Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 14 of 250
Found at i:4057688 original size:53 final size:53
Alignment explanation
Indices: 4057608--4057714 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
4057598 TCATTAAAAA
4057608 CGGATTAAAAATACATAACAAATTGGACAAAATAAGCTTGCCGAAACTTTAAG
1 CGGATTAAAAATACATAACAAATTGGACAAAATAAGCTTGCCGAAACTTTAAG
4057661 CGGATTAAAAATACATAACAAATTGGACAAAATAAGCTTGCCGAAACTTTAAG
1 CGGATTAAAAATACATAACAAATTGGACAAAATAAGCTTGCCGAAACTTTAAG
4057714 C
1 C
4057715 TTCCATGATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (53 bp):
CGGATTAAAAATACATAACAAATTGGACAAAATAAGCTTGCCGAAACTTTAAG
Found at i:4062924 original size:25 final size:25
Alignment explanation
Indices: 4062896--4062946 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4062886 AAAATCTGGT
*
4062896 TACTTATTGCAAAGTTCGAAAGCGA
1 TACTTATTGCAAAGTTCGAAAACGA
4062921 TACTTATTGCAAAGTTCGAAAACGA
1 TACTTATTGCAAAGTTCGAAAACGA
4062946 T
1 T
4062947 CACCACGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (25 bp):
TACTTATTGCAAAGTTCGAAAACGA
Found at i:4063194 original size:31 final size:31
Alignment explanation
Indices: 4063148--4063222 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
4063138 ACAGTTACTA
* *
4063148 GGCCGAAGCCATTTCATAAATCATACCACTG
1 GGCCGAAGCCTTTTCATAAATCATACAACTG
*
4063179 GGCTGAAGCCTTTTCATAAATCATACAACTG
1 GGCCGAAGCCTTTTCATAAATCATACAACTG
*
4063210 GGCCAAAGCCTTT
1 GGCCGAAGCCTTT
4063223 ACTGTAAACG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (31 bp):
GGCCGAAGCCTTTTCATAAATCATACAACTG
Found at i:4063536 original size:11 final size:11
Alignment explanation
Indices: 4063517--4063569 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
4063507 GTATATCATA
4063517 GCATATCATGT
1 GCATATCATGT
* *
4063528 GCATCTCAT-A
1 GCATATCATGT
4063538 GCATATCATGT
1 GCATATCATGT
**
4063549 GCATGCCATGT
1 GCATATCATGT
4063560 -CATATCATGT
1 GCATATCATGT
4063570 ATAACAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (11 bp):
GCATATCATGT
Found at i:4063536 original size:21 final size:22
Alignment explanation
Indices: 4063512--4063569 Score: 86
Period size: 21 Copynumber: 2.7 Consensus size: 22
4063502 AATGAGTATA
4063512 TCATAGCATATCATGTGCAT-C
1 TCATAGCATATCATGTGCATGC
4063533 TCATAGCATATCATGTGCATGC
1 TCATAGCATATCATGTGCATGC
4063555 -CAT-GTCATATCATGT
1 TCATAG-CATATCATGT
4063570 ATAACAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATAGCATATCATGTGCATGC
Found at i:4066490 original size:104 final size:104
Alignment explanation
Indices: 4066322--4066533 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 104
4066312 GGGTTGTTGT
* *
4066322 GTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTTTGAAATGTGAAA
1 GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAA
4066387 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
* *
4066426 GTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCTTTGAAATGTGAA
*
4066490 AGGGGGTTGCTATGTGTTGATTCCCCCGAGGGGTTGCTAA
65 AGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
4066530 GTGC
1 GTGC
4066534 GATATCCATT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
104 101 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (104 bp):
GTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAA
GGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:4066586 original size:71 final size:72
Alignment explanation
Indices: 4066452--4066603 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
4066442 TCATTGGTGG
* * *
4066452 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGTTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4066517 GAGGGGT
66 GAGGGGT
***
4066524 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4066588 GAGGGGT
66 GAGGGGT
4066595 TGCTAAGTG
1 TGCTAAGTG
4066604 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
71 44 0.59
72 30 0.41
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:4068219 original size:19 final size:20
Alignment explanation
Indices: 4068195--4068232 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4068185 CACAACCAAA
*
4068195 TACCAAATT-TTAAAAATTT
1 TACCAAATTCTCAAAAATTT
4068214 TACCAAATTCTCAAAAATT
1 TACCAAATTCTCAAAAATT
4068233 ACGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (20 bp):
TACCAAATTCTCAAAAATTT
Found at i:4084107 original size:24 final size:24
Alignment explanation
Indices: 4084074--4084121 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4084064 TTGGATATAG
*
4084074 AACAATCATATAGTGATATATGGT
1 AACAACCATATAGTGATATATGGT
4084098 AACAACCATATAGTGATATATGGT
1 AACAACCATATAGTGATATATGGT
4084122 GCGCCATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (24 bp):
AACAACCATATAGTGATATATGGT
Found at i:4088099 original size:25 final size:25
Alignment explanation
Indices: 4088071--4088122 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
4088061 AAAGGGTGAT
4088071 ATAGTTAACTTAATAATAAGTAGAA
1 ATAGTTAACTTAATAATAAGTAGAA
* *
4088096 ATAGTTACCTTAATAATAAGTGGAA
1 ATAGTTAACTTAATAATAAGTAGAA
4088121 AT
1 AT
4088123 TTTGAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (25 bp):
ATAGTTAACTTAATAATAAGTAGAA
Found at i:4091594 original size:18 final size:18
Alignment explanation
Indices: 4091571--4091607 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4091561 TAGCACATTA
4091571 TGATGTTGTTTGAGGATG
1 TGATGTTGTTTGAGGATG
4091589 TGATGTTGTTTGAGGATG
1 TGATGTTGTTTGAGGATG
4091607 T
1 T
4091608 TTTTAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (18 bp):
TGATGTTGTTTGAGGATG
Found at i:4091797 original size:13 final size:14
Alignment explanation
Indices: 4091770--4091798 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4091760 CTCAAAAATT
4091770 GGTTAGTAGAATCG
1 GGTTAGTAGAATCG
4091784 GGTTAGTA-AATCG
1 GGTTAGTAGAATCG
4091797 GG
1 GG
4091799 AGTTAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (14 bp):
GGTTAGTAGAATCG
Found at i:4104631 original size:46 final size:46
Alignment explanation
Indices: 4104561--4104651 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
4104551 GGGTTTTTGT
*
4104561 TACACACTTGATATGGATTCGACGTAATGATAATACTCTAAAATGG
1 TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATGG
*
4104607 TACACACTTGATATGGATTTGACGTAACGATAATACTCTAAAATG
1 TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATG
4104652 ACATACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (46 bp):
TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATGG
Found at i:4108484 original size:19 final size:18
Alignment explanation
Indices: 4108454--4108490 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
4108444 AGGCAACCCA
4108454 ATTTTATCTTTATTTTCT
1 ATTTTATCTTTATTTTCT
4108472 ATTTTATTCTTTATTTTCT
1 ATTTTA-TCTTTATTTTCT
4108491 TGCATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTATCTTTATTTTCT
Found at i:4109395 original size:102 final size:102
Alignment explanation
Indices: 4109269--4109465 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
4109259 GAATTAAATA
4109269 ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
1 ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
*
4109334 TTCATGTCAAAAGGG-AAAACATTCTTAACCAAAAAC
66 TTCACGTCAAAAGGGCAAAACATTCTTAACCAAAAAC
* *
4109370 ATAATAATAAAATATA-AGTGTGTTGGGCTGAGTAATTGGGGTGGGGTGCTTGGGTTGTCATCCC
1 ATAATAAT-AAATA-AGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCC
* * *
4109434 TCTTCGCGTCAAAAGGGCCAATACATTCTTAA
64 ACTTCACGTCAAAAGGG-CAAAACATTCTTAA
4109466 GAAAAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
101 8 0.09
102 65 0.76
103 1 0.01
104 12 0.14
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
TTCACGTCAAAAGGGCAAAACATTCTTAACCAAAAAC
Found at i:4111504 original size:9 final size:8
Alignment explanation
Indices: 4111475--4111513 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
4111465 AATGATAGGC
4111475 AAAAAGAA
1 AAAAAGAA
*
4111483 AAGAAAGTA
1 AA-AAAGAA
4111492 AAAAAGAA
1 AAAAAGAA
4111500 GAAAAAGAA
1 -AAAAAGAA
4111509 AAAAA
1 AAAAA
4111514 ACAGTAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:4111513 original size:17 final size:17
Alignment explanation
Indices: 4111475--4111513 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4111465 AATGATAGGC
*
4111475 AAAAAGAAAAGAAAGTA
1 AAAAAGAAAAGAAAGAA
4111492 AAAAAGAAGAA-AAAGAA
1 AAAAAGAA-AAGAAAGAA
4111509 AAAAA
1 AAAAA
4111514 ACAGTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAAGAA
Found at i:4118807 original size:22 final size:21
Alignment explanation
Indices: 4118776--4118821 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4118766 ATTTCTATCT
4118776 TTACTTTTATCATTAACATTA
1 TTACTTTTATCATTAACATTA
* **
4118797 TTACTATTTATTATTATTATTA
1 TTACT-TTTATCATTAACATTA
4118819 TTA
1 TTA
4118822 TTTACACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (21 bp):
TTACTTTTATCATTAACATTA
Found at i:4118893 original size:9 final size:10
Alignment explanation
Indices: 4118862--4119070 Score: 58
Period size: 9 Copynumber: 21.1 Consensus size: 10
4118852 TTTTGCATAC
4118862 ATATATTATT
1 ATATATTATT
4118872 ATTTATATTATT
1 A--TATATTATT
4118884 ATA-ATTATT
1 ATATATTATT
*
4118893 ACTAT-TTCTT
1 A-TATATTATT
*
4118903 -TCATGTCTATT
1 AT-ATAT-TATT
*
4118914 -T-T-TTATA
1 ATATATTATT
4118921 ATACTATTATT
1 ATA-TATTATT
4118932 ATA-ATCTCATT
1 ATATAT-T-ATT
4118943 -T-TATTATT
1 ATATATTATT
*
4118951 ATCATTCTTATT
1 AT-A-TATTATT
*
4118963 AATACATTATT
1 -ATATATTATT
4118974 AT-TATT-TT
1 ATATATTATT
*
4118982 ACCATATTATT
1 A-TATATTATT
4118993 AT-T-TTA-T
1 ATATATTATT
*
4119000 ATATTATTACT
1 ATA-TATTATT
* **
4119011 GT-TATTAAC
1 ATATATTATT
4119020 ATATTATTATT
1 ATA-TATTATT
4119031 AT-TATTATT
1 ATATATTATT
4119040 AT-TATTATT
1 ATATATTATT
4119049 ATAT-TTATT
1 ATATATTATT
4119058 ATTAATATTATT
1 A-T-ATATTATT
4119070 A
1 A
4119071 GTACTAGTAT
Statistics
Matches: 151, Mismatches: 16, Indels: 62
0.66 0.07 0.27
Matches are distributed among these distances:
7 6 0.04
8 12 0.08
9 49 0.32
10 26 0.17
11 33 0.22
12 23 0.15
13 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:4118933 original size:3 final size:3
Alignment explanation
Indices: 4118925--4119070 Score: 99
Period size: 3 Copynumber: 49.7 Consensus size: 3
4118915 TTTATAATAC
* * * * *
4118925 TAT TAT TAT AAT CTCAT T-T TAT TAT TAT CAT TCT TAT TAA TA- CAT
1 TAT TAT TAT TAT -T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4118970 TAT TAT TAT T-T TAC CA- TAT TAT TAT T-T TAT ATAT TAT TAC TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
4119013 TAT TAA CA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
4119057 TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TA
4119071 GTACTAGTAT
Statistics
Matches: 111, Mismatches: 21, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
2 11 0.10
3 92 0.83
4 6 0.05
5 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:4119220 original size:23 final size:24
Alignment explanation
Indices: 4119171--4119271 Score: 72
Period size: 23 Copynumber: 4.4 Consensus size: 24
4119161 TTTCTAATAT
* *
4119171 ATATATAT-AT-TGTATATGTTTA
1 ATATATATCATGTATATATTTTTA
4119193 TATATATATCATGTATAT-TTTTTA
1 -ATATATATCATGTATATATTTTTA
* *
4119217 ATAT-TATTA-GTTATATATTTTTT
1 ATATATATCATG-TATATATTTTTA
* *
4119240 ATACTATTTCATATATATATTTTT-
1 ATA-TATATCATGTATATATTTTTA
4119264 ATAT-TATC
1 ATATATATC
4119272 CTTGTTATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
21 1 0.02
22 12 0.19
23 21 0.33
24 11 0.17
25 18 0.29
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
ATATATATCATGTATATATTTTTA
Found at i:4119233 original size:24 final size:23
Alignment explanation
Indices: 4119189--4119270 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
4119179 ATTGTATATG
*
4119189 TTTATA-TATATATCATGTATATTT
1 TTTATATTAT-TA-CATATATATTT
**
4119213 TTTAATATTATTAGTTATATATTT
1 TTT-ATATTATTACATATATATTT
* *
4119237 TTTATACTATTTCATATATATATT
1 TTTATATTATTACATATATAT-TT
4119261 TTTATATTAT
1 TTTATATTAT
4119271 CCTTGTTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 14 0.30
24 25 0.53
25 5 0.11
26 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTATATTATTACATATATATTT
Found at i:4119320 original size:21 final size:20
Alignment explanation
Indices: 4119288--4119328 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4119278 ATTATTATTG
* *
4119288 GTATATGTTTTATTATATAT
1 GTATATATTTTAATATATAT
4119308 GTATATATCTTTAATATATAT
1 GTATATAT-TTTAATATATAT
4119329 TTATGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (20 bp):
GTATATATTTTAATATATAT
Found at i:4119427 original size:22 final size:21
Alignment explanation
Indices: 4119378--4119428 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
4119368 TTCTAATATG
*
4119378 TATATATTATGTAATATTTAA
1 TATATATTATGTAACATTTAA
**
4119399 TACTATATTATGTATACATTTTT
1 TA-TATATTATGTA-ACATTTAA
4119422 TATATAT
1 TATATAT
4119429 ATTACGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATTATGTAACATTTAA
Found at i:4119429 original size:24 final size:23
Alignment explanation
Indices: 4119378--4119443 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
4119368 TTCTAATATG
4119378 TATATATTATG--TAATATTTAA
1 TATATATTATGTATAATATTTAA
* *
4119399 TACTATATTATGTATACATTTTTTA
1 TA-TATATTATGTATA-ATATTTAA
*
4119424 TATATATTACGTATATATAT
1 TATATATTATGTATA-ATAT
4119444 CTTTTTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 9 0.25
24 17 0.47
25 8 0.22
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TATATATTATGTATAATATTTAA
Found at i:4119545 original size:25 final size:25
Alignment explanation
Indices: 4119473--4119590 Score: 102
Period size: 25 Copynumber: 4.8 Consensus size: 25
4119463 ATATATATCG
**
4119473 TGTATATATTTCAAATACTATATTA
1 TGTATATATTTTTAATACTATATTA
* *
4119498 --TAT-T-TTTTTACATATTATCTTA
1 TGTATATATTTTTA-ATACTATATTA
4119520 TGTATATA-TTTTAATAACTATATTA
1 TGTATATATTTTTAAT-ACTATATTA
* * * *
4119545 TATATGTATTTTTAATGCCATATTA
1 TGTATATATTTTTAATACTATATTA
*
4119570 TGTACATATTTTTAATACTAT
1 TGTATATATTTTTAATACTAT
4119591 GCATACACAT
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
21 4 0.06
22 10 0.14
23 3 0.04
24 5 0.07
25 42 0.59
26 7 0.10
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (25 bp):
TGTATATATTTTTAATACTATATTA
Found at i:4119736 original size:19 final size:19
Alignment explanation
Indices: 4119693--4119749 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
4119683 CTGTTTTCAA
*
4119693 TATATATTGTA-TATAT-T
1 TATATATAGTATTATATGT
*
4119710 TTTAATATAGTATTATATGT
1 TAT-ATATAGTATTATATGT
4119730 TATATATA-TATATATATGT
1 TATATATAGTAT-TATATGT
4119749 T
1 T
4119750 CCCTACTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 10 0.30
19 18 0.55
20 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TATATATAGTATTATATGT
Found at i:4127983 original size:7 final size:7
Alignment explanation
Indices: 4127971--4127995 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4127961 AAATTAATAA
4127971 AATAAAT
1 AATAAAT
4127978 AATAAAT
1 AATAAAT
4127985 AATAAAT
1 AATAAAT
4127992 AATA
1 AATA
4127996 GAACTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:4128015 original size:27 final size:27
Alignment explanation
Indices: 4127960--4128016 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
4127950 TAGCCTAACC
*
4127960 TAAATTAATAAAATAAATAATAAATAA
1 TAAATTAATAAAATAAATAATAAAAAA
*
4127987 TAAA-TAATAGAACTAAATAA-AACAAAA
1 TAAATTAATA-AAATAAATAATAA-AAAA
4128014 TAA
1 TAA
4128017 TATCTTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (27 bp):
TAAATTAATAAAATAAATAATAAAAAA
Found at i:4128340 original size:23 final size:24
Alignment explanation
Indices: 4128305--4128349 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4128295 TTATTCAACA
4128305 GAAAAACAAG-TTTA-TGTTTTCT
1 GAAAAACAAGTTTTAGTGTTTTCT
*
4128327 GAAACAACATGTTTTAGTGTTTT
1 GAAA-AACAAGTTTTAGTGTTTT
4128350 TAAGCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 5 0.26
24 4 0.21
25 6 0.32
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (24 bp):
GAAAAACAAGTTTTAGTGTTTTCT
Found at i:4135442 original size:42 final size:42
Alignment explanation
Indices: 4135395--4135480 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
4135385 TTTATAGTTG
* *
4135395 ATATTGAAATAACCAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATAACAAAGATGAGAAATGAATATGAGATGACAA
* ** *
4135437 ATATTGAATTGGCAAATATGAGAAATGAATATGAGATGACAA
1 ATATTGAAATAACAAAGATGAGAAATGAATATGAGATGACAA
4135479 AT
1 AT
4135481 GTGATATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (42 bp):
ATATTGAAATAACAAAGATGAGAAATGAATATGAGATGACAA
Found at i:4135793 original size:123 final size:123
Alignment explanation
Indices: 4135654--4135882 Score: 449
Period size: 123 Copynumber: 1.9 Consensus size: 123
4135644 ATAAAGAATA
4135654 AAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCACATTTT
1 AAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCACATTTT
*
4135719 GATTACTTATATTAAGTTAGATTGTTCGGATTATAGAAATAACGCTGAGTTATAATGG
66 GATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATAACGCTGAGTTATAATGG
4135777 AAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCACATTTT
1 AAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCACATTTT
4135842 GATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATA
66 GATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATA
4135883 CCATTGAGTT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 105 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (123 bp):
AAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCACATTTT
GATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATAACGCTGAGTTATAATGG
Found at i:4136543 original size:42 final size:42
Alignment explanation
Indices: 4136497--4136579 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
4136487 AGTTAGTAAG
*
4136497 TTACACGGGCTGAGAAACGGCCGTGTGTCTCAAGTCAGTGAA
1 TTACACGGGCTAAGAAACGGCCGTGTGTCTCAAGTCAGTGAA
* * * *
4136539 TTACATGGGCTAAGACATGGCTGTGTGTCTCAAGTCAGTGA
1 TTACACGGGCTAAGAAACGGCCGTGTGTCTCAAGTCAGTGA
4136580 GTTATAAGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (42 bp):
TTACACGGGCTAAGAAACGGCCGTGTGTCTCAAGTCAGTGAA
Found at i:4140466 original size:20 final size:20
Alignment explanation
Indices: 4140441--4140478 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4140431 GACCATTTCA
*
4140441 AAAAAAATCAAAAAAATTTG
1 AAAAAAATAAAAAAAATTTG
*
4140461 AAAAAAGTAAAAAAAATT
1 AAAAAAATAAAAAAAATT
4140479 AGGAAATAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATTTG
Found at i:4141328 original size:6 final size:6
Alignment explanation
Indices: 4141317--4141343 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4141307 ATATGCTTAC
4141317 ATATTT ATATTT ATATTT ATATTT ATA
1 ATATTT ATATTT ATATTT ATATTT ATA
4141344 AGCCAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:4142343 original size:45 final size:45
Alignment explanation
Indices: 4142281--4142444 Score: 213
Period size: 45 Copynumber: 3.7 Consensus size: 45
4142271 CGTCGTGTTA
* * * *
4142281 CCATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTCGTTATG
1 CCATAATGTCTTTCAACTATGGTCTTACTCGATCGAATCGTTATG
*
4142326 CCATAATGTCTGTCAACTATGGTCTTACTCGATCGAATCG-TATG
1 CCATAATGTCTTTCAACTATGGTCTTACTCGATCGAATCGTTATG
* ** ** * *
4142370 TCATAACATCTTTCAGTTATGGTCTTACTCGATGGAATCGTGATG
1 CCATAATGTCTTTCAACTATGGTCTTACTCGATCGAATCGTTATG
4142415 CCATAATGTCTTTCAACTATGGTCTTACTC
1 CCATAATGTCTTTCAACTATGGTCTTACTC
4142445 ATTTCTGGTA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 37 0.37
45 63 0.63
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (45 bp):
CCATAATGTCTTTCAACTATGGTCTTACTCGATCGAATCGTTATG
Found at i:4142470 original size:45 final size:45
Alignment explanation
Indices: 4142416--4142539 Score: 176
Period size: 45 Copynumber: 2.8 Consensus size: 45
4142406 ATCGTGATGC
* * *
4142416 CATAATGTCTTTCAACTATGGTCTTACTCATTTCTGGTATGGTGT
1 CATAGTGTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGT
* * *
4142461 TATAGTGTCTTTCAACTATGGTCTTATTTATTTCTGGTATAGTGT
1 CATAGTGTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGT
* *
4142506 CATAGTGTTTTTCAACTATGGTTTTAATCATTTC
1 CATAGTGTCTTTCAACTATGGTCTTAATCATTTC
4142540 CTTCAAGCCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (45 bp):
CATAGTGTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGT
Found at i:4147811 original size:34 final size:34
Alignment explanation
Indices: 4147739--4147811 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
4147729 CATGGTACTT
* **
4147739 TTAATTAGTGAAAATCATTGTATTGTATTACATG
1 TTAATTAGTGAAAATCATTGTATTGGATTACAAA
*
4147773 TTAATTAGTGAAAATC-TTTTAATTGGAGTTA-AAA
1 TTAATTAGTGAAAATCATTGT-ATTGGA-TTACAAA
4147807 TTAAT
1 TTAAT
4147812 GTTTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 27 0.82
35 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (34 bp):
TTAATTAGTGAAAATCATTGTATTGGATTACAAA
Found at i:4148824 original size:62 final size:62
Alignment explanation
Indices: 4148727--4148851 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
4148717 CTCGAAAGAA
4148727 TAAACTGATCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
1 TAAACTGATCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
*
4148789 TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
1 TAAACTGATCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
4148851 T
1 T
4148852 CAGCACAGTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (62 bp):
TAAACTGATCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
Found at i:4157912 original size:3 final size:3
Alignment explanation
Indices: 4157898--4157932 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4157888 CCCCATTTCT
*
4157898 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4157933 TTCTCCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4166038 original size:11 final size:13
Alignment explanation
Indices: 4166012--4166106 Score: 52
Period size: 12 Copynumber: 8.1 Consensus size: 13
4166002 ATAGGGTCTC
4166012 CAAATTCACATTT
1 CAAATTCACATTT
4166025 CAAA-TCAC-TTT
1 CAAATTCACATTT
4166036 C-AATGTCA-ATTT
1 CAAAT-TCACATTT
**
4166048 CACTTTCA-A-TT
1 CAAATTCACATTT
*
4166059 CAAATTCACAATT
1 CAAATTCACATTT
4166072 C-AATTCA-ATTCT
1 CAAATTCACATT-T
*
4166084 C--ATT--CAGTT
1 CAAATTCACATTT
4166093 CAAATTCACATTT
1 CAAATTCACATTT
4166106 C
1 C
4166107 CATTTTCTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 20 0.32
12 24 0.38
13 13 0.21
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (13 bp):
CAAATTCACATTT
Found at i:4166050 original size:18 final size:17
Alignment explanation
Indices: 4166029--4166081 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
4166019 ACATTTCAAA
4166029 TCACTTTCAATGTCAATT
1 TCACTTTCAAT-TCAATT
*
4166047 TCACTTTCAATTCAAAT
1 TCACTTTCAATTCAATT
*
4166064 TCACAATTCAATTCAATT
1 TCAC-TTTCAATTCAATT
4166082 CTCATTCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (17 bp):
TCACTTTCAATTCAATT
Found at i:4166061 original size:34 final size:34
Alignment explanation
Indices: 4166023--4166106 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
4166013 AAATTCACAT
4166023 TTCAAA-TCAC-TTTCAATGTCAATT-TCACTTTCAA
1 TTCAAATTCACATTTCAAT-TCAATTCTCA--TTCAA
* *
4166057 TTCAAATTCACAATTCAATTCAATTCTCATTCAG
1 TTCAAATTCACATTTCAATTCAATTCTCATTCAA
4166091 TTCAAATTCACATTTC
1 TTCAAATTCACATTTC
4166107 CATTTTCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 25 0.57
35 10 0.23
36 9 0.20
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (34 bp):
TTCAAATTCACATTTCAATTCAATTCTCATTCAA
Found at i:4166082 original size:17 final size:17
Alignment explanation
Indices: 4166023--4166104 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
4166013 AAATTCACAT
*
4166023 TTCAAA-TCACTTTCAA
1 TTCAAATTCACATTCAA
* *
4166039 TGTCAATTTCACTTTCAA
1 T-TCAAATTCACATTCAA
4166057 TTCAAATTCACAATTCAA
1 TTCAAATTCAC-ATTCAA
* *
4166075 TTC-AATTCTCATTCAG
1 TTCAAATTCACATTCAA
4166091 TTCAAATTCACATT
1 TTCAAATTCACATT
4166105 TCCATTTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 9 0.16
17 28 0.50
18 19 0.34
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (17 bp):
TTCAAATTCACATTCAA
Found at i:4166255 original size:15 final size:16
Alignment explanation
Indices: 4166235--4166267 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4166225 ATTCTTAAAC
4166235 TAATTC-ATTTTTATT
1 TAATTCAATTTTTATT
4166250 TAATTCATATTTTTATT
1 TAATTCA-ATTTTTATT
4166267 T
1 T
4166268 CATTTTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTCAATTTTTATT
Found at i:4172803 original size:13 final size:13
Alignment explanation
Indices: 4172785--4172811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4172775 TGGAAAAACA
4172785 ATAATTTTTCCAC
1 ATAATTTTTCCAC
4172798 ATAATTTTTCCAC
1 ATAATTTTTCCAC
4172811 A
1 A
4172812 CGTTTCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTTTCCAC
Found at i:4174330 original size:21 final size:22
Alignment explanation
Indices: 4174306--4174350 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4174296 TACGGTTTTG
4174306 TTGTTCCA-TATGAGGGTTCTT
1 TTGTTCCATTATGAGGGTTCTT
*
4174327 TTGTTCCATTATGAGGTTTCTT
1 TTGTTCCATTATGAGGGTTCTT
4174349 TT
1 TT
4174351 CTTATTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (22 bp):
TTGTTCCATTATGAGGGTTCTT
Found at i:4174977 original size:30 final size:30
Alignment explanation
Indices: 4174919--4174978 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4174909 GTTATGTTTT
** *
4174919 ATTTTAATTCTGTTTGAATAGATGTTTAAA
1 ATTTTAATTAGGTTTGAATAGATATTTAAA
* *
4174949 ATTTTAATTAGGTTTGAATTGCTATTTAAA
1 ATTTTAATTAGGTTTGAATAGATATTTAAA
4174979 TCGAATTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
ATTTTAATTAGGTTTGAATAGATATTTAAA
Found at i:4177187 original size:35 final size:35
Alignment explanation
Indices: 4177148--4177214 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
4177138 GTGCCCAGCA
*
4177148 TCGTGCCCACGACTCCAGCCGTGACAGAATAAGCG
1 TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
4177183 TCGTGCCCACGACTCCAACCGTGACAGAATAA
1 TCGTGCCCACGACTCCAACCGTGACAGAATAA
4177215 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.15
Consensus pattern (35 bp):
TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
Found at i:4177967 original size:22 final size:21
Alignment explanation
Indices: 4177939--4177999 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
4177929 AATCATCATT
4177939 CTTTTTTTCTTTTTTTTTTGAA
1 CTTTTTTTCTTTTTTTTTTG-A
* *
4177961 CTTTTTTTC-TTTTCTTTTGT
1 CTTTTTTTCTTTTTTTTTTGA
*
4177981 CTTTTCTTTCTTTCTTTTT
1 CTTTT-TTTCTTTTTTTTT
4178000 CTTTTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.15
21 13 0.39
22 15 0.45
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (21 bp):
CTTTTTTTCTTTTTTTTTTGA
Found at i:4178005 original size:20 final size:20
Alignment explanation
Indices: 4177938--4178007 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
4177928 AAATCATCAT
*
4177938 TCTTTTTTTCTTTTTTTTTTG
1 TCTTTTTTTC-TTTTCTTTTG
*
4177959 AACTTTTTTTCTTTTCTTTTG
1 -TCTTTTTTTCTTTTCTTTTG
4177980 TCTTTTCTTTC-TTTCTTTT-
1 TCTTTT-TTTCTTTTCTTTTG
4177999 TCTTTTTTT
1 TCTTTTTTT
4178008 TGAATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.07
19 6 0.14
20 13 0.30
21 13 0.30
22 9 0.20
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (20 bp):
TCTTTTTTTCTTTTCTTTTG
Found at i:4178009 original size:51 final size:52
Alignment explanation
Indices: 4177937--4178056 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 52
4177927 CAAATCATCA
*
4177937 TTCTTTTTTTCTTTTTTTTTTGAACT-TTTTTTCTTTTCTTT-TGT-CTTTTCT
1 TTCTTTCTTT-TTTTTTTTTTGAACTATTTTTTCTTTTCTTTGTGTGCTTTT-T
* *
4177988 TTCTTTCTTTTTCTTTTTTTTGAATTATTTTTTCTTTTTTTTGTGTGCTTTTT
1 TTCTTTCTTTTT-TTTTTTTTGAACTATTTTTTCTTTTCTTTGTGTGCTTTTT
*
4178041 TTCTCTCTTTTTTTTT
1 TTCTTTCTTTTTTTTT
4178057 GTTGAACATG
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
50 2 0.03
51 21 0.34
52 18 0.30
53 15 0.25
54 5 0.08
ACGTcount: A:0.04, C:0.12, G:0.05, T:0.78
Consensus pattern (52 bp):
TTCTTTCTTTTTTTTTTTTTGAACTATTTTTTCTTTTCTTTGTGTGCTTTTT
Found at i:4178022 original size:31 final size:30
Alignment explanation
Indices: 4177962--4178029 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
4177952 TTTTTTGAAC
**
4177962 TTTTTTTCTTTTCTTTTGTCTTTTCTTTCT
1 TTTTTTTCTTTTCTTTTGAATTTTCTTTCT
*
4177992 TTCTTTTTCTTTT-TTTTGAATTATTTTTTCT
1 TT-TTTTTCTTTTCTTTTGAATT-TTCTTTCT
4178023 TTTTTTT
1 TTTTTTT
4178030 GTGTGCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.04, C:0.12, G:0.03, T:0.81
Consensus pattern (30 bp):
TTTTTTTCTTTTCTTTTGAATTTTCTTTCT
Found at i:4185454 original size:35 final size:35
Alignment explanation
Indices: 4185415--4185481 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
4185405 GTGCCCAGCA
*
4185415 TCGTGCCCACGACTCCAGCCGTGACAGAATAAGCG
1 TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
4185450 TCGTGCCCACGACTCCAACCGTGACAGAATAA
1 TCGTGCCCACGACTCCAACCGTGACAGAATAA
4185482 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.15
Consensus pattern (35 bp):
TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
Found at i:4189184 original size:18 final size:18
Alignment explanation
Indices: 4189161--4189196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4189151 GACCATTTAT
4189161 GGCACTATTCACGTATAC
1 GGCACTATTCACGTATAC
* *
4189179 GGCACTGTTCATGTATAC
1 GGCACTATTCACGTATAC
4189197 AGTAATTGAG
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:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (18 bp):
GGCACTATTCACGTATAC
Found at i:4191980 original size:32 final size:32
Alignment explanation
Indices: 4191939--4192006 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
4191929 GTATTGTGAT
4191939 AGTCAAAGTGCTATTCATTTAGCAAAGAATCA
1 AGTCAAAGTGCTATTCATTTAGCAAAGAATCA
4191971 AGTCAAAGTGCTATTCATTTAGCAAAGAATCA
1 AGTCAAAGTGCTATTCATTTAGCAAAGAATCA
4192003 AGTC
1 AGTC
4192007 TATCATGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (32 bp):
AGTCAAAGTGCTATTCATTTAGCAAAGAATCA
Found at i:4194865 original size:25 final size:25
Alignment explanation
Indices: 4194819--4194866 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4194809 AATAATTTAA
* *
4194819 AATTATAAAAATATTCACAAAAAAC
1 AATTATAAAAATATCCAAAAAAAAC
4194844 AATTATAAAAA-ATCCAAAAAAAA
1 AATTATAAAAATATCCAAAAAAAA
4194867 GTAAGTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (25 bp):
AATTATAAAAATATCCAAAAAAAAC
Found at i:4196192 original size:26 final size:28
Alignment explanation
Indices: 4196163--4196225 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
4196153 TTATTCAACA
*
4196163 TTTAGGGTTC-ATGGTTC-GGGTTTG-AG
1 TTTAGGGTTCAAT-GTTCAAGGTTTGTAG
4196189 TTTAGGGTTCAATGTTCAAGGTTTGTAG
1 TTTAGGGTTCAATGTTCAAGGTTTGTAG
4196217 TTTAGGGTT
1 TTTAGGGTT
4196226 TAAGGTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 14 0.42
27 8 0.24
28 11 0.33
ACGTcount: A:0.16, C:0.06, G:0.33, T:0.44
Consensus pattern (28 bp):
TTTAGGGTTCAATGTTCAAGGTTTGTAG
Found at i:4203748 original size:3 final size:3
Alignment explanation
Indices: 4203740--4203765 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4203730 AATTGTGGGG
4203740 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4203766 TACTTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4219817 original size:14 final size:14
Alignment explanation
Indices: 4219794--4219833 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4219784 ACAAAAAAGT
*
4219794 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
4219808 AAATCATTTTACGG
1 AAAACATTTTACAG
4219822 AAAACATTTTAC
1 AAAACATTTTAC
4219834 TGACAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:4220188 original size:19 final size:19
Alignment explanation
Indices: 4220135--4220200 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
4220125 TTCAAAATTT
* *
4220135 TTATAAAAA-TTCCAAAAT
1 TTATAAAAATTTCAAAAAA
* ** *
4220153 TTATATATTTTTAAAAAAA
1 TTATAAAAATTTCAAAAAA
4220172 TTATAAAAATTTCAAAAAA
1 TTATAAAAATTTCAAAAAA
* *
4220191 ATCTAAAAAT
1 TTATAAAAAT
4220201 ATATAAAGAA
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
TTATAAAAATTTCAAAAAA
Found at i:4224837 original size:51 final size:52
Alignment explanation
Indices: 4224746--4224865 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 52
4224736 TCTTATTAAT
*
4224746 TTAAATTAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
1 TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
* * * *
4224798 TTAAAATAATTAAGTGAT-AATATTAAATGA-TTATTTTATCTTTAATT--AA
1 TTAAAATAATTAAGAGATAAATATTAAA-AATTTATATTATCATTAATTAAAA
*
4224847 TTAAATTAA-TAAGAGATAA
1 TTAAAATAATTAAGAGATAA
4224866 GTTGTAAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 7 0.12
49 11 0.19
51 24 0.41
52 17 0.29
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (52 bp):
TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
Found at i:4226337 original size:33 final size:33
Alignment explanation
Indices: 4226295--4226360 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4226285 TTCATGTGAT
4226295 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
4226328 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
4226361 CTCTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (33 bp):
TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
Found at i:4232609 original size:17 final size:16
Alignment explanation
Indices: 4232576--4232606 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4232566 AAAATAATTT
*
4232576 AAAACTTTAAATTTTG
1 AAAACTTAAAATTTTG
4232592 AAAACTTAAAATTTT
1 AAAACTTAAAATTTT
4232607 TGAGAAACGA
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:4232843 original size:23 final size:23
Alignment explanation
Indices: 4232802--4232860 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
4232792 CTATTGATGT
* *
4232802 GCCAGAGAAT-CTTACTGTTCT-T
1 GCCAGAGAATATTTACTGTT-TAC
*
4232824 GCCAGGGAATATTTACTGTTTAC
1 GCCAGAGAATATTTACTGTTTAC
4232847 GCCAGAGAATATTT
1 GCCAGAGAATATTT
4232861 CTTGTTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (23 bp):
GCCAGAGAATATTTACTGTTTAC
Found at i:4239688 original size:42 final size:42
Alignment explanation
Indices: 4239640--4239746 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
4239630 GAGATTACGT
* **
4239640 GTAAGACCATAACTGGGATATGACATC-AGTGTGAGATTTCAC
1 GTAAGACCATAACTGGGATATGACATCGA-TATGAGATCCCAC
* * * *
4239682 GTAAGACCATAACTAGGCTATTGGCATCGATATGAGATCCCAT
1 GTAAGACCATAACTGGGATA-TGACATCGATATGAGATCCCAC
*
4239725 GTAAGACCATATCTGGGATATG
1 GTAAGACCATAACTGGGATATG
4239747 GCATTGGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 20 0.38
43 32 0.60
44 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (42 bp):
GTAAGACCATAACTGGGATATGACATCGATATGAGATCCCAC
Found at i:4242184 original size:28 final size:29
Alignment explanation
Indices: 4242152--4242214 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
4242142 ACTAAGAATG
*
4242152 AACAA-AATGTACTAAAAACATGCAAATT
1 AACAACAATGTACTAAAAACAGGCAAATT
**
4242180 AACAACCTTGTACTAAAAACAGGCAAATT
1 AACAACAATGTACTAAAAACAGGCAAATT
4242209 AACAAC
1 AACAAC
4242215 CTATCCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (29 bp):
AACAACAATGTACTAAAAACAGGCAAATT
Found at i:4242191 original size:29 final size:29
Alignment explanation
Indices: 4242159--4242216 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
4242149 ATGAACAAAA
*
4242159 TGTACTAAAAACATGCAAATTAACAACCT
1 TGTACTAAAAACAGGCAAATTAACAACCT
4242188 TGTACTAAAAACAGGCAAATTAACAACCT
1 TGTACTAAAAACAGGCAAATTAACAACCT
4242217 ATCCTAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.21, G:0.09, T:0.22
Consensus pattern (29 bp):
TGTACTAAAAACAGGCAAATTAACAACCT
Found at i:4242224 original size:28 final size:29
Alignment explanation
Indices: 4242161--4242224 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
4242151 GAACAAAATG
* *
4242161 TACTAAAAACATGCAAATTAACAACCTTG
1 TACTAAAAACAGGCAAATTAACAACCTTA
4242190 TACTAAAAACAGGCAAATTAACAACC-TA
1 TACTAAAAACAGGCAAATTAACAACCTTA
*
4242218 TCCTAAA
1 TACTAAA
4242225 CTCTAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (29 bp):
TACTAAAAACAGGCAAATTAACAACCTTA
Found at i:4249069 original size:23 final size:23
Alignment explanation
Indices: 4249043--4249087 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4249033 TGGAAATGTG
*
4249043 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
4249066 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
4249088 TTGAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:4249880 original size:8 final size:8
Alignment explanation
Indices: 4249867--4249895 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4249857 AATTTGTGAA
4249867 AAAAAAAT
1 AAAAAAAT
4249875 -AAAAAAT
1 AAAAAAAT
4249882 AAAAAAAT
1 AAAAAAAT
4249890 AAAAAA
1 AAAAAA
4249896 CACACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4249887 original size:15 final size:15
Alignment explanation
Indices: 4249867--4249895 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4249857 AATTTGTGAA
4249867 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
4249882 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
4249896 CACACAGATT
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:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:4251173 original size:18 final size:19
Alignment explanation
Indices: 4251150--4251193 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
4251140 CTAAATATTT
4251150 ATTTTAATATTT-TTAT-AC
1 ATTTTAAT-TTTATTATCAC
4251168 ATTTTAATTTTATTATGCAC
1 ATTTTAATTTTATTAT-CAC
4251188 ATTTTA
1 ATTTTA
4251194 TTACCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAATTTTATTATCAC
Found at i:4258065 original size:24 final size:24
Alignment explanation
Indices: 4258036--4258085 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
4258026 ATAAAAATAT
4258036 TTATAATTTTAAAATTTTTATAAC
1 TTATAATTTTAAAATTTTTATAAC
4258060 TTATAATTTTAAAATTTTTATAAC
1 TTATAATTTTAAAATTTTTATAAC
4258084 TT
1 TT
4258086 CTTTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATAATTTTAAAATTTTTATAAC
Found at i:4288156 original size:2 final size:2
Alignment explanation
Indices: 4288149--4288179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4288139 AGAAAATTGT
4288149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4288180 GAATGTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4289281 original size:13 final size:13
Alignment explanation
Indices: 4289263--4289288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4289253 ACCTGATTCA
4289263 TCATAAACCAGAT
1 TCATAAACCAGAT
4289276 TCATAAACCAGAT
1 TCATAAACCAGAT
4289289 GTCTTCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
TCATAAACCAGAT
Found at i:4291584 original size:22 final size:22
Alignment explanation
Indices: 4291556--4291599 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4291546 CAATGTGTGC
*
4291556 CATGCATCTCATATGAAGATAT
1 CATGCATCTCATATGAAAATAT
4291578 CATGCATCTCATATGAAAATAT
1 CATGCATCTCATATGAAAATAT
4291600 TTACCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
CATGCATCTCATATGAAAATAT
Found at i:4292506 original size:19 final size:21
Alignment explanation
Indices: 4292465--4292508 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4292455 ATTTTGCAAG
4292465 AAAAAAAATTATATAATAAATT
1 AAAAAAAATTATATAAT-AATT
*
4292487 AAAATAAATT-TATAAT-ATT
1 AAAAAAAATTATATAATAATT
4292506 AAA
1 AAA
4292509 CATATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAAAATTATATAATAATT
Found at i:4292778 original size:19 final size:20
Alignment explanation
Indices: 4292738--4292778 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4292728 CATTCAAATG
*
4292738 ATATATAAAAAATCATCTATT
1 ATATATAAAAAA-CATCCATT
4292759 ATATATAAAAAA-ATCCATT
1 ATATATAAAAAACATCCATT
4292778 A
1 A
4292779 AAATCACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATATAAAAAACATCCATT
Found at i:4293286 original size:6 final size:6
Alignment explanation
Indices: 4293275--4293352 Score: 70
Period size: 6 Copynumber: 12.7 Consensus size: 6
4293265 AATAAATTAT
* * *
4293275 AAAACC AAAACC AAAACC AAAACC AAAA-C AAAAGC AATAGCA ATATTAACC
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AA-AACC A-A--AACC
*
4293326 AAAACC AAAATC AAAACC AAAA-C AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAA
4293353 GCAATAGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
5 10 0.16
6 43 0.70
7 2 0.03
8 2 0.03
9 4 0.07
ACGTcount: A:0.67, C:0.24, G:0.03, T:0.06
Consensus pattern (6 bp):
AAAACC
Found at i:4293341 original size:39 final size:39
Alignment explanation
Indices: 4293283--4293358 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
4293273 ATAAAACCAA
*
4293283 AACCAAAACCAAAACCAAAA-CAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAA-CAAAAGCAATATT
*
4293322 AACCAAAACCAAAATCAAAACCAAAACAAAAGCAATA
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATA
4293359 GCAATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.64, C:0.24, G:0.04, T:0.08
Consensus pattern (39 bp):
AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATATT
Found at i:4293341 original size:45 final size:45
Alignment explanation
Indices: 4293277--4293368 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
4293267 TAAATTATAA
4293277 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
*
4293322 AACCAAAACCAAAATCAAAACCAAAACAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
4293367 AA
1 AA
4293369 GTTGTTAACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.63, C:0.23, G:0.04, T:0.10
Consensus pattern (45 bp):
AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
Found at i:4293875 original size:28 final size:28
Alignment explanation
Indices: 4293835--4293889 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4293825 ATTCATCATA
4293835 AACCAGATGTCTTCTTAAAGAACAAATT
1 AACCAGATGTCTTCTTAAAGAACAAATT
* *
4293863 AACCAGATGTCTTCTTGAAGAATAAAT
1 AACCAGATGTCTTCTTAAAGAACAAAT
4293890 CATCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (28 bp):
AACCAGATGTCTTCTTAAAGAACAAATT
Found at i:4294531 original size:15 final size:15
Alignment explanation
Indices: 4294498--4294538 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4294488 TCTGTTGTGT
4294498 TTTTTAGTTTT-GGA
1 TTTTTAGTTTTAGGA
*
4294512 CTTTTAGTTTTAGGA
1 TTTTTAGTTTTAGGA
*
4294527 TTTTTATTTTTA
1 TTTTTAGTTTTA
4294539 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (15 bp):
TTTTTAGTTTTAGGA
Found at i:4294841 original size:20 final size:21
Alignment explanation
Indices: 4294804--4294844 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4294794 ATTAACCGAA
4294804 TTCAATTGTTAACCGAATTTT
1 TTCAATTGTTAACCGAATTTT
*
4294825 TTCAATT-TTACCCGAATTTT
1 TTCAATTGTTAACCGAATTTT
4294845 GCACGCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (21 bp):
TTCAATTGTTAACCGAATTTT
Found at i:4304555 original size:25 final size:25
Alignment explanation
Indices: 4304527--4304597 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
4304517 ATCGATACTT
* *
4304527 AGCTCATATGAGCTTACTGTTATTC
1 AGCTCAGAGGAGCTTACTGTTATTC
**
4304552 AGCTTGGAGGAGCTTACTGTTATTC
1 AGCTCAGAGGAGCTTACTGTTATTC
* *
4304577 AGCTCGGAGGATCTTACTGTT
1 AGCTCAGAGGAGCTTACTGTT
4304598 TATAGCTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (25 bp):
AGCTCAGAGGAGCTTACTGTTATTC
Found at i:4307012 original size:16 final size:15
Alignment explanation
Indices: 4306991--4307022 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4306981 ATGGCGTCGG
4306991 AGAAAAATGGCGATA
1 AGAAAAATGGCGATA
4307006 AGAAAAATGGCGATA
1 AGAAAAATGGCGATA
4307021 AG
1 AG
4307023 GGTATATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.12
Consensus pattern (15 bp):
AGAAAAATGGCGATA
Found at i:4308939 original size:47 final size:47
Alignment explanation
Indices: 4308870--4308964 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
4308860 AATCATAATA
4308870 ATTCTACTTTAAAAACAAAATATGTAAATTCATCACGTACTTACAAT
1 ATTCTACTTTAAAAACAAAATATGTAAATTCATCACGTACTTACAAT
4308917 ATTCTACTTTAAAAACAAAATATGTAAATTCATCACGTACTTACAAT
1 ATTCTACTTTAAAAACAAAATATGTAAATTCATCACGTACTTACAAT
4308964 A
1 A
4308965 AGACTTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (47 bp):
ATTCTACTTTAAAAACAAAATATGTAAATTCATCACGTACTTACAAT
Found at i:4311391 original size:36 final size:36
Alignment explanation
Indices: 4311332--4311404 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
4311322 CTTCAAGGTA
* * *
4311332 TAAGTTTTTTAAGTAAAAAC-TTTTAGGTATTAATT
1 TAAGTTTTTGAAATAAAAACTTTTTAGGTATAAATT
4311367 TAAGTTTTTGAAATACAAAACTTTTTAGGTATAAATT
1 TAAGTTTTTGAAATA-AAAACTTTTTAGGTATAAATT
4311404 T
1 T
4311405 TTGAAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 13 0.39
36 5 0.15
37 15 0.45
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (36 bp):
TAAGTTTTTGAAATAAAAACTTTTTAGGTATAAATT
Found at i:4316945 original size:21 final size:20
Alignment explanation
Indices: 4316898--4316945 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4316888 ATAAAATACC
4316898 TAATAT-GTAAAAGAATTTA
1 TAATATAGTAAAAGAATTTA
* *
4316917 TATTTATAGTAAAATAATTATA
1 TA-ATATAGTAAAAGAATT-TA
4316939 TAATATA
1 TAATATA
4316946 TATGAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 3 0.13
21 14 0.61
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (20 bp):
TAATATAGTAAAAGAATTTA
Found at i:4317298 original size:35 final size:36
Alignment explanation
Indices: 4317244--4317311 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
4317234 ACAATACAAG
*
4317244 TAAAAAATATAGATAATAATGTAA-AATAATAATTTA
1 TAAAAAATATAGATAATAAT-AAATAATAATAATTTA
4317280 TAAAAAA-ATA-ATACATAATAAATAATAATAAT
1 TAAAAAATATAGATA-ATAATAAATAATAATAAT
4317312 ATGAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 5 0.17
35 17 0.59
36 7 0.24
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (36 bp):
TAAAAAATATAGATAATAATAAATAATAATAATTTA
Found at i:4317300 original size:18 final size:19
Alignment explanation
Indices: 4317265--4317312 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
4317255 GATAATAATG
*
4317265 TAAAATAATAATTTATAAA
1 TAAAATAATAATTAATAAA
4317284 -AAAATAATACA-TAATAAA
1 TAAAATAATA-ATTAATAAA
4317302 TAATAATAATA
1 TAA-AATAATA
4317313 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 15 0.60
19 3 0.12
20 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATAATAATTAATAAA
Found at i:4322314 original size:11 final size:11
Alignment explanation
Indices: 4322298--4322340 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4322288 TAGAATATAC
4322298 CCCATACCTTG
1 CCCATACCTTG
*
4322309 CCCATACCTTT
1 CCCATACCTTG
*
4322320 CCCATACC-TA
1 CCCATACCTTG
4322330 CCCATACCTTG
1 CCCATACCTTG
4322341 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:4322335 original size:21 final size:22
Alignment explanation
Indices: 4322298--4322339 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4322288 TAGAATATAC
*
4322298 CCCATACCTTGCCCATACCTTT
1 CCCATACCTTACCCATACCTTT
4322320 CCCATACC-TACCCATACCTT
1 CCCATACCTTACCCATACCTT
4322340 GGAAAGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCATACCTTACCCATACCTTT
Found at i:4322899 original size:18 final size:18
Alignment explanation
Indices: 4322872--4322945 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
4322862 TACGACCGTT
*
4322872 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
* * *
4322890 TACGACACTATTTACATA
1 TACGGCACTATTCACGTA
*
4322908 TACGGCACTATTCATGTA
1 TACGGCACTATTCACGTA
*
4322926 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
4322944 TA
1 TA
4322946 TAGTAGTTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:4326938 original size:11 final size:11
Alignment explanation
Indices: 4326922--4326964 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4326912 TAGAATATAC
4326922 CCCATACCTTG
1 CCCATACCTTG
*
4326933 CCCATACCTTT
1 CCCATACCTTG
*
4326944 CCCATACC-TA
1 CCCATACCTTG
4326954 CCCATACCTTG
1 CCCATACCTTG
4326965 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:4326959 original size:21 final size:22
Alignment explanation
Indices: 4326922--4326963 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4326912 TAGAATATAC
*
4326922 CCCATACCTTGCCCATACCTTT
1 CCCATACCTTACCCATACCTTT
4326944 CCCATACC-TACCCATACCTT
1 CCCATACCTTACCCATACCTT
4326964 GGAAAGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCATACCTTACCCATACCTTT
Found at i:4329025 original size:43 final size:43
Alignment explanation
Indices: 4328977--4329200 Score: 286
Period size: 43 Copynumber: 5.2 Consensus size: 43
4328967 CGAAAAAAAT
4328977 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
*
4329020 GCCGCTAAAGACCATGACCTTTAACGGCGCTTTTTTCGCAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
** * * *
4329063 GCAACTAAAGACCATGACCTGTAGCGGCGCTTTTTTAGCAAGC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
* * *
4329106 GCCGCTAAAGACCATGACTTTTAGCGACGCTTTTTTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
* * * * * * * *
4329149 ACCGCTAAAGATCATAAACTTTAGCGACACTTTTTCCCCAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
*
4329192 GCCACTAAA
1 GCCGCTAAA
4329201 AGTCATGAAA
Statistics
Matches: 156, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 156 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (43 bp):
GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTCGCAAAC
Found at i:4334238 original size:15 final size:14
Alignment explanation
Indices: 4334218--4334254 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
4334208 AACCATTAAA
4334218 CTTAAACCATAGAAC
1 CTTAAACCATAG-AC
4334233 CTTAAACCATAGAC
1 CTTAAACCATAGAC
4334247 CTTAAACC
1 CTTAAACC
4334255 TTAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (14 bp):
CTTAAACCATAGAC
Found at i:4334255 original size:7 final size:7
Alignment explanation
Indices: 4334208--4334275 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
4334198 GTTTACGACG
4334208 AACCATTA
1 AACC-TTA
4334216 AA-CTTA
1 AACCTTA
*
4334222 AACCATA
1 AACCTTA
4334229 GAACCTTA
1 -AACCTTA
*
4334237 AACCATA
1 AACCTTA
*
4334244 GACCTTA
1 AACCTTA
4334251 AACCTTA
1 AACCTTA
**
4334258 AATATTA
1 AACCTTA
*
4334265 AACCCTA
1 AACCTTA
4334272 AACC
1 AACC
4334276 CAAAAATAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
6 5 0.11
7 34 0.72
8 8 0.17
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (7 bp):
AACCTTA
Found at i:4334572 original size:41 final size:41
Alignment explanation
Indices: 4334515--4334733 Score: 275
Period size: 41 Copynumber: 5.4 Consensus size: 41
4334505 GTTATATGAC
*
4334515 TTTTAGCGGTGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * *
4334556 TTTTAGCGGCGTTTTACAGAAAGCGACGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
4334597 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGAT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
4334638 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGAC-CT-GT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATG-CTCTGGT
* ** * * *
4334678 TTTTAGCAGCGTTTT-TTGTTAAAACGCTGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTACCG--AAAGCGCCGCTAATGCTCTGGT
4334719 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
4334734 TGGTAAAACG
Statistics
Matches: 158, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 16 0.10
41 140 0.89
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:4334734 original size:41 final size:40
Alignment explanation
Indices: 4334515--4334764 Score: 256
Period size: 41 Copynumber: 6.1 Consensus size: 40
4334505 GTTATATGAC
* * *
4334515 TTTTAGCGGTGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAACGCCGCTATTGCTCT-GT
* * *
4334556 TTTTAGCGGCGTTTTACAGAAAGCGACGCTAATT-CTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAACGCCGCT-ATTGCTCT-GT
* *
4334597 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGAT
1 TTTTAGCGGCGTTTTACCGAAAACGCCGCTATTGCTCTG-T
*
4334638 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGAC-CTGT
1 TTTTAGCGGCGTTTTACCGAAAACGCCGCTATTG-CTCTGT
* ** *
4334678 TTTTAGCAGCGTTTT-TTGTTAAAACGCTGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCG--AAAACGCCGCTATTGCTCTGT
**
4334719 TTTTAGCGGCGTTTT-TGGTAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCG-AAAACGCCGCTATTGCTCTGT
4334759 GTTTTA
1 -TTTTA
4334765 CAATTTTTGC
Statistics
Matches: 185, Mismatches: 16, Indels: 16
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.01
40 40 0.22
41 141 0.76
42 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCGAAAACGCCGCTATTGCTCTGT
Found at i:4334764 original size:122 final size:123
Alignment explanation
Indices: 4334515--4334757 Score: 293
Period size: 122 Copynumber: 2.0 Consensus size: 123
4334505 GTTATATGAC
* * *
4334515 TTTTAGCGGTGTTTTACCGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACAGAAAGC
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGCGTTTTACAGAAAAC
*
4334580 GACGCTAATTCTCTGGTTTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGAT
66 GACGCTAATTCTCTGGTTTTTAGCGGCGTTTTACCGAAAACGCCGCTAATGCTCTGAT
* **
4334638 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTATTGAC-CT-GTTTTTAGCAGCGTTTT-TTGTTAA
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATG-CTCTGGTTTTTAGCAGCGTTTTACAG--AA
** *
4334700 AACG-CTGCT-ATTGCTCT-GTTTTTAGCGGCGTTTT-TGGTAAAACGCCGCTATTGCTCTG
63 AACGAC-GCTAATT-CTCTGGTTTTTAGCGGCGTTTTACCG-AAAACGCCGCTAATGCTCTG
4334758 TGTTTTACAA
Statistics
Matches: 104, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
121 2 0.02
122 55 0.53
123 46 0.44
124 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (123 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTTTTTAGCAGCGTTTTACAGAAAAC
GACGCTAATTCTCTGGTTTTTAGCGGCGTTTTACCGAAAACGCCGCTAATGCTCTGAT
Found at i:4336534 original size:33 final size:33
Alignment explanation
Indices: 4336492--4336557 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4336482 ATCTTCACAG
4336492 TTTCCTCACAATCAAGCTAAAGTTTTCCAATTC
1 TTTCCTCACAATCAAGCTAAAGTTTTCCAATTC
4336525 TTTCCTCACAATCAAGCTAAAGTTTTCCAATTC
1 TTTCCTCACAATCAAGCTAAAGTTTTCCAATTC
4336558 AGAATCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (33 bp):
TTTCCTCACAATCAAGCTAAAGTTTTCCAATTC
Found at i:4341694 original size:26 final size:26
Alignment explanation
Indices: 4341665--4341718 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
4341655 CTAAACAAAT
4341665 ACCTAACACCACTAAATTACATTGAA
1 ACCTAACACCACTAAATTACATTGAA
4341691 ACCTAACACCACTAAATTACATTGAA
1 ACCTAACACCACTAAATTACATTGAA
4341717 AC
1 AC
4341719 TTGCTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22
Consensus pattern (26 bp):
ACCTAACACCACTAAATTACATTGAA
Found at i:4346481 original size:20 final size:20
Alignment explanation
Indices: 4346456--4346493 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4346446 TGTACTTCTA
4346456 GAATTAAAATGAAGTAACTG
1 GAATTAAAATGAAGTAACTG
4346476 GAATTAAAATGAAGTAAC
1 GAATTAAAATGAAGTAAC
4346494 CGAGTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (20 bp):
GAATTAAAATGAAGTAACTG
Found at i:4348839 original size:3 final size:3
Alignment explanation
Indices: 4348833--4348861 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4348823 ATAATAATTA
4348833 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4348862 GTTTAGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4353362 original size:17 final size:16
Alignment explanation
Indices: 4353336--4353373 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
4353326 TATGTGGTAA
4353336 AAAAATAATAAAAAAT
1 AAAAATAATAAAAAAT
*
4353352 AAAAATCAATAAAAGAT
1 AAAAAT-AATAAAAAAT
4353369 AAAAA
1 AAAAA
4353374 AATTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAATAATAAAAAAT
Found at i:4353394 original size:20 final size:20
Alignment explanation
Indices: 4353349--4353456 Score: 64
Period size: 19 Copynumber: 5.5 Consensus size: 20
4353339 AATAATAAAA
* * **
4353349 AATAAAAATCAATAAAAGAT
1 AATAAAAATTATTAAAATTT
4353369 AA-AAAAATTATTAAAATTT
1 AATAAAAATTATTAAAATTT
* *
4353388 AATAAAAA-TATTTAGAAGTT
1 AATAAAAATTA-TTAAAATTT
* *
4353408 ATTAAAAATTATAAAAAAATTGT
1 AATAAAAATTAT--TAAAATT-T
4353431 -A-AAAAATTA-TAAAATTT
1 AATAAAAATTATTAAAATTT
*
4353448 TATAAAAAT
1 AATAAAAAT
4353457 CATAAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
17 1 0.01
18 7 0.10
19 23 0.34
20 22 0.32
21 10 0.15
22 4 0.06
23 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (20 bp):
AATAAAAATTATTAAAATTT
Found at i:4353412 original size:30 final size:31
Alignment explanation
Indices: 4353370--4353456 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 31
4353360 ATAAAAGATA
4353370 AAAAAATTATTAAAATTTAATAAAAATATT-T
1 AAAAAATTATTAAAATTT-ATAAAAATATTGT
* * * *
4353401 -AGAAGTTATTAAAAATTATAAAAAAATTGT
1 AAAAAATTATTAAAATTTATAAAAATATTGT
4353431 AAAAAATTA-TAAAATTTTATAAAAAT
1 AAAAAATTATTAAAA-TTTATAAAAAT
4353457 CATAAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 10 0.22
30 20 0.44
31 15 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAATTATTAAAATTTATAAAAATATTGT
Found at i:4353424 original size:10 final size:10
Alignment explanation
Indices: 4353370--4353465 Score: 63
Period size: 10 Copynumber: 9.6 Consensus size: 10
4353360 ATAAAAGATA
4353370 AAAAAATTAT
1 AAAAAATTAT
* *
4353380 TAAAATTTAAT
1 AAAAAATT-AT
4353391 AAAAATATT-T
1 AAAAA-ATTAT
* *
4353401 -AGAAGTTAT
1 AAAAAATTAT
*
4353410 TAAAAATTAT
1 AAAAAATTAT
*
4353420 AAAAAAATTGT
1 -AAAAAATTAT
4353431 AAAAAATTAT
1 AAAAAATTAT
**
4353441 AAAATTTTAT
1 AAAAAATTAT
*
4353451 -AAAAATCAT
1 AAAAAATTAT
4353460 AAAAAA
1 AAAAAA
4353466 ATAAAATATA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
8 2 0.03
9 10 0.16
10 36 0.56
11 14 0.22
12 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:4353425 original size:11 final size:11
Alignment explanation
Indices: 4353411--4353444 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
4353401 AGAAGTTATT
4353411 AAAAATTATAA
1 AAAAATTATAA
*
4353422 AAAAATTGT-A
1 AAAAATTATAA
4353432 AAAAATTATAA
1 AAAAATTATAA
4353443 AA
1 AA
4353445 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:4353444 original size:29 final size:29
Alignment explanation
Indices: 4353408--4353495 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
4353398 TTTAGAAGTT
**
4353408 ATTA-AAAATTATAAAAAAATTGTAAAAA
1 ATTATAAAATTATAAAAAAATCATAAAAA
* *
4353436 ATTATAAAATTTTATAAAAATCATAAAAA
1 ATTATAAAATTATAAAAAAATCATAAAAA
* *
4353465 A--ATAAAA-TATATAGAAAT-ATAAAAAA
1 ATTATAAAATTATAAAAAAATCAT-AAAAA
4353491 ATTAT
1 ATTAT
4353496 GATTTTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 2 0.04
26 15 0.30
27 6 0.12
28 6 0.12
29 21 0.42
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
ATTATAAAATTATAAAAAAATCATAAAAA
Found at i:4353465 original size:21 final size:20
Alignment explanation
Indices: 4353410--4353465 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
4353400 TAGAAGTTAT
4353410 TAAAAATTATAAAAAAATTGTA
1 TAAAAA-TAT-AAAAAATTGTA
* *
4353432 -AAAAAT-TATAAAATTTTA
1 TAAAAATATAAAAAATTGTA
4353450 TAAAAATCATAAAAAA
1 TAAAAAT-ATAAAAAA
4353466 ATAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 1 0.04
21 11 0.39
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAAATATAAAAAATTGTA
Found at i:4354200 original size:18 final size:18
Alignment explanation
Indices: 4354167--4354201 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4354157 ACTCCTCTAA
*
4354167 TAATTTAATTTAATTAAT
1 TAATTTAATCTAATTAAT
*
4354185 TAATTTAATCTCATTAA
1 TAATTTAATCTAATTAA
4354202 GTATTAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTAATCTAATTAAT
Found at i:4355618 original size:28 final size:28
Alignment explanation
Indices: 4355578--4355635 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
4355568 CTATGAAAAG
* * *
4355578 TTACAAAATGGTTATTGAATTATTTAAT
1 TTACAAAACGGTTATCGAACTATTTAAT
4355606 TTACAAAACGGTTATCGAACTATTTAAT
1 TTACAAAACGGTTATCGAACTATTTAAT
4355634 TT
1 TT
4355636 TATCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (28 bp):
TTACAAAACGGTTATCGAACTATTTAAT
Found at i:4357189 original size:18 final size:19
Alignment explanation
Indices: 4357166--4357203 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4357156 TATATATTAG
*
4357166 TGTATA-ATTTTTTATATA
1 TGTATATATTTTTAATATA
4357184 TGTATATATTTTTAATATA
1 TGTATATATTTTTAATATA
4357203 T
1 T
4357204 TTATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TGTATATATTTTTAATATA
Found at i:4357306 original size:30 final size:30
Alignment explanation
Indices: 4357251--4357325 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
4357241 TTTATTCCTA
*
4357251 ATAT-TTATGTATTATGTAAATA-TTTTAAT
1 ATATATTATGTA-TATCTAAATATTTTTAAT
* **
4357280 ATTATATTATGTATATCTATATATTTTTCGT
1 A-TATATTATGTATATCTAAATATTTTTAAT
4357311 ATATATTATGTATAT
1 ATATATTATGTATAT
4357326 ATGTTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 25 0.64
31 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.56
Consensus pattern (30 bp):
ATATATTATGTATATCTAAATATTTTTAAT
Found at i:4357338 original size:24 final size:25
Alignment explanation
Indices: 4357297--4357352 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
4357287 TATGTATATC
*
4357297 TATATATTTTTCGTATATAT-TATG-
1 TATATATTTTTCGAATAT-TGTATGT
4357321 TATATATGTTTTC-AATATTGTATGT
1 TATATAT-TTTTCGAATATTGTATGT
4357346 TATATAT
1 TATATAT
4357353 ATTATTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 15 0.54
25 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (25 bp):
TATATATTTTTCGAATATTGTATGT
Found at i:4357433 original size:19 final size:19
Alignment explanation
Indices: 4357409--4357445 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4357399 CTATTTTATA
*
4357409 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
4357428 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
4357446 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Done.