Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 103 of 160
Found at i:19524852 original size:40 final size:40
Alignment explanation
Indices: 19524680--19524987 Score: 213
Period size: 40 Copynumber: 7.7 Consensus size: 40
19524670 CTTACTCCGA
* *
19524680 ATCTTGAAAATCATTCACAAAATTTAAAACTCTATAC--GGAG
1 ATCTTGAAAATCATTCA-AAAATTTAAAA-T-TATGCTTGAAG
* * * *
19524721 ATCTTGGAAATCGTTAAAAAATTTAAGATTCTAT-CTTG-AG
1 ATCTTGAAAATCATTCAAAAATTTAA-AAT-TATGCTTGAAG
* * * * * * *
19524761 GTCTTGAAAATCATTCAAGAGTTTAAAATTCTACCCTAAAG
1 ATCTTGAAAATCATTCAAAAATTTAAAATTAT-GCTTGAAG
*
19524802 A-CTTGAAAATCATTCAAAAATTTAAAATTATGCTTGGAG
1 ATCTTGAAAATCATTCAAAAATTTAAAATTATGCTTGAAG
* * * * * *
19524841 ATTTTGGAAATCATTCAAATATTTAAAATTTTACTT-AATC
1 ATCTTGAAAATCATTCAAAAATTTAAAATTATGCTTGAA-G
* * *
19524881 ATCATGAAAATAATTCAAAAATTTAAAATTTTG--TGCAAAG
1 ATCTTGAAAATCATTCAAAAATTTAAAATTATGCTTG--AAG
* * *
19524921 GTCTTG-AAATCATTCAAAAATTTAAAATTATGC-TCAAA
1 ATCTTGAAAATCATTCAAAAATTTAAAATTATGCTTGAAG
*
19524959 AGTCTTGAAAATCATTTAAAAATTTAAAA
1 A-TCTTGAAAATCATTCAAAAATTTAAAA
19524988 ATTTTGTTCA
Statistics
Matches: 209, Mismatches: 44, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
38 5 0.02
39 38 0.18
40 146 0.70
41 20 0.10
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (40 bp):
ATCTTGAAAATCATTCAAAAATTTAAAATTATGCTTGAAG
Found at i:19534864 original size:9 final size:10
Alignment explanation
Indices: 19534847--19534872 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19534837 TAAATCGAAG
19534847 AGAAAAAAAA
1 AGAAAAAAAA
19534857 AGAAAAAAAA
1 AGAAAAAAAA
19534867 AGAAAA
1 AGAAAA
19534873 CGAGGAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:19535991 original size:20 final size:20
Alignment explanation
Indices: 19535963--19536011 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
19535953 GCTTCTGTGC
19535963 CTAAAAAAATTAAATAATGTT
1 CTAAAAAAA-TAAATAATGTT
*
19535984 CTAAAAAAATAAATGATGTT
1 CTAAAAAAATAAATAATGTT
*
19536004 TTAAAAAA
1 CTAAAAAA
19536012 GCAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (20 bp):
CTAAAAAAATAAATAATGTT
Found at i:19548657 original size:7 final size:7
Alignment explanation
Indices: 19548641--19548686 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
19548631 GGGATTTGTT
19548641 AAAAAGAG
1 AAAAA-AG
19548649 AAAAAAG
1 AAAAAAG
19548656 -AAAAAG
1 AAAAAAG
19548662 AAAAAAAG
1 -AAAAAAG
19548670 AAAAAAG
1 AAAAAAG
19548677 AAAAAA-
1 AAAAAAG
19548683 AAAA
1 AAAA
19548687 GAGGTGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.28
7 15 0.42
8 11 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:19548661 original size:15 final size:15
Alignment explanation
Indices: 19548641--19548686 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
19548631 GGGATTTGTT
19548641 AAAAAGAGAAAAAAG
1 AAAAAGAGAAAAAAG
19548656 AAAAAGA-AAAAAAG
1 AAAAAGAGAAAAAAG
19548670 AAAAA-AGAAAAAA-
1 AAAAAGAGAAAAAAG
19548683 AAAA
1 AAAA
19548687 GAGGTGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.17
14 18 0.60
15 7 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAAG
Found at i:19548671 original size:21 final size:20
Alignment explanation
Indices: 19548641--19548686 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
19548631 GGGATTTGTT
*
19548641 AAAAAGAGAAAAAAGAAAAA
1 AAAAAAAGAAAAAAGAAAAA
19548661 GAAAAAAAGAAAAAAGAAAAA
1 -AAAAAAAGAAAAAAGAAAAA
19548682 AAAAA
1 AAAAA
19548687 GAGGTGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAAAAGAAAAA
Found at i:19549147 original size:33 final size:33
Alignment explanation
Indices: 19549084--19549147 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
19549074 GTCTCCCTTC
* *
19549084 TTATTTTCTAACTTGCGATTTAATATTGATCCT
1 TTATTTTCTAACTTACGATTTAATACTGATCCT
*
19549117 TTATTTTCTAACTTACGATTTAATCCTGATC
1 TTATTTTCTAACTTACGATTTAATACTGATC
19549148 ATTTTATCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (33 bp):
TTATTTTCTAACTTACGATTTAATACTGATCCT
Found at i:19549221 original size:72 final size:72
Alignment explanation
Indices: 19549138--19549318 Score: 231
Period size: 72 Copynumber: 2.5 Consensus size: 72
19549128 CTTACGATTT
*
19549138 AATCCTGATCATTTTATCTCCCTATTCACGATTTAGTCCTAGTCAT-TCTTCTTAGTTTTC-TAC
1 AATCCTGATCATTTTATCTCCCAATTCACGATTTAGTCCTAGTCATCT-TTCTTAG-TTTCATAC
*
19549201 TTGTAGTTC
64 TTGCAGTTC
* * *
19549210 AATCCTAATCATTTTATTTCCCAATTCACAATTTAGTCCTAGTCATCTTTCTTAGTTTCATACTT
1 AATCCTGATCATTTTATCTCCCAATTCACGATTTAGTCCTAGTCATCTTTCTTAGTTTCATACTT
*
19549275 GCATTTC
66 GCAGTTC
* * * * *
19549282 AATCCGGTTCATCTTGTCTCCCAATTCATGATTTAGT
1 AATCCTGATCATTTTATCTCCCAATTCACGATTTAGT
19549319 TTTGATCATT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
71 4 0.04
72 88 0.95
73 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (72 bp):
AATCCTGATCATTTTATCTCCCAATTCACGATTTAGTCCTAGTCATCTTTCTTAGTTTCATACTT
GCAGTTC
Found at i:19551682 original size:15 final size:15
Alignment explanation
Indices: 19551662--19551690 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19551652 AAATATTTAA
19551662 AAATTTTAAAAAATT
1 AAATTTTAAAAAATT
19551677 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
19551691 AGGGCCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTTAAAAAATT
Found at i:19555358 original size:124 final size:124
Alignment explanation
Indices: 19555204--19555570 Score: 556
Period size: 124 Copynumber: 3.0 Consensus size: 124
19555194 GTGCCATCAA
* * * * *
19555204 TATTTTATATTTTATCTAGTCATTCCTAATGTGCATGTAGACACGTAGATTAATTCTTGGATCAT
1 TATTTCATATTTTATCTAGTCATTCCTAATGTGCATGTAGCCACATAGATCAATTCTTAGATCAT
19555269 ACCATTGACCTTGATGATATGCCTCTCAATATTATCATTTGAATCCATTCGGTAATTAG
66 ACCATTGACCTTGATGATATGCCTCTCAATATTATCATTTGAATCCATTCGGTAATTAG
* * *
19555328 TATTTCATATTTTATCTTGTCATTCCTAATGTGCATGTCA-CCATATAGATCAATTATTAGATCA
1 TATTTCATATTTTATCTAGTCATTCCTAATGTGCATGT-AGCCACATAGATCAATTCTTAGATCA
* * *
19555392 TACTATTGACCTTGATGATATGCCTCTCAATATTATAATTTGAATCCATTCAGTAATTAG
65 TACCATTGACCTTGATGATATGCCTCTCAATATTATCATTTGAATCCATTCGGTAATTAG
* * * *
19555452 TATTTCACATTTTATCTGGTCATTCATAATGTGCATGTAGCCACATAGATCAATTCTTAGATTAT
1 TATTTCATATTTTATCTAGTCATTCCTAATGTGCATGTAGCCACATAGATCAATTCTTAGATCAT
* * *
19555517 ACCATTGACCTTGATGATATGCCTCTAAATATTATCATTTGAATCTATTTGGTA
66 ACCATTGACCTTGATGATATGCCTCTCAATATTATCATTTGAATCCATTCGGTA
19555571 TTGCATCAAT
Statistics
Matches: 218, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
123 1 0.00
124 216 0.99
125 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (124 bp):
TATTTCATATTTTATCTAGTCATTCCTAATGTGCATGTAGCCACATAGATCAATTCTTAGATCAT
ACCATTGACCTTGATGATATGCCTCTCAATATTATCATTTGAATCCATTCGGTAATTAG
Found at i:19560507 original size:14 final size:14
Alignment explanation
Indices: 19560488--19560518 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19560478 ACTCTCTCTC
19560488 AATTAATGCATCCT
1 AATTAATGCATCCT
19560502 AATTAATGCATCCT
1 AATTAATGCATCCT
19560516 AAT
1 AAT
19560519 CTAACGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (14 bp):
AATTAATGCATCCT
Found at i:19560968 original size:36 final size:36
Alignment explanation
Indices: 19560921--19560994 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
19560911 TAGGATAAAG
*
19560921 TAAGATATGCTTGGAA-CCTAAAACATTACTAGCAAT
1 TAAGATATGCTT-AAAGCCTAAAACATTACTAGCAAT
19560957 TAAGATATGCTTAAAGCCTAAAACATTACTAGCAAT
1 TAAGATATGCTTAAAGCCTAAAACATTACTAGCAAT
19560993 TA
1 TA
19560995 CTAGCAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (36 bp):
TAAGATATGCTTAAAGCCTAAAACATTACTAGCAAT
Found at i:19561023 original size:46 final size:46
Alignment explanation
Indices: 19560945--19561040 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
19560935 AACCTAAAAC
19560945 ATTACTAGCAATTAAGATATGCTTAAAGCCTAAAACATTACTAGCA
1 ATTACTAGCAATTAAGATATGCTTAAAGCCTAAAACATTACTAGCA
* *
19560991 ATTACTAGCAATTAAGATATGTTTGGAA-CCTAAAACATTACTAGCA
1 ATTACTAGCAATTAAGATATGCTT-AAAGCCTAAAACATTACTAGCA
19561037 ATTA
1 ATTA
19561041 AGCATAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (46 bp):
ATTACTAGCAATTAAGATATGCTTAAAGCCTAAAACATTACTAGCA
Found at i:19562275 original size:10 final size:10
Alignment explanation
Indices: 19562260--19562287 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
19562250 CAAAATGTAG
19562260 GCTCATTTAA
1 GCTCATTTAA
19562270 GCTCATTTAA
1 GCTCATTTAA
19562280 GCTCATTT
1 GCTCATTT
19562288 CAAGTTCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (10 bp):
GCTCATTTAA
Found at i:19566084 original size:1 final size:1
Alignment explanation
Indices: 19566078--19566120 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
19566068 TGCTAAATGT
19566078 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19566121 CACTGTTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19567444 original size:21 final size:17
Alignment explanation
Indices: 19567420--19567471 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
19567410 TGTTTGGTGC
19567420 ATAAGATTATGATATGATAGA
1 ATAAGATTAT-AT-T-AT-GA
*
19567441 ATAAGATCATATTATGA
1 ATAAGATTATATTATGA
*
19567458 ATAAGATTAGATTA
1 ATAAGATTATATTA
19567472 AATAATGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.50
18 2 0.07
19 1 0.04
20 2 0.07
21 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (17 bp):
ATAAGATTATATTATGA
Found at i:19580068 original size:18 final size:20
Alignment explanation
Indices: 19580028--19580069 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
19580018 TTTAATAATT
*
19580028 TAAATTATTAATATTTTATA
1 TAAATTATTAATATTTTAAA
19580048 TAAATTATT-AT-TTTTAAA
1 TAAATTATTAATATTTTAAA
19580066 TAAA
1 TAAA
19580070 ATTGAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATTATTAATATTTTAAA
Found at i:19581535 original size:13 final size:12
Alignment explanation
Indices: 19581513--19581546 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
19581503 TTTTTTTTCA
19581513 TCTTTT-TTTTT
1 TCTTTTCTTTTT
19581524 TCTTTCTCTTTTT
1 TCTTT-TCTTTTT
19581537 TCTTTTCTTT
1 TCTTTTCTTT
19581547 GCCGAACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 6 0.29
13 10 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTCTTTTT
Found at i:19581543 original size:18 final size:18
Alignment explanation
Indices: 19581501--19581546 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
19581491 TGATTGTTGG
19581501 TTTTTTT-TTTCATCTTT
1 TTTTTTTCTTTCATCTTT
19581518 TTTTTTTCTTTC-TCTTT
1 TTTTTTTCTTTCATCTTT
19581535 TTTCTTTTCTTT
1 TTT-TTTTCTTT
19581547 GCCGAACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTCTTTCATCTTT
Found at i:19582011 original size:21 final size:22
Alignment explanation
Indices: 19581987--19582029 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
19581977 TTCATTTACT
19581987 TAAAAATAAAAAATAA-AAAAA
1 TAAAAATAAAAAATAACAAAAA
** *
19582008 TAAATGTATAAAATAACAAAAA
1 TAAAAATAAAAAATAACAAAAA
19582030 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
TAAAAATAAAAAATAACAAAAA
Found at i:19592278 original size:1 final size:1
Alignment explanation
Indices: 19592272--19592307 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
19592262 GCCTAAAAGT
* *
19592272 AAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19592308 CTCAGATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:19594348 original size:19 final size:19
Alignment explanation
Indices: 19594312--19594348 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19594302 TTTAAAAAAT
* *
19594312 TAAAATAACATAATATATA
1 TAAAATAACAAAAAATATA
19594331 TAAAATAACAAAAAATAT
1 TAAAATAACAAAAAATAT
19594349 TTTTTTATAA
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:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAATAACAAAAAATATA
Found at i:19594570 original size:27 final size:26
Alignment explanation
Indices: 19594525--19594575 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
19594515 TGGTTCTAAT
*
19594525 TTATTTTTTTCAAATAAAAATAAAATA
1 TTATTTTTTTCAAA-AAAAAAAAAATA
19594552 TTATTTTTTAT-AAAAAAAAAAAAA
1 TTATTTTTT-TCAAAAAAAAAAAAA
19594576 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 12 0.55
28 1 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TTATTTTTTTCAAAAAAAAAAAAATA
Found at i:19596722 original size:46 final size:46
Alignment explanation
Indices: 19596636--19596724 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
19596626 ACATAAAATT
* * *
19596636 TAAAATTTTAATTCTAAAGTGTTAAAAATTATTGACTAAAATACTC
1 TAAAATTTTAATTCAAAAATGTTAAAAATTATGGACTAAAATACTC
* *
19596682 TAAAATTTTAATTCCAAAAATGTT-AAAGTTATGGATTAAAATA
1 TAAAATTTTAATT-CAAAAATGTTAAAAATTATGGACTAAAATA
19596725 TCCTTAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 29 0.78
47 8 0.22
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (46 bp):
TAAAATTTTAATTCAAAAATGTTAAAAATTATGGACTAAAATACTC
Found at i:19598041 original size:22 final size:20
Alignment explanation
Indices: 19597998--19598037 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19597988 ATTATGTATT
19597998 TTAAATTTTTATATACTAAA
1 TTAAATTTTTATATACTAAA
19598018 TTAAATTTTTATATACTAAA
1 TTAAATTTTTATATACTAAA
19598038 AATTTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTTTTATATACTAAA
Found at i:19599871 original size:24 final size:26
Alignment explanation
Indices: 19599821--19599874 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
19599811 AACTTAATAA
** *
19599821 TTTTATAAAATTGTTATTTTTTTAAT
1 TTTTATAAAATTGTTATTTACTAAAT
19599847 TTTTAT-AAATT-TTATTTACTAAAT
1 TTTTATAAAATTGTTATTTACTAAAT
19599871 TTTT
1 TTTT
19599875 TGTTACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 5 0.20
26 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTATAAAATTGTTATTTACTAAAT
Found at i:19600382 original size:21 final size:20
Alignment explanation
Indices: 19600342--19600425 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
19600332 ATAGAACATA
* *
19600342 TTAGTAAATAATC-GATAAC
1 TTAGTAATTAATCACATAAC
19600361 TTAGTAATTAATCACCATAAC
1 TTAGTAATTAATCA-CATAAC
* *
19600382 TTA-AAAGTAATCACTATAAC
1 TTAGTAATTAATCAC-ATAAC
19600402 GTAATAGTAATT-ATCA-ATAAC
1 -T--TAGTAATTAATCACATAAC
19600423 TTA
1 TTA
19600426 ATAGTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.04
19 13 0.25
20 14 0.27
21 14 0.27
23 6 0.12
24 3 0.06
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.33
Consensus pattern (20 bp):
TTAGTAATTAATCACATAAC
Found at i:19600394 original size:20 final size:20
Alignment explanation
Indices: 19600369--19600426 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
19600359 ACTTAGTAAT
*
19600369 TAATCACCATAACTTAAAAG
1 TAATCACAATAACTTAAAAG
* * *
19600389 TAATCACTATAACGTAATAG
1 TAATCACAATAACTTAAAAG
*
19600409 TAATTATCAATAACTTAA
1 TAATCA-CAATAACTTAA
19600427 TAGTTAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (20 bp):
TAATCACAATAACTTAAAAG
Found at i:19600450 original size:43 final size:42
Alignment explanation
Indices: 19600362--19600459 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 42
19600352 ATCGATAACT
*
19600362 TAGTAATTAATCACCATAACTTAAAAGTAATCACTATAACGTAA
1 TAGTAATT-ATCA-CATAACTTAAAAGTAATAACTATAACGTAA
* * *
19600406 TAGTAATTATCA-ATAACTTAATAGTTAATAAGTGATAACTTAA
1 TAGTAATTATCACATAACTTAAAAG-TAATAACT-ATAACGTAA
19600449 TAGTAAATTAT
1 TAGT-AATTAT
19600460 GATTTGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 11 0.23
42 6 0.13
43 16 0.34
44 14 0.30
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (42 bp):
TAGTAATTATCACATAACTTAAAAGTAATAACTATAACGTAA
Found at i:19600718 original size:22 final size:22
Alignment explanation
Indices: 19600693--19600900 Score: 62
Period size: 22 Copynumber: 9.8 Consensus size: 22
19600683 AATTTAGTAA
*
19600693 TAAATCAATTATAACTTAATAG
1 TAAATCAATGATAACTTAATAG
* * *
19600715 TAAATTAGTGATAATTTAATAG
1 TAAATCAATGATAACTTAATAG
** **
19600737 TAAAT-AAGTTTTAGGTTAATAG
1 TAAATCAA-TGATAACTTAATAG
* * *
19600759 T-AATTAAT--TGA--TAGTAG
1 TAAATCAATGATAACTTAATAG
* * *
19600776 TGAATC-ATAAATAACTTAGTAG
1 TAAATCAAT-GATAACTTAATAG
* * *
19600798 AAAATCAATGATAATTTAATAA
1 TAAATCAATGATAACTTAATAG
* *
19600820 TAAAT-AATTGATAATTTATTAG
1 TAAATCAA-TGATAACTTAATAG
* * * *
19600842 TTAATCATTAGA-AATTTAGTAG
1 TAAATCAAT-GATAACTTAATAG
*
19600864 TAAAT---TGATAACTTAACAG
1 TAAATCAATGATAACTTAATAG
* *
19600883 TAAATCACTAATAACTTA
1 TAAATCAATGATAACTTA
19600901 GTTATAAAGA
Statistics
Matches: 139, Mismatches: 31, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
17 8 0.06
18 5 0.04
19 14 0.10
20 2 0.01
21 7 0.05
22 98 0.71
23 5 0.04
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.38
Consensus pattern (22 bp):
TAAATCAATGATAACTTAATAG
Found at i:19601191 original size:22 final size:22
Alignment explanation
Indices: 19601114--19601305 Score: 92
Period size: 22 Copynumber: 8.8 Consensus size: 22
19601104 AATTAGCTTC
19601114 AATTTAATAGT-AATTAATTGAT
1 AATTTAATAGTAAATTAA-TGAT
19601136 AAATTTAATAGTAAATCATAA--AT
1 -AATTTAATAGTAAAT--TAATGAT
**
19601159 AGCTTAATAGTAAATTAATGAT
1 AATTTAATAGTAAATTAATGAT
* * * *
19601181 AATTTAGTAGTTAATTATTGAA
1 AATTTAATAGTAAATTAATGAT
* * * *
19601203 AACTTAAAAGTCAATCAAT-AT
1 AATTTAATAGTAAATTAATGAT
* *
19601224 AACTTAATAGTCAATT-ATCGAT
1 AATTTAATAGTAAATTAAT-GAT
* * * ** *
19601246 AACTTAATAATTAATTGGTAAT
1 AATTTAATAGTAAATTAATGAT
* * *
19601268 AACTTAATGGTAAA-TCATGAAT
1 AATTTAATAGTAAATTAATG-AT
19601290 AATTTAATA-TAAATTA
1 AATTTAATAGTAAATTA
19601306 GCAATAACTT
Statistics
Matches: 129, Mismatches: 30, Indels: 21
0.72 0.17 0.12
Matches are distributed among these distances:
20 5 0.04
21 21 0.16
22 83 0.64
23 14 0.11
24 3 0.02
26 3 0.02
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTAATAGTAAATTAATGAT
Found at i:19601241 original size:43 final size:44
Alignment explanation
Indices: 19601161--19601252 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 44
19601151 TCATAAATAG
* * * * * *
19601161 CTTAATAGTAAATTAATGATAATTTAGTAGTTAATTATTGAAAA
1 CTTAAAAGTAAATCAATGATAACTTAATAGTCAATTATCGAAAA
* *
19601205 CTTAAAAGTCAATCAAT-ATAACTTAATAGTCAATTATCGATAA
1 CTTAAAAGTAAATCAATGATAACTTAATAGTCAATTATCGAAAA
19601248 CTTAA
1 CTTAA
19601253 TAATTAATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 26 0.65
44 14 0.35
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (44 bp):
CTTAAAAGTAAATCAATGATAACTTAATAGTCAATTATCGAAAA
Found at i:19601247 original size:65 final size:68
Alignment explanation
Indices: 19601089--19601305 Score: 175
Period size: 65 Copynumber: 3.3 Consensus size: 68
19601079 AATAATTAGT
* * * *
19601089 AATAACTTAATAATAAATT-A-GCTTCAATTTAATAG-TAATTAATTGATAAATTTAATAGTAAA
1 AATAACTTAATAGTAAATTAATG-AT-AATTTAATAGTTAATTAATTGATAAACTTAAAAGTAAA
19601151 TCATA
64 TCATA
* * *
19601156 AATAGCTTAATAGTAAATTAATGATAATTTAGTAGTTAATT-ATTGA-AAACTTAAAAGTCAATC
1 AATAACTTAATAGTAAATTAATGATAATTTAATAGTTAATTAATTGATAAACTTAAAAGTAAATC
19601219 A-A
66 ATA
* * * * ** * **
19601221 TATAACTTAATAGTCAATT-ATCGATAACTTAATAATTAATT-GGTAAT-AACTTAATGGTAAAT
1 AATAACTTAATAGTAAATTAAT-GATAATTTAATAGTTAATTAATTGATAAACTTAAAAGTAAAT
*
19601283 CATG
65 CATA
*
19601287 AATAATTTAATA-TAAATTA
1 AATAACTTAATAGTAAATTA
19601306 GCAATAACTT
Statistics
Matches: 120, Mismatches: 23, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
64 2 0.02
65 54 0.45
66 25 0.21
67 31 0.26
68 7 0.06
69 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.38
Consensus pattern (68 bp):
AATAACTTAATAGTAAATTAATGATAATTTAATAGTTAATTAATTGATAAACTTAAAAGTAAATC
ATA
Found at i:19601297 original size:44 final size:43
Alignment explanation
Indices: 19601222--19601319 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 43
19601212 GTCAATCAAT
* * * * *
19601222 ATAACTTAATAGTCAATTATCGATAACTTAATAATTAATTGGTA
1 ATAACTTAATAGTAAATCATCGATAACTTAAT-ATAAATTAGCA
* *
19601266 ATAACTTAATGGTAAATCAT-GAATAATTTAATATAAATTAGCA
1 ATAACTTAATAGTAAATCATCG-ATAACTTAATATAAATTAGCA
19601309 ATAACTTAATA
1 ATAACTTAATA
19601320 ATTTAGCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
43 19 0.42
44 26 0.58
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (43 bp):
ATAACTTAATAGTAAATCATCGATAACTTAATATAAATTAGCA
Found at i:19601430 original size:22 final size:22
Alignment explanation
Indices: 19601405--19601709 Score: 116
Period size: 22 Copynumber: 13.5 Consensus size: 22
19601395 AGGTAAAAAG
*
19601405 TAATAGTAAATCATTGATAATT
1 TAATAGTAAATCATTAATAATT
* *
19601427 TAATAAG-AAATTATTGATAATT
1 TAAT-AGTAAATCATTAATAATT
* * * **
19601449 TAGTAGGAAATCACTAATAACA
1 TAATAGTAAATCATTAATAATT
** * * *
19601471 TGGTAGTAAATTACTAATATTT
1 TAATAGTAAATCATTAATAATT
*
19601493 TAATTA-TAAATCAGTAATAATT
1 TAA-TAGTAAATCATTAATAATT
* * *
19601515 TAGTAGTAAATTAGTTAATCATT
1 TAATAGTAAATCA-TTAATAATT
* * *
19601538 GATAACTTTGTAATAAATCATTGATAAAT
1 --TAA-----TAGTAAATCATTAATAATT
* *
19601567 TAGTAGTAAATCAACT-ATAACTT
1 TAATAGTAAATC-ATTAATAA-TT
* * *
19601590 T-ATAATAAATCATCAATAACT
1 TAATAGTAAATCATTAATAATT
** *
19601611 TAATAGTAAATCAACAACAATT
1 TAATAGTAAATCATTAATAATT
* * **
19601633 TAGTAGTAAATCATTTATAACA
1 TAATAGTAAATCATTAATAATT
* *
19601655 TAAT-GATAAATCATTCATAAAT
1 TAATAG-TAAATCATTAATAATT
* *
19601677 TAATAGTAAATTATTGATAATT
1 TAATAGTAAATCATTAATAATT
* *
19601699 TAGTAATAAAT
1 TAATAGTAAAT
19601710 TTTTATTAGC
Statistics
Matches: 208, Mismatches: 57, Indels: 36
0.69 0.19 0.12
Matches are distributed among these distances:
21 8 0.04
22 166 0.80
23 16 0.08
25 2 0.01
27 2 0.01
29 6 0.03
30 8 0.04
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TAATAGTAAATCATTAATAATT
Found at i:19601602 original size:66 final size:66
Alignment explanation
Indices: 19601531--19601709 Score: 187
Period size: 66 Copynumber: 2.7 Consensus size: 66
19601521 TAAATTAGTT
* ** * * * *
19601531 AATCATTGATAACTTTGTAATAAATCATTGATAAATTAGTAGTAAATCAACTATAACTTTATAAT
1 AATCATTAATAACTTAATAGTAAATCATTGATAATTTAGTAGTAAATCAACTATAACATAATAAT
19601596 A
66 A
* *** * ** *
19601597 AATCATCAATAACTTAATAGTAAATCAACAACAATTTAGTAGTAAATCATTTATAACATAATGAT
1 AATCATTAATAACTTAATAGTAAATCATTGATAATTTAGTAGTAAATCAACTATAACATAATAAT
19601662 A
66 A
* * * *
19601663 AATCATTCATAAATTAATAGTAAATTATTGATAATTTAGTAATAAAT
1 AATCATTAATAACTTAATAGTAAATCATTGATAATTTAGTAGTAAAT
19601710 TTTTATTAGC
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
66 89 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (66 bp):
AATCATTAATAACTTAATAGTAAATCATTGATAATTTAGTAGTAAATCAACTATAACATAATAAT
A
Found at i:19601621 original size:118 final size:118
Alignment explanation
Indices: 19601408--19601643 Score: 264
Period size: 118 Copynumber: 2.0 Consensus size: 118
19601398 TAAAAAGTAA
* *
19601408 TAGTAAATCATTGATAATTTAATAAGAAATTATTGATAATTTAGTAGGAAATCACTAATAACATG
1 TAGTAAATCATTGATAATTTAATAAGAAATCATTGATAAATTAGTAGGAAATCACTAATAACATG
* * * ** ** *
19601473 GTAGTAAATTACTAATATTTTAATTATAAATCAGTAATAATTTAGTAGTAAAT
66 ATAATAAATCACTAATAACTTAATTATAAATCAACAACAATTTAGTAGTAAAT
* * * * *
19601526 TAGTTAATCATTGATAACTTT-GTAATAAATCATTGATAAATTAGTAGTAAATCAACT-ATAACT
1 TAGTAAATCATTGATAA-TTTAATAAGAAATCATTGATAAATTAGTAGGAAATC-ACTAATAACA
*
19601589 TTATAATAAATCA-TCAATAACTTAA-TAGTAAATCAACAACAATTTAGTAGTAAAT
64 TGATAATAAATCACT-AATAACTTAATTA-TAAATCAACAACAATTTAGTAGTAAAT
19601644 CATTTATAAC
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
117 3 0.03
118 89 0.91
119 6 0.06
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (118 bp):
TAGTAAATCATTGATAATTTAATAAGAAATCATTGATAAATTAGTAGGAAATCACTAATAACATG
ATAATAAATCACTAATAACTTAATTATAAATCAACAACAATTTAGTAGTAAAT
Found at i:19601653 original size:44 final size:44
Alignment explanation
Indices: 19601541--19601667 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
19601531 AATCATTGAT
* * * * * *
19601541 AACTTTGTAATAAATCATTGATAAATTAGTAGTAAATCAACTAT
1 AACTTTATAATAAATCATTAATAACTTAATAGTAAATCAACAAC
*
19601585 AACTTTATAATAAATCATCAATAACTTAATAGTAAATCAACAAC
1 AACTTTATAATAAATCATTAATAACTTAATAGTAAATCAACAAC
* * *
19601629 AA-TTTAGTAGTAAATCATTTATAACATAAT-GATAAATCA
1 AACTTTA-TAATAAATCATTAATAACTTAATAG-TAAATCA
19601668 TTCATAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 5 0.07
44 65 0.93
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (44 bp):
AACTTTATAATAAATCATTAATAACTTAATAGTAAATCAACAAC
Found at i:19602046 original size:21 final size:21
Alignment explanation
Indices: 19602022--19602318 Score: 115
Period size: 21 Copynumber: 14.2 Consensus size: 21
19602012 ATTGATTACA
*
19602022 AAAATTATATCATAAGTTATC
1 AAAATTATATCAAAAGTTATC
*
19602043 AAAATTATATAAAAAGTTATC
1 AAAATTATATCAAAAGTTATC
* *
19602064 AAAATTACATCAAGA-TGTATC
1 AAAATTATATCAAAAGT-TATC
* * * *
19602085 AAAGTT-TAT-TAAAGATGACC
1 AAAATTATATCAAAAG-TTATC
* * ** *
19602105 TAAATTGTATCAATGGTTACC
1 AAAATTATATCAAAAGTTATC
* * * *
19602126 AAAATTATCTTATAAGTTACC
1 AAAATTATATCAAAAGTTATC
* * ** *
19602147 AAACTAATATTGAAGGTTA-C
1 AAAATTATATCAAAAGTTATC
* ** * *
19602167 TAAAATTGTATCAATGGCTACC
1 -AAAATTATATCAAAAGTTATC
* * *
19602189 AAAATTATATTATAACTTA-C
1 AAAATTATATCAAAAGTTATC
*
19602209 CAAATTAGTAT-AGAAAGTTATC
1 AAAATTA-TATCA-AAAGTTATC
** *
19602231 AAAATTGCATTAAAAGTTATC
1 AAAATTATATCAAAAGTTATC
*
19602252 AAAATTTTATC-AAAGATTATC
1 AAAATTATATCAAAAG-TTATC
* * * * *
19602273 AAACTTCTAACAAAGGTTACC
1 AAAATTATATCAAAAGTTATC
*
19602294 AAAA-CATATCAAAAGTTATC
1 AAAATTATATCAAAAGTTATC
19602314 AAAAT
1 AAAAT
19602319 CAAAATTATA
Statistics
Matches: 198, Mismatches: 64, Indels: 28
0.68 0.22 0.10
Matches are distributed among these distances:
19 2 0.01
20 37 0.19
21 146 0.74
22 13 0.07
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATTATATCAAAAGTTATC
Found at i:19602235 original size:63 final size:63
Alignment explanation
Indices: 19602106--19602237 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 63
19602096 AAGATGACCT
* * * * *
19602106 AAATTGTATCAATGGTTACCAAAATTATCTTATAAGTTACCAAACTAATATTGAAGGTTACTA
1 AAATTGTATCAATGGCTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACTA
* *
19602169 AAATTGTATCAATGGCTACCAAAATTATATTATAACTTACCAAATTAGTATAGAAAGTTA-TCA
1 AAATTGTATCAATGGCTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACT-A
19602232 AAATTG
1 AAATTG
19602238 CATTAAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 1 0.02
63 60 0.98
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (63 bp):
AAATTGTATCAATGGCTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACTA
Found at i:19602255 original size:63 final size:63
Alignment explanation
Indices: 19602106--19602257 Score: 153
Period size: 63 Copynumber: 2.4 Consensus size: 63
19602096 AAGATGACCT
* ** * * * *
19602106 AAATTGTATCAATGGTTACCAAAATTATCTTATAAGTTACCAAACTAATATTGAAGGTTACTA
1 AAATTGCATCAAAAGTTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACTA
* ** * * *
19602169 AAATTGTATCAATGGCTACCAAAATTATATTATAACTTACCAAATTAGTATAGAAAGTTA-TCA
1 AAATTGCATCAAAAGTTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACT-A
* *
19602232 AAATTGCATTAAAAGTTATCAAAATT
1 AAATTGCATCAAAAGTTACCAAAATT
19602258 TTATCAAAGA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
62 1 0.01
63 74 0.99
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (63 bp):
AAATTGCATCAAAAGTTACCAAAATTATATTATAACTTACCAAACTAATATAGAAAGTTACTA
Found at i:19602699 original size:33 final size:31
Alignment explanation
Indices: 19602633--19602701 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 31
19602623 TAAAACTTTC
* **
19602633 AATTATTTTTTTTTATTTTTAATTTTTAAAA
1 AATTATTTTTTTTTATTTATAATTGATAAAA
19602664 AATTATTTTTAGTTTTATTTAT-ATTGATAATAA
1 AATTATTTTT--TTTTATTTATAATTGATAA-AA
19602697 AATTA
1 AATTA
19602702 ATAACTTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.31
32 6 0.19
33 16 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
AATTATTTTTTTTTATTTATAATTGATAAAA
Found at i:19608981 original size:32 final size:32
Alignment explanation
Indices: 19608944--19609008 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
19608934 AAATTAAAAT
* * *
19608944 AAATTTGTTTATTAGTTTATTATATACTAATA
1 AAATTTATTTATTAATTTATTATATAATAATA
19608976 AAATTTATTTATTAATTTATTATATAATAATA
1 AAATTTATTTATTAATTTATTATATAATAATA
19609008 A
1 A
19609009 TAATAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
AAATTTATTTATTAATTTATTATATAATAATA
Found at i:19610450 original size:182 final size:182
Alignment explanation
Indices: 19610155--19610497 Score: 589
Period size: 182 Copynumber: 1.9 Consensus size: 182
19610145 GTGTTCATTA
*
19610155 CTGTGTTAAGACTAACGAATCCATCTCCTTCATCATAACCCATGTCTGTAAGAGGTAGTTAATTG
1 CTGTGTTAAGACTAAAGAATCCATCTCCTTCATCATAACCCATGTCTGTAAGAGGTAGTTAATTG
* * * *
19610220 GTTGTAGGACTCCCAATAAACATATTGGGGTAAACTCAATCCATTTCTCATTGATAACATCTGTA
66 GCTGTAGGACTCCCAATAAACATATCGAGGTAAACTCAATCCATTTCTCATTGATAACATCTATA
*
19610285 AAAGTAGTGACAACAAATCAAATTGGCTTTTATGATGAAAATGTATTTACTC
131 AAAGTAGTGACAACAAATCAAACTGGCTTTTATGATGAAAATGTATTTACTC
*
19610337 CTGTGTTAAGACTAAAGAATCCATCTCCTTCATCATAACCTATGTCTG-AAGGAGGTAGTTAATT
1 CTGTGTTAAGACTAAAGAATCCATCTCCTTCATCATAACCCATGTCTGTAA-GAGGTAGTTAATT
* *
19610401 GGCTGTAGGACTCCCAATAAATATATCGAGGTAAACTCAATCTATTTCTCATTGATAACATCTAT
65 GGCTGTAGGACTCCCAATAAACATATCGAGGTAAACTCAATCCATTTCTCATTGATAACATCTAT
19610466 AAAAGTAGTGACAACAAATCAAACTGGCTTTT
130 AAAAGTAGTGACAACAAATCAAACTGGCTTTT
19610498 CATAATTCTA
Statistics
Matches: 151, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
181 2 0.01
182 149 0.99
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (182 bp):
CTGTGTTAAGACTAAAGAATCCATCTCCTTCATCATAACCCATGTCTGTAAGAGGTAGTTAATTG
GCTGTAGGACTCCCAATAAACATATCGAGGTAAACTCAATCCATTTCTCATTGATAACATCTATA
AAAGTAGTGACAACAAATCAAACTGGCTTTTATGATGAAAATGTATTTACTC
Found at i:19611900 original size:53 final size:52
Alignment explanation
Indices: 19611804--19611913 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 52
19611794 TTTAGTTCAA
* * *
19611804 AAAAATTGATATTTCAAGTTTTCCTTAATATTCTCAAATTTTTATTTTAAGG
1 AAAAATTGATATTTCAAGTTTTCCTAAATATTCTCAAAATTTTATTCTAAGG
* * *
19611856 AAAAATTGATATTTCAATTTTTTTCC-AAATATTTTTAAAATTTTATTCTAAGG
1 AAAAATTGATATTTCAA--GTTTTCCTAAATATTCTCAAAATTTTATTCTAAGG
19611909 AAAAA
1 AAAAA
19611914 ATTTTAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 17 0.34
53 27 0.54
54 6 0.12
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (52 bp):
AAAAATTGATATTTCAAGTTTTCCTAAATATTCTCAAAATTTTATTCTAAGG
Found at i:19612219 original size:23 final size:23
Alignment explanation
Indices: 19612188--19612244 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
19612178 GCACAAAAAT
*
19612188 AAAATAAATATCTATAAAAA-T-AG
1 AAAAAAAATAT-TA-AAAAATTGAG
19612211 AAAAAAAATTATTAAAAAATTGAG
1 AAAAAAAA-TATTAAAAAATTGAG
*
19612235 CAAAAAAATA
1 AAAAAAAATA
19612245 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 5 0.17
23 12 0.41
24 12 0.41
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAAAAATATTAAAAAATTGAG
Found at i:19615087 original size:22 final size:23
Alignment explanation
Indices: 19615062--19615105 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19615052 TTTAGGATCC
*
19615062 TTTTAATTAT-ACTTATAGATTT
1 TTTTAATTATAAATTATAGATTT
*
19615084 TTTTAATTGTAAATTATAGATT
1 TTTTAATTATAAATTATAGATT
19615106 ATAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTTAATTATAAATTATAGATTT
Found at i:19615277 original size:17 final size:17
Alignment explanation
Indices: 19615240--19615277 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
19615230 TTTATATATT
*
19615240 TATATTTTTTCTTTTAG
1 TATATTTTTTATTTTAG
19615257 TATATTTTTTTATTTTA-
1 TATA-TTTTTTATTTTAG
19615274 TATA
1 TATA
19615278 AAAACAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TATATTTTTTATTTTAG
Found at i:19615383 original size:3 final size:3
Alignment explanation
Indices: 19615375--19615409 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19615365 CTTAAATCCT
19615375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19615410 TCATAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19619141 original size:2 final size:2
Alignment explanation
Indices: 19619136--19619161 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19619126 TATATATATA
19619136 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
19619162 CTCTTTTTGT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19619843 original size:22 final size:22
Alignment explanation
Indices: 19619812--19619853 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19619802 TCAGGAATAC
19619812 GGGATCTTTTATTTAATTTTAT
1 GGGATCTTTTATTTAATTTTAT
*
19619834 GGGATTTTTTATTTAATTTT
1 GGGATCTTTTATTTAATTTT
19619854 TAGTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.62
Consensus pattern (22 bp):
GGGATCTTTTATTTAATTTTAT
Found at i:19619865 original size:22 final size:22
Alignment explanation
Indices: 19619813--19619864 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19619803 CAGGAATACG
* *
19619813 GGATCTTTTATTTAATTTTATG
1 GGATTTTTTATTTAATTTTATA
19619835 GGATTTTTTATTTAATTTT-TA
1 GGATTTTTTATTTAATTTTATA
*
19619856 GTATTTTTT
1 GGATTTTTT
19619865 TGAAGTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (22 bp):
GGATTTTTTATTTAATTTTATA
Found at i:19641637 original size:2 final size:2
Alignment explanation
Indices: 19641632--19641722 Score: 78
Period size: 2 Copynumber: 45.5 Consensus size: 2
19641622 CTAGTTGCTT
* * *
19641632 TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
19641674 TA TCA -A AA TA TA CA AA T- TGA TA TA TA TA TA TA TA TA TA CA TA
1 TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
*
19641716 TT TA TA T
1 TA TA TA T
19641723 CCAAAATATA
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
1 2 0.03
2 67 0.94
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19645407 original size:35 final size:35
Alignment explanation
Indices: 19645363--19645430 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
19645353 TTTTTGCTAA
*
19645363 ATTAGAAACTTTTTATTTTTTAAAGAGACAAAGGC
1 ATTAAAAACTTTTTATTTTTTAAAGAGACAAAGGC
*
19645398 ATTAAAAACTTTTTATTTTTTAAAGGGACAAAG
1 ATTAAAAACTTTTTATTTTTTAAAGAGACAAAG
19645431 AGATTGGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (35 bp):
ATTAAAAACTTTTTATTTTTTAAAGAGACAAAGGC
Found at i:19650431 original size:12 final size:12
Alignment explanation
Indices: 19650391--19650431 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
19650381 CTTTTTGAAA
19650391 TTTTTATTTTTT
1 TTTTTATTTTTT
*
19650403 TGTTTATTTTTT
1 TTTTTATTTTTT
*
19650415 CTTTTTCTTTTTT
1 -TTTTTATTTTTT
19650428 TTTT
1 TTTT
19650432 GTTGATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.05, C:0.05, G:0.02, T:0.88
Consensus pattern (12 bp):
TTTTTATTTTTT
Found at i:19652190 original size:18 final size:18
Alignment explanation
Indices: 19652164--19652208 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19652154 GTTCTAACAC
* *
19652164 TTTAAGGTTTAGGTTTGA
1 TTTAGGGTTTAGGTTAGA
*
19652182 TTTAGGGTTTGGGTTAGA
1 TTTAGGGTTTAGGTTAGA
19652200 TTTAGGGTT
1 TTTAGGGTT
19652209 AGAGATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (18 bp):
TTTAGGGTTTAGGTTAGA
Found at i:19653273 original size:21 final size:20
Alignment explanation
Indices: 19653248--19653292 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
19653238 GAAAACTACA
*
19653248 TTTTTAAGCTTTTCCATTTTT
1 TTTTTAAGCTTTTCC-TTTTC
**
19653269 TTTTTAATTTTTTCCTTTTC
1 TTTTTAAGCTTTTCCTTTTC
19653289 TTTT
1 TTTT
19653293 ATGGTTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTAAGCTTTTCCTTTTC
Found at i:19665775 original size:19 final size:17
Alignment explanation
Indices: 19665753--19665787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
19665743 ATAAAAGTTT
19665753 ATAAAAAGTCAAAAAAGAA
1 ATAAAAAG--AAAAAAGAA
19665772 ATAAAAAGAAAAAAGA
1 ATAAAAAGAAAAAAGA
19665788 GTCAATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.09
Consensus pattern (17 bp):
ATAAAAAGAAAAAAGAA
Found at i:19669240 original size:3 final size:3
Alignment explanation
Indices: 19669234--19669266 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19669224 ATTGTTGTTG
19669234 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19669267 AAAAATGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19669709 original size:22 final size:23
Alignment explanation
Indices: 19669669--19669712 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
19669659 TAGCAAAGTC
19669669 AAAAATTTTTTCAAAAACAAAAAT
1 AAAAATTTTTT-AAAAACAAAAAT
*
19669693 AAAAATTTTTT-ATAACAAAA
1 AAAAATTTTTTAAAAACAAAA
19669713 TTTTTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATTTTTTAAAAACAAAAAT
Found at i:19669811 original size:11 final size:10
Alignment explanation
Indices: 19669788--19669823 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
19669778 AAAAAGATCA
*
19669788 TTTTAAGAAT
1 TTTTAAAAAT
19669798 TTTTAAAAAT
1 TTTTAAAAAT
19669808 TTTTAAAATAT
1 TTTTAAAA-AT
19669819 TTTTA
1 TTTTA
19669824 GAGTCTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTAAAAAT
Found at i:19670186 original size:13 final size:12
Alignment explanation
Indices: 19670164--19670199 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
19670154 GTTTGGTAGG
19670164 TTTTTCTTTTTT
1 TTTTTCTTTTTT
19670176 TTTTTCTTTTTT
1 TTTTTCTTTTTT
19670188 TTTTTCTATTTT
1 TTTTTCT-TTTT
19670200 GATTTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:19670211 original size:20 final size:19
Alignment explanation
Indices: 19670188--19670232 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
19670178 TTTCTTTTTT
*
19670188 TTTTTCTATTTTGATTTTGA
1 TTTTTCTATTTTG-TGTTGA
*
19670208 TTTTATTTATTTTGTGTTGA
1 TTTT-TCTATTTTGTGTTGA
19670228 TTTTT
1 TTTTT
19670233 ATGTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.73
Consensus pattern (19 bp):
TTTTTCTATTTTGTGTTGA
Found at i:19670233 original size:21 final size:22
Alignment explanation
Indices: 19670185--19670242 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
19670175 TTTTTTCTTT
* *
19670185 TTTTTTTTCTATTTTGATTTTGA
1 TTTTTATT-TATTTTGATGTTGA
19670208 -TTTTATTTATTTTG-TGTTGA
1 TTTTTATTTATTTTGATGTTGA
19670228 TTTTTATGTTATTTT
1 TTTTTAT-TTATTTT
19670243 TATATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 13 0.42
22 13 0.42
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.74
Consensus pattern (22 bp):
TTTTTATTTATTTTGATGTTGA
Found at i:19670837 original size:12 final size:12
Alignment explanation
Indices: 19670820--19670844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19670810 TTTATATAAT
19670820 AAAAATAATTAA
1 AAAAATAATTAA
19670832 AAAAATAATTAA
1 AAAAATAATTAA
19670844 A
1 A
19670845 CAATAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATAATTAA
Found at i:19670866 original size:23 final size:22
Alignment explanation
Indices: 19670815--19670860 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
19670805 ATTTTTTTAT
*
19670815 ATAA-TAAAAATAATTAAAAAA
1 ATAATTAAAAATAAATAAAAAA
19670836 ATAATTAAACAATAAATAATAAAA
1 ATAATTAAA-AATAAATAA-AAAA
19670860 A
1 A
19670861 ATTTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 4 0.19
23 8 0.38
24 5 0.24
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
ATAATTAAAAATAAATAAAAAA
Found at i:19671479 original size:2 final size:2
Alignment explanation
Indices: 19671472--19671504 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19671462 CAATCACACC
19671472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19671505 AGATTGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19676667 original size:69 final size:70
Alignment explanation
Indices: 19676543--19676673 Score: 160
Period size: 69 Copynumber: 1.9 Consensus size: 70
19676533 GCCTAGCTGA
* * * *
19676543 ATGAATTTTGAGCCTATTACCATCTTTTATGAATAGAAACCAAGTGTTAACATTGAT-AACCCAA
1 ATGAATTTTGAGCCTATCACCATCTTTTATGAATAAAAACCAAGTGCTAAAATTGATGAACCCAA
19676607 TTTGT
66 TTTGT
** *
19676612 ATGAATTTTGAG-CTCATCACCATCTTTTAT-AATGAAAAATTAATTGCTAAAATTGATGAACC
1 ATGAATTTTGAGCCT-ATCACCATCTTTTATGAAT-AAAAACCAAGTGCTAAAATTGATGAACC
19676674 AGTTTATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
68 5 0.10
69 43 0.83
70 4 0.08
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (70 bp):
ATGAATTTTGAGCCTATCACCATCTTTTATGAATAAAAACCAAGTGCTAAAATTGATGAACCCAA
TTTGT
Found at i:19680957 original size:47 final size:47
Alignment explanation
Indices: 19680856--19681138 Score: 250
Period size: 49 Copynumber: 5.8 Consensus size: 47
19680846 TTATTTCTTA
* * * * * * *
19680856 TCTTGGAAA-AGCTCTTATCAGCAGAGGCTTAACAGCTTCAAAATCTTC
1 TCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA--ATC
*
19680904 TCTTGGAAAGGGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATC
1 TCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC
19680951 TCTTGGAAAGGGCTCCTCTCAGCAGAGG-TCCAACAACTTTAAAAATCTC
1 TCTTGGAAAGGGCTCCTCTCAGCAGAGGCT-CAACAACTTTAAAAA--TC
* * * * *
19681000 ATATCTTGAAAAGGGCTCCTCTCAGTAAAGGCTCAACAATTTTAAAATTC
1 ---TCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC
* *
19681050 TCATCTGGAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTC
1 TC-T-TGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC
** * *
19681098 TTATCTT-GAAAAAGCTTCTCTTAGCAGAGGCTCAACAACTT
1 ---TCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTT
19681139 CAACAACTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
46 1 0.00
47 46 0.23
48 47 0.23
49 62 0.31
50 3 0.01
51 2 0.01
52 38 0.19
53 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (47 bp):
TCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC
Found at i:19681181 original size:107 final size:106
Alignment explanation
Indices: 19681032--19681344 Score: 301
Period size: 107 Copynumber: 3.0 Consensus size: 106
19681022 CAGTAAAGGC
* * *
19681032 TCAACAATTTTAAAATTCTCATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT
1 TCAACAACTTTAAAATTCTCATCTGAAAAAGCGCCTCTCAGCAGAGGCTCAACAACTTTAAAATT
* *
19681097 CTTATCTTGA-AAAAGCTTCTCTTAGCAGAGGCTCAACAACT
66 CTTATCTT-ACAAAAGCTCCTCTCAGCAGAGGCTCAACAACT
*
19681138 TCAACAACTTTAAAA-TCTCATATCTTGAAAAAG-GCCTCTCAGCAGAGGCTCAATAACTTTAAA
1 TCAACAACTTTAAAATTCTC--ATC-TGAAAAAGCGCCTCTCAGCAGAGGCTCAACAACTTTAAA
* *
19681201 ATTTTTATCTTACAAAAGCTCCTCTCAGTAGAGGCTCAACAACT
63 ATTCTTATCTTACAAAAGCTCCTCTCAGCAGAGGCTCAACAACT
* *
19681245 TTAA-AA--TT----TTCTC-T-TGAAAAAGGACTG-CTCTCAGTAGAGGCTCAACAACTTTAAA
1 TCAACAACTTTAAAATTCTCATCTGAAAAA-G-C-GCCTCTCAGCAGAGGCTCAACAACTTT-AA
* * * * * *
19681300 AATCTCATATCTAAAAAAAGGCTCATCTTAGCAGAGACTCAACAA
62 AAT-TCTTATCTTACAAAA-GCTCCTCTCAGCAGAGGCTCAACAA
19681345 TTTTAAAATT
Statistics
Matches: 176, Mismatches: 19, Indels: 28
0.79 0.09 0.13
Matches are distributed among these distances:
96 7 0.04
97 1 0.01
98 1 0.01
99 23 0.13
100 6 0.03
101 15 0.09
102 21 0.12
104 2 0.01
105 4 0.02
106 17 0.10
107 72 0.41
108 7 0.04
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (106 bp):
TCAACAACTTTAAAATTCTCATCTGAAAAAGCGCCTCTCAGCAGAGGCTCAACAACTTTAAAATT
CTTATCTTACAAAAGCTCCTCTCAGCAGAGGCTCAACAACT
Found at i:19681182 original size:58 final size:57
Alignment explanation
Indices: 19681080--19681196 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 57
19681070 CAGCAGAGGC
* *
19681080 TCAACAACTTTAAAATTCTTATCTTGAAAAAGCTTCTCTTAGCAGAGGCTCAACAACT
1 TCAACAACTTTAAAATTCATATCTTGAAAAAGC-TCTCTCAGCAGAGGCTCAACAACT
*
19681138 TCAACAACTTTAAAATCTCATATCTTGAAAAAGGC-CTCTCAGCAGAGGCTCAATAACT
1 TCAACAACTTTAAAAT-TCATATCTTGAAAAA-GCTCTCTCAGCAGAGGCTCAACAACT
19681196 T
1 T
19681197 TAAAATTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
58 38 0.70
59 14 0.26
60 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (57 bp):
TCAACAACTTTAAAATTCATATCTTGAAAAAGCTCTCTCAGCAGAGGCTCAACAACT
Found at i:19681434 original size:47 final size:46
Alignment explanation
Indices: 19681138--19681551 Score: 267
Period size: 47 Copynumber: 8.4 Consensus size: 46
19681128 CTCAACAACT
*
19681138 TCAACAACTTTAAAATCTCATATCTTGAAAAAGG-CCTCTCAGCAGAGGC
1 TCAACAACTTTAAAAT-TC---TCTTGAAAAAGGTTCTCTCAGCAGAGGC
* * * * *
19681187 TCAATAACTTTAAAATTTTTATCTT-ACAAAAGCTCCTCTCAGTAGAGGC
1 TCAACAACTTTAAAA---TTCTCTTGA-AAAAGGTTCTCTCAGCAGAGGC
* *
19681236 TCAACAACTTTAAAATTTTCTCTTGAAAAAGGACTGCTCTCAGTAGAGGC
1 TCAACAACTTTAAAA--TTCTCTTGAAAAAGG--TTCTCTCAGCAGAGGC
** * * *
19681286 TCAACAACTTTAAAAATCTCATATCTAAAAAAAGGCTCATCTTAGCAGAGAC
1 TCAACAACTTT-AAAAT-TC---TCTTGAAAAAGGTTC-TCTCAGCAGAGGC
* * * * * * *
19681338 TCAACAATTTTAAAATTCTCATATGGAAAAGCTTTTCTTAGTAAAGGC
1 TCAACAACTTTAAAATTCTC-T-TGAAAAAGGTTCTCTCAGCAGAGGC
* *
19681386 TCAACAACTTTAAAATTCTCTTGGAAAGGGTTTCTCTCAGCAGAGGC
1 TCAACAACTTTAAAATTCTCTTGAAAAAGG-TTCTCTCAGCAGAGGC
* * * * *
19681433 TCAACAACTTTAAAAATCTTTTGGAAAGGGCTCATCTCA-CTAGAGGC
1 TCAACAACTTTAAAATTCTCTTGAAAAAGGTTC-TCTCAGC-AGAGGC
* * *
19681480 TTAACAACTTTAAAAATCTCATATCTTGAAAAAGGCTCATCTCAGCAAAGGC
1 TCAACAACTTT-AAAAT-TC---TCTTGAAAAAGGTTC-TCTCAGCAGAGGC
*
19681532 TTAACAACTTTAAAATTCTC
1 TCAACAACTTTAAAATTCTC
19681552 ATCTGTTTTC
Statistics
Matches: 299, Mismatches: 41, Indels: 52
0.76 0.10 0.13
Matches are distributed among these distances:
46 10 0.03
47 67 0.22
48 56 0.19
49 52 0.17
50 32 0.11
51 16 0.05
52 55 0.18
53 11 0.04
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (46 bp):
TCAACAACTTTAAAATTCTCTTGAAAAAGGTTCTCTCAGCAGAGGC
Found at i:19693856 original size:11 final size:11
Alignment explanation
Indices: 19693831--19693865 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
19693821 ATAATAATAA
*
19693831 TTAAAAAACTCT
1 TTAAAAAAAT-T
19693843 TTAAAAAAATT
1 TTAAAAAAATT
19693854 TTAAAAAAATT
1 TTAAAAAAATT
19693865 T
1 T
19693866 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:19694001 original size:36 final size:37
Alignment explanation
Indices: 19693930--19694013 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 37
19693920 TCGATGGCTT
* *
19693930 GGTTCGGTCTGGCAGTTCAGCGGTTCAAGCGCGGTCC
1 GGTTCGGTCTGACAGTTCAGCGGTTCAAGCACGGTCC
*
19693967 GGTTCGGTCTGACGGTTCA-CGGTTCAAGCACGGTCC
1 GGTTCGGTCTGACAGTTCAGCGGTTCAAGCACGGTCC
*
19694003 AGTTCGGTCTG
1 GGTTCGGTCTG
19694014 GTTCGGTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 26 0.60
37 17 0.40
ACGTcount: A:0.12, C:0.26, G:0.36, T:0.26
Consensus pattern (37 bp):
GGTTCGGTCTGACAGTTCAGCGGTTCAAGCACGGTCC
Found at i:19694903 original size:3 final size:3
Alignment explanation
Indices: 19694890--19694928 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
19694880 AGATTAAATA
19694890 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19694929 ATGGTGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19697276 original size:40 final size:40
Alignment explanation
Indices: 19697227--19697485 Score: 289
Period size: 40 Copynumber: 6.6 Consensus size: 40
19697217 CCCTTTCAGA
* * * *
19697227 TTTTAAATTTAAAGTTTCATTGCCTCTAGTTAGAGGAGCA
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
* * *
19697267 TTCTGAATTTAAAGTTTCATTACCTCTGGTTAGAGGAGCC
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
* * *
19697307 TTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAAAAGCC
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
** ** *
19697347 TTTTGAATTTAAAGTTTTGTTTTCTCTGGTCAGAAGAGCC
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
* * *
19697387 TTTTGAATTTAAAGTTTCACTGCCTTTGGTCA-AAGAAGCC
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAG-AGCC
19697427 ------ATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
1 TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
*
19697461 TTTTAAATTTAAAGTTTCATTGCCT
1 TTTTGAATTTAAAGTTTCATTGCCT
19697486 TTAGTCAAAT
Statistics
Matches: 183, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
34 27 0.15
35 3 0.02
39 3 0.02
40 150 0.82
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (40 bp):
TTTTGAATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
Found at i:19697319 original size:80 final size:79
Alignment explanation
Indices: 19697227--19697490 Score: 322
Period size: 80 Copynumber: 3.4 Consensus size: 79
19697217 CCCTTTCAGA
* *
19697227 TTTTAAATTTAAAGTTTCATTGCCTCTAGTTAGAGGAGCATTCTGAATTTAAAGTTTCATTACCT
1 TTTTAAATTTAAAGTTTCATTGCCTTTAGTTAGAGAAGC-TTCTGAATTTAAAGTTTCATTACCT
*
19697292 CTGGTTAGAGGAGCC
65 CTGGTTAGAAGAGCC
* * * ** **
19697307 TTTTAAATTTAAAGTTTCATTGCCTTTGGTTAGAAAAGCCTTTTGAATTTAAAGTTTTGTTTTCT
1 TTTTAAATTTAAAGTTTCATTGCCTTTAGTTAGAGAAG-CTTCTGAATTTAAAGTTTCATTACCT
*
19697372 CTGGTCAGAAGAGCC
65 CTGGTTAGAAGAGCC
* * * * * *
19697387 TTTTGAATTTAAAGTTTCACTGCCTTTGGTCAAAGAAGC--C---ATTTAAAGTTTCATTGCCTC
1 TTTTAAATTTAAAGTTTCATTGCCTTTAGTTAGAGAAGCTTCTGAATTTAAAGTTTCATTACCTC
19697447 TGGTTAGAAGAGCC
66 TGGTTAGAAGAGCC
19697461 TTTTAAATTTAAAGTTTCATTGCCTTTAGT
1 TTTTAAATTTAAAGTTTCATTGCCTTTAGT
19697491 CAAATGAGCC
Statistics
Matches: 158, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
74 56 0.35
79 1 0.01
80 100 0.63
81 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (79 bp):
TTTTAAATTTAAAGTTTCATTGCCTTTAGTTAGAGAAGCTTCTGAATTTAAAGTTTCATTACCTC
TGGTTAGAAGAGCC
Found at i:19697436 original size:34 final size:33
Alignment explanation
Indices: 19697393--19697533 Score: 129
Period size: 34 Copynumber: 4.0 Consensus size: 33
19697383 AGCCTTTTGA
*
19697393 ATTTAAAGTTTCACTGCCTTTGGTCAAAGAAGCC
1 ATTTAAAGTTTCATTGCCTTTGGTCAAAG-AGCC
* *
19697427 ATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCC
1 ATTTAAAGTTTCATTGCCTTTGGTCA-AAGAGCC
*
19697461 TTTTAAATTTAAAGTTTCATTGCCTTTAGTCAAATGAGCC
1 ------ATTTAAAGTTTCATTGCCTTTGGTCAAA-GAGCC
* * *
19697501 ATTTATAGTTTTATAGCCTTTGGTCAAATGAGC
1 ATTTAAAGTTTCATTGCCTTTGGTCAAA-GAGC
19697534 TTTTTAATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
34 56 0.63
35 3 0.03
39 2 0.02
40 28 0.31
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (33 bp):
ATTTAAAGTTTCATTGCCTTTGGTCAAAGAGCC
Found at i:19697470 original size:74 final size:74
Alignment explanation
Indices: 19697273--19697511 Score: 284
Period size: 74 Copynumber: 3.1 Consensus size: 74
19697263 AGCATTCTGA
* *
19697273 ATTTAAAGTTTCATTACCTCTGGTTAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTT
1 ATTTAAAGTTTCATTACCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTC
19697338 AGAA-AAGCC
66 A-AAGAAGCC
** ** * * *
19697347 TTTTGAATTTAAAGTTTTGTTTTCTCTGGTCAGAAGAGCCTTTTGAATTTAAAGTTTCACTGCCT
1 ------ATTTAAAGTTTCATTACCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCT
19697412 TTGGTCAAAGAAGCC
60 TTGGTCAAAGAAGCC
* *
19697427 ATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTAGTC
1 ATTTAAAGTTTCATTACCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTC
19697492 AAATG-AGCC
66 AAA-GAAGCC
*
19697501 ATTTATAGTTT
1 ATTTAAAGTTT
19697512 TATAGCCTTT
Statistics
Matches: 139, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
74 74 0.53
75 1 0.01
79 2 0.01
80 62 0.45
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (74 bp):
ATTTAAAGTTTCATTACCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTC
AAAGAAGCC
Found at i:19697539 original size:74 final size:74
Alignment explanation
Indices: 19697273--19697540 Score: 247
Period size: 74 Copynumber: 3.5 Consensus size: 74
19697263 AGCATTCTGA
* * * *
19697273 ATTTAAAGTTTCATTA-CCTCTGGTTAGAGGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGT
1 ATTTAAAGTTTCA-TAGCCTCTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCACTGCCTTTAGT
*
19697337 TAGAA-AAGCC
65 CA-AAGAAGCC
** *** *
19697347 TTTTGAATTTAAAGTTTTGTTTTCTCTGGTCAGAAGAGCCTTTTGAATTTAAAGTTTCACTGCCT
1 ------ATTTAAAGTTTCATAGCCTCTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCACTGCCT
*
19697412 TTGGTCAAAGAAGCC
60 TTAGTCAAAGAAGCC
* * *
19697427 ATTTAAAGTTTCATTGCCTCTGGTTAGAAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTAGTC
1 ATTTAAAGTTTCATAGCCTCTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCACTGCCTTTAGTC
19697492 AAATG-AGCC
66 AAA-GAAGCC
* * * *
19697501 ATTTATAGTTTTATAGCCTTTGGTCA-AATGAGCTTTTTAA
1 ATTTAAAGTTTCATAGCCTCTGGTCAGAA-GAGCCTTTTAA
19697541 TTTTTATAGC
Statistics
Matches: 161, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
73 2 0.01
74 95 0.59
75 1 0.01
79 3 0.02
80 60 0.37
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (74 bp):
ATTTAAAGTTTCATAGCCTCTGGTCAGAAGAGCCTTTTAAATTTAAAGTTTCACTGCCTTTAGTC
AAAGAAGCC
Found at i:19697688 original size:40 final size:40
Alignment explanation
Indices: 19697626--19697908 Score: 250
Period size: 40 Copynumber: 7.1 Consensus size: 40
19697616 TCCTCTCAGA
* *
19697626 TTTTGAATTTAAAGTTTCGTTGCGTCTGGTTAGAGAAGCC
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
* * * * *
19697666 TTTTAAATTTAAAGTTTTGTTGCTTCTAGTTAAAGGAG-C
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
* * ** * * * *
19697705 TTTTAAATTTAAAATTTTTTTGCCTCTGGTCAGAAAAGCT
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
* * *
19697745 TTTTAAATTTAAAGTTTCGTTGCCTTTAGTCA-ATGGAA-CC
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGA--GAAGCC
* * *
19697785 TTTCGAATTTAAAGTTTTGTTGCCT-TTGATTAGAGAAGCC
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAG-TTAGAGAAGCC
* *
19697825 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGATAAGCT
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
* * * * **
19697865 TTTTGAATTTAAAATTTCATTGCCTTTAGTCAGAGGGGCC
1 TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
19697905 TTTT
1 TTTT
19697909 TAAATTTTTA
Statistics
Matches: 196, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
39 37 0.19
40 154 0.79
41 5 0.03
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (40 bp):
TTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGAGAAGCC
Found at i:19697891 original size:80 final size:78
Alignment explanation
Indices: 19697626--19697889 Score: 287
Period size: 80 Copynumber: 3.3 Consensus size: 78
19697616 TCCTCTCAGA
* * * *
19697626 TTTTGAATTTAAAGTTTCGTTGCGTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTTGTTGCTT
1 TTTTGAATTTAAAATTTCGTTGCCTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTCGTTGCCT
19697691 CTAGTTAA-AGGAGC
66 CTAGTTAATA--AGC
* ** * * *
19697705 TTTTAAATTTAAAATTTTTTTGCCTCTGGTCAGAAAAGCTTTTTAAATTTAAAGTTTCGTTGCCT
1 TTTTGAATTTAAAATTTCGTTGCCTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTCGTTGCCT
* * *
19697770 TTAGTCAATGGAACC
66 CTAGTTAAT--AAGC
* * * * * *
19697785 TTTCGAATTTAAAGTTTTGTTGCCTTTGATTAGAGAAGCCTTTTGAATTTAAAGTTTCGTTGCCT
1 TTTTGAATTTAAAATTTCGTTGCCTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTCGTTGCCT
19697850 CTAGTTAGATAAGC
66 CTAGTTA-ATAAGC
*
19697864 TTTTTGAATTTAAAATTTCATTGCCT
1 -TTTTGAATTTAAAATTTCGTTGCCT
19697890 TTAGTCAGAG
Statistics
Matches: 150, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
79 64 0.43
80 83 0.55
81 2 0.01
82 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (78 bp):
TTTTGAATTTAAAATTTCGTTGCCTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTCGTTGCCT
CTAGTTAATAAGC
Found at i:19697907 original size:120 final size:119
Alignment explanation
Indices: 19697626--19697907 Score: 318
Period size: 120 Copynumber: 2.4 Consensus size: 119
19697616 TCCTCTCAGA
* * * * * *
19697626 TTTTGAATTTAAAGTTTCGTTGCGTCTGGTTAGAGAAGCCTTTTAAATTTAAAGTTTTGTTGCTT
1 TTTTGAATTTAAAGTTTCGTTGCCTTTAGTCAGAGGAGCCTTTCAAATTTAAAGTTTTGTTGCTT
* ** *
19697691 CTAGTTAAAGGAGCTTTTAAATTTAAAATTTTTTTGCCTCTGGTCAGAAAAGCT
66 CTAGTTAAAGAAGCTTTTAAATTTAAAATTTCGTTGCCTCTAGTCAGAAAAGCT
* * *
19697745 TTTTAAATTTAAAGTTTCGTTGCCTTTAGTCA-ATGGAACCTTTCGAATTTAAAGTTTTGTTGCC
1 TTTTGAATTTAAAGTTTCGTTGCCTTTAGTCAGA-GGAGCCTTTCAAATTTAAAGTTTTGTTG-C
* * * * *
19697809 TT-T-GATTAGAGAAGCCTTTTGAATTTAAAGTTTCGTTGCCTCTAGTTAGATAAGCT
64 TTCTAG-TTAAAGAAG-CTTTTAAATTTAAAATTTCGTTGCCTCTAGTCAGAAAAGCT
* * *
19697865 TTTTGAATTTAAAATTTCATTGCCTTTAGTCAGAGGGGCCTTT
1 TTTTGAATTTAAAGTTTCGTTGCCTTTAGTCAGAGGAGCCTTT
19697908 TTAAATTTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
118 2 0.01
119 59 0.44
120 73 0.54
121 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (119 bp):
TTTTGAATTTAAAGTTTCGTTGCCTTTAGTCAGAGGAGCCTTTCAAATTTAAAGTTTTGTTGCTT
CTAGTTAAAGAAGCTTTTAAATTTAAAATTTCGTTGCCTCTAGTCAGAAAAGCT
Found at i:19698645 original size:389 final size:389
Alignment explanation
Indices: 19698087--19698865 Score: 1409
Period size: 389 Copynumber: 2.0 Consensus size: 389
19698077 GGAGTTGCTA
19698087 TAAGCACCAATTTTGTTTGATTCTATTTTAATTTAAATATAATTTTTTTATATTATTATTATTAT
1 TAAGCACCAATTTTGTTTGATTCTATTTTAATTTAAATATAATTTTTTTATATTATTATTATTAT
19698152 TATTATTTGGTAAAAAAAAGGGAAAAAAAGTCAAAACAAAAAAAAAATTGGTTTCAACTTTGGTA
66 TATTATTTGGTAAAAAAAA-GGAAAAAAAGTCAAAACAAAAAAAAAATTGGTTTCAACTTTGGTA
* *
19698217 GCTGAAATCAAGCTACCAAAGTAATTTTTTCTTCCCTGACACTACATAATGTTGTAGCATGAAAT
130 GCTAAAATCAAGCTACCAAAGTAATTTTTTCTCCCCTGACACTACATAATGTTGTAGCATGAAAT
*
19698282 CCAGTGACCTTTGGTCA-TCGAACAAATTTTTTCACAAACCTGAGAAAGTCCACAAAAATCTCAG
195 CCAGTGACCTTTGGTCACT-GAACAAATTTTTCCACAAACCTGAGAAAGTCCACAAAAATCTCAG
*
19698346 ATTTTCTAAGATTTTGATATCTTGCTTAACTCTATAAATAAAGCAAAGTTTTCACAAAATGAAGG
259 ATTTTCTAAGATTTTGATATCTTGCTTAACTCTATAAATAAAGCAAAGTGTTCACAAAATGAAGG
*
19698411 GATGAAAGAACAACACAGTGAAAAGCCTAAGAAAAAAATACACAATGAACCAAGGGAGTGGAGAA
324 GATGAAAGAACAACACAATGAAAAGCCTAAGAAAAAAATACACAATGAACCAAGGGAGTGGAGAA
19698476 C
389 C
19698477 TAAGCACCAATTTTGTTTGATTCTATTTTAATTTAAATATAATTTTGTTTATATTATTATTATTA
1 TAAGCACCAATTTTGTTTGATTCTATTTTAATTTAAATATAATTTT-TTTATATTATTATTATTA
*
19698542 TTATTATTTGGTAAAAAAAA-GAAAAAAAGTCAAAACAAAAAAAAATTTGGTTTCAACTTTGGTA
65 TTATTATTTGGTAAAAAAAAGGAAAAAAAGTCAAAACAAAAAAAAAATTGGTTTCAACTTTGGTA
19698606 GCTAAAATCAAGCTACCAAAGTAATTTTTTCTCCCCTGACACTACATAATGTTGTAGCATGAAAT
130 GCTAAAATCAAGCTACCAAAGTAATTTTTTCTCCCCTGACACTACATAATGTTGTAGCATGAAAT
* *
19698671 CCAGTGACCTTTGGTCACTGAACAAGTTTTTCCACAAACCTGAGAAAGTCCACAAAAATCTTAGA
195 CCAGTGACCTTTGGTCACTGAACAAATTTTTCCACAAACCTGAGAAAGTCCACAAAAATCTCAGA
* *
19698736 TTTTCTAAGATTTTGATATCTTGCTTAGCTCTATAAATAAAGCGAAGTGTTCACAAAATGAAGGG
260 TTTTCTAAGATTTTGATATCTTGCTTAACTCTATAAATAAAGCAAAGTGTTCACAAAATGAAGGG
* *
19698801 ATGAAAGAACAACATAATGCAAAGCCTAAGAAAAAAATACACAATGAACCAAGGGAGTGGAGAAC
325 ATGAAAGAACAACACAATGAAAAGCCTAAGAAAAAAATACACAATGAACCAAGGGAGTGGAGAAC
19698866 AAGAAGAGAA
Statistics
Matches: 375, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
389 290 0.77
390 47 0.13
391 38 0.10
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (389 bp):
TAAGCACCAATTTTGTTTGATTCTATTTTAATTTAAATATAATTTTTTTATATTATTATTATTAT
TATTATTTGGTAAAAAAAAGGAAAAAAAGTCAAAACAAAAAAAAAATTGGTTTCAACTTTGGTAG
CTAAAATCAAGCTACCAAAGTAATTTTTTCTCCCCTGACACTACATAATGTTGTAGCATGAAATC
CAGTGACCTTTGGTCACTGAACAAATTTTTCCACAAACCTGAGAAAGTCCACAAAAATCTCAGAT
TTTCTAAGATTTTGATATCTTGCTTAACTCTATAAATAAAGCAAAGTGTTCACAAAATGAAGGGA
TGAAAGAACAACACAATGAAAAGCCTAAGAAAAAAATACACAATGAACCAAGGGAGTGGAGAAC
Found at i:19699522 original size:19 final size:19
Alignment explanation
Indices: 19699500--19699562 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
19699490 TTCCTTTTCC
* *
19699500 TTTTCCTTTTATTTTTTTA
1 TTTTCATTTTATTTATTTA
*
19699519 TTTTGATTTTATTTATTTA
1 TTTTCATTTTATTTATTTA
*
19699538 TTGTTGATTTTTATGTTATTT-
1 TT-TTCA-TTTTAT-TTATTTA
19699559 TTTT
1 TTTT
19699563 ATGATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 18 0.47
20 6 0.16
21 8 0.21
22 6 0.16
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTTCATTTTATTTATTTA
Found at i:19699556 original size:26 final size:24
Alignment explanation
Indices: 19699507--19699564 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
19699497 TCCTTTTCCT
*
19699507 TTTATTT-TTTTATTTTGATTTTA
1 TTTATTTATTTTATTTTGATGTTA
*
19699530 TTTATTTATTGTTGATTTTTATGTTA
1 TTTATTTATT-TT-ATTTTGATGTTA
*
19699556 TTTTTTTAT
1 TTTATTTAT
19699565 GATTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.24
24 2 0.07
25 2 0.07
26 18 0.62
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTATTTATTTTATTTTGATGTTA
Found at i:19699567 original size:22 final size:20
Alignment explanation
Indices: 19699506--19699571 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 20
19699496 TTCCTTTTCC
19699506 TTTTATTT-TTTTATTTTGA-
1 TTTTATTTATTTT-TTTTGAT
*
19699525 TTTTATTTATTTATTGTTGAT
1 TTTTATTTATTT-TTTTTGAT
19699546 TTTTATGTTATTTTTTTATGAT
1 TTTTAT-TTATTTTTTT-TGAT
19699568 TTTT
1 TTTT
19699572 TAATTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.20
20 8 0.20
21 10 0.25
22 14 0.35
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTATTTATTTTTTTTGAT
Found at i:19710041 original size:3 final size:3
Alignment explanation
Indices: 19710033--19710060 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19710023 TTTGCCTTGG
19710033 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19710061 CTTTGTGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19711636 original size:23 final size:22
Alignment explanation
Indices: 19711610--19711663 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
19711600 GTAAAACTAT
19711610 AAAAATAAGTTTAT-AATTTATCA
1 AAAAATAAGTTT-TCAATTTA-CA
*
19711633 AAAAGATAA-TTTTCAATTTACG
1 AAAA-ATAAGTTTTCAATTTACA
19711655 AAAAATAAG
1 AAAAATAAG
19711664 ATTAAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 13 0.48
24 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAATAAGTTTTCAATTTACA
Found at i:19712589 original size:6 final size:7
Alignment explanation
Indices: 19712568--19712597 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19712558 ATTGAAGGTC
*
19712568 TTGGATT
1 TTGGTTT
19712575 TTGGTTT
1 TTGGTTT
19712582 TTGGTTT
1 TTGGTTT
19712589 TTGGTTT
1 TTGGTTT
19712596 TT
1 TT
19712598 AGGGTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.27, T:0.70
Consensus pattern (7 bp):
TTGGTTT
Found at i:19712605 original size:15 final size:14
Alignment explanation
Indices: 19712568--19712606 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19712558 ATTGAAGGTC
*
19712568 TTGGATTTTGGTTT
1 TTGGGTTTTGGTTT
*
19712582 TTGGTTTTTGGTTT
1 TTGGGTTTTGGTTT
19712596 TTAGGGTTTTG
1 TT-GGGTTTTG
19712607 AAATTTAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.05, C:0.00, G:0.31, T:0.64
Consensus pattern (14 bp):
TTGGGTTTTGGTTT
Found at i:19712674 original size:15 final size:15
Alignment explanation
Indices: 19712654--19712687 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
19712644 GATTTTAGAT
19712654 TTTAGGGTTTCAGGG
1 TTTAGGGTTTCAGGG
19712669 TTTAGGGTTTCAGGG
1 TTTAGGGTTTCAGGG
19712684 TTTA
1 TTTA
19712688 AGATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (15 bp):
TTTAGGGTTTCAGGG
Found at i:19712732 original size:8 final size:8
Alignment explanation
Indices: 19712632--19712852 Score: 61
Period size: 8 Copynumber: 28.2 Consensus size: 8
19712622 GCTCTAAAGG
*
19712632 TTTAGGAT
1 TTTAGGGT
*
19712640 TTT-GGAT
1 TTTAGGGT
*
19712647 TTTA-GAT
1 TTTAGGGT
19712654 TTTAGGGT
1 TTTAGGGT
*
19712662 TTCAGGG-
1 TTTAGGGT
19712669 TTTAGGGT
1 TTTAGGGT
*
19712677 TTCAGGGT
1 TTTAGGGT
* **
19712685 TTAAGATT
1 TTTAGGGT
*
19712693 TTTA--AT
1 TTTAGGGT
19712699 ATTTAGGG-
1 -TTTAGGGT
19712707 TTTAGGGT
1 TTTAGGGT
*
19712715 TTTAAAGGT
1 TTT-AGGGT
19712724 TTTAGGGT
1 TTTAGGGT
**
19712732 TTT-GTAT
1 TTTAGGGT
19712739 TTTAGGGT
1 TTTAGGGT
* *
19712747 TTCAAAGGT
1 TT-TAGGGT
*
19712756 TTTAAGGT
1 TTTAGGGT
* *
19712764 TTGGAAAGG-
1 TT--TAGGGT
*
19712773 TTT-GGATT
1 TTTAGG-GT
19712781 TTTAGGG-
1 TTTAGGGT
*
19712788 TTTATGGT
1 TTTAGGGT
***
19712796 TTTAAAAT
1 TTTAGGGT
19712804 TTTAGGGT
1 TTTAGGGT
19712812 TTTGAGGG-
1 TTT-AGGGT
**
19712820 TTTATTGT
1 TTTAGGGT
19712828 TTTAGGG-
1 TTTAGGGT
* *
19712835 TTTCGAGT
1 TTTAGGGT
19712843 TTTAGGGT
1 TTTAGGGT
19712851 TT
1 TT
19712853 ATGGTTTTGA
Statistics
Matches: 155, Mismatches: 39, Indels: 38
0.67 0.17 0.16
Matches are distributed among these distances:
6 2 0.01
7 49 0.32
8 79 0.51
9 21 0.14
10 4 0.03
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (8 bp):
TTTAGGGT
Found at i:19712797 original size:32 final size:30
Alignment explanation
Indices: 19712768--19712859 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
19712758 TAAGGTTTGG
19712768 AAAGGTTTGGATTTTTAGGGTTTATGGTTTT
1 AAAGGTTTGGATTTTTAGGGTTTATGG-TTT
** * * *
19712799 AAAATTTTAGGGTTTTGAGGGTTTATTGTTT
1 AAAGGTTT-GGATTTTTAGGGTTTATGGTTT
* * * *
19712830 TAGGGTTTCGAGTTTTAGGGTTTATGGTTT
1 AAAGGTTTGGATTTTTAGGGTTTATGGTTT
19712860 TGAGCATTTT
Statistics
Matches: 46, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
30 17 0.37
31 13 0.28
32 16 0.35
ACGTcount: A:0.18, C:0.01, G:0.29, T:0.51
Consensus pattern (30 bp):
AAAGGTTTGGATTTTTAGGGTTTATGGTTT
Found at i:19712798 original size:15 final size:15
Alignment explanation
Indices: 19712780--19712860 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
19712770 AGGTTTGGAT
19712780 TTTTAGGGTTTATGG
1 TTTTAGGGTTTATGG
*** *
19712795 TTTTAAAATTTTAGGG
1 TTTT-AGGGTTTATGG
*
19712811 TTTTGAGGGTTTATTG
1 TTTT-AGGGTTTATGG
*
19712827 TTTTAGGGTTT-CGAG
1 TTTTAGGGTTTATG-G
19712842 TTTTAGGGTTTATGG
1 TTTTAGGGTTTATGG
19712857 TTTT
1 TTTT
19712861 GAGCATTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
15 28 0.56
16 22 0.44
ACGTcount: A:0.16, C:0.01, G:0.28, T:0.54
Consensus pattern (15 bp):
TTTTAGGGTTTATGG
Found at i:19712887 original size:16 final size:16
Alignment explanation
Indices: 19712866--19713070 Score: 100
Period size: 16 Copynumber: 12.7 Consensus size: 16
19712856 GTTTTGAGCA
19712866 TTTTAAGGTTTTGAAG
1 TTTTAAGGTTTTGAAG
*
19712882 TTTTAAGATTTTGAA-
1 TTTTAAGGTTTTGAAG
** ***
19712897 TTTTGGGGTTACAAAGG
1 TTTTAAGGTTTTGAA-G
*
19712914 TTTTAGGGTTTAT-AA-
1 TTTTAAGGTTT-TGAAG
* *
19712929 TTTT-AGATTTTTAAG
1 TTTTAAGGTTTTGAAG
* *
19712944 GTTTAAGGTTTTGAAA
1 TTTTAAGGTTTTGAAG
* *
19712960 TTTAAAGGTTTTGAAA
1 TTTTAAGGTTTTGAAG
* *
19712976 TTTAAAGGTTTAGAA-
1 TTTTAAGGTTTTGAAG
*
19712991 TTTTAAGGTTTT-CAG
1 TTTTAAGGTTTTGAAG
* *
19713006 TTTTAAGATTTAAAATTTAAGG
1 TTTTAAG-GTT----TTGAA-G
*
19713028 TTTTGAGGGTTTTGAAG
1 TTTT-AAGGTTTTGAAG
*
19713045 TTTTAAGATTTTGAA-
1 TTTTAAGGTTTTGAAG
19713060 TTTTAAGGTTT
1 TTTTAAGGTTT
19713071 CAAGGGTTTT
Statistics
Matches: 144, Mismatches: 30, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
13 1 0.01
14 7 0.05
15 43 0.30
16 61 0.42
17 16 0.11
18 4 0.03
20 2 0.01
21 1 0.01
22 7 0.05
23 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.21, T:0.49
Consensus pattern (16 bp):
TTTTAAGGTTTTGAAG
Found at i:19713055 original size:39 final size:40
Alignment explanation
Indices: 19713004--19713081 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
19712994 TAAGGTTTTC
**
19713004 AGTTTTAAGA-TTTAAAATTTAAGGTTTTGAGGGTTTTGA
1 AGTTTTAAGATTTTAAAATTTAAGGTTTCAAGGGTTTTGA
* *
19713043 AGTTTTAAGATTTTGAATTTTAAGGTTTCAAGGGTTTTG
1 AGTTTTAAGATTTTAAAATTTAAGGTTTCAAGGGTTTTG
19713082 GGGTTTGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 10 0.29
40 24 0.71
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.47
Consensus pattern (40 bp):
AGTTTTAAGATTTTAAAATTTAAGGTTTCAAGGGTTTTGA
Found at i:19713065 original size:15 final size:16
Alignment explanation
Indices: 19713037--19713066 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19713027 GTTTTGAGGG
19713037 TTTTGAAGTTTTAAGA
1 TTTTGAAGTTTTAAGA
19713053 TTTTGAA-TTTTAAG
1 TTTTGAAGTTTTAAG
19713067 GTTTCAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TTTTGAAGTTTTAAGA
Found at i:19713211 original size:140 final size:141
Alignment explanation
Indices: 19713044--19713352 Score: 401
Period size: 140 Copynumber: 2.2 Consensus size: 141
19713034 GGGTTTTGAA
* * * *
19713044 GTTTTAAGATTTTGAATTTTA-AGGTTTCAAGGGTTTTGGGGTTTGGAATTTTGGATTT-TAAGA
1 GTTTTAAGATTTTGAAGTTTAGA-GTTTCAAGGGTTTCGAGGTTTGAAATTTTGGATTTGT-AGA
* * * * *
19713107 TTTAGGGTTTTAAAATTTTAAGGTTTTGAGGATGTATGATTTCAGGGTTTTGA-GTTTTAGGGTT
64 GTTAGGGTTTTAAAATTTTAAGGTTTCGAGGATGTATGATTTCAGAGTTTTGAGGGTTTAGGATT
19713171 T-AAGATTTTAAGG
129 TAAAG-TTTTAAGG
* *
19713184 GTTTTAAGGTTTTGAAGTTTAGAGTTTCAAGGGTTTCGAGGTTTGAAATTTTGGATTTGTAGGGT
1 GTTTTAAGATTTTGAAGTTTAGAGTTTCAAGGGTTTCGAGGTTTGAAATTTTGGATTTGTAGAGT
* * * * *
19713249 TAGGGTTTTAAAATTTTAAGGTTTCGAGGGTTTATGGTTTTAGAGTTTTGAGGGTTTATGATTTA
66 TAGGGTTTTAAAATTTTAAGGTTTCGAGGATGTATGATTTCAGAGTTTTGAGGGTTTAGGATTTA
19713314 AAGTTTTAAGG
131 AAGTTTTAAGG
*
19713325 ATTTTAAGATTTTGAAGTTTTAGAGTTT
1 GTTTTAAGATTTTGAAG-TTTAGAGTTT
19713353 TGAATTTCAA
Statistics
Matches: 146, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
140 99 0.68
141 34 0.23
142 13 0.09
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (141 bp):
GTTTTAAGATTTTGAAGTTTAGAGTTTCAAGGGTTTCGAGGTTTGAAATTTTGGATTTGTAGAGT
TAGGGTTTTAAAATTTTAAGGTTTCGAGGATGTATGATTTCAGAGTTTTGAGGGTTTAGGATTTA
AAGTTTTAAGG
Found at i:19713417 original size:24 final size:24
Alignment explanation
Indices: 19713390--19713435 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
19713380 TTTTTAGGAT
*
19713390 TTTGAAATTGTAGGTTTTCGAGGG
1 TTTGAAATTGTAGGGTTTCGAGGG
** *
19713414 TTTGTGATTTTAGGGTTTCGAG
1 TTTGAAATTGTAGGGTTTCGAG
19713436 ACTTTAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.04, G:0.33, T:0.46
Consensus pattern (24 bp):
TTTGAAATTGTAGGGTTTCGAGGG
Found at i:19713551 original size:3 final size:3
Alignment explanation
Indices: 19713543--19713576 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
19713533 TTCATAAAAT
19713543 TTA TTA TTA TTA TTA TTA TTA TTTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TT
19713577 TGTTTGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19713845 original size:14 final size:14
Alignment explanation
Indices: 19713801--19713848 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
19713791 AATCATTTTC
19713801 ATTTTTATTATTGTT
1 ATTTTTATTA-TGTT
*
19713816 ATTATTATCTA-GTT
1 ATTTTTAT-TATGTT
*
19713830 ATTTTTATTATATT
1 ATTTTTATTATGTT
19713844 ATTTT
1 ATTTT
19713849 ATAAGGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 7 0.25
16 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (14 bp):
ATTTTTATTATGTT
Found at i:19714019 original size:3 final size:3
Alignment explanation
Indices: 19714011--19714060 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
19714001 AACATGCATA
19714011 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19714059 AA
1 AA
19714061 CTCAAAACGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19714884 original size:23 final size:22
Alignment explanation
Indices: 19714850--19714928 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
19714840 AGATGACTTT
19714850 TAATCT-GAGCTTGCGTGCCAAC
1 TAATCTAG-GCTTGCGTGCCAAC
* *
19714872 TAATTCTAGGCTTTCATGCCAAC
1 TAA-TCTAGGCTTGCGTGCCAAC
*
19714895 TAATCTAGGCTTGTGTGCCAAC
1 TAATCTAGGCTTGCGTGCCAAC
19714917 TACA-CTAGGCTT
1 TA-ATCTAGGCTT
19714929 AAAACTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 29 0.59
23 19 0.39
24 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
TAATCTAGGCTTGCGTGCCAAC
Found at i:19715026 original size:36 final size:33
Alignment explanation
Indices: 19714986--19715132 Score: 122
Period size: 32 Copynumber: 4.3 Consensus size: 33
19714976 CTAAATTGGA
*
19714986 GCTTAAAATCTTTTCATGGTGTGCCAGATAATTTAG
1 GCTTAAAA-C-TTTCATGG-GTGCCAAATAATTTAG
* *
19715022 GCTTAAAACTTT-ATTGGTG-CAAACTACA-CTAG
1 GCTTAAAACTTTCATGGGTGCCAAA-TA-ATTTAG
* * * *
19715054 GCTTAAAAC-TTCATTGGTGCCATATAAATTGG
1 GCTTAAAACTTTCATGGGTGCCAAATAATTTAG
*
19715086 GCTTAAAATCTTTTCATGGTGAGCCAAATAATTTAG
1 GCTTAAAA-C-TTTCATGG-GTGCCAAATAATTTAG
19715122 GCTTAAAACTT
1 GCTTAAAACTT
19715133 CATTAGTGTC
Statistics
Matches: 91, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
31 6 0.07
32 36 0.40
33 8 0.09
34 5 0.05
35 8 0.09
36 28 0.31
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (33 bp):
GCTTAAAACTTTCATGGGTGCCAAATAATTTAG
Found at i:19716115 original size:19 final size:17
Alignment explanation
Indices: 19716085--19716127 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
19716075 TTTCTTTTTC
19716085 TTTTTTTCTTTT-ACTCT
1 TTTTTTTCTTTTGAC-CT
19716102 ATTTTTTTCTTTTTGACCT
1 -TTTTTTTC-TTTTGACCT
19716121 TTTTTTT
1 TTTTTTT
19716128 TGTTATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.65
19 6 0.26
20 2 0.09
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTTGACCT
Found at i:19716505 original size:16 final size:16
Alignment explanation
Indices: 19716486--19716542 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
19716476 TTTTTTTCTT
19716486 TTTCTTTCTTTTATTC
1 TTTCTTTCTTTTATTC
*
19716502 TTTCTTTCATTTCA-TC
1 TTTCTTTC-TTTTATTC
*
19716518 TTTCCTT-TTTT-TTC
1 TTTCTTTCTTTTATTC
*
19716532 CTT-TTTCTTTT
1 TTTCTTTCTTTT
19716543 GTATTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
13 2 0.06
14 11 0.33
16 16 0.48
17 4 0.12
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTCTTTTATTC
Found at i:19720291 original size:10 final size:10
Alignment explanation
Indices: 19720264--19720301 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
19720254 TATACATATA
19720264 AAATAATAAAT
1 AAATAA-AAAT
19720275 AAATAAAACAT
1 AAATAAAA-AT
19720286 -AATAAAAAT
1 AAATAAAAAT
19720295 AAATAAA
1 AAATAAA
19720302 CAAATACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.08
10 15 0.60
11 8 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:19721866 original size:66 final size:64
Alignment explanation
Indices: 19721757--19721917 Score: 153
Period size: 66 Copynumber: 2.4 Consensus size: 64
19721747 CATAAATCTA
** * *** * **
19721757 AAAAATAAAATGACTTGGAC-AGAGCCAAGATCGAAGATAAGTGATTGGGATTTAACTGCAGGTC
1 AAAAATAAAATGAC-TGGACTA-AGCCAAGATAAAAAATAAGTGATTAAAATTAAACCACAGGT-
19721821 TG
63 TG
* *
19721823 AAAAATAAAATGATCTAGACTAAGCCAAGATAAAAAATGAGTGATTAAAATTAAACCACAGGTTG
1 AAAAATAAAATGA-CTGGACTAAGCCAAGATAAAAAATAAGTGATTAAAATTAAACCACAGGTTG
*
19721888 AAAAACTAAAATAACCTGGACTAAGCCAAG
1 AAAAA-TAAAATGA-CTGGACTAAGCCAAG
19721918 GTTGAAGATA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
65 7 0.09
66 69 0.88
67 2 0.03
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.20
Consensus pattern (64 bp):
AAAAATAAAATGACTGGACTAAGCCAAGATAAAAAATAAGTGATTAAAATTAAACCACAGGTTG
Found at i:19722355 original size:23 final size:23
Alignment explanation
Indices: 19722328--19722373 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19722318 CATCATTTGC
19722328 CCTCCTCTCTTTCAACTTTCCCA
1 CCTCCTCTCTTTCAACTTTCCCA
*
19722351 CCTCCTTTCTTTCAACTTTCCCA
1 CCTCCTCTCTTTCAACTTTCCCA
19722374 AAGTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.46, G:0.00, T:0.41
Consensus pattern (23 bp):
CCTCCTCTCTTTCAACTTTCCCA
Found at i:19737154 original size:36 final size:35
Alignment explanation
Indices: 19737106--19737173 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
19737096 TAAAAATAGT
* *
19737106 TAAAAATGATTGTTGGTGACTCTCCAACATCTTTG
1 TAAAAATAATTGTTAGTGACTCTCCAACATCTTTG
**
19737141 TAAAAGATAATTGTTAGTGACTCTTTAACATCT
1 TAAAA-ATAATTGTTAGTGACTCTCCAACATCT
19737174 AGGCAGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.18
36 23 0.82
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (35 bp):
TAAAAATAATTGTTAGTGACTCTCCAACATCTTTG
Found at i:19737768 original size:18 final size:17
Alignment explanation
Indices: 19737734--19737768 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19737724 TTTATGAATC
*
19737734 AAATTTAAGGTTTGGTT
1 AAATTTAAGATTTGGTT
19737751 AAATTTAAGATCTTGGTT
1 AAATTTAAGAT-TTGGTT
19737769 TTTGGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (17 bp):
AAATTTAAGATTTGGTT
Found at i:19737818 original size:21 final size:20
Alignment explanation
Indices: 19737789--19737828 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
19737779 TTGGTTTCAA
19737789 AATTTAGGGTTTAGGGTTTT
1 AATTTAGGGTTTAGGGTTTT
19737809 AATTCTAGGGTTTAGGGTTT
1 AATT-TAGGGTTTAGGGTTT
19737829 ATAGTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (20 bp):
AATTTAGGGTTTAGGGTTTT
Found at i:19737908 original size:39 final size:40
Alignment explanation
Indices: 19737865--19737970 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 40
19737855 ATTTGAAGGC
*
19737865 TTAGGGTTTTGAGTATTTGGGGTTTTAGGCTTT-AAGGGT
1 TTAGGGTTTTGAGTATTTAGGGTTTTAGGCTTTAAAGGGT
* * * * *
19737904 TTAGGGCTTTGAGTATTTAGGATTTAAGGTTTTAAAGGTT
1 TTAGGGTTTTGAGTATTTAGGGTTTTAGGCTTTAAAGGGT
*
19737944 TTAAGGTTTTCAGAGT-TTTAGGGTTTT
1 TTAGGGTTTT--GAGTATTTAGGGTTTT
19737971 TAGATTTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 28 0.52
40 13 0.24
41 9 0.17
42 4 0.07
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (40 bp):
TTAGGGTTTTGAGTATTTAGGGTTTTAGGCTTTAAAGGGT
Found at i:19737970 original size:25 final size:24
Alignment explanation
Indices: 19737940--19738145 Score: 115
Period size: 24 Copynumber: 8.6 Consensus size: 24
19737930 AGGTTTTAAA
19737940 GGTTTTAAGGTTTTCAGAGTTTTAG
1 GGTTTTAAGGTTTT-AGAGTTTTAG
* *
19737965 GGTTTTTAGATTTTA-AGGTTTTGAG
1 GGTTTTAAGGTTTTAGA-GTTTT-AG
*
19737990 AGTTTT-AGG-TTTAGAGTTTTAGG
1 GGTTTTAAGGTTTTAGAGTTTTA-G
* * *
19738013 GGTTTGAAGGGTTTAGAATTCTTAG
1 GGTTTTAAGGTTTTAGAGTT-TTAG
*
19738038 GGTTTTAA-ATTTTAG-GTTTTCGAG
1 GGTTTTAAGGTTTTAGAGTTTT--AG
* * * *
19738062 GG-CTTATGGTTTTAGGGTTTCA-
1 GGTTTTAAGGTTTTAGAGTTTTAG
* * *
19738084 AGTTTTAGGGTTTAAGA-TTTTAAG
1 GGTTTTAAGGTTTTAGAGTTTT-AG
* * *
19738108 GGTTTTATGGCTTT-GAATTTTAG
1 GGTTTTAAGGTTTTAGAGTTTTAG
19738131 GGTTTTAAGAGTTTT
1 GGTTTTAAG-GTTTT
19738146 GCAGTTTGGA
Statistics
Matches: 138, Mismatches: 27, Indels: 33
0.70 0.14 0.17
Matches are distributed among these distances:
22 7 0.05
23 44 0.32
24 45 0.33
25 39 0.28
26 3 0.02
ACGTcount: A:0.21, C:0.03, G:0.28, T:0.48
Consensus pattern (24 bp):
GGTTTTAAGGTTTTAGAGTTTTAG
Found at i:19738017 original size:16 final size:17
Alignment explanation
Indices: 19737926--19738010 Score: 90
Period size: 17 Copynumber: 5.2 Consensus size: 17
19737916 GTATTTAGGA
*
19737926 TTTAAGGTTTT-AAAGGT
1 TTTAAGGTTTTCAGA-GT
19737943 TTTAAGGTTTTCAGAGT
1 TTTAAGGTTTTCAGAGT
* *
19737960 TTTAGGGTTTTTAGA-T
1 TTTAAGGTTTTCAGAGT
*
19737976 TTTAAGGTTTTGAGAGT
1 TTTAAGGTTTTCAGAGT
19737993 TTT-AGG-TTT-AGAGT
1 TTTAAGGTTTTCAGAGT
19738007 TTTA
1 TTTA
19738011 GGGGTTTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 17 0.28
17 30 0.50
18 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.51
Consensus pattern (17 bp):
TTTAAGGTTTTCAGAGT
Found at i:19738096 original size:8 final size:8
Alignment explanation
Indices: 19737791--19738137 Score: 74
Period size: 8 Copynumber: 44.5 Consensus size: 8
19737781 GGTTTCAAAA
19737791 TTTAGGG-
1 TTTAGGGT
19737798 TTTAGGGT
1 TTTAGGGT
*
19737806 TTTA--AT
1 TTTAGGGT
*
19737812 TCTAGGG-
1 TTTAGGGT
19737819 TTTAGGGT
1 TTTAGGGT
19737827 TTATA--GT
1 TT-TAGGGT
*
19737834 TTT-GGCT
1 TTTAGGGT
19737841 TTTAAGGG-
1 TTT-AGGGT
*
19737849 TTTAGGAT
1 TTTAGGGT
* *
19737857 TTGAAGG-
1 TTTAGGGT
*
19737864 CTTAGGGT
1 TTTAGGGT
*
19737872 TTT-GAGT
1 TTTAGGGT
*
19737879 ATTTGGGGT
1 -TTTAGGGT
*
19737888 TTTAGGCT
1 TTTAGGGT
*
19737896 TTAAGGG-
1 TTTAGGGT
*
19737903 TTTAGGGC
1 TTTAGGGT
*
19737911 TTT-GAGT
1 TTTAGGGT
*
19737918 ATTTA-GGA
1 -TTTAGGGT
*
19737926 TTTAAGGT
1 TTTAGGGT
*
19737934 TTTAAAGGT
1 TTT-AGGGT
*
19737943 TTTAAGGT
1 TTTAGGGT
*
19737951 TTTCAGAGT
1 TTT-AGGGT
19737960 TTTAGGGTT
1 TTTAGGG-T
*
19737969 TTTA-GAT
1 TTTAGGGT
*
19737976 TTTAAGGT
1 TTTAGGGT
*
19737984 TTTGAGAGT
1 TTT-AGGGT
19737993 TTTA-GG-
1 TTTAGGGT
*
19737999 TTTAGAGT
1 TTTAGGGT
19738007 TTTAGGGGT
1 TTTA-GGGT
*
19738016 TTGAAGGG-
1 TT-TAGGGT
**
19738024 TTTAGAAT
1 TTTAGGGT
19738032 TCTTAGGGT
1 T-TTAGGGT
**
19738041 TTTA-AAT
1 TTTAGGGT
19738048 TTTA-GGT
1 TTTAGGGT
19738055 TTTCGAGGG-
1 TTT--AGGGT
* *
19738064 CTTATGGT
1 TTTAGGGT
19738072 TTTAGGGT
1 TTTAGGGT
* *
19738080 TTCA-AGT
1 TTTAGGGT
19738087 TTTAGGG-
1 TTTAGGGT
* *
19738094 TTTAAGAT
1 TTTAGGGT
19738102 TTTAAGGGT
1 TTT-AGGGT
* *
19738111 TTTATGGC
1 TTTAGGGT
**
19738119 TTT-GAAT
1 TTTAGGGT
19738126 TTTAGGGT
1 TTTAGGGT
19738134 TTTA
1 TTTA
19738138 AGAGTTTTGC
Statistics
Matches: 238, Mismatches: 66, Indels: 71
0.63 0.18 0.19
Matches are distributed among these distances:
6 9 0.04
7 77 0.32
8 94 0.39
9 55 0.23
10 3 0.01
ACGTcount: A:0.20, C:0.03, G:0.29, T:0.47
Consensus pattern (8 bp):
TTTAGGGT
Found at i:19738111 original size:16 final size:15
Alignment explanation
Indices: 19738070--19738112 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
19738060 AGGGCTTATG
19738070 GTTTTAGGGTTTCAA
1 GTTTTAGGGTTTCAA
19738085 GTTTTAGGGTTT-AA
1 GTTTTAGGGTTTCAA
19738099 GATTTTAAGGGTTT
1 G-TTTT-AGGGTTT
19738113 TATGGCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.12
15 16 0.62
16 7 0.27
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (15 bp):
GTTTTAGGGTTTCAA
Found at i:19738184 original size:8 final size:8
Alignment explanation
Indices: 19737949--19738208 Score: 57
Period size: 8 Copynumber: 32.8 Consensus size: 8
19737939 AGGTTTTAAG
19737949 GTTTTCAGA
1 GTTTT-AGA
*
19737958 GTTTTAGG
1 GTTTTAGA
19737966 GTTTTTAGA
1 G-TTTTAGA
19737975 -TTTTA-A
1 GTTTTAGA
19737981 GGTTTTGAGA
1 -GTTTT-AGA
19737991 GTTTTAG-
1 GTTTTAGA
19737998 G-TTTAGA
1 GTTTTAGA
*
19738005 GTTTTAGG
1 GTTTTAGA
*
19738013 GGTTT-GAA
1 GTTTTAG-A
*
19738021 GGGTTTAGA
1 -GTTTTAGA
* *
19738030 ATTCTTAGG
1 GTT-TTAGA
19738039 GTTTTA-A
1 GTTTTAGA
*
19738046 ATTTTAG-
1 GTTTTAGA
*
19738053 GTTTTCGA
1 GTTTTAGA
**
19738061 GGGCTTATG-
1 -GTTTTA-GA
*
19738070 GTTTTAGG
1 GTTTTAGA
*
19738078 GTTTCA-A
1 GTTTTAGA
*
19738085 GTTTTAGG
1 GTTTTAGA
*
19738093 GTTTAAGA
1 GTTTTAGA
*
19738101 -TTTTAAGG
1 GTTTT-AGA
19738109 GTTTTATG-
1 GTTTTA-GA
*
19738117 GCTTT-GA
1 GTTTTAGA
* *
19738124 ATTTTAGG
1 GTTTTAGA
19738132 GTTTTAAGA
1 GTTTT-AGA
19738141 GTTTT-GCA
1 GTTTTAG-A
*
19738149 G-TTTGGA
1 GTTTTAGA
* *
19738156 ATTTTGGA
1 GTTTTAGA
*
19738164 TTTTTAGA
1 GTTTTAGA
19738172 G-TTTAGA
1 GTTTTAGA
*
19738179 GTTTTAAA
1 GTTTTAGA
* *
19738187 ATTTTAGG
1 GTTTTAGA
19738195 GTTTT-GA
1 GTTTTAGA
19738202 GGTTTTA
1 -GTTTTA
19738209 TGGTTTTATG
Statistics
Matches: 180, Mismatches: 42, Indels: 58
0.64 0.15 0.21
Matches are distributed among these distances:
6 7 0.04
7 43 0.24
8 83 0.46
9 44 0.24
10 3 0.02
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (8 bp):
GTTTTAGA
Found at i:19738653 original size:3 final size:3
Alignment explanation
Indices: 19738638--19738685 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
19738628 ATTTTCATTT
* *
19738638 TTA TTA TTG TTA TTA TTA TTA TTA TCTA GTTA TTT TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA
19738684 TT
1 TT
19738686 CTATAAGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 4 0.11
5 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Done.