Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 171 of 310
Found at i:55964702 original size:25 final size:23
Alignment explanation
Indices: 55964658--55964705 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
55964648 ATGTGCATAC
**
55964658 TTTTAATATTATTATGTATTTAT
1 TTTTAATATTATTACATATTTAT
55964681 TTTTAATATATATGTACATATTTAT
1 TTTTAATAT-TAT-TACATATTTAT
55964706 GTAGTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTAATATTATTACATATTTAT
Found at i:55964805 original size:18 final size:18
Alignment explanation
Indices: 55964771--55964889 Score: 70
Period size: 18 Copynumber: 6.7 Consensus size: 18
55964761 TTATGTACAC
55964771 TTTTTTATT-TCTATTTTAT
1 TTTTTTATTAT-T-TTTTAT
55964790 TTTTTTATTATTTTTTAT
1 TTTTTTATTATTTTTTAT
** *
55964808 TTGTCAATATTATTTATTAT
1 TT-T-TTTATTATTTTTTAT
* * *
55964828 TTTTCTAATA-TTTTGAT
1 TTTTTTATTATTTTTTAT
* * *
55964845 ATTTTGA-TA--TTTTAA
1 TTTTTTATTATTTTTTAT
55964860 TTTTTTA-TATTTTTTAT
1 TTTTTTATTATTTTTTAT
55964877 ATTTTTTATTATT
1 -TTTTTTATTATT
55964890 CACATCATTA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
15 11 0.14
16 2 0.03
17 14 0.18
18 19 0.25
19 16 0.21
20 15 0.19
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTTATTATTTTTTAT
Found at i:55964820 original size:20 final size:21
Alignment explanation
Indices: 55964795--55964839 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
55964785 TTTATTTTTT
*
55964795 TATTATTTTTTATTTGTC-AA
1 TATTATTTATTATTTGTCTAA
*
55964815 TATTATTTATTATTTTTCTAA
1 TATTATTTATTATTTGTCTAA
55964836 TATT
1 TATT
55964840 TTGATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTATTTATTATTTGTCTAA
Found at i:55964865 original size:24 final size:24
Alignment explanation
Indices: 55964833--55964881 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
55964823 ATTATTTTTC
55964833 TAATATTTTGATA-TTTTGATATTT
1 TAATATTTT-ATATTTTTGATATTT
* *
55964857 TAATTTTTTATATTTTTTATATTT
1 TAATATTTTATATTTTTGATATTT
55964881 T
1 T
55964882 TTATTATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TAATATTTTATATTTTTGATATTT
Found at i:55964873 original size:9 final size:9
Alignment explanation
Indices: 55964784--55964885 Score: 65
Period size: 9 Copynumber: 11.7 Consensus size: 9
55964774 TTTATTTCTA
55964784 TTTTAT-TT
1 TTTTATATT
55964792 TTTTATTATT
1 TTTTA-TATT
55964802 TTTTAT-TT
1 TTTTATATT
* **
55964810 GTCAATATT
1 TTTTATATT
*
55964819 ATTTATTATT
1 TTTTA-TATT
55964829 TTTCTA-ATAT
1 TTT-TATAT-T
*
55964839 TTTGATA-T
1 TTTTATATT
*
55964847 TTTGATA--
1 TTTTATATT
55964854 TTTTA-ATT
1 TTTTATATT
55964862 TTTTATATT
1 TTTTATATT
55964871 TTTTATATT
1 TTTTATATT
55964880 TTTTAT
1 TTTTAT
55964886 TATTCACATC
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 23 0.31
9 27 0.36
10 18 0.24
11 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:55968431 original size:21 final size:21
Alignment explanation
Indices: 55968407--55968450 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55968397 ATAATAATAT
* * *
55968407 AATATAATAGAAGAATAAAGA
1 AATAAAATAGAAAAAGAAAGA
55968428 AATAAAATAGAAAAAGAAAGA
1 AATAAAATAGAAAAAGAAAGA
55968449 AA
1 AA
55968451 GAACAGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAAATAGAAAAAGAAAGA
Found at i:55969358 original size:6 final size:6
Alignment explanation
Indices: 55969349--55969380 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
55969339 CCTGACTATG
*
55969349 ACTGTT ACTGTT ACTGTC ACTGTT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
55969381 CCTACAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (6 bp):
ACTGTT
Found at i:55977411 original size:19 final size:19
Alignment explanation
Indices: 55977389--55977427 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
55977379 AGAATAATTG
*
55977389 AAAGCATCTTTCGATAGGC
1 AAAGCATCGTTCGATAGGC
55977408 AAAGCATCGTTCGATAGGC
1 AAAGCATCGTTCGATAGGC
55977427 A
1 A
55977428 GAAATTGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (19 bp):
AAAGCATCGTTCGATAGGC
Found at i:55978323 original size:21 final size:21
Alignment explanation
Indices: 55978299--55978342 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55978289 ATAATAATAT
* * *
55978299 AATATAATAGAAGAATAAAGA
1 AATAAAATAGAAAAAGAAAGA
55978320 AATAAAATAGAAAAAGAAAGA
1 AATAAAATAGAAAAAGAAAGA
55978341 AA
1 AA
55978343 GAACAGACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AATAAAATAGAAAAAGAAAGA
Found at i:55981188 original size:22 final size:19
Alignment explanation
Indices: 55981161--55981271 Score: 54
Period size: 19 Copynumber: 5.8 Consensus size: 19
55981151 AAATATGTTT
55981161 TTATTTATAAATATATATATA
1 TTATTT-TAAATAT-TATATA
*
55981182 TTGATTTGT-TATATTATATA
1 TT-ATTT-TAAATATTATATA
*
55981202 TTATTTTAAA-ATTAGTATG
1 TTATTTTAAATATTA-TATA
* *
55981221 TTA-TAT-AATATT-TAAA
1 TTATTTTAAATATTATATA
* * * *
55981237 TTGTTTTATAAAAATGTATA
1 TTATTTTA-AATATTATATA
55981257 TT-TTTTAAATATTAT
1 TTATTTTAAATATTAT
55981272 TACATATGTG
Statistics
Matches: 67, Mismatches: 15, Indels: 19
0.66 0.15 0.19
Matches are distributed among these distances:
16 4 0.06
17 4 0.06
18 15 0.22
19 20 0.30
20 13 0.19
21 6 0.09
22 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTATTTTAAATATTATATA
Found at i:55984188 original size:16 final size:18
Alignment explanation
Indices: 55984162--55984199 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
55984152 TGTTTTTATG
55984162 TTTTAAAAATAATTTT-A
1 TTTTAAAAATAATTTTAA
*
55984179 TTTT-AAAATATTTTTAA
1 TTTTAAAAATAATTTTAA
55984196 TTTT
1 TTTT
55984200 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAAAATAATTTTAA
Found at i:56005254 original size:27 final size:27
Alignment explanation
Indices: 56005216--56005271 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
56005206 TTAATTTATA
56005216 TAAAATATGTTACTATTATTATTCATT
1 TAAAATATGTTACTATTATTATTCATT
56005243 TAAAATATGTTACTATTATTATTCATT
1 TAAAATATGTTACTATTATTATTCATT
56005270 TA
1 TA
56005272 TTTATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (27 bp):
TAAAATATGTTACTATTATTATTCATT
Found at i:56005301 original size:14 final size:12
Alignment explanation
Indices: 56005268--56005294 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56005258 TTATTATTCA
56005268 TTTATTTATATT
1 TTTATTTATATT
56005280 TTTATTTATATT
1 TTTATTTATATT
56005292 TTT
1 TTT
56005295 TAATTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTATATT
Found at i:56009170 original size:35 final size:35
Alignment explanation
Indices: 56009131--56009200 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
56009121 AGGTATGAGA
* * *
56009131 TAGTTTGAAAATATTCTTGATTTCATATAGATAAC
1 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
56009166 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
1 TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
56009201 GGTATCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (35 bp):
TAGTTCGAAAATATTCCTGATTTCATATAAATAAC
Found at i:56012148 original size:21 final size:21
Alignment explanation
Indices: 56012124--56012167 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
56012114 TGTTTCTTTT
* *
56012124 ATATTTTATTTTATTATAATA
1 ATATTATATTATATTATAATA
*
56012145 ATATTATATTATATTATATTA
1 ATATTATATTATATTATAATA
56012166 AT
1 AT
56012168 TTCTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTATATTATATTATAATA
Found at i:56012153 original size:5 final size:5
Alignment explanation
Indices: 56012122--56012165 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
56012112 TTTGTTTCTT
* * *
56012122 TTATA TTTTA TTTTA TTATAA TAATA TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTA
56012166 ATTTCTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:56017561 original size:56 final size:56
Alignment explanation
Indices: 56017475--56017587 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
56017465 AATTATTGCG
56017475 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
1 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
*
56017531 AAAGTCTTGGTGAAGCGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
1 AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
56017587 A
1 A
56017588 TAGGCTTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (56 bp):
AAAGTCTTGGTGAAACGTATGAGTGCAATGTTGGGATATTGTATTAATAAAGCCCA
Found at i:56018909 original size:15 final size:17
Alignment explanation
Indices: 56018889--56018922 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
56018879 CTTTTTACTT
56018889 TTCCTC-AAA-TTTTTA
1 TTCCTCAAAACTTTTTA
56018904 TTCCTCAAAACTTTTTA
1 TTCCTCAAAACTTTTTA
56018921 TT
1 TT
56018923 TTCCCCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
TTCCTCAAAACTTTTTA
Found at i:56019095 original size:18 final size:18
Alignment explanation
Indices: 56019072--56019117 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
56019062 TTATTTATAT
56019072 TATTGAATTTT-TTTGTCA
1 TATTGAATTTTATTT-TCA
56019090 TATTGAATATTTATTTTCA
1 TATTGAAT-TTTATTTTCA
*
56019109 AATTGAATT
1 TATTGAATT
56019118 ATTAATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 13 0.52
20 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (18 bp):
TATTGAATTTTATTTTCA
Found at i:56023467 original size:95 final size:95
Alignment explanation
Indices: 56023304--56023489 Score: 372
Period size: 95 Copynumber: 2.0 Consensus size: 95
56023294 TCATCGGCGG
56023304 CTGCCATGAAACAAGCTGACCGGGCGCAATGAAAATCATACGTTGGAACATCCGTGGTTTGGGGA
1 CTGCCATGAAACAAGCTGACCGGGCGCAATGAAAATCATACGTTGGAACATCCGTGGTTTGGGGA
56023369 ATCTACAGGCAGTTCACAGATTTCGGGGGC
66 ATCTACAGGCAGTTCACAGATTTCGGGGGC
56023399 CTGCCATGAAACAAGCTGACCGGGCGCAATGAAAATCATACGTTGGAACATCCGTGGTTTGGGGA
1 CTGCCATGAAACAAGCTGACCGGGCGCAATGAAAATCATACGTTGGAACATCCGTGGTTTGGGGA
56023464 ATCTACAGGCAGTTCACAGATTTCGG
66 ATCTACAGGCAGTTCACAGATTTCGG
56023490 CATTTGTTGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 91 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (95 bp):
CTGCCATGAAACAAGCTGACCGGGCGCAATGAAAATCATACGTTGGAACATCCGTGGTTTGGGGA
ATCTACAGGCAGTTCACAGATTTCGGGGGC
Found at i:56028710 original size:26 final size:26
Alignment explanation
Indices: 56028681--56028731 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
56028671 AGGTTTTTTA
* *
56028681 TTTTTAAAGTATTAAAATTTTAAAAC
1 TTTTGAAAGTATTAAAATTTGAAAAC
* *
56028707 TTTTGATAGTGTTAAAATTTGAAAA
1 TTTTGAAAGTATTAAAATTTGAAAA
56028732 AAGATTTAAT
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:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TTTTGAAAGTATTAAAATTTGAAAAC
Found at i:56039851 original size:28 final size:28
Alignment explanation
Indices: 56039795--56039855 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
56039785 TCTATGAATT
* * *
56039795 AAAAGTTGTAAAATTATTTCTACTAAAA
1 AAAAGTTGTAAAACTATCTCAACTAAAA
*
56039823 AAAAGTTGTAAAACTATCTGAACTTAAAA
1 AAAAGTTGTAAAACTATCTCAAC-TAAAA
56039852 AAAA
1 AAAA
56039856 AAAATGACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (28 bp):
AAAAGTTGTAAAACTATCTCAACTAAAA
Found at i:56042486 original size:12 final size:12
Alignment explanation
Indices: 56042469--56042498 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
56042459 TCAAAATGTT
56042469 ATATTTTTATAA
1 ATATTTTTATAA
56042481 ATA-TTTTATAA
1 ATATTTTTATAA
56042492 ATATTTT
1 ATATTTT
56042499 AATACTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTTTATAA
Found at i:56042489 original size:11 final size:11
Alignment explanation
Indices: 56042473--56042499 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
56042463 AATGTTATAT
56042473 TTTTATAAATA
1 TTTTATAAATA
56042484 TTTTATAAATA
1 TTTTATAAATA
56042495 TTTTA
1 TTTTA
56042500 ATACTTACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:56045174 original size:171 final size:171
Alignment explanation
Indices: 56044889--56045234 Score: 595
Period size: 171 Copynumber: 2.0 Consensus size: 171
56044879 GTTTGAAGTA
* * *
56044889 ATATGCGCTCTGTGCCTTATCGATATAAATCGACGTAAACCCCATACATTAATCTTATGACATGC
1 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
* ** *
56044954 CAATTATACGCGACTCTGTTTGAGACTGTTTAATAAAGTATTCAATGATTCTATTCATACATGTC
66 CAATTATACGCAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGTC
56045019 CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
131 CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
*
56045060 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGGCATGC
1 ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
56045125 CAATTATAC-CTAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGT
66 CAATTATACGC-AACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGT
*
56045189 CCACATATCATTCATATCACTTTTAATTACATTAACATTAGC
130 CCACATATCATTCATATCACTTTTAATCACATTAACATTAGC
56045231 ATAT
1 ATAT
56045235 CAATATCTTA
Statistics
Matches: 165, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
170 1 0.01
171 164 0.99
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (171 bp):
ATATGCGCTCTGTGCCTCATCGATATAAATCGAAGTAAACCCCATACATTAATCCTATGACATGC
CAATTATACGCAACTCTGTTCAAGACTGTTTAATAAAGAATTCAATGATTCTATTCATACATGTC
CACATATCATTCATATCACTTTTAATCACATTAACATTAGC
Found at i:56047824 original size:27 final size:28
Alignment explanation
Indices: 56047768--56047858 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 28
56047758 TTTAATTTAT
* *
56047768 TTAATAATAATACCAATTAAATAATTATAAC
1 TTAAT-ATAAAACCAA-T-AATAATAATAAC
* *
56047799 TTAATATGAAACCATAATAATAATAATAAT
1 TTAATATAAAACC--AATAATAATAATAAC
56047829 TTAATATAAAACCATACTAATAATTAATAA
1 TTAATATAAAACCA-A-TAATAA-TAATAA
56047859 TAATAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 34 0.68
31 12 0.24
32 2 0.04
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (28 bp):
TTAATATAAAACCAATAATAATAATAAC
Found at i:56047833 original size:30 final size:30
Alignment explanation
Indices: 56047787--56047859 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
56047777 ATACCAATTA
* * *
56047787 AATAATTATAACTTAATATGAAACCATAAT
1 AATAATAATAATTTAATATAAAACCATAAT
*
56047817 AATAATAATAATTTAATATAAAACCATACT
1 AATAATAATAATTTAATATAAAACCATAAT
56047847 AATAATTAATAAT
1 AATAA-TAATAAT
56047860 AATAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 31 0.82
31 7 0.18
ACGTcount: A:0.56, C:0.08, G:0.01, T:0.34
Consensus pattern (30 bp):
AATAATAATAATTTAATATAAAACCATAAT
Found at i:56047868 original size:30 final size:30
Alignment explanation
Indices: 56047787--56047869 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
56047777 ATACCAATTA
*
56047787 AATAATT-ATAACTTAATATGAAACCATAAT
1 AATAATTAATAA-TTAATATAAAACCATAAT
*
56047817 AATAA-TAATAATTTAATATAAAACCATACT
1 AATAATTAATAA-TTAATATAAAACCATAAT
56047847 AATAATTAATAA-TAATAATAAAA
1 AATAATTAATAATTAAT-ATAAAA
56047870 TCTTAGATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.11
30 36 0.77
31 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (30 bp):
AATAATTAATAATTAATATAAAACCATAAT
Found at i:56053449 original size:53 final size:53
Alignment explanation
Indices: 56053364--56053473 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
56053354 GGGAAAGCTT
* * *
56053364 ACACGAAGTGTGCCTTTACATATAATCGTAACCTTTCTTTTACATCAATGCTC
1 ACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAATGCTC
56053417 ACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAATGCTC
1 ACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAATGCTC
56053470 ACAC
1 ACAC
56053474 GAGCTATAGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (53 bp):
ACACAAAGTGTGCCTTTACATATAACCGTAACCTTTCCTTTACATCAATGCTC
Found at i:56055926 original size:109 final size:109
Alignment explanation
Indices: 56055790--56055991 Score: 352
Period size: 109 Copynumber: 1.9 Consensus size: 109
56055780 TAAATTCAAT
*
56055790 AGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
56055855 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
* *
56055899 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
56055963 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
56055992 GGAAACATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 87 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTAAA
Found at i:56065426 original size:13 final size:13
Alignment explanation
Indices: 56065408--56065435 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56065398 TATATATATA
56065408 CAAACTAATTTTG
1 CAAACTAATTTTG
56065421 CAAACTAATTTTG
1 CAAACTAATTTTG
56065434 CA
1 CA
56065436 GTTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (13 bp):
CAAACTAATTTTG
Found at i:56071983 original size:31 final size:30
Alignment explanation
Indices: 56071948--56072010 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
56071938 CAATTTAACA
56071948 AATAAATGCCTCTAAAATAATAATAAAAATT
1 AATAAATGCCTCTAAAATAATAA-AAAAATT
* *
56071979 AATAAATGCCTTTAAAATAATAACAAAATT
1 AATAAATGCCTCTAAAATAATAAAAAAATT
56072009 AA
1 AA
56072011 CAAGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AATAAATGCCTCTAAAATAATAAAAAAATT
Found at i:56072068 original size:22 final size:22
Alignment explanation
Indices: 56072043--56072085 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56072033 TATCCAAACA
56072043 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
56072065 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
56072086 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:56072098 original size:22 final size:22
Alignment explanation
Indices: 56072050--56072098 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
56072040 ACAATAACAA
* *
56072050 TAAAATAGTAGCAACATAATAG
1 TAAAATAGTAGCAAAATAAGAG
*
56072072 TAAAATGGTAGCAAAATAGAGAG
1 TAAAATAGTAGCAAAATA-AGAG
56072095 -AAAA
1 TAAAA
56072099 CAACAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.18
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAAGAG
Found at i:56074233 original size:16 final size:16
Alignment explanation
Indices: 56074212--56074246 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
56074202 AGATCGACTG
56074212 ATTGACGTGGGTTTGA
1 ATTGACGTGGGTTTGA
56074228 ATTGACGTGGGTTTGA
1 ATTGACGTGGGTTTGA
56074244 ATT
1 ATT
56074247 TTTTCGGTCA
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:0.20, C:0.06, G:0.34, T:0.40
Consensus pattern (16 bp):
ATTGACGTGGGTTTGA
Found at i:56074424 original size:19 final size:19
Alignment explanation
Indices: 56074402--56074439 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
56074392 TATTTATATA
*
56074402 TTTTAATAATTTTTGTGAT
1 TTTTAATAATTTTTATGAT
56074421 TTTTAATAATTTTTATGAT
1 TTTTAATAATTTTTATGAT
56074440 AAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTTAATAATTTTTATGAT
Found at i:56076817 original size:32 final size:32
Alignment explanation
Indices: 56076721--56076803 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
56076711 TATCCAAATG
* *
56076721 GTACAATTTGAAAATGTTATGTACACTTTGTAT
1 GTACAA-TTGAAAAGGTTATGTACACTTTGTGT
*
56076754 GTACACTTGAAAAGGTTATGTACACTTTGTGT
1 GTACAATTGAAAAGGTTATGTACACTTTGTGT
*
56076786 GTACAATTGGAAAGGTTA
1 GTACAATTGAAAAGGTTA
56076804 GATATGCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 40 0.89
33 5 0.11
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
GTACAATTGAAAAGGTTATGTACACTTTGTGT
Found at i:56077487 original size:12 final size:11
Alignment explanation
Indices: 56077468--56077498 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
56077458 TGTATAAAAC
56077468 TTATTTTATTA
1 TTATTTTATTA
56077479 TTAATTTTATTA
1 TT-ATTTTATTA
56077491 TTATTTTA
1 TTATTTTA
56077499 AAGGCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:56077513 original size:30 final size:30
Alignment explanation
Indices: 56077479--56077538 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
56077469 TATTTTATTA
56077479 TTAATTTTATTATTATTTTAAAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* *
56077509 TTAATTTTATTATTATTTTAGAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
56077539 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:56080716 original size:28 final size:28
Alignment explanation
Indices: 56080680--56080777 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
56080670 ACAAAGTGCA
*
56080680 AATAACGATAAGCACCAAAGTGCAAAAT
1 AATAACGATAAGCACTAAAGTGCAAAAT
*
56080708 AATAACGATAAGCACTAAAGTGCAAATTTT
1 AATAACGATAAGCACTAAAGTGCAAA--AT
* * * *
56080738 TACAATGATAAGCACTGAAGTGCAAAAT
1 AATAACGATAAGCACTAAAGTGCAAAAT
56080766 AAT-ACGATAAGC
1 AATAACGATAAGC
56080778 GCGCTAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.14
28 27 0.47
30 23 0.40
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.20
Consensus pattern (28 bp):
AATAACGATAAGCACTAAAGTGCAAAAT
Found at i:56084850 original size:16 final size:16
Alignment explanation
Indices: 56084812--56084850 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
56084802 AAAAAAATAT
*
56084812 AAATAAAATATTCAAA
1 AAATAAAACATTCAAA
56084828 AACATAAAACATTCAAA
1 AA-ATAAAACATTCAAA
56084845 AAATAA
1 AAATAA
56084851 TCAATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAAACATTCAAA
Found at i:56091830 original size:23 final size:22
Alignment explanation
Indices: 56091783--56091832 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
56091773 TTATCCATTC
*
56091783 ATAAATCTATACACTATATGCT
1 ATAAATCTATACACTATATACT
* *
56091805 ATAATATCTATACTCTATATATT
1 ATAA-ATCTATACACTATATACT
56091828 ATAAA
1 ATAAA
56091833 CAAATTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAATCTATACACTATATACT
Found at i:56094448 original size:9 final size:9
Alignment explanation
Indices: 56094434--56094647 Score: 89
Period size: 9 Copynumber: 22.8 Consensus size: 9
56094424 TATTTTTCTC
56094434 ATAAAAATT
1 ATAAAAATT
**
56094443 ATAAAAAAA
1 ATAAAAATT
*
56094452 ACAAAAAGTT
1 ATAAAAA-TT
56094462 ATAAAAATT
1 ATAAAAATT
* *
56094471 CAGGAAACATT
1 -A-TAAAAATT
56094482 ATTAAAAA-T
1 A-TAAAAATT
*
56094491 ATTAAAATT
1 ATAAAAATT
*
56094500 GATATAAACTT
1 -ATA-AAAATT
* *
56094511 ATTAAAACT
1 ATAAAAATT
*
56094520 ATAAACA-T
1 ATAAAAATT
56094528 ATAAAAACTT
1 ATAAAAA-TT
*
56094538 ATAAATATT
1 ATAAAAATT
56094547 ATAAAAA-T
1 ATAAAAATT
56094555 AT-AAAATT
1 ATAAAAATT
*
56094563 AATAAAATTT
1 -ATAAAAATT
*
56094573 ATTTAAAA-T
1 A-TAAAAATT
56094582 A-AAAAATTT
1 ATAAAAA-TT
* *
56094591 ATTAGAATTCT
1 A-TAAAAAT-T
* *
56094602 TTAAAAATA
1 ATAAAAATT
56094611 ATAAAAATT
1 ATAAAAATT
*
56094620 GTAAAAAATT
1 AT-AAAAATT
56094630 ATAAAAATAT
1 ATAAAAAT-T
56094640 ATTAAAAA
1 A-TAAAAA
56094648 CTTGAACTAG
Statistics
Matches: 149, Mismatches: 36, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
7 8 0.05
8 16 0.11
9 56 0.38
10 48 0.32
11 21 0.14
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:56094524 original size:17 final size:17
Alignment explanation
Indices: 56094502--56094569 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
56094492 TTAAAATTGA
*
56094502 TATAAACTTATTAAAAC
1 TATAAAATTATTAAAAC
*
56094519 TATAAACA-TATAAAAAC
1 TATAAA-ATTATTAAAAC
*
56094536 TTATAAATATTA-TAAAAA
1 -TATAAA-ATTATTAAAAC
*
56094554 TATAAAATTAATAAAA
1 TATAAAATTATTAAAA
56094570 TTTATTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 4 0.10
17 25 0.60
18 11 0.26
19 2 0.05
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAAAATTATTAAAAC
Found at i:56095031 original size:19 final size:19
Alignment explanation
Indices: 56094999--56095046 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
56094989 TTTTGATTAC
56094999 TTTTTAT-ATATTTTAATAA
1 TTTTTATGAT-TTTTAATAA
*
56095018 TTTTTGTGATTTTTAATAA
1 TTTTTATGATTTTTAATAA
56095037 TTTTTATGAT
1 TTTTTATGAT
56095047 AAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTATGATTTTTAATAA
Found at i:56095605 original size:26 final size:26
Alignment explanation
Indices: 56095576--56095628 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
56095566 TGCGGACGTA
56095576 GCAAAACTGCTGTATTTGTAAACTTC
1 GCAAAACTGCTGTATTTGTAAACTTC
56095602 GCAAAACTGCTGTATTTGTAAACTTC
1 GCAAAACTGCTGTATTTGTAAACTTC
56095628 G
1 G
56095629 TTTTGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (26 bp):
GCAAAACTGCTGTATTTGTAAACTTC
Found at i:56099919 original size:11 final size:10
Alignment explanation
Indices: 56099903--56099958 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
56099893 AAAAAAATAT
56099903 TATTTTTATA
1 TATTTTTATA
56099913 TATTTTTA-A
1 TATTTTTATA
*
56099922 TA--TTTATT
1 TATTTTTATA
56099930 TATTTTTA-A
1 TATTTTTATA
56099939 TA-TTTTATTA
1 TATTTTTA-TA
56099949 TATTTTTATA
1 TATTTTTATA
56099959 AAACACTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 4 0.11
8 7 0.18
9 5 0.13
10 17 0.45
11 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTTTATA
Found at i:56099933 original size:17 final size:18
Alignment explanation
Indices: 56099906--56099956 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
56099896 AAAATATTAT
*
56099906 TTTTATATATTTTTAATA
1 TTTTATTTATTTTTAATA
56099924 -TTTATTTATTTTTAATA
1 TTTTATTTATTTTTAATA
56099941 TTTTATTATATTTTTA
1 TTTTATT-TATTTTTA
56099957 TAAAACACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 16 0.53
18 6 0.20
19 8 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTATTTTTAATA
Found at i:56099933 original size:27 final size:27
Alignment explanation
Indices: 56099902--56099953 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
56099892 AAAAAAAATA
56099902 TTATTTTTATATATTTT-TAATATTTAT
1 TTATTTTTA-ATATTTTATAATATTTAT
*
56099929 TTATTTTTAATATTTTATTATATTT
1 TTATTTTTAATATTTTATAATATTT
56099954 TTATAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTATTTTTAATATTTTATAATATTTAT
Found at i:56102685 original size:21 final size:19
Alignment explanation
Indices: 56102651--56102712 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
56102641 TAAGCTATAT
56102651 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
56102673 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
56102695 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
56102713 GTATTTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:56102765 original size:22 final size:22
Alignment explanation
Indices: 56102737--56102779 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56102727 AAAATATGGT
*
56102737 AAAATAAATAGTATAAAAAAAC
1 AAAATAAATAATATAAAAAAAC
*
56102759 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATAAAAAAA
56102780 TATAAGAAAG
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:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATAAAAAAAC
Found at i:56107112 original size:10 final size:10
Alignment explanation
Indices: 56107080--56107131 Score: 56
Period size: 11 Copynumber: 5.3 Consensus size: 10
56107070 TTATTATGAT
56107080 TTTTTAATAA
1 TTTTTAATAA
56107090 TTATTTAATAA
1 TT-TTTAATAA
*
56107101 TTTTTGATAA
1 TTTTTAATAA
56107111 -TTTT-AT-A
1 TTTTTAATAA
56107118 TTTTTAAATAA
1 TTTTT-AATAA
56107129 TTT
1 TTT
56107132 GTTGCAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 1 0.03
8 6 0.17
9 4 0.11
10 11 0.31
11 14 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:56108800 original size:14 final size:14
Alignment explanation
Indices: 56108775--56108810 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
56108765 TCTTTTTATG
*
56108775 TTTTAAATTTTTTA
1 TTTTAAATATTTTA
56108789 -TTTAAATATTTTA
1 TTTTAAATATTTTA
56108802 TTTTAAATA
1 TTTTAAATA
56108811 AAATATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATATTTTA
Found at i:56119393 original size:20 final size:20
Alignment explanation
Indices: 56119368--56119409 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
56119358 ATTTGTAGAG
*
56119368 TATTGATGAATATTTTATAT
1 TATTGATGAATATTTCATAT
*
56119388 TATTGATGGATATTTCATAT
1 TATTGATGAATATTTCATAT
56119408 TA
1 TA
56119410 AAAATTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (20 bp):
TATTGATGAATATTTCATAT
Found at i:56120159 original size:22 final size:22
Alignment explanation
Indices: 56120134--56120177 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56120124 TAGTCTTATA
56120134 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
56120156 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
56120178 TATTTCATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:56120290 original size:15 final size:15
Alignment explanation
Indices: 56120270--56120326 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
56120260 ATTCAATATT
56120270 AATATTTTAATAATA
1 AATATTTTAATAATA
*
56120285 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
56120304 AATATATTAATAATA
1 AATATTTTAATAATA
*
56120319 AATGTTTT
1 AATATTTT
56120327 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:56125377 original size:37 final size:37
Alignment explanation
Indices: 56125323--56125400 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
56125313 TATTTCAAGA
56125323 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
1 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
*
56125360 CAAGATTAATTATTAAAATAGTTATTTTTGTTTGTCT
1 CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
56125397 CAAG
1 CAAG
56125401 TTATATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (37 bp):
CAAGATTAATTACTAAAATAGTTATTTTTGTTTGTCT
Found at i:56127789 original size:2 final size:2
Alignment explanation
Indices: 56127784--56127823 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
56127774 CAAGTTTTAC
* *
56127784 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56127824 TACTTAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56128441 original size:25 final size:23
Alignment explanation
Indices: 56128385--56128449 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
56128375 TCTTATTTTT
*
56128385 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
56128404 TATTTGTTTTTATATTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
56128427 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
56128450 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 5 0.13
21 2 0.05
23 6 0.15
24 3 0.08
25 12 0.31
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:56132118 original size:40 final size:39
Alignment explanation
Indices: 56131997--56132130 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 39
56131987 GACTTCAAGT
* * *
56131997 CGATGAGACATTGGATGTCAAATTATTACTTC-AGATTAATT
1 CGATGAGACACTGGGTGTC-AATTATTACTTCGA-ATT-ATC
* * * ** *
56132038 TGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
*
56132075 CGATGAGACACTGGGTGTCAACTTATTGCTTCGAATTATC
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGAATTATC
**
56132115 CGATGAGGTACTGGGT
1 CGATGAGACACTGGGT
56132131 ACCAAGCTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
37 19 0.27
38 9 0.13
39 2 0.03
40 27 0.38
41 14 0.20
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGAATTATC
Found at i:56134989 original size:15 final size:16
Alignment explanation
Indices: 56134969--56135005 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
56134959 CCATGTAAAC
*
56134969 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
56134984 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
56135000 ACAAAA
1 ACAAAA
56135006 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:56134990 original size:11 final size:11
Alignment explanation
Indices: 56134965--56135006 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
56134955 GGGCCCATGT
56134965 AAACACAAAAC-
1 AAACA-AAAACA
56134976 AAACAAAAACA
1 AAACAAAAACA
56134987 AAACAAAAA-A
1 AAACAAAAACA
56134997 AATACAAAAA
1 AA-ACAAAAA
56135007 ATATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:56137229 original size:131 final size:131
Alignment explanation
Indices: 56137044--56137403 Score: 431
Period size: 131 Copynumber: 2.7 Consensus size: 131
56137034 ATAAGCATTC
* * * * *
56137044 ATTC-AAAAATTCTTCAAAAACGAAGACGAGATTCGTTGTTTGGCAATTCGCGGAATCGTGCCCT
1 ATTCTAAAAATTCTTC-AAAACGAAGGCGAGATTCGATATTT-GAAATTCGCGGAATCATGCCCT
56137108 AACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCA
64 AACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCA
**
56137173 TGT
129 CAT
* * *
56137176 CTT-TTAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTAGTAATTCGCGGAATCATGCCCTA
1 ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTT-GAAATTCGCGGAATCATGCCCTA
* * * *
56137240 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCAC
65 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCAC
56137305 AT
130 AT
* * * * * *
56137307 ATTCTAAAAATTATTTAAAACGAAGGCAATATTC-ACATTTGAAAATTCG-AGAATCATGCCCTA
1 ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTG-AAATTCGCGGAATCATGCCCTA
* * ** *
56137370 TCGTGCTGGGTTGTGATTTCTCGTTTGCTCAAAA
65 ACGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAA
56137404 CGATCGAACA
Statistics
Matches: 197, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
130 43 0.22
131 117 0.59
132 37 0.19
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (131 bp):
ATTCTAAAAATTCTTCAAAACGAAGGCGAGATTCGATATTTGAAATTCGCGGAATCATGCCCTAA
CGTGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACA
T
Found at i:56141825 original size:13 final size:14
Alignment explanation
Indices: 56141803--56141834 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
56141793 GAGATCTTCA
56141803 AAAAATAATAAAAT
1 AAAAATAATAAAAT
56141817 AAAAA-AATAAAAT
1 AAAAATAATAAAAT
56141830 AAAAA
1 AAAAA
56141835 GAAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:56143300 original size:132 final size:132
Alignment explanation
Indices: 56143063--56143683 Score: 1161
Period size: 132 Copynumber: 4.7 Consensus size: 132
56143053 TGGGCCTATG
* * * * * * **
56143063 AGGCTAAAATTTTAGATCTTGTTTCCTTGAAATTGAAATGAAGCAGATCGAAGACGGTGAATCTG
1 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
56143128 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
56143193 GT
131 GT
56143195 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
56143260 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
56143325 GT
131 GT
56143327 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
56143392 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
56143457 GT
131 GT
56143459 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
56143524 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
66 AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
56143589 GT
131 GT
56143591 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
1 AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
*
56143656 AGCTTCCTGAAGTTGCAGTGAAACAGAT
66 AGCTTCCTGAAGTTGCAGTGAAGCAGAT
56143684 CGAAGACGGC
Statistics
Matches: 480, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 480 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (132 bp):
AGGCTAAAATTTCAGATCTCGTTTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTG
AGCTTCCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGA
GT
Found at i:56143701 original size:177 final size:177
Alignment explanation
Indices: 56143481--56143860 Score: 586
Period size: 177 Copynumber: 2.1 Consensus size: 177
56143471 CAGATCTCGT
*
56143481 TTCCTTGAAGTTGCAGT-AAAGCAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAGTGA
1 TTCC-TGAAGTTGCAGTGAAA-CAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGA
*
56143545 AGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATCT
64 AGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATAT
56143610 CG-TTTCCTTGAAGTTGCAGT-AAAGCAGATCGAAGACGGCAAATCTGAGC
129 CGTTTTCC-TGAAGTTGCAGTGAAA-CAGATCGAAGACGGCAAATCTGAGC
*
56143659 TTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTGAGCTTCATGAAGTTGCAGTGAAG
1 TTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGAAG
* ** * * * *
56143724 GAGATTTAAGCCACCATTCTAGTTTCCTAAGGTTGTAGTGGAGTAGGCTAAAATTTCAGATATTG
66 CAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATATCG
* *
56143789 TTTTCCTGAAGTTGCAGTGAAATAGATCGAAGACGGCGAATCTGAGC
131 TTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGC
*
56143836 TTCCTGAAGTTGCAGTGAAGCAGAT
1 TTCCTGAAGTTGCAGTGAAACAGAT
56143861 TTAAGCCACC
Statistics
Matches: 186, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
177 171 0.92
178 15 0.08
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (177 bp):
TTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGAAG
CAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATATCG
TTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGC
Found at i:56143781 original size:309 final size:310
Alignment explanation
Indices: 56143349--56143975 Score: 926
Period size: 309 Copynumber: 2.0 Consensus size: 310
56143339 CAGATCTCGT
*
56143349 TTCCTTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAGTGAA
1 TTCC-TGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGAA
*
56143414 GCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATCTC
65 GCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATATC
56143479 G-TTTCCTTGAAGTTGCAGT-AAAGCAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAG
130 GTTTTCC-TGAAGTTGCAGTGAAA-CAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAG
56143542 TGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCT-AAAATT-TCA
193 TGAAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAAATTAT-A
*
56143605 GATCTCGTTTCCTTGA-AGTTGCAGTAAAGCAGATCGAAGACGGCAAATCT-GAGC
257 GATCTCGTTTCCCTGAGA-TTGCAGTAAAGCAGATCGAAGACGGCAAATCTAG-GC
*
56143659 TTCCTGAAGTTGCAGTGAAA-CAGATCGAAGACGGCGAATCTGAGCTTCATGAAGTTGCAGTGAA
1 TTCCTGAAGTTGCAGT-AAAGCAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGAA
* ** * * * *
56143723 GGAGATTTAAGCCACCATTCTAGTTTCCTAAGGTTGTAGTGGAGTAGGCTAAAATTTCAGATATT
65 GCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATATC
* *
56143788 GTTTTCCTGAAGTTGCAGTGAAATAGATCGAAGACGGCGAATCTGAGCTTCCTGAAGTTGCAGTG
130 GTTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAGTG
* * * *
56143853 AAGCAGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGAT
195 AAGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAAATTATAGAT
* * *** **
56143918 CTTGTTTCCCTGAGATTGTAGTGGGGCAGATCGAAGACGGTGAATCTAGGC
260 CTCGTTTCCCTGAGATTGCAGTAAAGCAGATCGAAGACGGCAAATCTAGGC
56143969 TTCCTGA
1 TTCCTGA
56143976 TGATGCAGCG
Statistics
Matches: 286, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
309 213 0.74
310 70 0.24
311 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (310 bp):
TTCCTGAAGTTGCAGTAAAGCAGATCGAAGACGGCAAATCTGAGCTTCATGAAGTTGCAGTGAAG
CAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTAAAATTTCAGATATCG
TTTTCCTGAAGTTGCAGTGAAACAGATCGAAGACGGCAAATCTGAGCTTCCTGAAGTTGCAGTGA
AGCAGATTTAAGCCACCAACCTAGCTCCCTAAAGTTGTAGTGGAGTAGGCTGAAAATTATAGATC
TCGTTTCCCTGAGATTGCAGTAAAGCAGATCGAAGACGGCAAATCTAGGC
Found at i:56144059 original size:129 final size:129
Alignment explanation
Indices: 56143661--56144569 Score: 1092
Period size: 129 Copynumber: 7.0 Consensus size: 129
56143651 ATCTGAGCTT
* * * * *
56143661 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCT-GAGCTTCATGAAGTTGCAGTGAAGG
1 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAG-GCTTCCTGATGATGCAGCGAAGC
* * * * *
56143725 AGATTTAAGCCACCATTCTAGTTTCCTAAGGTTGTAGTGGAGTAGGCT-AAAATT-TCAGATATT
65 AGATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTAT-AGATCTT
*
56143788 GTTTT
125 GTTTC
* * * *
56143793 CCTGAAGTTGCAGTGAAATAGATCGAAGACGGCGAATCT-GAGCTTCCTGAAGTTGCAGTGAAGC
1 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAG-GCTTCCTGATGATGCAGCGAAGC
*
56143857 AGATTTAAGCCACCATCCTAGCTTCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTG
65 AGATTTAAG----CATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTG
56143922 TTTC
126 TTTC
* *** *
56143926 CCTG-AGATTGTAGTGGGGCAGATCGAAGACGGTGAATCTAGGCTTCCTGATGATGCAGCGAAGC
1 CCTGAAG-TTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGC
* * *
56143990 AAATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAAGATTATAGATCTTGTTTT
65 AGATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTGTTTC
*
56144055 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATTCAGCGAAGCA
1 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGCA
* *
56144120 GATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAAGATTATAGATCTTGTTTT
66 GATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTGTTTC
*
56144184 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATTCAGCGAAGCA
1 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGCA
*
56144249 GATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAAGCTGAAGATTATAGATCTTGTTTC
66 GATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTGTTTC
*** * * **
56144313 CCTG-AGATTGCAGTGGGGCAGATCGAAGACGGTGAATCTAGGCTTCCTGATGTTGCAGTAAAGC
1 CCTGAAG-TTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGC
* ** * * * * *
56144377 AAATTTAAGCAAGTCCTAGCTTTCTAAAGTTGTAGTGGAGTAGGCTGAGGATTGTAGATCTCGTC
65 AGATTTAAGC-A-TCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTGTT
56144442 TC
128 TC
** * * *** * *
56144444 CCTGAAGTTGCAGTGAGGCAAATCAAAGACGATAAATCTTGGCTTCCTGAAGATGCAGCGAAGCA
1 CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGCA
* * * * * *
56144509 GATTTAAGCAAGTCCTAGCTCCTTAAAGTTGTAGTGAAGTGGGCTGAAGATTGTAGGTCTT
66 GATTTAAGC-A-TCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTT
56144570 ATCTTCTCGA
Statistics
Matches: 703, Mismatches: 65, Indels: 19
0.89 0.08 0.02
Matches are distributed among these distances:
128 2 0.00
129 362 0.51
130 3 0.00
131 150 0.21
132 111 0.16
133 73 0.10
134 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (129 bp):
CCTGAAGTTGCAGTGAAACAGATCGAAGACGGCGAATCTAGGCTTCCTGATGATGCAGCGAAGCA
GATTTAAGCATCCTAGCTCCCTAAGGTTGTAGTGGAGTAGGCTGAAGATTATAGATCTTGTTTC
Found at i:56144867 original size:44 final size:44
Alignment explanation
Indices: 56144749--56145724 Score: 1319
Period size: 44 Copynumber: 22.1 Consensus size: 44
56144739 CAAGACCAGA
* *
56144749 CAGATTTGGCGTCTTTGTATTGGCAGAGAGCAGATCGAAGCTAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
56144793 CAGATTTGGGCGTCTCTGTATTGCCAGAGAGCAGATCAAAGATAG
1 CAGATTT-GGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
56144838 CAGATTTGGCGTCTCTGTATTGGCGGAGAGTCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAG-CAGATCGAAGATAG
* * *
56144883 CAGATTTGACTTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
56144927 CAGATTTGGCGTCTCTGTATTGGCAAAAAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
56144971 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCATATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
56145015 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
56145059 CAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
56145103 TAGATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
56145147 TAGATTTGGCGTCTCTGTATTAGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
**
56145191 CAGATTTGGCGTCTCTGTATTGGTGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
56145235 TAGATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* ** * *
56145279 TAGATTTGGTATCTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
56145323 CAGATTTGGCGTCTCTGTATCGTCGGAGGGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
56145367 CAGATTTGGTGTCTCTGTATTGTCAGAGGGCAGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
56145410 TTAAATTTGGTGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *** *
56145455 CAGATTTGGCGTCTCTGTATCGTTGGAGGGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
56145499 TAAATTTGGCGTCTTTGTATTGGCGGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * *
56145543 TAGATTTGGCGTCTCTGTATTGTCAGAGAGCGGATCGAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
56145586 ACAGATTTGGCGTCTCTGTATTGGCAGAGGGCAGATCGAAGATGG
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * **
56145631 CAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATTAAAGAT-G
1 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
56145674 ACAGATTTGGCATCTCTGTATTGGCAGAGAACAGCTCGAAAATAA
1 -CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
56145719 CAGATT
1 CAGATT
56145725 GGTGTTCCTG
Statistics
Matches: 832, Mismatches: 92, Indels: 16
0.89 0.10 0.02
Matches are distributed among these distances:
43 2 0.00
44 747 0.90
45 83 0.10
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
Found at i:56145963 original size:15 final size:16
Alignment explanation
Indices: 56145943--56145979 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
56145933 CCGTGTAAAC
*
56145943 ACAAAACAAACAAAA-
1 ACAAAACAAAAAAAAT
56145958 ACAAAACAAAAAAAAT
1 ACAAAACAAAAAAAAT
56145974 ACAAAA
1 ACAAAA
56145980 AATATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.03
Consensus pattern (16 bp):
ACAAAACAAAAAAAAT
Found at i:56145964 original size:11 final size:11
Alignment explanation
Indices: 56145939--56145980 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
56145929 GGGCCCGTGT
56145939 AAACACAAAAC-
1 AAACA-AAAACA
56145950 AAACAAAAACA
1 AAACAAAAACA
56145961 AAACAAAAA-A
1 AAACAAAAACA
56145971 AATACAAAAA
1 AA-ACAAAAA
56145981 ATATATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACAAAAACA
Found at i:56148270 original size:131 final size:132
Alignment explanation
Indices: 56148020--56148303 Score: 428
Period size: 131 Copynumber: 2.2 Consensus size: 132
56148010 GCATTCATTC
* *
56148020 AAAAATTCTTCAAAAACGAAGACGAGATTCATTGTTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTCTTC-AAAACGAAGACGAGATTCATTATTTAGCAATTCGCGGAATCGTGCCCTAACGT
**
56148085 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCATGTCT
65 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
56148150 T-T
130 TCT
* *
56148152 TAAAATTCTTCAAAACGAAGACGAGATTCGA-TATTTAGTAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTCTTCAAAACGAAGACGAGATTC-ATTATTTAGCAATTCGCGGAATCGTGCCCTAACGT
* * * *
56148216 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCACATCT
65 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
56148281 TCT
130 TCT
* *
56148284 AAAAATTATTTAAAACGAAG
1 AAAAATTCTTCAAAACGAAG
56148304 GAAATATTCG
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
131 108 0.79
132 29 0.21
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (132 bp):
AAAAATTCTTCAAAACGAAGACGAGATTCATTATTTAGCAATTCGCGGAATCGTGCCCTAACGTG
TTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCTT
CT
Found at i:56148334 original size:131 final size:131
Alignment explanation
Indices: 56148020--56148347 Score: 394
Period size: 131 Copynumber: 2.5 Consensus size: 131
56148010 GCATTCATTC
* * ** *
56148020 AAAAATTCTTCAAAAACGAAGACGAGATTC-ATTGTTTGGCAATTCGCGGAATCGTGCCCTAACG
1 AAAAATTATTC-AAAACGAAGACAAGATTCGA-CATTTGACAATTCGCGGAATCGTGCCCTAACG
**
56148084 TGTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCATGTC
64 TGTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATC
56148149 TTT
129 TTT
* * * * *
56148152 TAAAATTCTTCAAAACGAAGACGAGATTCGATATTT-AGTAATTCGCGGAATCGTGCCCTAACGT
1 AAAAATTATTCAAAACGAAGACAAGATTCGACATTTGA-CAATTCGCGGAATCGTGCCCTAACGT
* * * *
56148216 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAATCGAGTATCCCTTCAAGATTTCATTCACATCT
65 GTTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCT
56148281 TCT
130 T-T
* * * * *
56148284 AAAAATTATTTAAAACGAAGGA-AATATTCGACATTTGACAATTCG-AGAATCATGCCCTATCGT
1 AAAAATTATTCAAAACGAA-GACAAGATTCGACATTTGACAATTCGCGGAATCGTGCCCTAACGT
56148347 G
65 G
56148348 CTGTGTTGTG
Statistics
Matches: 171, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
131 123 0.72
132 45 0.26
133 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (131 bp):
AAAAATTATTCAAAACGAAGACAAGATTCGACATTTGACAATTCGCGGAATCGTGCCCTAACGTG
TTGGGTTACAATTTCGCGTTTGCTCAAAATAACCGAATATCACTTCAAAATTTCATTCACATCTT
T
Found at i:56149271 original size:20 final size:20
Alignment explanation
Indices: 56149248--56149289 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
56149238 TTCTTTCTTG
*
56149248 TTTT-GTATTTTTATCATTTA
1 TTTTAGTATATTTAT-ATTTA
*
56149268 TTTTATTATATTTATATTTA
1 TTTTAGTATATTTATATTTA
56149288 TT
1 TT
56149290 CTTTAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTAGTATATTTATATTTA
Found at i:56149287 original size:15 final size:16
Alignment explanation
Indices: 56149253--56149289 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
56149243 TCTTGTTTTG
56149253 TATTT-TTATCATTTA
1 TATTTATTATCATTTA
56149268 T-TTTATTAT-ATTTA
1 TATTTATTATCATTTA
56149282 TATTTATT
1 TATTTATT
56149290 CTTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTATCATTTA
Found at i:56149731 original size:3 final size:3
Alignment explanation
Indices: 56149723--56149747 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56149713 GCATATGTGA
56149723 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
56149748 TTGATAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:56152584 original size:19 final size:19
Alignment explanation
Indices: 56152548--56152598 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
56152538 TGGCACACAT
*
56152548 AGCGCATACTAGCA-CACGA
1 AGCGCATACT-GGAGCACGA
*
56152567 AGTGCATACTGGAGCACGA
1 AGCGCATACTGGAGCACGA
*
56152586 AGCGCATCCTGGA
1 AGCGCATACTGGA
56152599 ACCTGAGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.14
Consensus pattern (19 bp):
AGCGCATACTGGAGCACGA
Found at i:56155355 original size:9 final size:9
Alignment explanation
Indices: 56155341--56155429 Score: 54
Period size: 10 Copynumber: 9.2 Consensus size: 9
56155331 CGTTTGTATA
56155341 TATAATTTT
1 TATAATTTT
56155350 TATAATTTT
1 TATAATTTT
* *
56155359 TAAAAATTT
1 TATAATTTT
*
56155368 TAAAAGTTATT
1 TATAA-TT-TT
56155379 TA-AATTTTCT
1 TATAA-TTT-T
*
56155389 TATAATTCAT
1 TATAATT-TT
*
56155399 AATAATTTT
1 TATAATTTT
*
56155408 TAAATATTTT
1 TATA-ATTTT
56155418 TATAATTATT
1 TATAATT-TT
56155428 TA
1 TA
56155430 AGAATCCACT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 28 0.44
10 29 0.46
11 6 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (9 bp):
TATAATTTT
Found at i:56156393 original size:31 final size:30
Alignment explanation
Indices: 56156335--56156409 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
56156325 AAGTATAAAC
56156335 TCATAATATAAA-ATAAATCATCACCAAAAG
1 TCATAATATAAATATAAA-CATCACCAAAAG
56156365 TCATAATATAAATATTAAA-AGTCACCAAAAG
1 TCATAATATAAATA-TAAACA-TCACCAAAAG
*
56156396 TCATAATGTAAATA
1 TCATAATATAAATA
56156410 AAGTAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 13 0.32
31 24 0.59
32 4 0.10
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
TCATAATATAAATATAAACATCACCAAAAG
Found at i:56164547 original size:17 final size:18
Alignment explanation
Indices: 56164525--56164559 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
56164515 ACAATCACAC
56164525 TCATAT-ATATATATAAG
1 TCATATCATATATATAAG
56164542 TCATATCCATATATATAA
1 TCATAT-CATATATATAA
56164560 ATTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (18 bp):
TCATATCATATATATAAG
Found at i:56176019 original size:12 final size:12
Alignment explanation
Indices: 56176002--56176031 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
56175992 TTTGATTAGA
56176002 TTATTTCATGAG
1 TTATTTCATGAG
56176014 TTATTTCATGAG
1 TTATTTCATGAG
56176026 TTATTT
1 TTATTT
56176032 TTTTGATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTATTTCATGAG
Found at i:56176148 original size:45 final size:46
Alignment explanation
Indices: 56176096--56176188 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
56176086 TAACTTATAT
56176096 ATCAAAATTGTTAAGTGA-TTGTTTTTGTGCTCTATTAATGAATAA
1 ATCAAAATTGTTAAGTGATTTGTTTTTGTGCTCTATTAATGAATAA
*
56176141 ATCAAAATTGTTAAGTGATTTTTTTTTTGTGCTCTATTAATGAATAA
1 ATCAAAATTGTTAAGTGA-TTTGTTTTTGTGCTCTATTAATGAATAA
56176188 A
1 A
56176189 ACAATTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 18 0.40
47 27 0.60
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (46 bp):
ATCAAAATTGTTAAGTGATTTGTTTTTGTGCTCTATTAATGAATAA
Found at i:56177275 original size:30 final size:30
Alignment explanation
Indices: 56177241--56177301 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
56177231 TATTAGTATG
*
56177241 TCAATTTTAGGATTTTTTTATAATCCATAT
1 TCAATTTTAGGATTTTTATATAATCCATAT
56177271 TCAATTTTAGGATTTTTATATAATCCATAT
1 TCAATTTTAGGATTTTTATATAATCCATAT
56177301 T
1 T
56177302 AAGGAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (30 bp):
TCAATTTTAGGATTTTTATATAATCCATAT
Found at i:56180505 original size:161 final size:161
Alignment explanation
Indices: 56180233--56180541 Score: 476
Period size: 161 Copynumber: 1.9 Consensus size: 161
56180223 CCCAAGACGG
* * *
56180233 ATTGAAAAAAATTGCCACTTACAAAGCTGTTGAGTTCGTTGAGATGAGTTCGGGCACAGGTCCAA
1 ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
*
56180298 TAGCCAAACATGTCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
66 TAGCCAAACATATCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
56180363 CAAAACCCTTTTGATAATGCTCCGACAAGGA
131 CAAAACCCTTTTGATAATGCTCCGACAAGGA
* * ** **
56180394 ATTGAAAAAAATTTCCACTTACAAAGCTATTGAGTTAGTTGAGTTGAGTCCGGGCAGGGGTTTAA
1 ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
* * * *
56180459 TCGCCAAACATATCGT-GGATCGAATCGGGGAGTTGCTCCGACAAGGCATTGTTCATCTACCACA
66 TAGCCAAACATATCATAGG-TCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACA
56180523 CCAAAACCCTTTTGATAAT
130 CCAAAACCCTTTTGATAAT
56180542 ACTCTAAAAT
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
160 2 0.02
161 131 0.98
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (161 bp):
ATTGAAAAAAATTGCCACTTACAAAGCTATTGAGTTAGTTGAGATGAGTCCGGGCACAGGTCCAA
TAGCCAAACATATCATAGGTCGAATCGGGGAGTTACTCCAACAAGGCATTGTTCATCTACCACAC
CAAAACCCTTTTGATAATGCTCCGACAAGGA
Found at i:56183701 original size:13 final size:15
Alignment explanation
Indices: 56183667--56183701 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
56183657 CATAAATGTA
56183667 TTTTTTTCACTTATT
1 TTTTTTTCACTTATT
56183682 TTTTTTTCACTT-TT
1 TTTTTTTCACTTATT
56183696 TTTTTT
1 TTTTTT
56183702 GAGAACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTCACTTATT
Found at i:56184843 original size:22 final size:22
Alignment explanation
Indices: 56184818--56184922 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 22
56184808 AGAAATAGCA
56184818 AAATAAAAATAATAATTATAAT
1 AAATAAAAATAATAATTATAAT
* *
56184840 AAATTAAAAAT-ATAAGTATAAG
1 AAA-TAAAAATAATAATTATAAT
*
56184862 AAA-AATAAATTAATTAATTAATTATT
1 AAATAA-AAA-TAA-TAATT-A-TAAT
*
56184888 AAAATAAAAATAAATAA-TATAAC
1 -AAATAAAAAT-AATAATTATAAT
*
56184911 AATTAAAAATAA
1 AAATAAAAATAA
56184923 AACAAAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 25 0.38
23 10 0.15
24 5 0.08
25 2 0.03
26 6 0.09
27 8 0.12
28 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAAAAATAATAATTATAAT
Found at i:56188119 original size:17 final size:18
Alignment explanation
Indices: 56188086--56188122 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
56188076 GTTAGTAAAT
56188086 TAAAAGTAAAACAAAAAA
1 TAAAAGTAAAACAAAAAA
56188104 TAAAA-TAAAA-ATAAAAA
1 TAAAAGTAAAACA-AAAAA
56188121 TA
1 TA
56188123 GCTAAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 12 0.67
18 5 0.28
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (18 bp):
TAAAAGTAAAACAAAAAA
Found at i:56188205 original size:115 final size:114
Alignment explanation
Indices: 56188032--56188261 Score: 390
Period size: 115 Copynumber: 2.0 Consensus size: 114
56188022 GGGTTTCTTC
* *
56188032 TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAATGTTAGTAAATTAAAAGTAAAA
1 TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAAA
*
56188097 CAAAAAATAAAATAAAAATAAAAATAGCTAAAGTAATAAAAATCTAGTGT
66 -AAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
56188147 TAGTCATAAACTAAAGGA-ACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAA
1 TAGTCATAAACTAAA-GACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAA
**
56188211 AATGAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
65 AAAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
56188261 T
1 T
56188262 CCTAATATTT
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
114 47 0.43
115 60 0.55
116 2 0.02
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (114 bp):
TAGTCATAAACTAAAGACACCTGCCAGAAGCAAATAAAAGAAACGTAAGTAAATTAAAAGTAAAA
AAAAAATAAAATAAAAATAAAAATAGATAAAGTAATAAAAATCTAGTGT
Found at i:56188236 original size:17 final size:17
Alignment explanation
Indices: 56188196--56188233 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
56188186 GAAACGTAAG
*
56188196 TAAATTAAAAGTAAAAA
1 TAAAATAAAAGTAAAAA
*
56188213 TGAAATAAAA-TAAAAA
1 TAAAATAAAAGTAAAAA
56188229 TAAAA
1 TAAAA
56188234 ATAGATAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAGTAAAAA
Found at i:56189348 original size:30 final size:30
Alignment explanation
Indices: 56189314--56189371 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
56189304 CACAGACTGG
*
56189314 CACATGGGCGTGTGGCCAGCCAGTGTGGCT
1 CACATGGGCGTATGGCCAGCCAGTGTGGCT
*
56189344 CACATGGGCGTATGGCCAGCCCGTGTGG
1 CACATGGGCGTATGGCCAGCCAGTGTGG
56189372 AAATGTCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.19
Consensus pattern (30 bp):
CACATGGGCGTATGGCCAGCCAGTGTGGCT
Found at i:56200151 original size:20 final size:20
Alignment explanation
Indices: 56200126--56200175 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
56200116 TGGCTTAAAA
56200126 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
56200146 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
56200163 GTGGTAGTGGATT
1 TTGGTAGTGGATT
56200176 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:56204790 original size:20 final size:20
Alignment explanation
Indices: 56204765--56204814 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
56204755 TGGCTTAAAA
56204765 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
56204785 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
56204802 GTGGTAGTGGATT
1 TTGGTAGTGGATT
56204815 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:56207757 original size:28 final size:28
Alignment explanation
Indices: 56207725--56207794 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 28
56207715 TAAAATTTCA
56207725 AAAAATTATAAAAATTATTTTTAAAAAT-T
1 AAAAATTATAAAAATTA--TTTAAAAATAT
* *
56207754 AAAAATCAT-TAAATTATTTAAAAATAT
1 AAAAATTATAAAAATTATTTAAAAATAT
*
56207781 GAAAATTATAAAAA
1 AAAAATTATAAAAA
56207795 AAATATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 9 0.26
27 8 0.24
28 9 0.26
29 8 0.24
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAAATTATAAAAATTATTTAAAAATAT
Found at i:56210687 original size:17 final size:17
Alignment explanation
Indices: 56210665--56210699 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
56210655 AAATTATTTG
56210665 TTTTGTTTACTATTCAC
1 TTTTGTTTACTATTCAC
56210682 TTTTGTTTACTATTCAC
1 TTTTGTTTACTATTCAC
56210699 T
1 T
56210700 CCCTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTGTTTACTATTCAC
Found at i:56211289 original size:16 final size:17
Alignment explanation
Indices: 56211263--56211295 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
56211253 TATACAATAT
*
56211263 AAAATTATAAATTTATG
1 AAAATTATAAAATTATG
56211280 AAAA-TATAAAATTATG
1 AAAATTATAAAATTATG
56211296 TACCATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAAATTATAAAATTATG
Found at i:56211366 original size:22 final size:21
Alignment explanation
Indices: 56211334--56211375 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
56211324 ATATTTTGAA
*
56211334 ATATATATAAAAATTTATAAT
1 ATATATATAAAAATTAATAAT
56211355 ATATAATATAAAAATTAATAA
1 ATAT-ATATAAAAATTAATAA
56211376 AAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATATAAAAATTAATAAT
Found at i:56211384 original size:32 final size:33
Alignment explanation
Indices: 56211340--56211401 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
56211330 TGAAATATAT
*
56211340 ATAAAAATTTAT-AATATATAATA-TAAAAATTA
1 ATAAAAAATTATAAATATAT-ATACTAAAAATTA
56211372 ATAAAAAATTATAAATATATATACTAAAAA
1 ATAAAAAATTATAAATATATATACTAAAAA
56211402 GCATGTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (33 bp):
ATAAAAAATTATAAATATATATACTAAAAATTA
Found at i:56211541 original size:16 final size:16
Alignment explanation
Indices: 56211490--56211543 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
56211480 TAATGTAAAT
56211490 TTTTTATAT-TTTTAA
1 TTTTTATATATTTTAA
* *
56211505 TAATTTATATAATTTAAAA
1 T-TTTTATAT-ATTT-TAA
56211524 TTTTTATATATTTTAA
1 TTTTTATATATTTTAA
56211540 TTTT
1 TTTT
56211544 CAATTGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.42
17 4 0.13
18 10 0.32
19 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTATATATTTTAA
Found at i:56219101 original size:26 final size:26
Alignment explanation
Indices: 56219065--56219116 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
56219055 GGGGTTATTT
56219065 TAAATTGCCTGTAAAATTGTATCAGA
1 TAAATTGCCTGTAAAATTGTATCAGA
56219091 TAAATTGCCTGTAAAATTGTATCAGA
1 TAAATTGCCTGTAAAATTGTATCAGA
56219117 ATAAGCCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (26 bp):
TAAATTGCCTGTAAAATTGTATCAGA
Found at i:56219939 original size:21 final size:21
Alignment explanation
Indices: 56219914--56219964 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
56219904 TAGCCAACAC
56219914 GGCCGTGTGAATTTTGGGCCA
1 GGCCGTGTGAATTTTGGGCCA
*
56219935 GGCCGTGTGAATTTTGGGCTA
1 GGCCGTGTGAATTTTGGGCCA
56219956 GGCCGTGTG
1 GGCCGTGTG
56219965 GGCCACACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.12, C:0.18, G:0.41, T:0.29
Consensus pattern (21 bp):
GGCCGTGTGAATTTTGGGCCA
Found at i:56223386 original size:30 final size:30
Alignment explanation
Indices: 56223324--56223386 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
56223314 AACTTATTTA
*
56223324 TTGTTAATTTTGTTATTATTTTAAAAGTAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
56223354 TTGTTAATTTTGTTATTATTTTAGAAA-CAT
1 TTGTTAATTTTGTTATTATTTTA-AAAGCAT
56223384 TTG
1 TTG
56223387 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAAGCAT
Found at i:56226490 original size:14 final size:14
Alignment explanation
Indices: 56226471--56226500 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56226461 TCTCTTAATT
56226471 TTTAAAATAATTAA
1 TTTAAAATAATTAA
56226485 TTTAAAATAATTAA
1 TTTAAAATAATTAA
56226499 TT
1 TT
56226501 ACATTATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAATAATTAA
Found at i:56229373 original size:21 final size:20
Alignment explanation
Indices: 56229347--56229391 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
56229337 CTACGTGGCA
*
56229347 AGTTAACTGGCCACATTAGC
1 AGTTAACTGGCCACATCAGC
*
56229367 TAGTTAACTTGCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
56229388 AGTT
1 AGTT
56229392 CTGTTAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:56229956 original size:21 final size:21
Alignment explanation
Indices: 56229907--56229961 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
56229897 ATTGTAAATG
56229907 TAATATTAA-TTATGATTTTT
1 TAATATTAATTTATGATTTTT
*
56229927 TAA-ATTTAATTTAT-TTTTATT
1 TAATA-TTAATTTATGATTT-TT
56229948 TAATATTAAGTTTA
1 TAATATTAA-TTTA
56229962 AAATAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.03
20 10 0.34
21 13 0.45
22 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TAATATTAATTTATGATTTTT
Found at i:56231500 original size:21 final size:21
Alignment explanation
Indices: 56231474--56231513 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56231464 CGCACAGTAG
**
56231474 CCTGTGTTGTGACATAGGGGC
1 CCTGTGTTGCAACATAGGGGC
56231495 CCTGTGTTGCAACATAGGG
1 CCTGTGTTGCAACATAGGG
56231514 TCTGTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (21 bp):
CCTGTGTTGCAACATAGGGGC
Found at i:56234799 original size:28 final size:29
Alignment explanation
Indices: 56234745--56234808 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
56234735 ATTAAACCAA
* * *
56234745 AATTTTATTATTTTTAGGGGGCAAAATGT
1 AATTTTATTATTTTTAGGAGGAAAAATAT
*
56234774 AATTTTATTATTTTTA-GATGAAAAATAT
1 AATTTTATTATTTTTAGGAGGAAAAATAT
56234802 AATTTTA
1 AATTTTA
56234809 CCATTACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (29 bp):
AATTTTATTATTTTTAGGAGGAAAAATAT
Found at i:56237628 original size:15 final size:17
Alignment explanation
Indices: 56237593--56237625 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56237583 AATGCAGTAA
*
56237593 TAAAATATATTATATTT
1 TAAAAAATATTATATTT
56237610 TAAAAAATATTA-ATTT
1 TAAAAAATATTATATTT
56237626 AAACTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAAATATTATATTT
Found at i:56237648 original size:21 final size:20
Alignment explanation
Indices: 56237594--56237649 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
56237584 ATGCAGTAAT
* *
56237594 AAAATA-TATTATATTTTAA
1 AAAATATTATTAAATTTAAA
56237613 AAAATATTAATTTAAACTTTAAA
1 AAAATATT-A-TTAAA-TTTAAA
56237636 AAAATATTATTAAA
1 AAAATATTATTAAA
56237650 AAATAACTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 6 0.19
22 5 0.16
23 13 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATTATTAAATTTAAA
Found at i:56243102 original size:23 final size:23
Alignment explanation
Indices: 56243076--56243123 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
56243066 ATTGACTTTA
*
56243076 TCATTATGTAATGTTGTTCATTC
1 TCATTATATAATGTTGTTCATTC
56243099 TCATTATATAATGTTGTTCATTC
1 TCATTATATAATGTTGTTCATTC
56243122 TC
1 TC
56243124 TTTTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (23 bp):
TCATTATATAATGTTGTTCATTC
Found at i:56247948 original size:15 final size:16
Alignment explanation
Indices: 56247928--56247958 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56247918 TTATAGTTGT
56247928 TAAAAT-AAATAAAAA
1 TAAAATAAAATAAAAA
56247943 TAAAATAAAATAAAAA
1 TAAAATAAAATAAAAA
56247959 AACACACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAATAAAAA
Found at i:56249778 original size:70 final size:70
Alignment explanation
Indices: 56249665--56249799 Score: 245
Period size: 70 Copynumber: 1.9 Consensus size: 70
56249655 TACAACCCGG
*
56249665 GAGAACACATCTGTGAAGCCTACTCTTGGAATTTGGCTGTAACCCTTTGCAACAAGCCTTACTTT
1 GAGAACACATCTGTGAAGCCTACTCTTGGAATTTGACTGTAACCCTTTGCAACAAGCCTTACTTT
56249730 CTAGA
66 CTAGA
56249735 GAGAACACATCTGTGAAGTCC-ACTCTTGGAATTTGACTGTAACCCTTTGCAACAAGCCTTACTT
1 GAGAACACATCTGTGAAG-CCTACTCTTGGAATTTGACTGTAACCCTTTGCAACAAGCCTTACTT
56249799 T
65 T
56249800 ATATCTGGGT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
70 61 0.97
71 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (70 bp):
GAGAACACATCTGTGAAGCCTACTCTTGGAATTTGACTGTAACCCTTTGCAACAAGCCTTACTTT
CTAGA
Found at i:56249925 original size:42 final size:42
Alignment explanation
Indices: 56249874--56249956 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
56249864 CAACCTTTTT
* *
56249874 ACCTTTAAGAAGTTTCGCAAGGTCCCATGTTCTGTTTTTGTA
1 ACCTTTAAGAAGTTTCACAAGATCCCATGTTCTGTTTTTGTA
*
56249916 ACCTTTAAGAAGTTTCACAAGATCCCATGTTTTGTTTTTGT
1 ACCTTTAAGAAGTTTCACAAGATCCCATGTTCTGTTTTTGT
56249957 GGAGTGATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (42 bp):
ACCTTTAAGAAGTTTCACAAGATCCCATGTTCTGTTTTTGTA
Found at i:56257017 original size:51 final size:51
Alignment explanation
Indices: 56256941--56257057 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
56256931 CGGATCACAT
* *
56256941 TTATCACTTGTCACTTGTCAGTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
56256992 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
56257043 TTATCCCTTGTCACT
1 TTATCACTTGTCACT
56257058 GATCAAAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:56263286 original size:12 final size:12
Alignment explanation
Indices: 56263269--56263302 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
56263259 CCGTCCGGCC
56263269 TATATTAATTTT
1 TATATTAATTTT
56263281 TATATT-ATTTT
1 TATATTAATTTT
56263292 TATA-TAATTTT
1 TATATTAATTTT
56263303 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:56266578 original size:15 final size:14
Alignment explanation
Indices: 56266545--56266578 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
56266535 TTTAGAACTT
*
56266545 TAATTATTTAATTA
1 TAATTATTTAATAA
56266559 TAATTATTTAAATAA
1 TAATTATTT-AATAA
56266574 TAATT
1 TAATT
56266579 TAAAAATATT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTATTTAATAA
Found at i:56290349 original size:310 final size:310
Alignment explanation
Indices: 56289787--56290409 Score: 1158
Period size: 310 Copynumber: 2.0 Consensus size: 310
56289777 AATACACGCC
*
56289787 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGGAAACTTGTTTTCTCTCTTTTCAAT
1 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
56289852 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
66 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
* * *
56289917 GTTCTTCACACTCCGATTTGCCAATAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
131 GTTATTCAAACTCCGATTTGCCAAGAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
*
56289982 TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCGAACATCGCCTTTCATTCATCTTTATGCCTATCT
196 TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATCT
*
56290047 TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTCTCTTTTATGAA
261 TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
56290097 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
1 CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
*
56290162 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTGGTT
66 ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
*
56290227 GTTATTCAAACTCCGATTTGCCAAGAAACCTTTAT-TGGAGGGTCGGTTAGAGCCTTTGGTGGAG
131 GTTATTCAAACTCCGATTTGCCAAGAAACCTTT-TCTGGAGGGTCGGTTAAAGCCTTTGGTGGAG
56290291 TTTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATC
195 TTTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATC
56290356 TTTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
260 TTTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
56290407 CCT
1 CCT
56290410 TCTTCTAACA
Statistics
Matches: 304, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
310 303 1.00
311 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (310 bp):
CCTCATATGTACATCATTCAGTTTCATTCATTTATGAATGAAAACTTGTTTTCTCTCTTTTCAAT
ATTATTTTCTTGTAATTTCTTACAAGTGCTTTTAACTTGATTTCTTTTCAAGAATCGTGGTAGTT
GTTATTCAAACTCCGATTTGCCAAGAAACCTTTTCTGGAGGGTCGGTTAAAGCCTTTGGTGGAGT
TTGTTGAAGTCTTTCTTCAAAGGGTTCCATCAAACATCGCCTTTCATTCATCTTTATGCCTATCT
TTTTTCCATCACTCCCTAATCTTTTTCAATCTTGATTTATCTTTTATGAA
Found at i:56296894 original size:6 final size:6
Alignment explanation
Indices: 56296883--56296909 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56296873 ACAACATAAT
56296883 TATACA TATACA TATACA TATACA TAT
1 TATACA TATACA TATACA TATACA TAT
56296910 TAATTCAATG
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
TATACA
Found at i:56302790 original size:15 final size:15
Alignment explanation
Indices: 56302770--56302801 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56302760 ATGCATGCAA
*
56302770 AAATATGAAAGACAT
1 AAATATAAAAGACAT
56302785 AAATATAAAAGACAT
1 AAATATAAAAGACAT
56302800 AA
1 AA
56302802 CAGTGGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:56302897 original size:26 final size:26
Alignment explanation
Indices: 56302868--56302924 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
56302858 GTTGACTACA
*
56302868 ATAGTGACTATTCCGAAATGTC-TTCT
1 ATAGTGACTATTACGAAATGTCATT-T
*
56302894 ATAGTGACTATTACGAGATGTCATTT
1 ATAGTGACTATTACGAAATGTCATTT
56302920 ATAGT
1 ATAGT
56302925 TCCAACTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (26 bp):
ATAGTGACTATTACGAAATGTCATTT
Found at i:56303755 original size:155 final size:155
Alignment explanation
Indices: 56303473--56303790 Score: 539
Period size: 155 Copynumber: 2.1 Consensus size: 155
56303463 TATAAGGGTC
* *
56303473 ATACACATGACAAGGTCAATGGATAAAGTAGTTGGATGAATTACTTACATAAAGAGTATATAATA
1 ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
*
56303538 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTTGCCAGAA
66 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
56303603 TAGGGTTA-CGAGGTATTACCGGATA
131 TAGGGTTATC-AGGTATTACCGGATA
* *
56303628 ATACACATGACAAGGTCAATTGATAAAGCAGTTGGATGAATTATTTACATAAAGAGTAAATAATA
1 ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
* *
56303693 AGGAGTTTTCAATCATGGTACTTATTGTAGACTGTAACACCCCTAACTCGTATTCGTCGCCAGAA
66 AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
* *
56303758 TAGGGTTATCATGTATTATCGGATA
131 TAGGGTTATCAGGTATTACCGGATA
56303783 ATACACAT
1 ATACACAT
56303791 CATTCACATA
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
155 152 0.99
156 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (155 bp):
ATACACATGACAAGGTCAATGGATAAAGCAGTTGGATGAATTACTTACATAAAGAGTAAATAATA
AGGAGTTTTCAATCATGATACTTATTGTAGACTGTAACACCCCTAACCCGTATTCGTCGCCAGAA
TAGGGTTATCAGGTATTACCGGATA
Done.