCAACGCCACAGCTACCAATAAGTATCTTCACAAAATCAAATGAGACAGGTTGAACT
ACC
Found at i:22436426 original size:2 final size:2
Alignment explanation
Indices: 22436419--22436443 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22436409 GGCAGTGAGT
22436419 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22436444 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22436763 original size:20 final size:21
Alignment explanation
Indices: 22436734--22436779 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
22436724 TAGTAAATAT
*
22436734 AAACTCTTATTTT-ATTTAAA
1 AAACTCTTATTTTAATATAAA
*
22436754 AAACTTTTATTTTAATATAAA
1 AAACTCTTATTTTAATATAAA
22436775 AAACT
1 AAACT
22436780 AATTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
AAACTCTTATTTTAATATAAA
Found at i:22438156 original size:9 final size:9
Alignment explanation
Indices: 22438142--22438167 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22438132 TCTGAAGAAA
22438142 GTATGTCTG
1 GTATGTCTG
22438151 GTATGTCTG
1 GTATGTCTG
22438160 GTATGTCT
1 GTATGTCT
22438168 ATGCCCTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.46
Consensus pattern (9 bp):
GTATGTCTG
Found at i:22444168 original size:13 final size:13
Alignment explanation
Indices: 22444150--22444174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22444140 GTAAAAAAAA
22444150 TTTAAAATATAAT
1 TTTAAAATATAAT
22444163 TTTAAAATATAA
1 TTTAAAATATAA
22444175 ACAATAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAAATATAAT
Found at i:22444180 original size:22 final size:22
Alignment explanation
Indices: 22444153--22444210 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
22444143 AAAAAAATTT
22444153 AAAATATAATTTTAAA-ATATAA
1 AAAATATAATTTTAAATAT-TAA
* *
22444175 ACAATAAGAATTTTAAATATTAA
1 AAAAT-ATAATTTTAAATATTAA
22444198 AAAATATAATTTT
1 AAAATATAATTTT
22444211 GAGACATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.37
23 17 0.57
24 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATAATTTTAAATATTAA
Found at i:22452588 original size:22 final size:21
Alignment explanation
Indices: 22452508--22452588 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 21
22452498 CATAAATTAT
* * * *
22452508 ATTTTTTATTAAATATATATA
1 ATTTTTTATCATATTTAAATA
22452529 A-TTTTTATCA-ATTTAAATA
1 ATTTTTTATCATATTTAAATA
* * *
22452548 ATTTTGTTTTAATATTTTAATATT
1 ATTTT-TTATCATA-TTTAA-ATA
22452572 ATTTTTTATCATATTTA
1 ATTTTTTATCATATTTA
22452589 TAATTATCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
19 8 0.17
20 11 0.23
21 5 0.11
22 5 0.11
23 11 0.23
24 7 0.15
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (21 bp):
ATTTTTTATCATATTTAAATA
Found at i:22452592 original size:24 final size:24
Alignment explanation
Indices: 22452530--22452592 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
22452520 ATATATATAA
22452530 TTTTTATCA-ATTTA-AATAATTT
1 TTTTTATCATATTTATAATAATTT
22452552 TGTTTTA--ATATTT-TAAT-ATTAT
1 T-TTTTATCATATTTATAATAATT-T
22452574 TTTTTATCATATTTATAAT
1 TTTTTATCATATTTATAAT
22452593 TATCAAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
21 9 0.26
22 10 0.29
23 11 0.32
24 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTATCATATTTATAATAATTT
Found at i:22453058 original size:63 final size:63
Alignment explanation
Indices: 22452977--22453095 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
22452967 AATTTAAAAT
* *
22452977 TTTAATAATTATTATTTATA-AATTTAATAAAAT-TAAAAATATATATTTT-ATATTTTCATGTC
1 TTTAATAATAATTATTTATATAA---AATAAAATATAAAAATATAAATTTTAATATTTTCATGTC
22453039 A
63 A
*
22453040 TTTAATATATAATT-TTTATATAAAATATAATATAAAAATATAAATTTTAATATTTT
1 TTTAATA-ATAATTATTTATATAAAATAAAATATAAAAATATAAATTTTAATATTTT
22453096 ATACGATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 7 0.14
62 15 0.31
63 20 0.41
64 7 0.14
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (63 bp):
TTTAATAATAATTATTTATATAAAATAAAATATAAAAATATAAATTTTAATATTTTCATGTCA
Found at i:22460418 original size:2 final size:2
Alignment explanation
Indices: 22460411--22460442 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22460401 ATCTATCTAC
22460411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22460443 GCACACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22469622 original size:82 final size:82
Alignment explanation
Indices: 22469485--22469649 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
22469475 AAATCCCTCC
*
22469485 AAAACGGCTTAAACACCAGCACAATTACCACTTGACTATCACAAGTTGATAATAATAACAACTTC
1 AAAACGGCTTAAACACCAGCACAATCACCACTTGACTATCACAAGTTGATAATAATAACAACTTC
22469550 TTAACATTTCAAATTGT
66 TTAACATTTCAAATTGT
22469567 AAAACGGCTTAAACACCAGCACAATCACCACTTGACTATC-CAAAGTTGATAATAATAACAACTT
1 AAAACGGCTTAAACACCAGCACAATCACCACTTGACTATCAC-AAGTTGATAATAATAACAACTT
22469631 CTTAACATTTCAAATTGT
65 CTTAACATTTCAAATTGT
22469649 A
1 A
22469650 TCAGAACTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 1 0.01
82 80 0.99
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.27
Consensus pattern (82 bp):
AAAACGGCTTAAACACCAGCACAATCACCACTTGACTATCACAAGTTGATAATAATAACAACTTC
TTAACATTTCAAATTGT
Found at i:22473452 original size:32 final size:33
Alignment explanation
Indices: 22473401--22473467 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
22473391 AAAAAATAAG
22473401 ATTCAATTATTTTTTATTTAAATATTTACATGA
1 ATTCAATTATTTTTTATTTAAATATTTACATGA
*
22473434 ATTCAATTA-TTTTTATTTAAATATTTATATGA
1 ATTCAATTATTTTTTATTTAAATATTTACATGA
22473466 AT
1 AT
22473468 GTACATGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 24 0.73
33 9 0.27
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (33 bp):
ATTCAATTATTTTTTATTTAAATATTTACATGA
Found at i:22487268 original size:29 final size:30
Alignment explanation
Indices: 22487221--22487277 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
22487211 AATTAAGATA
*
22487221 AAAATAAATATTTAAAAATTTAATTGATCC
1 AAAATAAATAATTAAAAATTTAATTGATCC
22487251 AAAATAAA-AATTAAAAATTTAATTGAT
1 AAAATAAATAATTAAAAATTTAATTGAT
22487278 TATAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATAAATAATTAAAAATTTAATTGATCC
Found at i:22488675 original size:13 final size:12
Alignment explanation
Indices: 22488653--22488688 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
22488643 TTGTGAAATT
22488653 TTTTAA-AAAAA
1 TTTTAATAAAAA
22488664 TATTTAATAAAAA
1 T-TTTAATAAAAA
22488677 TTTTAATAAAAA
1 TTTTAATAAAAA
22488689 AATTCAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 16 0.70
13 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TTTTAATAAAAA
Found at i:22488689 original size:13 final size:14
Alignment explanation
Indices: 22488658--22488689 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
22488648 AAATTTTTTA
22488658 AAAAAATATTTAAT
1 AAAAAATATTTAAT
22488672 -AAAAAT-TTTAAT
1 AAAAAATATTTAAT
22488684 AAAAAA
1 AAAAAA
22488690 ATTCAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATATTTAAT
Found at i:22492026 original size:7 final size:7
Alignment explanation
Indices: 22492014--22492046 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
22492004 CTTTCTGTGC
22492014 CCCACGT
1 CCCACGT
22492021 CCCACGT
1 CCCACGT
22492028 CCCACGT
1 CCCACGT
22492035 CCCACGT
1 CCCACGT
22492042 CCCAC
1 CCCAC
22492047 CTCCTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.61, G:0.12, T:0.12
Consensus pattern (7 bp):
CCCACGT
Found at i:22492727 original size:24 final size:22
Alignment explanation
Indices: 22492695--22492746 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 22
22492685 TAAAACATTA
22492695 AATTTTATA-TTTAAATTCAATTT
1 AATTTTATAGTTTAAATT--ATTT
22492718 AATTTATATATGTTTAAATTATTT
1 AATTT-TATA-GTTTAAATTATTT
22492742 AATTT
1 AATTT
22492747 GAAATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.19
24 13 0.50
26 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTATAGTTTAAATTATTT
Found at i:22495902 original size:26 final size:26
Alignment explanation
Indices: 22495845--22495895 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
22495835 TAAACTTTTT
* *
22495845 ATAAATATATATTAATATTTTTTAAA
1 ATAAAAATATATTAATATTTATTAAA
22495871 ATAAAAATATATTAAT-TTTAATTAA
1 ATAAAAATATATTAATATTT-ATTAA
22495896 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAAAAATATATTAATATTTATTAAA
Found at i:22503635 original size:24 final size:24
Alignment explanation
Indices: 22503599--22503644 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
22503589 AAAAAACAAA
22503599 TAAATAAATAGAT-AAATATTATTC
1 TAAATAAATAGATGAAA-ATTATTC
22503623 TAAA-AAATAAGATGAAAATTAT
1 TAAATAAAT-AGATGAAAATTAT
22503645 AAGTATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (24 bp):
TAAATAAATAGATGAAAATTATTC
Found at i:22512005 original size:2 final size:2
Alignment explanation
Indices: 22511998--22512032 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22511988 AGAAAAATCA
22511998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22512033 TACATGAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22512997 original size:29 final size:28
Alignment explanation
Indices: 22512951--22513007 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
22512941 TATATTTTAT
22512951 AATTTTTATTAATATAAAAATATAAAATA
1 AATTTTTATTAATATAAAAA-ATAAAATA
* *
22512980 AATTTTTATT-TTATTAAATAATAAAATA
1 AATTTTTATTAATA-TAAAAAATAAAATA
22513008 TTATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTTTTATTAATATAAAAAATAAAATA
Found at i:22513829 original size:21 final size:21
Alignment explanation
Indices: 22513804--22513847 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22513794 GATTACTTCA
*
22513804 AATAA-AATTTAAATTTAATTT
1 AATAATAATTTAAA-TAAATTT
*
22513825 AATAATTATTTAAATAAATTT
1 AATAATAATTTAAATAAATTT
22513846 AA
1 AA
22513848 AGTTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATAATTTAAATAAATTT
Found at i:22518183 original size:31 final size:31
Alignment explanation
Indices: 22518133--22518204 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
22518123 TATAAATTTT
* * *
22518133 TTTAATTTA-TTTATTAATGAAATATTATTA
1 TTTAATTTACTTCATTAATGAAATAATATCA
22518163 TTTAATTTACTTCATTAATGAAATAATATCA
1 TTTAATTTACTTCATTAATGAAATAATATCA
22518194 TTTAATTTACT
1 TTTAATTTACT
22518205 AATAGTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATTTACTTCATTAATGAAATAATATCA
Found at i:22518566 original size:16 final size:17
Alignment explanation
Indices: 22518537--22518570 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22518527 AATTTAAAAT
*
22518537 AAAATTTATATTATTAA
1 AAAATTAATATTATTAA
22518554 AAAATTAAT-TTATTAA
1 AAAATTAATATTATTAA
22518570 A
1 A
22518571 TATATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAATATTATTAA
Found at i:22520391 original size:27 final size:27
Alignment explanation
Indices: 22520361--22520419 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
22520351 TATTTAAATT
22520361 TAAATTTATAAGATATTTTT-TA-TAAAA
1 TAAATTTATAA-A-ATTTTTATATTAAAA
*
22520388 TAAAATTATAAAATTTTTATATTAAAA
1 TAAATTTATAAAATTTTTATATTAAAA
*
22520415 CAAAT
1 TAAAT
22520420 AATATTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 6 0.22
26 3 0.11
27 18 0.67
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAATTTATAAAATTTTTATATTAAAA
Found at i:22528351 original size:13 final size:13
Alignment explanation
Indices: 22528333--22528366 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
22528323 TAAAAGTATT
*
22528333 ATTTAATATTTTA
1 ATTTAATATGTTA
*
22528346 ATTTAAGATGTTA
1 ATTTAATATGTTA
22528359 ATTTAATA
1 ATTTAATA
22528367 AAAATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
ATTTAATATGTTA
Found at i:22528400 original size:18 final size:18
Alignment explanation
Indices: 22528379--22528414 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22528369 AATATTATAT
22528379 TTATATATAATTAAAATA
1 TTATATATAATTAAAATA
* *
22528397 TTATTTATATTTAAAATA
1 TTATATATAATTAAAATA
22528415 ATATTTTATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATATAATTAAAATA
Found at i:22528424 original size:19 final size:18
Alignment explanation
Indices: 22528384--22528425 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22528374 TATATTTATA
*
22528384 TATAATTAAAATATTATT
1 TATAATTAAAATAATATT
*
22528402 TATATTTAAAATAATATTT
1 TATAATTAAAATAATA-TT
22528421 TATAA
1 TATAA
22528426 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAATTAAAATAATATT
Found at i:22531967 original size:20 final size:20
Alignment explanation
Indices: 22531927--22531967 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22531917 TTGAATCAAA
*
22531927 TTATATATTTTTATAATTTT
1 TTATATATTTTTATAAATTT
22531947 TTATATATTTTTCA-AAATTT
1 TTATATATTTTT-ATAAATTT
22531967 T
1 T
22531968 ATAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATATTTTTATAAATTT
Found at i:22533450 original size:33 final size:32
Alignment explanation
Indices: 22533383--22533461 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
22533373 TAAATTTGAT
* *
22533383 AATTTATATATTTATATTATATAAAATATTAA
1 AATTTATGTATTTATATTATATAAAATATAAA
***
22533415 AATTTATGTATTTTATATTATATTTTATATAAA
1 AATTTATGTA-TTTATATTATATAAAATATAAA
22533448 AA-TTATGT-TTTATA
1 AATTTATGTATTTATA
22533462 ATTCATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
32 15 0.37
33 20 0.49
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (32 bp):
AATTTATGTATTTATATTATATAAAATATAAA
Found at i:22533542 original size:27 final size:26
Alignment explanation
Indices: 22533511--22533578 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
22533501 TTGTTAAATT
*
22533511 TATATATAATTTAAATCATATTATTT
1 TATATATAATTTAAATCATATTATTA
*
22533537 TCATATCAT-ATTTATATCATATTATTA
1 T-ATAT-ATAATTTAAATCATATTATTA
*
22533564 TAT-TATATTTTAAAT
1 TATATATAATTTAAAT
22533579 TATCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.06
25 7 0.20
26 3 0.09
27 21 0.60
28 2 0.06
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATATAATTTAAATCATATTATTA
Found at i:22533886 original size:32 final size:29
Alignment explanation
Indices: 22533809--22533892 Score: 80
Period size: 32 Copynumber: 2.8 Consensus size: 29
22533799 ACCAAATACA
*
22533809 ATATTATATAAAAAT-ATATTTTTAATTAT
1 ATATTTTA-AAAAATAATATTTTTAATTAT
* * *
22533838 ATATATTAATATAATAATATTTTTAAATATTTT
1 ATATTTTAA-AAAATAATATTTTT--A-ATTAT
22533871 ATATTTTAAAAAATAATATTTT
1 ATATTTTAAAAAATAATATTTT
22533893 ATTAATTTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 1 0.02
29 10 0.23
30 8 0.18
32 13 0.30
33 12 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
ATATTTTAAAAAATAATATTTTTAATTAT
Found at i:22534119 original size:2 final size:2
Alignment explanation
Indices: 22534112--22534156 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
22534102 AAAGAAAATA
*
22534112 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22534154 AT A
1 AT A
22534157 ATGTATGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:22536229 original size:22 final size:21
Alignment explanation
Indices: 22536188--22536230 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
22536178 TATTTGATGC
*
22536188 ATAAAATAATAAAAATTTAAT
1 ATAAAATAATAAAAAATTAAT
22536209 ATAAAAGT-ATAAAAAGATTAAT
1 ATAAAA-TAATAAAAA-ATTAAT
22536231 TAATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAAAATAATAAAAAATTAAT
Found at i:22536322 original size:21 final size:20
Alignment explanation
Indices: 22536296--22536344 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
22536286 TTCTACCTTT
*
22536296 AAAAATTATTT-ATATAAATTA
1 AAAAATTATTTCA-A-AAAATA
*
22536317 AAAAATAATTTCAAAAAATA
1 AAAAATTATTTCAAAAAATA
22536337 AAAAATTA
1 AAAAATTA
22536345 AATTATCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTATTTCAAAAAATA
Found at i:22536841 original size:19 final size:19
Alignment explanation
Indices: 22536791--22536867 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
22536781 TAATAAAAAT
*
22536791 TTTAAATTTAATTCATATTTAA
1 TTTAAATTTAATT--T-TTAAA
* *
22536813 TTGAATTTTAATTTTTAAA
1 TTTAAATTTAATTTTTAAA
***
22536832 TTTAAATTTAATTAAAAAA
1 TTTAAATTTAATTTTTAAA
**
22536851 AATAAATTTAATTTTTA
1 TTTAAATTTAATTTTTA
22536868 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
19 30 0.71
20 1 0.02
22 11 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (19 bp):
TTTAAATTTAATTTTTAAA
Found at i:22537020 original size:22 final size:22
Alignment explanation
Indices: 22536969--22537025 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
22536959 AATATTAAAA
22536969 TTAAA-TAAATTTATAAATTAT
1 TTAAATTAAATTTATAAATTAT
22536990 TTAAATTAAATATT-TAAA-TAT
1 TTAAATTAAAT-TTATAAATTAT
*
22537011 TTAAATTTAATTTAT
1 TTAAATTAAATTTAT
22537026 TCGATAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.06
21 19 0.59
22 9 0.28
23 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAATTAAATTTATAAATTAT
Found at i:22537685 original size:23 final size:24
Alignment explanation
Indices: 22537627--22537686 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
22537617 GTGAAAAAAA
22537627 TAAATTAAAATTATATTATTTGATT
1 TAAATT-AAATTATATTATTTGATT
** * * *
22537652 GGATTTCAATT-TTTTATTTGATT
1 TAAATTAAATTATATTATTTGATT
22537675 TAAATTAAATTA
1 TAAATTAAATTA
22537687 AAATATTAAA
Statistics
Matches: 25, Mismatches: 9, Indels: 3
0.68 0.24 0.08
Matches are distributed among these distances:
23 18 0.72
24 4 0.16
25 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (24 bp):
TAAATTAAATTATATTATTTGATT
Found at i:22537695 original size:18 final size:18
Alignment explanation
Indices: 22537674--22537755 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
22537664 TTTATTTGAT
22537674 TTAAATTAAATTAAAATA
1 TTAAATTAAATTAAAATA
* *
22537692 TTAAA-TATA-TATAAT-
1 TTAAATTAAATTAAAATA
*
22537707 TTAAATTAAATTTCAAATA
1 TTAAATTAAA-TTAAAATA
*
22537726 -AAAATTAAAATT-AAATA
1 TTAAATT-AAATTAAAATA
* *
22537743 TTATATTATATTA
1 TTAAATTAAATTA
22537756 TTTAATTTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
15 5 0.10
16 8 0.17
17 12 0.25
18 20 0.42
19 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTAAAATA
Found at i:22537763 original size:44 final size:43
Alignment explanation
Indices: 22537681--22537797 Score: 136
Period size: 44 Copynumber: 2.7 Consensus size: 43
22537671 GATTTAAATT
* *
22537681 AAATTAAAATATTAAATATATATAATT-TAAATTAAATTTCAAATAA
1 AAATT-AAA-ATTAAATAT-TAT-ATTATATATTTAATTTCAAATAA
22537727 AAATTAAAATTAAATATTATATTATATTATTTAATTTCAAATAA
1 AAATTAAAATTAAATATTATATTATA-TATTTAATTTCAAATAA
22537771 AAATT-AAA-T--ATATTATATTATATATTT
1 AAATTAAAATTAAATATTATATTATATATTT
22537798 TTATTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
39 5 0.07
40 13 0.19
42 4 0.06
43 8 0.12
44 29 0.43
45 3 0.04
46 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (43 bp):
AAATTAAAATTAAATATTATATTATATATTTAATTTCAAATAA
Found at i:22537903 original size:22 final size:23
Alignment explanation
Indices: 22537860--22537914 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
22537850 AATTTATTTG
* *
22537860 AATATATTAAAACTATATTAAAAT
1 AATATA-TAAAAATATAATAAAAT
22537884 AATATATAAAAATA-AATAAAAT
1 AATATATAAAAATATAATAAAAT
*
22537906 ACTAT-TAAA
1 AATATATAAA
22537915 TTAAACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 11 0.39
23 7 0.25
24 6 0.21
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATATAAAAATATAATAAAAT
Found at i:22537958 original size:17 final size:17
Alignment explanation
Indices: 22537936--22537989 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
22537926 TAAATTTTAT
22537936 AATTTAAATTATATAAA
1 AATTTAAATTATATAAA
* * **
22537953 AATTTAATTTAAATTCA
1 AATTTAAATTATATAAA
22537970 AA-TTAAATT-T-TAAA
1 AATTTAAATTATATAAA
22537984 AATTTA
1 AATTTA
22537990 TAAATTTATA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 6 0.21
17 15 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATTATATAAA
Found at i:22537977 original size:22 final size:22
Alignment explanation
Indices: 22537935--22537982 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
22537925 TTAAATTTTA
*
22537935 TAATTTAAATTATATAAAAATT
1 TAATTTAAATTAAATAAAAATT
* *
22537957 TAATTTAAATTCAAATTAAATTT
1 TAATTTAAATT-AAATAAAAATT
22537980 TAA
1 TAA
22537983 AAATTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTTAAATTAAATAAAAATT
Found at i:22538522 original size:13 final size:14
Alignment explanation
Indices: 22538496--22538532 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
22538486 TTTAAACATA
22538496 TTAAAAAT-AAA-T
1 TTAAAAATAAAATT
*
22538508 TTAAAATTAAAATT
1 TTAAAAATAAAATT
22538522 TTAAAAATAAA
1 TTAAAAATAAA
22538533 TTGGTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 7 0.33
13 3 0.14
14 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAATAAAATT
Found at i:22538533 original size:13 final size:13
Alignment explanation
Indices: 22538496--22538534 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
22538486 TTTAAACATA
22538496 TTAAAAATAAA-T
1 TTAAAAATAAATT
*
22538508 TTAAAATTAAAATT
1 TTAAAAAT-AAATT
22538522 TTAAAAATAAATT
1 TTAAAAATAAATT
22538535 GGTTCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 8 0.35
14 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATAAATT
Found at i:22538856 original size:11 final size:11
Alignment explanation
Indices: 22538840--22538882 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
22538830 TATTTATGAA
22538840 ATTTGTTTATT
1 ATTTGTTTATT
*
22538851 ATTTGTTTGTT
1 ATTTGTTTATT
*
22538862 ATTTATTTATT
1 ATTTGTTTATT
22538873 ATTTGTTTAT
1 ATTTGTTTAT
22538883 AATAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
ATTTGTTTATT
Found at i:22538893 original size:22 final size:22
Alignment explanation
Indices: 22538845--22538895 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
22538835 ATGAAATTTG
* * *
22538845 TTTATTATTTGTTTGTTATTTA
1 TTTATTATTTGTTTATAATATA
22538867 TTTATTATTTGTTTATAATA-A
1 TTTATTATTTGTTTATAATATA
22538888 TATTATTA
1 T-TTATTA
22538896 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (22 bp):
TTTATTATTTGTTTATAATATA
Found at i:22538977 original size:20 final size:21
Alignment explanation
Indices: 22538932--22538988 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
22538922 CAAATCTTAT
*
22538932 TTTAAGATTCATTTATATTAG
1 TTTAAGATTTATTTATATTAG
*
22538953 CTTAA-ATTTATTTATATTCA-
1 TTTAAGATTTATTTATATT-AG
*
22538973 TTTAAGGTTTATTTAT
1 TTTAAGATTTATTTAT
22538989 TTAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTAAGATTTATTTATATTAG
Found at i:22538986 original size:25 final size:25
Alignment explanation
Indices: 22538957--22539024 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
22538947 TATTAGCTTA
22538957 AATTTATTTATATTCATTTAAGGTT-T
1 AATTTATTTATATTCATTTAA--TTAT
* *
22538983 -ATTTATTTAAATTTATTTAATTAT
1 AATTTATTTATATTCATTTAATTAT
22539007 AATTTATTTATTATTCAT
1 AATTTATTTA-TATTCAT
22539025 AAATATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 27 0.77
26 5 0.14
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (25 bp):
AATTTATTTATATTCATTTAATTAT
Found at i:22538990 original size:15 final size:13
Alignment explanation
Indices: 22538958--22539018 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 13
22538948 ATTAGCTTAA
22538958 ATTT-ATTTATATT
1 ATTTAATTTAT-TT
22538971 CATTTAAGGTTTATTT
1 -ATTTAA--TTTATTT
22538987 ATTTAAATTTATTT
1 ATTT-AATTTATTT
22539001 AATTATAATTTATTT
1 -ATT-TAATTTATTT
22539016 ATT
1 ATT
22539019 ATTCATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
14 14 0.34
15 17 0.41
16 5 0.12
17 5 0.12
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (13 bp):
ATTTAATTTATTT
Found at i:22538999 original size:14 final size:15
Alignment explanation
Indices: 22538980--22539018 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
22538970 TCATTTAAGG
22538980 TTTATTTATTTA-AA
1 TTTATTTATTTATAA
*
22538994 TTTATTTAATTATAA
1 TTTATTTATTTATAA
22539009 TTTATTTATT
1 TTTATTTATT
22539019 ATTCATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTTATTTATAA
Found at i:22539387 original size:2 final size:2
Alignment explanation
Indices: 22539374--22539410 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
22539364 ATTATAACAT
* *
22539374 TA TA TC TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22539411 CAAGGGGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:22540107 original size:2 final size:2
Alignment explanation
Indices: 22540100--22540134 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22540090 TCGTAGAATT
22540100 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22540135 ATGTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22540309 original size:21 final size:20
Alignment explanation
Indices: 22540266--22540306 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22540256 GAAGAGTTAA
*
22540266 TAATATATGTTAAAATAATT
1 TAATATATATTAAAATAATT
22540286 TAATA-ATATTAAAATCAATT
1 TAATATATATTAAAAT-AATT
22540306 T
1 T
22540307 TAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATATATATTAAAATAATT
Found at i:22540316 original size:18 final size:18
Alignment explanation
Indices: 22540275--22540317 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
22540265 ATAATATATG
*
22540275 TTAAAATAATTTAATAATA
1 TTAAAATAATTT-ATAAAA
22540294 TTAAAATCAATTT-TAAAA
1 TTAAAAT-AATTTATAAAA
22540312 TTAAAA
1 TTAAAA
22540318 ATCTCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATAATTTATAAAA
Found at i:22541595 original size:32 final size:31
Alignment explanation
Indices: 22541507--22541595 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 31
22541497 TATTAAGATA
* *
22541507 ATATAAA--AAATTAAAATTTAAAAATAAAT
1 ATATAAATCAAATCAAATTTTAAAAATAAAT
** *
22541536 ATATAAATCAAATCAAATCATATAAAATAATT
1 ATATAAATCAAATCAAATTTTA-AAAATAAAT
*
22541568 ATTTAAATTCAAATCAAATTTTAAAAAT
1 ATATAAA-TCAAATCAAATTTTAAAAAT
22541596 TTATATTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 7 0.15
31 9 0.19
32 19 0.40
33 13 0.27
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.34
Consensus pattern (31 bp):
ATATAAATCAAATCAAATTTTAAAAATAAAT
Found at i:22564023 original size:21 final size:21
Alignment explanation
Indices: 22563975--22564021 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
22563965 AATATATTTT
*
22563975 TATTTATCAAATTCACATATA
1 TATTTATCAAATTCACATACA
*
22563996 TATTTATCAAATTCATATACCA
1 TATTTATCAAATTCACATA-CA
22564018 TATT
1 TATT
22564022 ATTTTGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTATCAAATTCACATACA
Found at i:22578028 original size:22 final size:24
Alignment explanation
Indices: 22577991--22578034 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
22577981 ATATAATATA
22577991 AAAATGATAGTTTAAAATTTTAAT
1 AAAATGATAGTTTAAAATTTTAAT
*
22578015 AAAAT-ATA-TTTAAATTTTTA
1 AAAATGATAGTTTAAAATTTTA
22578035 TATTGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 3 0.16
24 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
AAAATGATAGTTTAAAATTTTAAT
Done.