Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 214 of 228
Found at i:62538404 original size:19 final size:20
Alignment explanation
Indices: 62538363--62538408 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
62538353 TTATGATCTT
* *
62538363 TTTTATAATTTTTATGATAA
1 TTTTATGATTTTTATAATAA
*
62538383 TTTTATGATTTTT-TAATTA
1 TTTTATGATTTTTATAATAA
62538402 TTTTATG
1 TTTTATG
62538409 GAAAAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTATGATTTTTATAATAA
Found at i:62541767 original size:19 final size:19
Alignment explanation
Indices: 62541739--62541778 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
62541729 TTTGATTAAG
62541739 AGTGACATGGTTACAACTA
1 AGTGACATGGTTACAACTA
*
62541758 AGTGATATGGTTACAACTA
1 AGTGACATGGTTACAACTA
62541777 AG
1 AG
62541779 AAATTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (19 bp):
AGTGACATGGTTACAACTA
Found at i:62559246 original size:17 final size:19
Alignment explanation
Indices: 62559224--62559263 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
62559214 AATTATTGTT
62559224 TAAAAA-GAAA-AAAAATA
1 TAAAAATGAAATAAAAATA
*
62559241 TAAAAATTAAATAAAAATA
1 TAAAAATGAAATAAAAATA
62559260 TAAA
1 TAAA
62559264 TATCTCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (19 bp):
TAAAAATGAAATAAAAATA
Found at i:62566066 original size:29 final size:29
Alignment explanation
Indices: 62566015--62566073 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
62566005 TTTTTTTGTA
*
62566015 TTTCCTTTTGAAGAATTCATGGAAAGCTT
1 TTTCCTTTTGAAGAATGCATGGAAAGCTT
* **
62566044 TTTCCTTTTGAAGGATGGTTGGAAAGCTT
1 TTTCCTTTTGAAGAATGCATGGAAAGCTT
62566073 T
1 T
62566074 ATTATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (29 bp):
TTTCCTTTTGAAGAATGCATGGAAAGCTT
Found at i:62566616 original size:12 final size:12
Alignment explanation
Indices: 62566581--62566639 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
62566571 GTTCACGAAC
* *
62566581 AAGCTTATTTAA
1 AAGCTTGTTTAT
*
62566593 AAGCTCGTTTAT
1 AAGCTTGTTTAT
62566605 AAGCTTGTTTAT
1 AAGCTTGTTTAT
*
62566617 -TGACTTGTTTAT
1 AAG-CTTGTTTAT
*
62566629 AA-CTTATTTAT
1 AAGCTTGTTTAT
62566640 TTATTAATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (12 bp):
AAGCTTGTTTAT
Found at i:62566859 original size:23 final size:23
Alignment explanation
Indices: 62566811--62566865 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
62566801 ATTATTTATT
**
62566811 AACATTGTTCGTTTAATGTTCGTG
1 AACA-TGTTCGTTTAATGTTAATG
62566835 AACATGTTCGTTTAA-GTTAAATG
1 AACATGTTCGTTTAATGTT-AATG
*
62566858 AACGTGTT
1 AACATGTT
62566866 TGTGAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (23 bp):
AACATGTTCGTTTAATGTTAATG
Found at i:62579460 original size:35 final size:36
Alignment explanation
Indices: 62579414--62579490 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 36
62579404 TTATGATGAA
62579414 AAAAAATTATAAATGTACTTTATTTAATTTTAA-TT
1 AAAAAATTATAAATGTACTTTATTTAATTTTAATTT
*
62579449 AAAATATTATAAATGTACTTTATTTAATTTTAATTT
1 AAAAAATTATAAATGTACTTTATTTAATTTTAATTT
62579485 AAAAAA
1 AAAAAA
62579491 AAATTTTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 32 0.82
36 7 0.18
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (36 bp):
AAAAAATTATAAATGTACTTTATTTAATTTTAATTT
Found at i:62591658 original size:18 final size:18
Alignment explanation
Indices: 62591615--62591659 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
62591605 GTTTGAAAAA
**
62591615 AAATATAAATATGTACAT
1 AAATATAAATATACACAT
*
62591633 AAAAATAAATATACACAT
1 AAATATAAATATACACAT
*
62591651 ATATATAAA
1 AAATATAAA
62591660 GATAAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATATAAATATACACAT
Found at i:62591678 original size:28 final size:30
Alignment explanation
Indices: 62591647--62591713 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
62591637 ATAAATATAC
62591647 ACATATATATAAA-GAT-AAAATAATAATT
1 ACATATATATAAATGATAAAAATAATAATT
*
62591675 ACATATA-A-AAATTATAAAAATAATAATT
1 ACATATATATAAATGATAAAAATAATAATT
62591703 ACAT-TAT-TAAA
1 ACATATATATAAA
62591714 ATTAAGTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 3 0.09
27 5 0.15
28 26 0.76
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (30 bp):
ACATATATATAAATGATAAAAATAATAATT
Found at i:62599018 original size:41 final size:41
Alignment explanation
Indices: 62598973--62599050 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
62598963 TGGCAATTCT
*
62598973 AATGGCTTTGGTTCAGACTTTCAATTGGTTGCTTTACTTTG
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTG
*
62599014 AATGGCTTTGGTTGACACTTTCAATTGGTTGCTTTAC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTAC
62599051 ATTTAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (41 bp):
AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTG
Found at i:62605404 original size:18 final size:16
Alignment explanation
Indices: 62605367--62605401 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
62605357 ATAATTTTTT
62605367 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
62605383 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
62605399 TAT
1 TAT
62605402 ATTAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTTAATCAAATA
Found at i:62618320 original size:8 final size:8
Alignment explanation
Indices: 62618309--62618333 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
62618299 CCACCTACCC
62618309 CCCACTTG
1 CCCACTTG
62618317 CCCACTTG
1 CCCACTTG
62618325 CCCACTTG
1 CCCACTTG
62618333 C
1 C
62618334 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:62618917 original size:11 final size:11
Alignment explanation
Indices: 62618901--62618935 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
62618891 TCCTTCCTCC
62618901 CTCCCTTCTCT
1 CTCCCTTCTCT
62618912 CTCCCTTCTCT
1 CTCCCTTCTCT
62618923 CTTCCC-TCTCT
1 C-TCCCTTCTCT
62618934 CT
1 CT
62618936 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:62619424 original size:3 final size:3
Alignment explanation
Indices: 62619400--62619466 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
62619390 AATATCCTTG
* * * *
62619400 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA GTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
62619448 TTA GTA TATA TT- TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
62619467 GTACGTGTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:62619476 original size:22 final size:23
Alignment explanation
Indices: 62619407--62619477 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
62619397 TTGTTATTTT
* *
62619407 TATATTATTAGTAT-TATTAGTA
1 TATATTATTATTATGTAGTAGTA
*
62619429 TTAGTATTATTATTATGTATTAGTA
1 -TA-TATTATTATTATGTAGTAGTA
62619454 TATATT-TTATTATGTACGT-GTA
1 TATATTATTATTATGTA-GTAGTA
62619476 TA
1 TA
62619478 CATCTATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 15 0.35
23 7 0.16
24 13 0.30
25 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.55
Consensus pattern (23 bp):
TATATTATTATTATGTAGTAGTA
Found at i:62619582 original size:3 final size:3
Alignment explanation
Indices: 62619569--62619616 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
62619559 TATTCCAATG
* * *
62619569 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62619617 GTTTATGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:62619856 original size:10 final size:9
Alignment explanation
Indices: 62619818--62619933 Score: 62
Period size: 8 Copynumber: 12.6 Consensus size: 9
62619808 TTTTTATGTC
62619818 ATATTATTAT
1 ATATTA-TAT
*
62619828 ATTTTAATATT
1 ATATT-ATA-T
62619839 ATATTATAT
1 ATATTATAT
62619848 A-ATTATAT
1 ATATTATAT
*
62619856 ATA-CATAT
1 ATATTATAT
*
62619864 ATATTTTAT
1 ATATTATAT
62619873 ATA-TAT-T
1 ATATTATAT
*
62619880 ATCATTGTAT
1 AT-ATTATAT
*
62619890 ATATTTTA-
1 ATATTATAT
62619898 ATATTATTAGTT
1 ATATTA-TA--T
* *
62619910 ATATTTTAC
1 ATATTATAT
62619919 ACTATTATAT
1 A-TATTATAT
62619929 ATATT
1 ATATT
62619934 TTTCTAATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
7 3 0.04
8 23 0.28
9 23 0.28
10 19 0.23
11 8 0.10
12 5 0.06
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (9 bp):
ATATTATAT
Found at i:62619904 original size:64 final size:64
Alignment explanation
Indices: 62619825--62619956 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
62619815 GTCATATTAT
*
62619825 TATATTTTAATATTA-TA-TTATATAATTATA-TATACATATATA-TTTTATATATATTATCATT
1 TATATTTTAATATTATTAGTTATAT-ATTACACTAT-CATATATATTTTTATA-ATATTAT-ATT
62619886 GTA
62 GTA
* * *
62619889 TATATTTTAATATTATTAGTTATATTTTACACTATTATATATATTTTTCTAATATTATATTGTA
1 TATATTTTAATATTATTAGTTATATATTACACTATCATATATATTTTTATAATATTATATTGTA
62619953 TATA
1 TATA
62619957 CTATTGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
64 25 0.42
65 20 0.33
66 15 0.25
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (64 bp):
TATATTTTAATATTATTAGTTATATATTACACTATCATATATATTTTTATAATATTATATTGTA
Found at i:62619931 original size:19 final size:18
Alignment explanation
Indices: 62619887--62619946 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
62619877 ATTATCATTG
62619887 TATATATTTTAATATTAT
1 TATATATTTTAATATTAT
62619905 TAGTTATATTTTACACTATTAT
1 TA--TATATTTTA-A-TATTAT
*
62619927 ATATATTTTTCTAATATTAT
1 -TATATATTT-TAATATTAT
62619947 ATTGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
20 15 0.43
21 8 0.23
22 8 0.23
23 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATATTTTAATATTAT
Found at i:62620386 original size:38 final size:37
Alignment explanation
Indices: 62620302--62620396 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
62620292 TATACGTACT
*
62620302 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
62620340 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
62620376 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
62620397 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:62622758 original size:21 final size:21
Alignment explanation
Indices: 62622710--62622752 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
62622700 AATGTATGGC
62622710 AAATTATCTCTAATAAATAAA
1 AAATTATCTCTAATAAATAAA
62622731 AAATTATCTCTAATAAATAAA
1 AAATTATCTCTAATAAATAAA
62622752 A
1 A
62622753 TTTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTATCTCTAATAAATAAA
Found at i:62657023 original size:20 final size:20
Alignment explanation
Indices: 62656998--62657041 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
62656988 TGTGTGAAGC
62656998 AAAATCTACATAGATAAAGA
1 AAAATCTACATAGATAAAGA
62657018 AAAATCTACATAGATAAAGA
1 AAAATCTACATAGATAAAGA
62657038 AAAA
1 AAAA
62657042 AACCAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAATCTACATAGATAAAGA
Found at i:62665209 original size:10 final size:10
Alignment explanation
Indices: 62665194--62665269 Score: 61
Period size: 10 Copynumber: 8.0 Consensus size: 10
62665184 ATCGTAAAAA
62665194 TATAAAAATT
1 TATAAAAATT
* *
62665204 TGTAAAATTT
1 TATAAAAATT
62665214 TATAAAAA-T
1 TATAAAAATT
*
62665223 CATAAAAA-T
1 TATAAAAATT
*
62665232 TAT-AAAATA
1 TATAAAAATT
* *
62665241 TATAGAAATA
1 TATAAAAATT
62665251 TA-AAAAATT
1 TATAAAAATT
*
62665260 TATAACAATT
1 TATAAAAATT
62665270 ATCGTATCAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
8 4 0.08
9 21 0.40
10 27 0.52
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (10 bp):
TATAAAAATT
Found at i:62665227 original size:9 final size:8
Alignment explanation
Indices: 62665214--62665256 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
62665204 TGTAAAATTT
62665214 TATAAAAA
1 TATAAAAA
62665222 TCATAAAAA
1 T-ATAAAAA
62665231 TTATAAAATA
1 -TATAAAA-A
*
62665241 TATAGAAA
1 TATAAAAA
62665249 TATAAAAA
1 TATAAAAA
62665257 ATTTATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 9 0.30
9 19 0.63
10 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (8 bp):
TATAAAAA
Found at i:62665236 original size:18 final size:17
Alignment explanation
Indices: 62665180--62665256 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
62665170 AAAATTAGAA
*
62665180 AAAAATCGTAAAAATAT
1 AAAAATCATAAAAATAT
** *
62665197 AAAAATTTGTAAAATTTTAT
1 AAAAA-TCATAAAA--ATAT
62665217 AAAAATCATAAAAATTAT
1 AAAAATCATAAAAA-TAT
*
62665235 AAAATAT-ATAGAAATAT
1 AAAA-ATCATAAAAATAT
62665252 AAAAA
1 AAAAA
62665257 ATTTATAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.02
17 12 0.24
18 20 0.41
19 8 0.16
20 8 0.16
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAAATCATAAAAATAT
Found at i:62665497 original size:16 final size:16
Alignment explanation
Indices: 62665476--62665506 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62665466 TTTTATAAAA
62665476 TTTTACAATTTTTATT
1 TTTTACAATTTTTATT
*
62665492 TTTTACGATTTTTAT
1 TTTTACAATTTTTAT
62665507 AAAAAATTCT
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:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTACAATTTTTATT
Found at i:62665521 original size:35 final size:35
Alignment explanation
Indices: 62665454--62665524 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
62665444 GCATTGTATA
** **
62665454 ATTTTTTATTATTTTTATAAAATTTTACAATTTTT
1 ATTTTTTACGATTTTTATAAAAAATTACAATTTTT
62665489 ATTTTTTACGATTTTTATAAAAAATT-CTAATTTTT
1 ATTTTTTACGATTTTTATAAAAAATTAC-AATTTTT
62665524 A
1 A
62665525 ATAAATATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
ATTTTTTACGATTTTTATAAAAAATTACAATTTTT
Found at i:62665776 original size:88 final size:88
Alignment explanation
Indices: 62665618--62665841 Score: 288
Period size: 88 Copynumber: 2.6 Consensus size: 88
62665608 AATTTTTAAT
* * * * * *
62665618 AAGAGTAGGGGCTTAATTGCTTGTTTGAAAAATTTTCAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAGAGTAGGGGCTTAATTGCTTTTTTTAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTT
62665683 CAAGTACCCAATTGAGTGCAAAA
66 CAAGTACCCAATTGAGTGCAAAA
* * *
62665706 AAGATTAGGGGCTTAATTGCTTTTTTTAAGAAGTTTGAGGGTCTTTTTAATGTATTTTAAAAGTT
1 AAGAGTAGGGGCTTAATTGCTTTTTTTAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTT
* *
62665771 TAAGTACTCAATTGAGTGCAAAA
66 CAAGTACCCAATTGAGTGCAAAA
* * * ***
62665794 AAAAGGAGGCGCTTAATTGCTTTTTTTTTTAAGTTTGAGGG-CTTTTTA
1 AAGAGTAGGGGCTTAATTGCTTTTTTTAAAAAGTTTGAGGGTCTTTTTA
62665842 CACTCTTAAC
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 7 0.06
88 111 0.94
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (88 bp):
AAGAGTAGGGGCTTAATTGCTTTTTTTAAAAAGTTTGAGGGTCTTTTTAATGCATTTTAAAAGTT
CAAGTACCCAATTGAGTGCAAAA
Found at i:62679003 original size:23 final size:24
Alignment explanation
Indices: 62678948--62679002 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
62678938 CAAATAAGAA
* *
62678948 ATATTAAAATTAGTTTT-AATTAT
1 ATATCAAAATTAGTTTTAAATAAT
*
62678971 ATTTCAAAATTAGTTTTAAATAAT
1 ATATCAAAATTAGTTTTAAATAAT
62678995 ATATCAAA
1 ATATCAAA
62679003 TATATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
ATATCAAAATTAGTTTTAAATAAT
Found at i:62681268 original size:18 final size:19
Alignment explanation
Indices: 62681237--62681279 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
62681227 TTAAAAAGTT
62681237 AAAATAAAATTTAAT-TTA
1 AAAATAAAATTTAATATTA
62681255 AAAAT-AAATATTAATATTA
1 AAAATAAAAT-TTAATATTA
*
62681274 CAAATA
1 AAAATA
62681280 TATTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAAAATTTAATATTA
Found at i:62683650 original size:16 final size:17
Alignment explanation
Indices: 62683619--62683656 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
62683609 AATTAGTTGT
*
62683619 GAAGCTAGACTGTTAAA
1 GAAGTTAGACTGTTAAA
62683636 GAAGTTAGA-TGTTAAA
1 GAAGTTAGACTGTTAAA
62683652 -AAGTT
1 GAAGTT
62683657 GTTAAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (17 bp):
GAAGTTAGACTGTTAAA
Found at i:62694356 original size:3 final size:3
Alignment explanation
Indices: 62694348--62694374 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
62694338 TTTAGCAATT
62694348 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
62694375 GTTTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62698310 original size:16 final size:16
Alignment explanation
Indices: 62698291--62698334 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
62698281 AATCAAAGTC
62698291 AAAATAGAAAAAAG-AG
1 AAAA-AGAAAAAAGAAG
*
62698307 AAAAAGAAGAAAGAAG
1 AAAAAGAAAAAAGAAG
62698323 AAAAAGAAAAAA
1 AAAAAGAAAAAA
62698335 AAGGAGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAG
Found at i:62699158 original size:16 final size:17
Alignment explanation
Indices: 62699139--62699175 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
62699129 ATGAAGATGA
*
62699139 AAAAAAATG-AATAATG
1 AAAAAAATGAAAAAATG
62699155 -AAAAAATGAAAAAATG
1 AAAAAAATGAAAAAATG
62699171 AAAAA
1 AAAAA
62699176 GTAAAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 6 0.33
17 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAAAAATGAAAAAATG
Found at i:62699166 original size:7 final size:8
Alignment explanation
Indices: 62699140--62699175 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
62699130 TGAAGATGAA
62699140 AAAAAATG
1 AAAAAATG
*
62699148 -AATAATG
1 AAAAAATG
62699155 AAAAAATG
1 AAAAAATG
62699163 AAAAAATG
1 AAAAAATG
62699171 AAAAA
1 AAAAA
62699176 GTAAAAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (8 bp):
AAAAAATG
Found at i:62700519 original size:88 final size:88
Alignment explanation
Indices: 62700370--62701842 Score: 2374
Period size: 88 Copynumber: 16.7 Consensus size: 88
62700360 AACAGATCAG
* * * * *
62700370 TGAAGACAACAGATCTTGCCTTCCAGCATTGACAGCAAAGTAGGTTGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62700435 CTCTCGGTTGTGATGGAGCTGAT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
62700458 TGAAGACAACAGATCTTGCCTTCCTGCACTGACAACGAAGCAGGTCAAAGACACAAACCTTGTCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62700523 CCCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
62700546 TGAAGACAATAGATCTTGCCTTCCTGCACTGTCAGCGAAGCAGGTCAAAGACAAAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62700611 CCCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * *
62700634 TGAAGACAACAGATCTTGCCTTCCTGCATTGTCAGCGAAGTAGGTCAAAGACA-AAAGCCTTGCC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCC
*
62700698 TCCCTCGGTTGTGATGGAGCTGGT
65 TCTCTCGGTTGTGATGGAGCTGGT
* *
62700722 TGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62700787 CTCTCGGTTGTGATAGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * *
62700810 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTTGAAGATACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62700875 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * *
62700898 TGAAGACAAAAGATCTTGCCTTCCAGAATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62700963 CTCTCGGTTGTGATGGTGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
62700986 TGAAGACAAAAGATCTTGGCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62701051 CTCTCGATTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
62701074 TGAAGACAAAAGATTTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
* *
62701139 CTCTCAGTTGTGATGGAGCTAGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
62701162 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62701227 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* *
62701250 TGAAAACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62701315 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
62701338 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62701403 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
** *
62701426 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAATGAAGCAGGTCAAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62701491 CTCTCGGTTGTGATGGTGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
62701514 TGAAGACAAAAGATCTTGGCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62701579 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
62701602 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTACCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
* *
62701667 CTCTTGATTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
62701690 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
62701755 CTCTCGGTTGT-AGTGGAGATGGT
66 CTCTCGGTTGTGA-TGGAGCTGGT
* * * * * *
62701778 TGAAGACAACAGATCTTTCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
62701843 TCCTGTACTG
Statistics
Matches: 1298, Mismatches: 84, Indels: 6
0.94 0.06 0.00
Matches are distributed among these distances:
87 4 0.00
88 1291 0.99
89 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
CTCTCGGTTGTGATGGAGCTGGT
Found at i:62701864 original size:44 final size:45
Alignment explanation
Indices: 62701704--62701922 Score: 157
Period size: 45 Copynumber: 4.9 Consensus size: 45
62701694 GACAAAAGAT
* * *
62701704 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACA-CAAAC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGAC
* * * * * * * *
62701748 CTTGCCTCTCTCGGT--TG-TAGTGGAG-ATGGTTGAAGACAACAGAT
1 CTTGCCT-TC-CTGTACTGACAGCGAAGCA-GATCGAAGACACCAGAC
* *
62701792 CTTTCCTTCCTG-CCTTGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTTCCTGTAC-TGACAGCGAAGCAGATCGAAGACACCAGAC
* * * *
62701836 CTTGCCTTCCTGTACTGACAGCGGAGCAGAAT-GAAGATAGCAGAT
1 CTTGCCTTCCTGTACTGACAGCGAAGCAG-ATCGAAGACACCAGAC
* * *
62701881 CTTGCCTTCTTGTACTAACAGCGAAGCAGATCGAAGAAACCA
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
62701923 CAGTTTTCAA
Statistics
Matches: 133, Mismatches: 29, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
42 3 0.02
43 16 0.12
44 55 0.41
45 56 0.42
46 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.22
Consensus pattern (45 bp):
CTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGAC
Found at i:62702199 original size:100 final size:97
Alignment explanation
Indices: 62701930--62702302 Score: 453
Period size: 100 Copynumber: 3.7 Consensus size: 97
62701920 CCACAGTTTT
* * *
62701930 CAATTCAAAAGATTGAAGCTACAACAGCGGATCTTACATTCCAAGCGGTGCAGCGGAACAGATTG
1 CAATT-AAAAGATTGAAGCTACAACAGCGAATCTTACTTTCC-AGC-GTGCAGTGGAACAGATTG
** *
62701995 AAGCTACAATGGCGGATCTCACTTCCCTGACATTG
63 AAGCTACAACAGCGGATCTTACTTCCCTGACATTG
* * * *
62702030 CAATCAAAAGATTGAGGCCACAACGGCGAATCTTA-TTTCCAGGCAGTGCAGTGGAACAGATTGA
1 CAATTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCA-GC-GTGCAGTGGAACAGATTGA
* *
62702094 AGCTACAACAACAGATCTTACTTCCCTGACATTG
64 AGCTACAACAGCGGATCTTACTTCCCTGACATTG
*
62702128 CAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTG
1 CAATTAA-AAGATTGAAGCTACAACAGCGAATCTTACTTTCC-AGCG-TGCAGTGGAACAGATTG
62702193 AAGCTACAACAGCGGATCTTACTTCCCTGACATTG
63 AAGCTACAACAGCGGATCTTACTTCCCTGACATTG
* * * *
62702228 CAATTAAGAAGATTGAAGCTACATCAGCAAATCTTAC-CTCTCAGGCGGTGCAGTGGAATAGATT
1 CAATTAA-AAGATTGAAGCTACAACAGCGAATCTTACTTTC-CA-GC-GTGCAGTGGAACAGATT
* *
62702292 AAAGCCACAAC
62 GAAGCTACAAC
62702303 GGTGAATCTT
Statistics
Matches: 238, Mismatches: 27, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
97 1 0.00
98 59 0.25
99 54 0.23
100 122 0.51
101 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (97 bp):
CAATTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCAGCGTGCAGTGGAACAGATTGAAG
CTACAACAGCGGATCTTACTTCCCTGACATTG
Found at i:62702229 original size:50 final size:49
Alignment explanation
Indices: 62701936--62702264 Score: 286
Period size: 50 Copynumber: 6.6 Consensus size: 49
62701926 TTTTCAATTC
** ** **
62701936 AAAAGATTGAAGCTACAACAGCGGATCTTACATTCCAAG-CGGTGCAGCGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTAC-TTCCCTGACATTGCA-ATG
* ** * *
62701986 AACAGATTGAAGCTACAATGGCGGATCTCACTTCCCTGACATTGCAATC
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATG
* * * * * * * * *
62702035 AAAAGATTGAGGCCACAACGGCGAATCTTA-TTTCCAGGCAGTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAAT-G
* * * *
62702084 AACAGATTGAAGCTACAACAACAGATCTTACTTCCCTGACATTGCAATT
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATG
* * *
62702133 AAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCGTTGCAGTGG
1 AA-AAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-G
* *
62702184 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATT
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATG
* **
62702233 AAGAAGATTGAAGCTACATCAGCAAATCTTAC
1 AA-AAGATTGAAGCTACAACAGCGGATCTTAC
62702265 CTCTCAGGCG
Statistics
Matches: 219, Mismatches: 52, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
48 12 0.05
49 57 0.26
50 147 0.67
51 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (49 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATG
Found at i:62702465 original size:125 final size:125
Alignment explanation
Indices: 62702238--62702600 Score: 534
Period size: 125 Copynumber: 2.9 Consensus size: 125
62702228 CAATTAAGAA
* * * * * * * *
62702238 GATTGAAGCTACATCAGCAAATCTTAC-CTCTCAGGCGGTGCAGTGGAATAGATTAAAGCCACAA
1 GATTAAAGCTACAACAGCGAATCTTACGC-CCCAAGCGATGCAGTGGAACAGATTAAAGCCACAT
* *
62702302 CGGTGAATCTTGCCTT-TCTGACATTGCGGTTAAAAAGATTAAAGCCATATCGGTGAATCTT
65 CGGTGAATCTTG-CTTCTCTGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
*
62702363 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATC
*
62702428 GGTGAATCTTGCTTCCCCT-ACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
66 GGTGAATCTTGCTT-CTCTGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
* *
62702488 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAGCCAAATT
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATC
* *
62702553 GGTGAATCTTGTTTCTCTGATATTGCAGTTAAAAAGATTAAAGCCACA
66 GGTGAATCTTGCTTCTCTGACATTGCAGTTAAAAAGATTAAAGCCACA
62702601 ATGACGAATC
Statistics
Matches: 216, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
124 6 0.03
125 207 0.96
126 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (125 bp):
GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATC
GGTGAATCTTGCTTCTCTGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
Found at i:62702509 original size:25 final size:25
Alignment explanation
Indices: 62702463--62702512 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
62702453 CAGTTAAAAA
* * *
62702463 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
62702488 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
62702513 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:62702844 original size:44 final size:45
Alignment explanation
Indices: 62702684--62702887 Score: 195
Period size: 44 Copynumber: 4.6 Consensus size: 45
62702674 AGAACCAAAG
* * * * * *
62702684 TCTTATCCCCCTGAAGATGCAGTGGGGCAAATTGAAGGTACA-A-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGAATT-AAAGTAGATAGA
* **
62702728 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCCGATA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGA-ATTAAAGTAGATAGA
* *
62702772 TCCTATCTCCCTGAAGTTGCAGAGGAGCGAATTAAAGTAG-TAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAGTAGATAGA
** * *
62702816 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGGTTAAAAT-GATTGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAGTAGATAGA
* *
62702860 TCTTATCTCTCTGAAGTTGCAGTAGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
62702888 AGATCGCATC
Statistics
Matches: 134, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
43 7 0.05
44 126 0.94
45 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAGTAGATAGA
Found at i:62704363 original size:3 final size:3
Alignment explanation
Indices: 62704348--62704383 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
62704338 TTTAGCAATT
*
62704348 TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62704384 GTTTCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:62710314 original size:16 final size:17
Alignment explanation
Indices: 62710280--62710314 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
62710270 AATACCATCA
*
62710280 ATGAATTTATATATTTC
1 ATGAATTTATATATATC
62710297 ATGAATTT-TATATATC
1 ATGAATTTATATATATC
62710313 AT
1 AT
62710315 AATATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (17 bp):
ATGAATTTATATATATC
Found at i:62714608 original size:24 final size:23
Alignment explanation
Indices: 62714581--62714626 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
62714571 AAAGTAAATC
*
62714581 TTAATATGATATTAATCTCTAATG
1 TTAATATAATATTAATC-CTAATG
* *
62714605 TTAATCTAATATTTATCCTAAT
1 TTAATATAATATTAATCCTAAT
62714627 ATTGTCGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (23 bp):
TTAATATAATATTAATCCTAATG
Found at i:62723092 original size:42 final size:42
Alignment explanation
Indices: 62722997--62723176 Score: 216
Period size: 42 Copynumber: 4.5 Consensus size: 42
62722987 AGTGATTCGG
*
62722997 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATT-TAAAATACGGT
**
62723040 GGAATCAGCACTTAGCAACCCCTTTCACATTTACGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
* * * *
62723082 GGGATCAGCACTTAGCAACCAC---CA-A--T--AATTCAG-
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
*
62723115 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
62723157 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
62723177 ACCAATGATT
Statistics
Matches: 116, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
33 20 0.17
34 4 0.03
36 3 0.03
37 1 0.01
38 1 0.01
39 3 0.03
41 5 0.04
42 48 0.41
43 31 0.27
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAAAATACGGT
Found at i:62723127 original size:33 final size:33
Alignment explanation
Indices: 62723085--62723209 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
62723075 ATACGGTGGG
*
62723085 ATCAGCACTTAGCAACCACCAATAATTCAGGGA
1 ATCAGCACTTAGCAACCACCAATAATTCGGGGA
* *
62723118 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
1 ATCAGCACTTAGCAA-CCAC--CA-A--T--AATTCGG-GGA
*
62723160 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
1 ATCAGCACTTAGCAACCACCAATAATTCGGGGA
*
62723193 ATCAGTACTTAGCAACC
1 ATCAGCACTTAGCAACC
62723210 CCCTTTATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 34 0.45
34 8 0.11
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
41 8 0.11
42 18 0.24
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATAATTCGGGGA
Found at i:62723129 original size:75 final size:75
Alignment explanation
Indices: 62723040--62723214 Score: 287
Period size: 75 Copynumber: 2.3 Consensus size: 75
62723030 AAAATACGGT
* ** *
62723040 GGAATCAGCACTTAGCAACCCCTTTCACATTTACGATACGGTGGGATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
62723105 AATAATTCAG
66 AATAATTCAG
62723115 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
* *
62723180 AATGATTCGG
66 AATAATTCAG
*
62723190 GGAATCAGTACTTAGCAACCCCCTT
1 GGAATCAGCACTTAGCAACCCCCTT
62723215 TATATTCAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (75 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
AATAATTCAG
Found at i:62730215 original size:21 final size:23
Alignment explanation
Indices: 62730167--62730217 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
62730157 CATATGATTT
62730167 TATATTTTTAATTTATTAAATAA
1 TATATTTTTAATTTATTAAATAA
62730190 TATATTTTATAA-TT-TTAAAT-A
1 TATATTTT-TAATTTATTAAATAA
62730211 TATATTT
1 TATATTT
62730218 ATGCTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.30
22 6 0.22
23 10 0.37
24 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTTTTAATTTATTAAATAA
Found at i:62738867 original size:22 final size:23
Alignment explanation
Indices: 62738818--62738870 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
62738808 GCATATGATT
* *
62738818 TTATATTTTTAATTTATTAAATA
1 TTATATTTTTAAATTATCAAATA
62738841 TTATATTTTTACAATT-TCAAATA
1 TTATATTTTTA-AATTATCAAATA
62738864 -TATATTT
1 TTATATTT
62738871 ATGCTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 17 0.63
24 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATATTTTTAAATTATCAAATA
Found at i:62739024 original size:18 final size:19
Alignment explanation
Indices: 62738978--62739017 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
62738968 AAAATGAACT
*
62738978 AATACATATACAACTATTAA
1 AATA-ATATACAAATATTAA
62738998 AATAATATACAAAT-TTAA
1 AATAATATACAAATATTAA
62739016 AA
1 AA
62739018 CTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATATACAAATATTAA
Found at i:62741724 original size:7 final size:8
Alignment explanation
Indices: 62741690--62741750 Score: 52
Period size: 9 Copynumber: 7.0 Consensus size: 8
62741680 CTTATTTTTT
62741690 AAATATAA
1 AAATATAA
62741698 AAA-ATAA
1 AAATATAA
62741705 ATAATATACA
1 A-AATATA-A
62741715 AAATATAA
1 AAATATAA
*
62741723 AAGCTATAA
1 AA-ATATAA
62741732 AAAGTATTAA
1 AAA-TA-TAA
62741742 AAAGTATAA
1 AAA-TATAA
62741751 TTTTTAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 5 0.11
8 8 0.18
9 21 0.47
10 11 0.24
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (8 bp):
AAATATAA
Found at i:62743839 original size:19 final size:19
Alignment explanation
Indices: 62743815--62743876 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
62743805 TTTGGTTCAG
62743815 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
* *
62743834 ACTTTCAA-TGGCTTTGGTTGAC
1 ACTTTCAATTGG--TTGCTT--T
62743856 ACTTTCAATTGGTTGCTTT
1 ACTTTCAATTGGTTGCTTT
62743875 AC
1 AC
62743877 ATTTAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 5 0.15
21 5 0.15
22 8 0.24
23 3 0.09
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (19 bp):
ACTTTCAATTGGTTGCTTT
Found at i:62743844 original size:41 final size:41
Alignment explanation
Indices: 62743799--62743876 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
62743789 AGGCAATTCT
*
62743799 AATGGCTTTGGTTCAGACTTTCAATTGGTTGCTTTACTTTC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
*
62743840 AATGGCTTTGGTTGACACTTTCAATTGGTTGCTTTAC
1 AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTAC
62743877 ATTTAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.45
Consensus pattern (41 bp):
AATGGCTTTGGTTCACACTTTCAATTGGTTGCTTTACTTTC
Found at i:62744327 original size:39 final size:38
Alignment explanation
Indices: 62744262--62744335 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
62744252 CACATTACGT
*
62744262 AAAACGCCGCTAAAGATTGAGCATTAGCGGCACTTTCAG
1 AAAACGCCGCTAAAGAATGAGCATTAGCGGC-CTTTCAG
62744301 AAAAGCGCCGCTAAA-AATGAGCATTAGCGGCCTTT
1 AAAA-CGCCGCTAAAGAATGAGCATTAGCGGCCTTT
62744336 TTTTGTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 4 0.12
39 19 0.58
40 10 0.30
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (38 bp):
AAAACGCCGCTAAAGAATGAGCATTAGCGGCCTTTCAG
Found at i:62744577 original size:76 final size:79
Alignment explanation
Indices: 62744395--62744650 Score: 288
Period size: 76 Copynumber: 3.2 Consensus size: 79
62744385 CCTTTCGGGG
** * *
62744395 CTTTAGCGGCGTTTTTAAAAAAAGCGCTGCTAATGC-CAGATCTTTAGCGGCGTTTTTGACAAAG
1 CTTTAGCGGCGTTTTT-GGAAAAGCGC-GCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAG
62744459 CGCCGCTAATGCTTAGAT
64 CG-CGCTAATGC-TAGAT
* *
62744477 CTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATTCTCAGATCTTTAGCGTCGTTTTTGAAAAAGC
1 CTTTAGCGGCGTTTTTGGAAAAGCG-CGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGC
*
62744542 G-TCT-AT-C-AGAT
65 GCGCTAATGCTAGAT
* * *
62744553 CTTTAGCGGTGTTTTTGGAAAAGCGCCGTTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGC
1 CTTTAGCGGCGTTTTTGGAAAAGCG-CGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGC
* **
62744618 GCCGCTAATGCTCGGGG
65 G-CGCTAATGCT-AGAT
62744635 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
62744651 TAAAAAGTGC
Statistics
Matches: 149, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
76 64 0.43
78 3 0.02
79 4 0.03
80 3 0.02
81 14 0.09
82 61 0.41
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (79 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCGCTAATACTCAGATCTTTAGCGGCGTTTTTGAAAAAGCG
CGCTAATGCTAGAT
Found at i:62744607 original size:117 final size:121
Alignment explanation
Indices: 62744394--62744657 Score: 358
Period size: 117 Copynumber: 2.2 Consensus size: 121
62744384 ACCTTTCGGG
62744394 GCTTTAGCGGCGTTTTTAAAAAAAGCGCTGCTAATGCCAGATCTTTAGCGGCGTTTTTGACAAAG
1 GCTTTAGCGGCGTTTTT-AAAAAAGCGCTGCTAAT-CCAGATCTTTAGCGGCGTTTTTGACAAAG
* * * *
62744459 CGCCGCTAATGCTTAGATCTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATTCTCAGA
64 CGCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
* * * *
62744517 TCTTTAGCGTCGTTTTTGAAAAAGCG-T-CT-AT-CAGATCTTTAGCGGTGTTTTTGGA-AAAGC
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATCCAGATCTTTAGCGGCGTTTTT-GACAAAGC
* * *
62744577 GCCGTTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCGGG
65 GCCGCTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
*
62744634 GCTTTAGCGGCGTTTTTTAAAAAG
1 GCTTTAGCGGCGTTTTTAAAAAAG
62744658 TGCCGCAAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
117 96 0.76
118 2 0.02
119 2 0.02
120 2 0.02
121 1 0.01
122 8 0.06
123 15 0.12
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (121 bp):
GCTTTAGCGGCGTTTTTAAAAAAGCGCTGCTAATCCAGATCTTTAGCGGCGTTTTTGACAAAGCG
CCGCTAATACTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGA
Found at i:62744657 original size:41 final size:41
Alignment explanation
Indices: 62744395--62744663 Score: 309
Period size: 41 Copynumber: 6.7 Consensus size: 41
62744385 CCTTTCGGGG
* *
62744395 CTTTAGCGGCGTTTTTAAAAAAAGCGCTGCTAATGC-CAGAT
1 CTTTAGCGGCGTTTTT-GAAAAAGCGCCGCTAATGCTCAGAT
* *
62744436 CTTTAGCGGCGTTTTTGACAAAGCGCCGCTAATGCTTAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * *
62744477 CTTTAGCGGCGTTTTTGGAAAAGCGTCGCTAATTCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* *
62744518 CTTTAGCGTCGTTTTTGAAAAAGCG--TCT-A---TCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * * *
62744553 CTTTAGCGGTGTTTTTGGAAAAGCGCCGTTAATACTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* * **
62744594 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
* *
62744635 CTTTAGCGGCGTTTTTTAAAAAGTGCCGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
62744664 AAAAACATTT
Statistics
Matches: 195, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.14
37 1 0.01
38 2 0.01
39 2 0.01
40 16 0.08
41 146 0.75
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:62744808 original size:26 final size:26
Alignment explanation
Indices: 62744760--62744810 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
62744750 AAAATGGATA
* * *
62744760 AATTTGAAATAATAACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
*
62744786 AATTTGAAATAAAAAAATATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
62744811 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.25
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:62745104 original size:14 final size:15
Alignment explanation
Indices: 62745071--62745104 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
62745061 TAAGGTTTAT
62745071 AGATTATGGAATTAG
1 AGATTATGGAATTAG
62745086 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
62745100 GGATT
1 AGATT
62745105 TTGATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:62745154 original size:14 final size:14
Alignment explanation
Indices: 62745135--62745161 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62745125 TAAGGTTTAT
62745135 GGGTTAGAGGTTAG
1 GGGTTAGAGGTTAG
62745149 GGGTTAGAGGTTA
1 GGGTTAGAGGTTA
62745162 AGAGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGGTTAGAGGTTAG
Found at i:62745276 original size:87 final size:89
Alignment explanation
Indices: 62745173--62745352 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 89
62745163 GAGTTATGAT
* * * *
62745173 TTAGGGTTTATGGATTCGATGTCAGGTTAGGGTTTAGGGTATAGATTAATTAGTGTGTTTTAATT
1 TTAGGGGTTAGGGATTCGAGGTCAGGTTAGGGTTTAAGGTATAGATTAATTAGTGTGTTTTAATT
* *
62745238 TATATAT-TAATAATGTTTA-GGG
66 TATATATCAAATAAGGTTTAGGGG
* * *
62745260 TTAGGGGTTAGGGATTCGGGGTCAGGTTAGGGTTTAAGGTTTAGATTAATTAGTGTTTTTTAATT
1 TTAGGGGTTAGGGATTCGAGGTCAGGTTAGGGTTTAAGGTATAGATTAATTAGTGTGTTTTAATT
62745325 TATATATCAAATAAGGTTTAGGGG
66 TATATATCAAATAAGGTTTAGGGG
62745349 TTAG
1 TTAG
62745353 TGTCTAAGGG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 65 0.79
88 10 0.12
89 7 0.09
ACGTcount: A:0.26, C:0.03, G:0.28, T:0.43
Consensus pattern (89 bp):
TTAGGGGTTAGGGATTCGAGGTCAGGTTAGGGTTTAAGGTATAGATTAATTAGTGTGTTTTAATT
TATATATCAAATAAGGTTTAGGGG
Found at i:62745370 original size:7 final size:7
Alignment explanation
Indices: 62745360--62745385 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62745350 TAGTGTCTAA
62745360 GGGTTTG
1 GGGTTTG
62745367 GGGTTTG
1 GGGTTTG
62745374 GGGTTTG
1 GGGTTTG
62745381 GGGTT
1 GGGTT
62745386 AGTGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (7 bp):
GGGTTTG
Found at i:62745830 original size:43 final size:43
Alignment explanation
Indices: 62745793--62746045 Score: 371
Period size: 43 Copynumber: 5.9 Consensus size: 43
62745783 CGTTTGTAAT
62745793 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * * *
62745836 AAAAGTGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTTTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * * * *
62745879 AAAAGTGTCGCTAAAGGTATTGGTCTTTAGTGGCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* * *
62745922 AGAAGCGCTGCTAAAGGTCTTAGTCTTTAGCGGCGCTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
*
62745965 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGCCGTTTGTGGG
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
* *
62746008 AGACGCACCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
62746046 TTTTCTATAA
Statistics
Matches: 188, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 188 1.00
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.30
Consensus pattern (43 bp):
AGAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGG
Found at i:62746166 original size:22 final size:22
Alignment explanation
Indices: 62746138--62746180 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
62746128 TAGCGGCACT
*
62746138 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
62746160 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
62746181 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:62760035 original size:24 final size:23
Alignment explanation
Indices: 62760008--62760052 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
62759998 AAGTAAATCC
*
62760008 TAATATGATATTAATCTCTAATGT
1 TAATATAATATTAATC-CTAATGT
* *
62760032 TAATCTAATATTTATCCTAAT
1 TAATATAATATTAATCCTAAT
62760053 ATTGTCGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
TAATATAATATTAATCCTAATGT
Found at i:62762429 original size:55 final size:55
Alignment explanation
Indices: 62762363--62762474 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
62762353 AATTAATATT
62762363 ATTCGAAAGTATTTTAATCTTTTTATGCAAACTTATCAATAAAAACATGAATCTA
1 ATTCGAAAGTATTTTAATCTTTTTATGCAAACTTATCAATAAAAACATGAATCTA
62762418 ATTCGAAAGTATTTTAATCTTTTTATGCAAACTTATCAATAAAAACATGAATCTA
1 ATTCGAAAGTATTTTAATCTTTTTATGCAAACTTATCAATAAAAACATGAATCTA
62762473 AT
1 AT
62762475 GGGATTTGAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (55 bp):
ATTCGAAAGTATTTTAATCTTTTTATGCAAACTTATCAATAAAAACATGAATCTA
Found at i:62766382 original size:34 final size:35
Alignment explanation
Indices: 62766322--62766388 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
62766312 CAAACACCAG
*
62766322 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCAATTTACAGAAAAGT
* *
62766357 AAAATATTTTCCCG-AAATCAATTTACGGAAAA
1 AAAATATTTTCCAGTAAATCAATTTACAGAAAA
62766389 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCAATTTACAGAAAAGT
Found at i:62767376 original size:16 final size:16
Alignment explanation
Indices: 62767352--62767382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62767342 ATCCTTACTT
62767352 TAAAAAGTATAATTAA
1 TAAAAAGTATAATTAA
*
62767368 TAAATAGTATAATTA
1 TAAAAAGTATAATTA
62767383 TTTTTCAAAA
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAAAGTATAATTAA
Found at i:62768122 original size:40 final size:41
Alignment explanation
Indices: 62768039--62768135 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
62768029 TTCGGGGGAA
*
62768039 TTAGTGGCGTTTTTTGTAAAGCGCCGCTAAGGCTAAGACTT
1 TTAGTGGCGTTTTTTGAAAAGCGCCGCTAAGGCTAAGACTT
* * * * **
62768080 TTAGTGGCGTTTTTTGAAAATCGTCGCTAA-TCTAGGTGTT
1 TTAGTGGCGTTTTTTGAAAAGCGCCGCTAAGGCTAAGACTT
*
62768120 TTAGCGGCGTTTTTTG
1 TTAGTGGCGTTTTTTG
62768136 TTTATGCGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 21 0.44
41 27 0.56
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.40
Consensus pattern (41 bp):
TTAGTGGCGTTTTTTGAAAAGCGCCGCTAAGGCTAAGACTT
Found at i:62773176 original size:13 final size:13
Alignment explanation
Indices: 62773166--62773256 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 13
62773156 GGTTAAATTT
62773166 ATTACTTAAATAC
1 ATTACTTAAATAC
62773179 ATTACTTACTAAAATAC
1 ATTAC-T--T-AAATAC
62773196 ATTACTTACTAA-A-
1 ATTACTTA--AATAC
** **
62773209 ATTTGTTTAAATTT
1 A-TTACTTAAATAC
*
62773223 ATTACTTAAATAT
1 ATTACTTAAATAC
*
62773236 GTTACTTAAATAC
1 ATTACTTAAATAC
62773249 ATTACTTA
1 ATTACTTA
62773257 CTAAAATTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
12 2 0.03
13 34 0.57
14 9 0.15
15 2 0.03
16 2 0.03
17 11 0.18
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTACTTAAATAC
Found at i:62773193 original size:17 final size:17
Alignment explanation
Indices: 62773167--62773210 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
62773157 GTTAAATTTA
*
62773167 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
62773184 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
62773201 TTACTAAAAT
1 TTACTAAAAT
62773211 TTGTTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:62773220 original size:57 final size:53
Alignment explanation
Indices: 62773151--62773265 Score: 167
Period size: 53 Copynumber: 2.1 Consensus size: 53
62773141 TTTGTAAGTT
62773151 AATTTGGTTAAATTTATTACTTAAATACATTACTTACTAAAATACATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAAT--A-T-CTTACTAAAATACATTACTTACTAA
* * *
62773208 AATTTGTTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAATATCTTACTAAAATACATTACTTACTAA
62773261 AATTT
1 AATTT
62773266 AAGTATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 28 0.51
54 1 0.02
55 1 0.02
57 25 0.45
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (53 bp):
AATTTGGTTAAATTTATTACTTAAATATCTTACTAAAATACATTACTTACTAA
Found at i:62773752 original size:9 final size:9
Alignment explanation
Indices: 62773734--62774112 Score: 232
Period size: 9 Copynumber: 43.8 Consensus size: 9
62773724 CTTGTGGTTA
*
62773734 AACTTGCAT
1 AACTTACAT
62773743 AACTTACAT
1 AACTTACAT
*
62773752 AA-TAACAT
1 AACTTACAT
62773760 AACAACTTACAT
1 ---AACTTACAT
62773772 AA--TACAT
1 AACTTACAT
* *
62773779 AGCATACAT
1 AACTTACAT
62773788 AACTTACAT
1 AACTTACAT
62773797 AACTTACAT
1 AACTTACAT
*
62773806 AA--TACAA
1 AACTTACAT
62773813 AACTTACAT
1 AACTTACAT
*
62773822 AACTTAAAT
1 AACTTACAT
* *
62773831 ATCTTACAC
1 AACTTACAT
62773840 AACTTACAT
1 AACTTACAT
*
62773849 AACGTACAT
1 AACTTACAT
62773858 AA--TACAT
1 AACTTACAT
62773865 AACTTACAT
1 AACTTACAT
62773874 AA--TACAT
1 AACTTACAT
*
62773881 AA-TAACTTAT
1 AACTTAC--AT
62773891 AACTTACAT
1 AACTTACAT
*
62773900 AACATACAT
1 AACTTACAT
* **
62773909 TACTTTGAT
1 AACTTACAT
62773918 AACTTACAT
1 AACTTACAT
62773927 AACTTACAT
1 AACTTACAT
*
62773936 AA--TACAC
1 AACTTACAT
**
62773943 AACTT-GTT
1 AACTTACAT
*
62773951 AAGCTTACTT
1 AA-CTTACAT
62773961 AA--TACAT
1 AACTTACAT
62773968 AACTTACAT
1 AACTTACAT
62773977 AA--TACAT
1 AACTTACAT
*
62773984 AA-TAACTTAT
1 AACTTAC--AT
62773994 AACTTACAT
1 AACTTACAT
*
62774003 AACATACAT
1 AACTTACAT
* **
62774012 TACTTTGAT
1 AACTTACAT
62774021 AACTTACAT
1 AACTTACAT
62774030 AACTTACAT
1 AACTTACAT
*
62774039 AA--TACAC
1 AACTTACAT
**
62774046 AACTT-GTT
1 AACTTACAT
*
62774054 AAGCTTACTT
1 AA-CTTACAT
62774064 AA--TACAT
1 AACTTACAT
62774071 AACTTACAT
1 AACTTACAT
62774080 AACTT--AT
1 AACTTACAT
*
62774087 ACACGTACAT
1 A-ACTTACAT
62774097 AACTTACAT
1 AACTTACAT
*
62774106 AATTTAC
1 AACTTAC
62774113 TTAATACATA
Statistics
Matches: 287, Mismatches: 50, Indels: 66
0.71 0.12 0.16
Matches are distributed among these distances:
7 60 0.21
8 16 0.06
9 179 0.62
10 19 0.07
11 8 0.03
12 5 0.02
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:62773787 original size:157 final size:157
Alignment explanation
Indices: 62773428--62773775 Score: 655
Period size: 157 Copynumber: 2.2 Consensus size: 157
62773418 TATTTATATA
62773428 AACTTACATAACTATCACAT-A-AACTTACATAATATATAACTTACATGTTACCTTACATAATAC
1 AACTTACATAA-TA--ACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATAC
62773491 ATAACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAG
63 ATAACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAG
62773556 TTATCTACAAGCTTGTGGTTAAACTTGCAT
128 TTATCTACAAGCTTGTGGTTAAACTTGCAT
62773586 AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
1 AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
62773651 ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
66 ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
62773716 TCTACAAGCTTGTGGTTAAACTTGCAT
131 TCTACAAGCTTGTGGTTAAACTTGCAT
62773743 AACTTACATAATAACATAACAACTTACATAATA
1 AACTTACATAATAACATAACAACTTACATAATA
62773776 CATAGCATAC
Statistics
Matches: 188, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
155 4 0.02
156 1 0.01
157 172 0.91
158 11 0.06
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (157 bp):
AACTTACATAATAACATAACAACTTACATAATATATAACTTACATGTTACCTTACATAATACATA
ACTTATATAAAATTTTTATATAAACTTACATAATACATTATTTACATATTAACTTACATAAGTTA
TCTACAAGCTTGTGGTTAAACTTGCAT
Found at i:62773788 original size:16 final size:16
Alignment explanation
Indices: 62773740--62774050 Score: 147
Period size: 16 Copynumber: 19.5 Consensus size: 16
62773730 GTTAAACTTG
62773740 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
62773757 CATAACAACTTACATAATA
1 CAT---AACTTACATAATA
* *
62773776 CATAGCATACATAACTTA
1 CATAACTTACATAA--TA
62773794 CATAACTTACATAATA
1 CATAACTTACATAATA
*
62773810 CAAAACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
62773828 AATATCTTACACAACTTA
1 CATAACTTACATAA--TA
*
62773846 CATAACGTACATAATA
1 CATAACTTACATAATA
62773862 CATAACTTACATAATA
1 CATAACTTACATAATA
*
62773878 CATAA-TAAC-T--T-
1 CATAACTTACATAATA
62773889 -ATAACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
62773906 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
62773924 CATAACTTACATAATA
1 CATAACTTACATAATA
* *
62773940 CACAACTT--GT--T-
1 CATAACTTACATAATA
* *
62773951 -A-AGCTTACTTAATA
1 CATAACTTACATAATA
62773965 CATAACTTACATAATA
1 CATAACTTACATAATA
*
62773981 CATAA-TAAC-T--T-
1 CATAACTTACATAATA
62773992 -ATAACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
62774009 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
62774027 CATAACTTACATAATA
1 CATAACTTACATAATA
*
62774043 CACAACTT
1 CATAACTT
62774051 GTTAAGCTTA
Statistics
Matches: 223, Mismatches: 37, Indels: 69
0.68 0.11 0.21
Matches are distributed among these distances:
9 4 0.02
10 9 0.04
11 7 0.03
12 5 0.02
13 1 0.00
14 3 0.01
15 7 0.03
16 84 0.38
17 5 0.02
18 82 0.37
19 4 0.02
20 12 0.05
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:62773794 original size:25 final size:25
Alignment explanation
Indices: 62773740--62774107 Score: 216
Period size: 25 Copynumber: 14.6 Consensus size: 25
62773730 GTTAAACTTG
62773740 CATAACTTACATAA-T--A-ACATA
1 CATAACTTACATAACTACATACATA
*
62773761 -ACAACTTACATAA-TACATAGCATA
1 CATAACTTACATAACTACATA-CATA
62773785 CATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* * *
62773810 CAAAACTTACATAACTTAAATATCTTA
1 CATAACTTACATAAC-TACATA-CATA
*
62773837 CACAACTTACATAACGTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
62773862 CATAACTTACATAA-TACATA-ATAA
1 CATAACTTACATAACTACATACAT-A
* *
62773886 CTTATAACTTACATAACATACATTACTTT
1 C--ATAACTTACATAAC-TACA-TACATA
*
62773915 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* ** *
62773940 CACAACTT-GTTAAGCTTACTTA-ATA
1 CATAACTTACATAA-C-TACATACATA
62773965 CATAACTTACATAA-TACATA-ATAA
1 CATAACTTACATAACTACATACAT-A
* *
62773989 CTTATAACTTACATAACATACATTACTTT
1 C--ATAACTTACATAAC-TACA-TACATA
*
62774018 GATAACTTACATAACTTACATA-ATA
1 CATAACTTACATAAC-TACATACATA
* ** *
62774043 CACAACTT-GTTAAGCTTACTTA-ATA
1 CATAACTTACATAA-C-TACATACATA
*
62774068 CATAACTTACATAACT-TATACACGTA
1 CATAACTTACATAACTACATACA--TA
62774094 CATAACTTACATAA
1 CATAACTTACATAA
62774108 TTTACTTAAT
Statistics
Matches: 276, Mismatches: 41, Indels: 55
0.74 0.11 0.15
Matches are distributed among these distances:
20 13 0.05
22 1 0.00
23 18 0.07
24 16 0.06
25 99 0.36
26 52 0.19
27 63 0.23
28 8 0.03
29 4 0.01
30 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
CATAACTTACATAACTACATACATA
Found at i:62773941 original size:34 final size:33
Alignment explanation
Indices: 62773763--62774108 Score: 211
Period size: 34 Copynumber: 10.4 Consensus size: 33
62773753 ATAACATAAC
* **
62773763 AACTTACATAATACATAGCATACATAACTTACAT
1 AACTTACATAATACATAAC-TTGATAACTTACAT
* * *
62773797 AACTTACATAATACAAAACTTACATAACTTAAAT
1 AACTTACATAATACATAACTT-GATAACTTACAT
* * **
62773831 ATCTTACACAACTTACATAACGTACATAA--TACAT
1 AACTTACATAA--TACATAAC-TTGATAACTTACAT
62773865 AACTTACATAATACAT-A----ATAACTT--AT
1 AACTTACATAATACATAACTTGATAACTTACAT
*
62773891 AACTTACATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACATAAC-TTGATAACTTACAT
* * *
62773927 AACTTACATAATACACAACTTGTTAAGCTTACTT
1 AACTTACATAATACATAACTTGATAA-CTTACAT
* *
62773961 AA--TACATAACTTACATAATACATAATAACTT--AT
1 AACTTACATAA--TACAT-A-ACTTGATAACTTACAT
*
62773994 AACTTACATAACATACATTACTTTGATAACTTACAT
1 AACTTACAT-A-ATACATAAC-TTGATAACTTACAT
* * *
62774030 AACTTACATAATACACAACTTGTTAAGCTTACTT
1 AACTTACATAATACATAACTTGATAA-CTTACAT
*
62774064 AA--TACATAACTTACATAACTT-ATACACGTACAT
1 AACTTACATAA--TACATAACTTGATA-ACTTACAT
62774097 AACTTACATAAT
1 AACTTACATAAT
62774109 TTACTTAATA
Statistics
Matches: 247, Mismatches: 31, Indels: 69
0.71 0.09 0.20
Matches are distributed among these distances:
26 15 0.06
27 1 0.00
28 7 0.03
29 1 0.00
31 1 0.00
32 19 0.08
33 28 0.11
34 109 0.44
35 23 0.09
36 41 0.17
37 2 0.01
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (33 bp):
AACTTACATAATACATAACTTGATAACTTACAT
Found at i:62774107 original size:103 final size:103
Alignment explanation
Indices: 62773763--62774081 Score: 434
Period size: 103 Copynumber: 3.1 Consensus size: 103
62773753 ATAACATAAC
* * ** *
62773763 AACTTACATAATACATAGCAT-A--CATAACTTACATAACTTACA-TA-ATACAAAACTTACATA
1 AACTTACATAATACATA--ATAACTCATAACTTACATAACATACATTACTTTGATAACTTACATA
* * ** * *
62773823 ACTTAAATATCTTACACAACTTACATAA-CGTACATAATACAT
64 ACTTACATA--ATACACAACTT-GTTAAGCTTACTTAATACAT
*
62773865 AACTTACATAATACATAATAACTTATAACTTACATAACATACATTACTTTGATAACTTACATAAC
1 AACTTACATAATACATAATAACTCATAACTTACATAACATACATTACTTTGATAACTTACATAAC
62773930 TTACATAATACACAACTTGTTAAGCTTACTTAATACAT
66 TTACATAATACACAACTTGTTAAGCTTACTTAATACAT
*
62773968 AACTTACATAATACATAATAACTTATAACTTACATAACATACATTACTTTGATAACTTACATAAC
1 AACTTACATAATACATAATAACTCATAACTTACATAACATACATTACTTTGATAACTTACATAAC
62774033 TTACATAATACACAACTTGTTAAGCTTACTTAATACAT
66 TTACATAATACACAACTTGTTAAGCTTACTTAATACAT
62774071 AACTTACATAA
1 AACTTACATAA
62774082 CTTATACACG
Statistics
Matches: 199, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
100 2 0.01
101 1 0.01
102 20 0.10
103 154 0.77
104 2 0.01
105 20 0.10
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (103 bp):
AACTTACATAATACATAATAACTCATAACTTACATAACATACATTACTTTGATAACTTACATAAC
TTACATAATACACAACTTGTTAAGCTTACTTAATACAT
Found at i:62777677 original size:20 final size:20
Alignment explanation
Indices: 62777652--62777691 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62777642 CATGACGGAA
62777652 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
62777672 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
62777692 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:62778644 original size:14 final size:14
Alignment explanation
Indices: 62778628--62778657 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62778618 TGCTCATTTA
62778628 TTTATTTATTATTAT
1 TTTA-TTATTATTAT
62778643 TTTATTATTATTAT
1 TTTATTATTATTAT
62778657 T
1 T
62778658 CATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:62780926 original size:19 final size:20
Alignment explanation
Indices: 62780886--62780929 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
62780876 GTCTCTTTAG
* *
62780886 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
62780905 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
62780924 GCATTA
1 GCATTA
62780930 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:62785360 original size:88 final size:88
Alignment explanation
Indices: 62785211--62785890 Score: 994
Period size: 88 Copynumber: 7.8 Consensus size: 88
62785201 CAATGAAGTT
* * * *
62785211 AAAGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACATAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
62785276 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * *
62785299 AAAGATCTTGCTTTTCTGTATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
62785364 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
*
62785387 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
* *
62785452 TGTGATGGAGCTGGTTCAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
62785475 AAAGATCTTGCTTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
62785540 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
62785563 AAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTTTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
62785628 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
62785651 AAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
62785716 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * * ** *
62785739 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATCCATCGA
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGG
* * *
62785802 TTG-CAGTAGAGCTAGTTAAAGA-A
65 TTGTGA-TAGAGCTGGTTGAAGACA
** * * * **
62785825 GCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGG
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGG
62785888 TTG
65 TTG
62785891 CATTGGAGCT
Statistics
Matches: 544, Mismatches: 45, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
85 3 0.01
86 63 0.12
87 29 0.05
88 449 0.83
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
TGTGATAGAGCTGGTTGAAGACA
Found at i:62786153 original size:43 final size:44
Alignment explanation
Indices: 62786053--62786158 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
62786043 GATCTTGTCC
* * *
62786053 CCCTGAAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCT
1 CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
* * **
62786097 CCCCG-AGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCT
1 CCCTGAAG-TTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
62786140 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTGGAG
62786159 TGGGTTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 24 0.47
44 27 0.53
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (44 bp):
CCCTGAAGTTACAGTGGAGCAGATCGAAGACAGAGATCCTATCT
Found at i:62787684 original size:14 final size:14
Alignment explanation
Indices: 62787668--62787697 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62787658 TGCTCATTTA
62787668 TTTATTTATTATTAT
1 TTTA-TTATTATTAT
62787683 TTTATTATTATTAT
1 TTTATTATTATTAT
62787697 T
1 T
62787698 CATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:62791122 original size:21 final size:21
Alignment explanation
Indices: 62791096--62791166 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
62791086 CTACAACTTA
*
62791096 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
62791117 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
62791138 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
62791159 AAGCAGAG
1 AAGCAGAG
62791167 CAGACCAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.30, C:0.20, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:62791604 original size:42 final size:43
Alignment explanation
Indices: 62791463--62791604 Score: 207
Period size: 42 Copynumber: 3.3 Consensus size: 43
62791453 ATCCCAAAAA
** *
62791463 TAGTGGCGTTTTTGTATAAAAACGCCGCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTT-TACCAAAGCGCCGCTAAAGAACATGGTCTT
*
62791507 TAGTGGCG-TTTTTACCAAAGCGCCCCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
*
62791549 TAGTGGCGTTTTTTA-CTAAGCGCCGCTAAAGAACATGGTCTT
1 TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
*
62791591 TAGCGGCGTTTTTT
1 TAGTGGCGTTTTTT
62791605 TGTAAACGCT
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 72 0.80
43 10 0.11
44 8 0.09
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (43 bp):
TAGTGGCGTTTTTTACCAAAGCGCCGCTAAAGAACATGGTCTT
Found at i:62792310 original size:11 final size:13
Alignment explanation
Indices: 62792282--62792323 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 13
62792272 TTTTTCAAAG
62792282 ATTTTATAATATAAA
1 ATTTTAT-ATA-AAA
62792297 ATTTT-T-TAAAA
1 ATTTTATATAAAA
62792308 ATTTTATATAAAA
1 ATTTTATATAAAA
62792321 ATT
1 ATT
62792324 AAATAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.32
12 3 0.12
13 8 0.32
14 1 0.04
15 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTATATAAAA
Found at i:62792311 original size:26 final size:25
Alignment explanation
Indices: 62792271--62792323 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
62792261 AAAAATATAT
*
62792271 TTTTTTCAAAGATTTTATAATATAAAA
1 TTTTTTCAAAAATTTTAT-ATA-AAAA
62792298 TTTTTT-AAAAATTTTATATAAAAA
1 TTTTTTCAAAAATTTTATATAAAAA
62792322 TT
1 TT
62792324 AAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 10 0.40
27 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTTCAAAAATTTTATATAAAAA
Found at i:62800401 original size:28 final size:28
Alignment explanation
Indices: 62800370--62800433 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
62800360 TAAAGTATAT
62800370 AAAAATTCATAAAAATCGTAAA-AAAATA
1 AAAAATTCATAAAAATC-TAAAGAAAATA
** * *
62800398 AAAAAAGCATAAAACTCTAAAGAAATTA
1 AAAAATTCATAAAAATCTAAAGAAAATA
62800426 ATAAAATT
1 A-AAAATT
62800434 TTATAAGCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 4 0.14
28 20 0.71
29 4 0.14
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.22
Consensus pattern (28 bp):
AAAAATTCATAAAAATCTAAAGAAAATA
Found at i:62800664 original size:20 final size:20
Alignment explanation
Indices: 62800637--62800680 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
62800627 TTTTTAATGG
62800637 TTTTTAAAAT-TTTATAA-TA
1 TTTTTAAAATGTTT-TAACTA
62800656 TTTTCTAAAATGTTTTAACTA
1 TTTT-TAAAATGTTTTAACTA
62800677 TTTT
1 TTTT
62800681 GGTCGTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 9 0.41
21 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATGTTTTAACTA
Found at i:62806051 original size:20 final size:20
Alignment explanation
Indices: 62806028--62806077 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
62806018 TTTATAATTT
* *
62806028 ATATCTATATATCTATATAC
1 ATATCTATATATATATACAC
* *
62806048 ATATTTATACATATATACAC
1 ATATCTATATATATATACAC
*
62806068 ATACCTATAT
1 ATATCTATAT
62806078 GTTTTATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATCTATATATATATACAC
Found at i:62810479 original size:16 final size:16
Alignment explanation
Indices: 62810458--62810526 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
62810448 TTTGGTTCGC
62810458 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62810474 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62810490 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
62810507 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62810523 TGTA
1 TGTA
62810527 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:62810504 original size:33 final size:32
Alignment explanation
Indices: 62810458--62810526 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
62810448 TTTGGTTCGC
62810458 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
62810490 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
62810523 TGTA
1 TGTA
62810527 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:62810591 original size:44 final size:45
Alignment explanation
Indices: 62810507--62810597 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
62810497 GGATTAGAGG
* * *
62810507 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
62810552 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
62810596 TG
1 TG
62810598 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:62815427 original size:97 final size:97
Alignment explanation
Indices: 62815320--62815509 Score: 235
Period size: 97 Copynumber: 2.0 Consensus size: 97
62815310 TTCATTTTGA
** **
62815320 ATCTTAGCAAAATTCGCTGT-TC-TGCTTAATTTATTTGTTTAGAGCTCTGCTCTCAATAAAATT
1 ATCTTAGCAAAATTCG-T-TATCTTGAATAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATT
62815383 TCATCTT-TCCCACTA-TGATAATCTTTTTCATCTT
64 TCATCTTAT-CCA-TATTGATAATCTTTTTCATCTT
* * * * *
62815417 ATCTTAGCAAAATTTGTTATCTTGAATAATTTATTCATTTTGAGCTTTGTTCTTAATAAAATTTC
1 ATCTTAGCAAAATTCGTTATCTTGAATAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
62815482 ATCTTATCCATATTGATAATCTTTTTCA
66 ATCTTATCCATATTGATAATCTTTTTCA
62815510 AGCATTTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 5 0.06
97 73 0.91
98 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.47
Consensus pattern (97 bp):
ATCTTAGCAAAATTCGTTATCTTGAATAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
ATCTTATCCATATTGATAATCTTTTTCATCTT
Found at i:62816447 original size:46 final size:46
Alignment explanation
Indices: 62816395--62816882 Score: 659
Period size: 46 Copynumber: 10.7 Consensus size: 46
62816385 AGTGGACTAG
*
62816395 AGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
62816441 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* *
62816487 AGATAGCAGATCTTGTTTTCCTGTATTTGGCAGC-AGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * * * *
62816533 AGATAGCAGATCTTGTCTTCTTATATTTGGCAGTGGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * *
62816579 AGATAGCAAATCTTGCCTTCCTGTATTTAGCAGCG-A--AG--CGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
**
62816620 AGATAGCAGATCTTGTCTTTTTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * * *
62816666 AGATAGCAGATCTTGTCTTCCTGTATTTGGTAGAGGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* *
62816712 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAG-TAGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * *
62816758 AGATAGCAGATATTGTCTTCCTGTATTTGGCAGCGAAGTAGATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* **
62816804 AGATAGCAGATCTTGTCTTCCTATATTTGGCA-ATAGAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
*
62816850 AGATAGTAGATCTTGTCTTCCTGTATTTGGCAG
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
62816883 TGGAGTTGGT
Statistics
Matches: 387, Mismatches: 44, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
41 32 0.08
42 1 0.00
43 2 0.01
44 2 0.01
45 3 0.01
46 346 0.89
47 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
Found at i:62822887 original size:22 final size:21
Alignment explanation
Indices: 62822849--62822889 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62822839 AGATTATTAT
**
62822849 CTCTTTTTCTTCTTTTGTTGA
1 CTCTTTTTCTTAGTTTGTTGA
62822870 CTCTTTTTCATTAGTTTGTT
1 CTCTTTTTC-TTAGTTTGTT
62822890 ATTTCTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.66
Consensus pattern (21 bp):
CTCTTTTTCTTAGTTTGTTGA
Found at i:62823352 original size:23 final size:23
Alignment explanation
Indices: 62823325--62823376 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
62823315 CATATAATTT
*
62823325 TATATTTTTTAT-TTTTTAAATA
1 TATATTTTTTATAATTTTAAATA
62823347 -ATATATTTTTATAATTTTAAATA
1 TATAT-TTTTTATAATTTTAAATA
62823370 TATATTT
1 TATATTT
62823377 ATGCTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 11 0.42
24 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATTTTTTATAATTTTAAATA
Found at i:62823358 original size:22 final size:22
Alignment explanation
Indices: 62823325--62823376 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
62823315 CATATAATTT
*
62823325 TATAT-TTTTTAT-TTTTTAAA
1 TATATATTTTTATAATTTTAAA
62823345 TAATATATTTTTATAATTTTAAA
1 T-ATATATTTTTATAATTTTAAA
62823368 TATATATTT
1 TATATATTT
62823377 ATGCTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 4 0.14
22 15 0.54
23 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATATTTTTATAATTTTAAA
Found at i:62823384 original size:23 final size:23
Alignment explanation
Indices: 62823338--62823385 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
62823328 ATTTTTTATT
*
62823338 TTTTAAATAATATATTTTTATAA
1 TTTTAAATAATATATTTTGATAA
*
62823361 TTTTAAAT-ATATATTTATGCTAA
1 TTTTAAATAATATATTT-TGATAA
62823384 TT
1 TT
62823386 AAACGAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTAAATAATATATTTTGATAA
Found at i:62824252 original size:28 final size:28
Alignment explanation
Indices: 62824188--62824252 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
62824178 TTTTATACTA
62824188 TTTAATATAACTTTAATAGTTTTTAATTT
1 TTTAA-ATAACTTTAATAGTTTTTAATTT
* * *
62824217 TTAAAAATAA-TTTTATATTTTTTGAATTT
1 TT-TAAATAACTTTAATAGTTTTT-AATTT
62824246 TTTAAAT
1 TTTAAAT
62824253 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.50
29 13 0.43
30 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAAATAACTTTAATAGTTTTTAATTT
Found at i:62827781 original size:40 final size:41
Alignment explanation
Indices: 62827737--62827843 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 41
62827727 AAATGCCACG
*
62827737 AATGCTC-ATTTTTAGCGGCGTTTTTTCAAAAATCGCCGCA
1 AATGCTCAATTTTTAGCGGCGTTTTTTCAAAAAGCGCCGCA
* * * * * * *
62827777 AATGCTCAATCTTTAGTGGCG-ATTTCCATAAAGCGCTGCT
1 AATGCTCAATTTTTAGCGGCGTTTTTTCAAAAAGCGCCGCA
* *
62827817 AATGCTCAATTTTTATCGGTGTTTTTT
1 AATGCTCAATTTTTAGCGGCGTTTTTT
62827844 GTCCAAGTGC
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
40 37 0.73
41 14 0.27
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
AATGCTCAATTTTTAGCGGCGTTTTTTCAAAAAGCGCCGCA
Found at i:62835226 original size:21 final size:22
Alignment explanation
Indices: 62835193--62835240 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
62835183 GTAGTTATGA
* *
62835193 CACATGCCCATGTG-AAGGAGG
1 CACACGCCCATGTGAAAAGAGG
*
62835214 CACACGCCTATGTGAAAAGAGG
1 CACACGCCCATGTGAAAAGAGG
62835236 CACAC
1 CACAC
62835241 ACACGACCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.12
Consensus pattern (22 bp):
CACACGCCCATGTGAAAAGAGG
Found at i:62836739 original size:33 final size:33
Alignment explanation
Indices: 62836674--62836752 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
62836664 TTTTAATATT
* * *
62836674 TAATTAATTTTAAATATTATATTTTTAATTGAAA
1 TAATTAATGTAAAATAATATATTTTTAATTG-AA
*
62836708 TAATTAATGTAAAATAATAT-TTTTTATTTGAA
1 TAATTAATGTAAAATAATATATTTTTAATTGAA
*
62836740 TTATTGAATGTAA
1 TAATT-AATGTAA
62836753 TTAAAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 6 0.15
33 16 0.41
34 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (33 bp):
TAATTAATGTAAAATAATATATTTTTAATTGAA
Found at i:62846189 original size:45 final size:44
Alignment explanation
Indices: 62846120--62846249 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 44
62846110 CTTGGTATGC
62846120 TTTACAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
1 TTTA-AAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
*
62846165 TTTAAAAACGAGGTTGAGATTTTGTTACATGTTTTG--T-TTTTT
1 TTT-AAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
* * * * *
62846207 TTT-AAATGAGATTGAAATTTTGTTACATATCTTATTTATTTTT
1 TTTAAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
62846250 CAAAAAATTC
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
40 25 0.34
42 9 0.12
43 6 0.08
45 33 0.45
46 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (44 bp):
TTTAAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
Found at i:62849942 original size:13 final size:13
Alignment explanation
Indices: 62849926--62849951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62849916 CTTTGCATAT
62849926 TGTCTTCAATAGG
1 TGTCTTCAATAGG
62849939 TGTCTTCAATAGG
1 TGTCTTCAATAGG
62849952 CTCGCACTTT
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:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TGTCTTCAATAGG
Found at i:62858347 original size:43 final size:43
Alignment explanation
Indices: 62858299--62858546 Score: 275
Period size: 43 Copynumber: 5.8 Consensus size: 43
62858289 GCGTCGCTAA
*
62858299 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
* *
62858342 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGAAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
* * *
62858385 CTTTAGCGACACTTTTCCTACAAACGCCGCTATAA-ATCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTA-AAGATCAGGAC
* * * *
62858428 CTTTAGCGGCACTTTT-ACACAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
*** * * *
62858470 CTTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
* * * ** *
62858513 TTTTAGCGACGTTTTTTTCGCAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
62858547 AGTGCCATTC
Statistics
Matches: 177, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 35 0.20
43 140 0.79
44 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATCAGGAC
Found at i:62858495 original size:85 final size:86
Alignment explanation
Indices: 62858299--62858520 Score: 297
Period size: 85 Copynumber: 2.6 Consensus size: 86
62858289 GCGTCGCTAA
* * * *
62858299 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTA-AAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAA-ATCAGGACCTTTAGCGGCACTTTTCACAC
62858363 AAACGCCGCTATAGATCAGAAC
65 AAACGCCGCTATAGATCAGAAC
* *
62858385 CTTTAGCGACACTTTTCCTACAAACGCCGCTATAAATCAGGACCTTTAGCGGCACTTTT-ACACA
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAAATCAGGACCTTTAGCGGCACTTTTCACACA
62858449 AACGCCGCTATAGATCA-AGAC
66 AACGCCGCTATAGATCAGA-AC
** * * * *
62858470 CTTTAGCGGCGCTTTTTTTATAAACGCCGCTATAGATCATGACTTTTAGCG
1 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAAATCAGGACCTTTAGCG
62858521 ACGTTTTTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 66 0.55
86 51 0.43
87 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTCCTACAAACGCCGCTATAAATCAGGACCTTTAGCGGCACTTTTCACACA
AACGCCGCTATAGATCAGAAC
Found at i:62863126 original size:21 final size:21
Alignment explanation
Indices: 62863102--62863142 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
62863092 AACCCTAAAT
62863102 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTCTTAACCCCTAAC
*
62863123 CCCTAACTCTTAATCCCTAA
1 CCCTAACTCTTAACCCCTAA
62863143 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTCTTAACCCCTAAC
Found at i:62863379 original size:23 final size:24
Alignment explanation
Indices: 62863340--62863393 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
62863330 TATATGAAAT
*
62863340 TATTTAATATATAAATTAAAAAAA
1 TATTTAATAAATAAATTAAAAAAA
62863364 TATTTAA-AAATAAATT-AAAAAA
1 TATTTAATAAATAAATTAAAAAAA
*
62863386 TAATTAAT
1 TATTTAAT
62863394 CTAAACCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTTAATAAATAAATTAAAAAAA
Found at i:62863458 original size:22 final size:22
Alignment explanation
Indices: 62863423--62863485 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
62863413 TTGACCCATG
* *
62863423 AACTCATAAACCCTAAATCCCT
1 AACTCATAACCCCTAAACCCCT
*
62863445 AACTCTTAACCCCTAAACCCCT
1 AACTCATAACCCCTAAACCCCT
62863467 AAC-CACTAACCCCTAAACC
1 AACTCA-TAACCCCTAAACC
62863486 TTAAATCTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (22 bp):
AACTCATAACCCCTAAACCCCT
Found at i:62863534 original size:15 final size:15
Alignment explanation
Indices: 62863498--62863538 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
62863488 AAATCTCAAC
62863498 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
62863512 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
62863526 CCTTAAATCCATA
1 CCTTAAATCCATA
62863539 CTCCATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:62863547 original size:15 final size:15
Alignment explanation
Indices: 62863501--62863547 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
62863491 TCTCAACCCT
*
62863501 TAAA-CCATAATCCC
1 TAAATCCATAATCCA
*
62863515 T-AATCCATAATCCT
1 TAAATCCATAATCCA
*
62863529 TAAATCCATACTCCA
1 TAAATCCATAATCCA
62863544 TAAA
1 TAAA
62863548 CCTTAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCA
Found at i:62863831 original size:41 final size:40
Alignment explanation
Indices: 62863771--62863886 Score: 162
Period size: 41 Copynumber: 2.8 Consensus size: 40
62863761 TAAAATGTTT
62863771 TTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCCTA-CCA
1 TTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGCCCC-AGCCA
* *
62863812 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCCAGGCA
1 TTAGCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCAGCCA
*
62863853 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCC
1 TTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGCC
62863887 ACGAAATGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
40 2 0.03
41 62 0.91
42 4 0.06
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCAGCCA
Found at i:62863972 original size:40 final size:39
Alignment explanation
Indices: 62863922--62864000 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
62863912 TGGGCTAAGG
* *
62863922 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGC-TTTTTTTGAAAAACGCCACTAATGCTCA
*
62863962 TTTTTAGCGGCTTTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCTTTTTTTGAAAAACGCCACTAATGCTCA
62864001 ATCTTTAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 26 0.72
40 10 0.28
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (39 bp):
TTTTTAGCGGCTTTTTTTGAAAAACGCCACTAATGCTCA
Found at i:62864008 original size:40 final size:40
Alignment explanation
Indices: 62863928--62864013 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 40
62863918 AAGGTTTTTT
* *
62863928 GCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCATTTTTA
1 GCGGCGTTTTTTTGAAAAACGCCACTAATGCTCATCTTTA
*
62863968 GCGGC-TTTTTTTTAAAAACGCCACTAATGCTCAATCTTTA
1 GCGGCGTTTTTTTGAAAAACGCCACTAATGCTC-ATCTTTA
*
62864008 GTGGCG
1 GCGGCG
62864014 ATTTCCAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 25 0.62
40 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (40 bp):
GCGGCGTTTTTTTGAAAAACGCCACTAATGCTCATCTTTA
Found at i:62883152 original size:15 final size:15
Alignment explanation
Indices: 62883134--62883171 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
62883124 GAAATTCAAC
62883134 TATATTTCAAAA-ATA
1 TATATTT-AAAATATA
*
62883149 TATATATAAAATATA
1 TATATTTAAAATATA
62883164 TATATTTA
1 TATATTTA
62883172 GGACTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATTTAAAATATA
Found at i:62883159 original size:13 final size:13
Alignment explanation
Indices: 62883143--62883168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62883133 CTATATTTCA
62883143 AAAATATATATAT
1 AAAATATATATAT
62883156 AAAATATATATAT
1 AAAATATATATAT
62883169 TTAGGACTTT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:62883742 original size:24 final size:24
Alignment explanation
Indices: 62883714--62883773 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
62883704 TGTAACTGCT
*
62883714 TATATATTATATGTACGTAATATG
1 TATATATTATATGTACGTAATACG
*
62883738 TATATATTATATGTATGTAATACG
1 TATATATTATATGTACGTAATACG
*
62883762 TACATATTATAT
1 TATATATTATAT
62883774 TATATATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (24 bp):
TATATATTATATGTACGTAATACG
Done.