Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 21 of 120
Found at i:5590986 original size:219 final size:219
Alignment explanation
Indices: 5590546--5590985 Score: 862
Period size: 221 Copynumber: 2.0 Consensus size: 219
5590536 TATTATTAAT
5590546 TAATATTAGAATATAATAATATAAATTATTATTTAATTGGTATTATTTATTAGATTAATGAAATA
1 TAATATTAGAATATAATAATATAAATTATTATTTAATTGGTATTATTTATTAGATTAATGAAATA
5590611 TATATATATAAATTAAAGCTAAATGTATGGTAATAAAATATAAATGTGTAAAAATTATATTTGTA
66 TATATATATAAATTAAAGCTAAATGTATGGTAATAAAATATAAATGTGTAAAAATTATATTTGTA
5590676 GATTTGTAAAATAAATATTAATTTACTTATTATTTAAGTAAATAGATATTTATAATTTATTAATA
131 GATTTGTAAAATAAATATTAATTTACTTATTATTTAAGTAAATAGATATTTATAATTTATTAATA
5590741 TTATTACTAATTAATATATATATA
196 TTATTACTAATTAATATATATATA
5590765 TAATATTAGAATATAATAATATAAATTATTATTTAATTGGTATTATTTATTAGATTAATGAAATA
1 TAATATTAGAATATAATAATATAAATTATTATTTAATTGGTATTATTTATTAGATTAATG-AA-A
5590830 TATATATATATAAATTAAAGCTAAATGTATGGTAATAAAATATAAATGTGTAAAAATTATATTTG
64 TATATATATATAAATTAAAGCTAAATGTATGGTAATAAAATATAAATGTGTAAAAATTATATTTG
5590895 TAGATTTGTAAAATAAATATTAATTTACTTATTATTTAAGTAAATAGATATTTATAATTTATTAA
129 TAGATTTGTAAAATAAATATTAATTTACTTATTATTTAAGTAAATAGATATTTATAATTTATTAA
5590960 TATTATTACTAATTAATATATATATA
194 TATTATTACTAATTAATATATATATA
5590986 AGATATAAAG
Statistics
Matches: 219, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
219 60 0.27
220 2 0.01
221 157 0.72
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (219 bp):
TAATATTAGAATATAATAATATAAATTATTATTTAATTGGTATTATTTATTAGATTAATGAAATA
TATATATATAAATTAAAGCTAAATGTATGGTAATAAAATATAAATGTGTAAAAATTATATTTGTA
GATTTGTAAAATAAATATTAATTTACTTATTATTTAAGTAAATAGATATTTATAATTTATTAATA
TTATTACTAATTAATATATATATA
Found at i:5591488 original size:17 final size:18
Alignment explanation
Indices: 5591466--5591501 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5591456 TAAATGAGTT
5591466 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5591483 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5591501 A
1 A
5591502 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5591820 original size:18 final size:18
Alignment explanation
Indices: 5591797--5591833 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5591787 ATTTGTGATA
5591797 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
5591815 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
5591833 A
1 A
5591834 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:5604160 original size:29 final size:30
Alignment explanation
Indices: 5604093--5604161 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
5604083 GGTAAAACGG
* *
5604093 TAATTTTTGAACACTCGGAGGGTAAAAATG
1 TAATTTTTGGACACTCGGAGGGTAAAAATA
* * *
5604123 GAATGTTTGGACATTC-GAGGGTAAAAATA
1 TAATTTTTGGACACTCGGAGGGTAAAAATA
5604152 TAATTTTTGG
1 TAATTTTTGG
5604162 GAAGTTTGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (30 bp):
TAATTTTTGGACACTCGGAGGGTAAAAATA
Found at i:5604173 original size:29 final size:30
Alignment explanation
Indices: 5604112--5604305 Score: 142
Period size: 29 Copynumber: 6.7 Consensus size: 30
5604102 AACACTCGGA
* *
5604112 GGGTAAAAATGGAATGTTT-GGACA--TTCG
1 GGGTAAAAATGGAATTTTTGGGA-AGTTTAG
**
5604140 AGGGTAAAAATATAATTTTTGGGAAGTTT-G
1 -GGGTAAAAATGGAATTTTTGGGAAGTTTAG
* * *
5604170 GGGTCAAAAATGGAA-ATTTAGGAAATTTAG
1 GGGT-AAAAATGGAATTTTTGGGAAGTTTAG
*
5604200 GGGT--AAATGGTAATTTTTGGAAAGTTTAG
1 GGGTAAAAATGG-AATTTTTGGGAAGTTTAG
* *
5604229 GGATAAAAATGGAATTTTT-AGAAGTTTAG
1 GGGTAAAAATGGAATTTTTGGGAAGTTTAG
*
5604258 GGGT-AAAATGGTAA-TTTTGGAGAA-TTCA-
1 GGGTAAAAATGG-AATTTTTGG-GAAGTTTAG
*
5604286 GGGTTAAAATGGAATTTTTG
1 GGGTAAAAATGGAATTTTTG
5604306 AAAATCTGAG
Statistics
Matches: 133, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
27 6 0.05
28 19 0.14
29 73 0.55
30 27 0.20
31 8 0.06
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (30 bp):
GGGTAAAAATGGAATTTTTGGGAAGTTTAG
Found at i:5604237 original size:58 final size:58
Alignment explanation
Indices: 5604111--5604334 Score: 187
Period size: 58 Copynumber: 3.9 Consensus size: 58
5604101 GAACACTCGG
* * * * * *
5604111 AGGGTAAAAATGGAATGTTTGGACA-TTCGAGGGTAAAAAT-ATAATTTTTGGGAAGTTT
1 AGGGTAAAAATGGAATATTTAGAAATTTAG-GGGT-AAAATGGTAATTTTTGGAAAGTTT
*
5604169 GGGGTCAAAAATGGAA-ATTTAGGAAATTTAGGGGT-AAATGGTAATTTTTGGAAAGTTT
1 AGGGT-AAAAATGGAATATTTA-GAAATTTAGGGGTAAAATGGTAATTTTTGGAAAGTTT
* * *
5604227 AGGGATAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGGTAA-TTTTGGAGAA-TTC
1 AGGG-TAAAAATGGAATATTTAGAAATTTAGGGGTAAAATGGTAATTTTTGGA-AAGTTT
* * *
5604285 AGGGTTAAAATGGAAT-TTTTGAAAATCT-GAGGGTAAAAAT-GTAATTTTTG
1 AGGGTAAAAATGGAATATTTAG-AAATTTAG-GGGT-AAAATGGTAATTTTTG
5604335 AAGAATTCGG
Statistics
Matches: 139, Mismatches: 15, Indels: 24
0.78 0.08 0.13
Matches are distributed among these distances:
56 5 0.04
57 27 0.19
58 71 0.51
59 33 0.24
60 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.33
Consensus pattern (58 bp):
AGGGTAAAAATGGAATATTTAGAAATTTAGGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:5604317 original size:29 final size:28
Alignment explanation
Indices: 5604176--5604342 Score: 113
Period size: 29 Copynumber: 5.8 Consensus size: 28
5604166 TTTGGGGTCA
* * * * *
5604176 AAAATGGAAATTTAGGAAATTTAGGGGT
1 AAAATGGAATTTTTGAAAATTCAGGGTT
* * *
5604204 -AAATGGTAATTTTTGGAAAGTTTAGGGATA
1 AAAATGG-AATTTTT-GAAAATTCAGGG-TT
* * *
5604234 AAAATGGAATTTTT-AGAAGTTTAGGGGT
1 AAAATGGAATTTTTGA-AAATTCAGGGTT
* *
5604262 AAAATGGTAATTTTGGAGAATTCAGGGTT
1 AAAATGG-AATTTTTGAAAATTCAGGGTT
* *
5604291 AAAATGGAATTTTTGAAAATCTGAGGGTA
1 AAAATGGAATTTTTGAAAAT-TCAGGGTT
*
5604320 AAAATGTAATTTTTGAAGAATTC
1 AAAATGGAATTTTTGAA-AATTC
5604343 GGGGGTCAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
27 6 0.05
28 24 0.22
29 64 0.58
30 11 0.10
31 6 0.05
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGAAAATTCAGGGTT
Found at i:5604362 original size:87 final size:84
Alignment explanation
Indices: 5604111--5604376 Score: 209
Period size: 88 Copynumber: 3.0 Consensus size: 84
5604101 GAACACTCGG
* * * * * * *
5604111 AGGGTAAAAATGGAATGTTTGGACATTCGAGGGTAAAAATATAATTTTTGGGAAGTTTGGGGTCA
1 AGGGTTAAAATGGAATTTTTGAAAATT-GAGGGTAAAAATGTAATTTTTGAGAAGTTAGGGGTCA
* *
5604176 AAA-ATGGAAATTTAGGAAATTT
65 AAATAT-G--ATTTTGGAAATTC
* * * *
5604198 AGGGGT-AAATGGTAATTTTTGGAAAGTTTAGGGATAAAAATGGAATTTTT-AGAAGTTTAGGGG
1 AGGGTTAAAATGG-AATTTTT-GAAAATTGAGGG-TAAAAATGTAATTTTTGAGAAG-TTAGGGG
* *
5604261 T-AAAATGGTAATTTTGGAGAATTC
62 TCAAAAT-ATGATTTTGGA-AATTC
*
5604285 AGGGTTAAAATGGAATTTTTGAAAATCTGAGGGTAAAAATGTAATTTTTGAAGAA-TTCGGGGGT
1 AGGGTTAAAATGGAATTTTTGAAAAT-TGAGGGTAAAAATGTAATTTTTG-AGAAGTT-AGGGGT
*
5604349 CAAAATATGATTTTTGGACAGTTC
63 CAAAATATGA-TTTTGGA-AATTC
5604373 AGGG
1 AGGG
5604377 ACCTACTGGG
Statistics
Matches: 141, Mismatches: 24, Indels: 27
0.73 0.12 0.14
Matches are distributed among these distances:
86 35 0.25
87 50 0.35
88 55 0.39
89 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (84 bp):
AGGGTTAAAATGGAATTTTTGAAAATTGAGGGTAAAAATGTAATTTTTGAGAAGTTAGGGGTCAA
AATATGATTTTGGAAATTC
Found at i:5605495 original size:3 final size:3
Alignment explanation
Indices: 5605483--5605525 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
5605473 TTTCCTTTCC
* * *
5605483 TAT T-T TAT TAT TAA TAT CAT TAT TAT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5605526 ATGCTATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5606309 original size:11 final size:10
Alignment explanation
Indices: 5606273--5606365 Score: 68
Period size: 11 Copynumber: 8.9 Consensus size: 10
5606263 GGACATTATT
5606273 AATTTAAATA
1 AATTTAAATA
5606283 AATTTAAACTTA
1 AATTTAAA--TA
5606295 AATTTATAATA
1 AATTTA-AATA
5606306 AATTTAAAT-
1 AATTTAAATA
*
5606315 --TTCAAATA
1 AATTTAAATA
5606323 AATTTAAACCTA
1 AATTTAAA--TA
*
5606335 AA-ATAAATTTA
1 AATTTAAA--TA
5606346 AATTTAAAATA
1 AATTT-AAATA
5606357 AATTTAAAT
1 AATTTAAAT
5606366 TCTGTTGGGC
Statistics
Matches: 67, Mismatches: 6, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
7 6 0.09
10 20 0.30
11 23 0.34
12 13 0.19
13 5 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTTAAATA
Found at i:5606312 original size:17 final size:17
Alignment explanation
Indices: 5606287--5606366 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
5606277 TAAATAAATT
* *
5606287 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
5606304 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
**
5606321 TAAATTTAAACCTAAAA
1 TAAATTTAAATTTAAAA
5606338 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
5606355 TAAATTTAAATT
1 TAAATTTAAATT
5606367 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5606313 original size:6 final size:6
Alignment explanation
Indices: 5606273--5606366 Score: 69
Period size: 6 Copynumber: 16.7 Consensus size: 6
5606263 GGACATTATT
*
5606273 AATTTA AA--TA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTT-A
** * *
5606319 AA--TA AATTTA AACCTA AA-ATA AATTTA AATTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
5606363 AATT
1 AATT
5606367 CTGTTGGGCC
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
4 9 0.13
5 11 0.16
6 45 0.64
7 5 0.07
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:5609630 original size:39 final size:38
Alignment explanation
Indices: 5609586--5609722 Score: 132
Period size: 39 Copynumber: 3.5 Consensus size: 38
5609576 ATAGTCTAGT
* *
5609586 AGTGTTTATAGTGTCACTACTGCTTCAGTATAGCATCGC
1 AGTGTTTACAGTGTCACTACTG-TTCAGTATAGCATTGC
* ** * *
5609625 GGTGTTTACAGTGTCACCGCCAGTTCAATATAGCATTGC
1 AGTGTTTACAGTGTCA-CTACTGTTCAGTATAGCATTGC
* *
5609664 AGTGTTTACAGTGTCACTGCTAG-TCTAGTATATCATTGC
1 AGTGTTTACAGTGTCACTACT-GTTC-AGTATAGCATTGC
* *
5609703 AGTGTTTATAGTGTTACTAC
1 AGTGTTTACAGTGTCACTAC
5609723 CAGTTTAGTG
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
38 4 0.05
39 72 0.91
40 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (38 bp):
AGTGTTTACAGTGTCACTACTGTTCAGTATAGCATTGC
Found at i:5611925 original size:12 final size:13
Alignment explanation
Indices: 5611901--5611936 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5611891 TTGTAATATA
5611901 TTTATTCATAATTT
1 TTTA-TCATAATTT
5611915 TTTAT-ATAATTT
1 TTTATCATAATTT
5611927 TTTATCATAA
1 TTTATCATAA
5611937 CATTTGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.57
13 5 0.24
14 4 0.19
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTATCATAATTT
Found at i:5614592 original size:16 final size:17
Alignment explanation
Indices: 5614564--5614600 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5614554 TAAAAATATA
5614564 ATTT-TATTATTTTAAT
1 ATTTATATTATTTTAAT
5614580 ATTTATATT-TTTTAAT
1 ATTTATATTATTTTAAT
*
5614596 TTTTA
1 ATTTA
5614601 AAGGATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTATATTATTTTAAT
Found at i:5616263 original size:30 final size:31
Alignment explanation
Indices: 5616207--5616266 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
5616197 AAAAATGTAT
* *
5616207 TTTTTAAAGGATTAAATTTTTAATTTTATCA
1 TTTTTAAAGGATTAAATGTGTAATTTTATCA
*
5616238 TTTTTAAAGGGTTAAA-GTGTAATTTTATC
1 TTTTTAAAGGATTAAATGTGTAATTTTATC
5616267 TTTACTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (31 bp):
TTTTTAAAGGATTAAATGTGTAATTTTATCA
Found at i:5619196 original size:2 final size:2
Alignment explanation
Indices: 5619189--5619243 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
5619179 TTTGTACTCT
5619189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5619231 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
5619244 GATTATAGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5619612 original size:21 final size:20
Alignment explanation
Indices: 5619559--5619612 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
5619549 TTTTTCTTTA
*
5619559 TTCTCCA-TTC-TTTTCTGC
1 TTCTCCATTTCTTTTTCTCC
*
5619577 TTCTCC-TTCTATTTTTCTCCC
1 TTCTCCATT-TCTTTTTCT-CC
5619598 TTCTCCATTTCTTTT
1 TTCTCCATTTCTTTT
5619613 AATGTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 7 0.25
19 1 0.04
20 6 0.21
21 12 0.43
22 2 0.07
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.59
Consensus pattern (20 bp):
TTCTCCATTTCTTTTTCTCC
Found at i:5620857 original size:41 final size:41
Alignment explanation
Indices: 5620800--5620895 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
5620790 GAATTTTATT
* *
5620800 TTAACAAGAATTCTAGTCACCCAATTCTAATAATCTCTACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
5620841 TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
5620882 TTGACAAGAATTCT
1 TTAACAAGAATTCT
5620896 CTACGAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:5635186 original size:27 final size:27
Alignment explanation
Indices: 5635156--5635235 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
5635146 GTTTGAGGAG
* *
5635156 TAATCTGACTCTAGCTCGAAAGAGCGT
1 TAATCTGATTCTGGCTCGAAAGAGCGT
* * *
5635183 TAATTTGATTCTGGCTTGAAGGAGCGT
1 TAATCTGATTCTGGCTCGAAAGAGCGT
*
5635210 TATTCTGATTCTGGCTCGAAAGAGCG
1 TAATCTGATTCTGGCTCGAAAGAGCG
5635236 ATATTATATC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (27 bp):
TAATCTGATTCTGGCTCGAAAGAGCGT
Found at i:5635257 original size:25 final size:25
Alignment explanation
Indices: 5635204--5635410 Score: 209
Period size: 25 Copynumber: 8.2 Consensus size: 25
5635194 TGGCTTGAAG
* *
5635204 GAGCGTTATTCTGATTCTGGCTCGAAA
1 GAGCGATATTCT-A-TCTGGCTCGTAA
* *
5635231 GAGCGATATTATATCTGGCTCATAA
1 GAGCGATATTCTATCTGGCTCGTAA
* * *
5635256 GAGCGATATTTTGTCTGACTCGTAA
1 GAGCGATATTCTATCTGGCTCGTAA
* * *
5635281 GAGTGATATTCTATCTGTCTCGTGA
1 GAGCGATATTCTATCTGGCTCGTAA
* * *
5635306 GAGTGATATTCTAACTGGCTCGTAG
1 GAGCGATATTCTATCTGGCTCGTAA
* *
5635331 GAGCGATATTTTGTCTGGCTCGTAA
1 GAGCGATATTCTATCTGGCTCGTAA
*
5635356 GAGCGATATTCTAAT-TGGCTTGTAA
1 GAGCGATATTCT-ATCTGGCTCGTAA
* *
5635381 GAGCAATATTCTGTCTGGACTCGTAA
1 GAGCGATATTCTATCTGG-CTCGTAA
5635407 GAGC
1 GAGC
5635411 TAAACTCTGT
Statistics
Matches: 149, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
24 1 0.01
25 126 0.85
26 12 0.08
27 10 0.07
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (25 bp):
GAGCGATATTCTATCTGGCTCGTAA
Found at i:5635390 original size:75 final size:75
Alignment explanation
Indices: 5635204--5635410 Score: 245
Period size: 75 Copynumber: 2.7 Consensus size: 75
5635194 TGGCTTGAAG
* * * *
5635204 GAGCGTTATTCTGATTCTGGCTCGAAAGAGCGATATTATATCTGGCTCATAAGAGCGATATTTTG
1 GAGCGATATTCT-A-TCTGGCTCGTAAGAGCGATATTCTATCTGGCTCGTAAGAGCGATATTTTG
5635269 TCTGACTCGTAA
64 TCTGACTCGTAA
* * * * * *
5635281 GAGTGATATTCTATCTGTCTCGTGAGAGTGATATTCTAACTGGCTCGTAGGAGCGATATTTTGTC
1 GAGCGATATTCTATCTGGCTCGTAAGAGCGATATTCTATCTGGCTCGTAAGAGCGATATTTTGTC
*
5635346 TGGCTCGTAA
66 TGACTCGTAA
* * *
5635356 GAGCGATATTCTAAT-TGGCTTGTAAGAGCAATATTCTGTCTGGACTCGTAAGAGC
1 GAGCGATATTCT-ATCTGGCTCGTAAGAGCGATATTCTATCTGG-CTCGTAAGAGC
5635411 TAAACTCTGT
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
75 85 0.79
76 13 0.12
77 10 0.09
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (75 bp):
GAGCGATATTCTATCTGGCTCGTAAGAGCGATATTCTATCTGGCTCGTAAGAGCGATATTTTGTC
TGACTCGTAA
Found at i:5635419 original size:26 final size:26
Alignment explanation
Indices: 5635377--5635440 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5635367 TAATTGGCTT
*
5635377 GTAAGAGC-AATATTCTGTCTGGACTC
1 GTAAGAGCTAA-ACTCTGTCTGGACTC
* * *
5635403 GTAAGAGCTAAACTCTGTTTGGGCTT
1 GTAAGAGCTAAACTCTGTCTGGACTC
*
5635429 GTATGAGCTAAA
1 GTAAGAGCTAAA
5635441 TTTTTGGAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (26 bp):
GTAAGAGCTAAACTCTGTCTGGACTC
Found at i:5636264 original size:18 final size:18
Alignment explanation
Indices: 5636243--5636277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5636233 AAAGATATAT
* *
5636243 TAATTAATAATATTATTA
1 TAATAAATAATAATATTA
5636261 TAATAAATAATAATATT
1 TAATAAATAATAATATT
5636278 TTATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAATAATAATATTA
Found at i:5636289 original size:18 final size:19
Alignment explanation
Indices: 5636240--5636290 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
5636230 TCAAAAGATA
5636240 TATTAATTAATAATATTAT
1 TATTAATTAATAATATTAT
*
5636259 TATAATAAATAATAATATT-T
1 TAT--TAATTAATAATATTAT
*
5636279 TATTATTTAATA
1 TATTAATTAATA
5636291 TAAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 4 0.15
21 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATTAATAATATTAT
Found at i:5637348 original size:17 final size:19
Alignment explanation
Indices: 5637321--5637359 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5637311 GATATGGGAC
*
5637321 AAAAATGAGAA-TGATGTG
1 AAAAATGAGAATTGAAGTG
5637339 AAAAAT-AGAATTGAAGTG
1 AAAAATGAGAATTGAAGTG
5637357 AAA
1 AAA
5637360 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
AAAAATGAGAATTGAAGTG
Found at i:5643563 original size:19 final size:20
Alignment explanation
Indices: 5643528--5643567 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5643518 GGGTTTTCCA
5643528 GAAAAAGTCAAAGGGTCAAT
1 GAAAAAGTCAAAGGGTCAAT
*
5643548 GAAAAAGTC-AATGGTCAAT
1 GAAAAAGTCAAAGGGTCAAT
5643567 G
1 G
5643568 GTTAACAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.10, G:0.25, T:0.17
Consensus pattern (20 bp):
GAAAAAGTCAAAGGGTCAAT
Found at i:5645420 original size:20 final size:20
Alignment explanation
Indices: 5645395--5645434 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5645385 CTCACATGCC
*
5645395 AAAGTGAAAAATTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
5645415 AAAGTGAAAAAGTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
5645435 GTGGTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (20 bp):
AAAGTGAAAAAGTGATTTTT
Found at i:5645539 original size:47 final size:47
Alignment explanation
Indices: 5645480--5645628 Score: 165
Period size: 47 Copynumber: 3.2 Consensus size: 47
5645470 AAGGTGGAAG
* * * *
5645480 AAGTAACAGTTTATCT-CTAAAACTTGTGGCTTGTCCATAATATTATA
1 AAGTGACAGTTTATCTAC-AAAAGTGGTGGCTTGTCCACAATATTATA
* * *
5645527 AAGTGACAGTTTATCTACAAAAGTGGTGGCTTGTTCACAGTCTTATA
1 AAGTGACAGTTTATCTACAAAAGTGGTGGCTTGTCCACAATATTATA
* * * * * *
5645574 AAGTGTCAATTTATCTGCAAAAGTGGTGGCTTTTCTACAATATTATT
1 AAGTGACAGTTTATCTACAAAAGTGGTGGCTTGTCCACAATATTATA
5645621 AAGTGACA
1 AAGTGACA
5645629 ATTCATTTAC
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
47 83 0.99
48 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (47 bp):
AAGTGACAGTTTATCTACAAAAGTGGTGGCTTGTCCACAATATTATA
Found at i:5645631 original size:47 final size:47
Alignment explanation
Indices: 5645505--5645631 Score: 166
Period size: 47 Copynumber: 2.7 Consensus size: 47
5645495 TCTAAAACTT
* * *
5645505 GTGGCTTGTCCATAATATTATAAAGTGACAGTTTATCTACAAAAGTG
1 GTGGCTTGTTCACAATATTATAAAGTGACAATTTATCTACAAAAGTG
* * * *
5645552 GTGGCTTGTTCACAGTCTTATAAAGTGTCAATTTATCTGCAAAAGTG
1 GTGGCTTGTTCACAATATTATAAAGTGACAATTTATCTACAAAAGTG
*
5645599 GTGGCTT-TTCTACAATATTATTAAGTGACAATT
1 GTGGCTTGTTC-ACAATATTATAAAGTGACAATT
5645632 CATTTACATT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 3 0.04
47 65 0.96
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (47 bp):
GTGGCTTGTTCACAATATTATAAAGTGACAATTTATCTACAAAAGTG
Found at i:5647528 original size:16 final size:16
Alignment explanation
Indices: 5647495--5647539 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5647485 TCTCAAAATA
* *
5647495 TAAATTATTTATTAAAT
1 TAAATAATTT-TTCAAT
*
5647512 TAATTAATTTTTCAAT
1 TAAATAATTTTTCAAT
5647528 TAAATAATTTTT
1 TAAATAATTTTT
5647540 TAATCCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATAATTTTTCAAT
Found at i:5660856 original size:50 final size:50
Alignment explanation
Indices: 5660761--5660991 Score: 275
Period size: 50 Copynumber: 4.6 Consensus size: 50
5660751 ATATTTATGT
* *
5660761 GTTTACGCTCATTAGC-TAATTTATGCATTTACACTCGCCAACTTGCACAC
1 GTTTACGCTCATCAGCTTAA-TTATGCATTTACACTCGCCAGCTTGCACAC
* ** * *
5660811 GTTTATGCTCATCAGCTTAATTATGTTTTTATACTAGCCAGCTTGCACAC
1 GTTTACGCTCATCAGCTTAATTATGCATTTACACTCGCCAGCTTGCACAC
* *
5660861 GTTTACGCTCATCAGCTTATTTATGCATTTACTCTCGCCAGCTTGCACAC
1 GTTTACGCTCATCAGCTTAATTATGCATTTACACTCGCCAGCTTGCACAC
* * * * *
5660911 GTTTGCGCTCGTCAGCTTATTTATGCTTTTACACTCGCCAGCTTGCACAT
1 GTTTACGCTCATCAGCTTAATTATGCATTTACACTCGCCAGCTTGCACAC
* ** * *
5660961 GTTTACGTTTGTCAGCTTATTTATGCGTTTA
1 GTTTACGCTCATCAGCTTAATTATGCATTTA
5660992 TATCTATATA
Statistics
Matches: 157, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
50 154 0.98
51 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (50 bp):
GTTTACGCTCATCAGCTTAATTATGCATTTACACTCGCCAGCTTGCACAC
Found at i:5660935 original size:100 final size:100
Alignment explanation
Indices: 5660761--5660991 Score: 318
Period size: 100 Copynumber: 2.3 Consensus size: 100
5660751 ATATTTATGT
* * *
5660761 GTTTACGCTCATTAGCTAATTTATGCATTTACACTCGCCAACTTGCACACGTTTATGCTCATCAG
1 GTTTACGCTCATCAGCTTATTTATGCATTTACACTCGCCAACTTGCACACGTTTACGCTCATCAG
* *
5660826 CTTAATTATGTTTTTATACTAGCCAGCTTGCACAC
66 CTTAATTATGCTTTTACACTAGCCAGCTTGCACAC
* * * *
5660861 GTTTACGCTCATCAGCTTATTTATGCATTTACTCTCGCCAGCTTGCACACGTTTGCGCTCGTCAG
1 GTTTACGCTCATCAGCTTATTTATGCATTTACACTCGCCAACTTGCACACGTTTACGCTCATCAG
* * *
5660926 CTTATTTATGCTTTTACACTCGCCAGCTTGCACAT
66 CTTAATTATGCTTTTACACTAGCCAGCTTGCACAC
* ** *
5660961 GTTTACGTTTGTCAGCTTATTTATGCGTTTA
1 GTTTACGCTCATCAGCTTATTTATGCATTTA
5660992 TATCTATATA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 115 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (100 bp):
GTTTACGCTCATCAGCTTATTTATGCATTTACACTCGCCAACTTGCACACGTTTACGCTCATCAG
CTTAATTATGCTTTTACACTAGCCAGCTTGCACAC
Found at i:5661970 original size:2 final size:2
Alignment explanation
Indices: 5661963--5661992 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5661953 CTTTCCTTTT
5661963 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5661993 CATTTACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5665028 original size:50 final size:50
Alignment explanation
Indices: 5664953--5665265 Score: 450
Period size: 50 Copynumber: 6.3 Consensus size: 50
5664943 CTCTTTATCA
* *
5664953 TAATTAT-CTGTTTACGCTCGCCAGCTTGAACACGTTTATGCTCGTCAGCT
1 TAATTATGC-GTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * *
5665003 TAATTATGCGTTTACGCTCGCCAGCTTTCACACGTTTAAGCTCGTCAGCC
1 TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * *
5665053 TAATTATGCATTTATGCTCGCTAGCTTGCACACGTTTATGCTCGTCAGCT
1 TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * *
5665103 TAATTATGCATTTACGCTCGCCAGTTTGCACACGCTTACGCTCGTCAGCT
1 TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
*
5665153 TAATTATACGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
1 TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
* * * *
5665203 TAATTATGCGTTTATGCTCGCCAGC-TGCACACATTTACACTCGTCTGCT
1 TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
5665252 TAATTATGCGTTTA
1 TAATTATGCGTTTA
5665266 TTCAAAATTT
Statistics
Matches: 238, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
49 35 0.15
50 202 0.85
51 1 0.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (50 bp):
TAATTATGCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCT
Found at i:5670196 original size:30 final size:29
Alignment explanation
Indices: 5670162--5670220 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
5670152 TTAATTTTGA
**
5670162 TACTTTTTTAAACAATTTTAATGATTTTTT
1 TACTTTTAAAAACAATTTTAAT-ATTTTTT
*
5670192 TACTTTTAAAAACAATTTTTATATTTTTT
1 TACTTTTAAAAACAATTTTAATATTTTTT
5670221 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (29 bp):
TACTTTTAAAAACAATTTTAATATTTTTT
Found at i:5670219 original size:21 final size:21
Alignment explanation
Indices: 5670185--5670224 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5670175 AATTTTAATG
*
5670185 ATTTTTTTACTTTTAAAAACA
1 ATTTTTATACTTTTAAAAACA
* *
5670206 ATTTTTATATTTTTTAAAA
1 ATTTTTATACTTTTAAAAA
5670225 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTATACTTTTAAAAACA
Found at i:5670229 original size:30 final size:30
Alignment explanation
Indices: 5670171--5670233 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5670161 ATACTTTTTT
* *
5670171 AAACAATTTTAATGATTTTTTTACTTTTAA
1 AAACAATTTTAATGATTTTTTAAATTTTAA
*
5670201 AAACAATTTTTAT-ATTTTTTAAAATTTTAA
1 AAACAATTTTAATGATTTTTT-AAATTTTAA
5670231 AAA
1 AAA
5670234 ATTAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (30 bp):
AAACAATTTTAATGATTTTTTAAATTTTAA
Found at i:5671001 original size:13 final size:13
Alignment explanation
Indices: 5670985--5671016 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5670975 TTTTTTTTCC
5670985 AATTTTGTACCTA
1 AATTTTGTACCTA
*
5670998 AATTTGGTACCTA
1 AATTTTGTACCTA
5671011 AATTTT
1 AATTTT
5671017 TTTTAGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (13 bp):
AATTTTGTACCTA
Found at i:5671510 original size:31 final size:32
Alignment explanation
Indices: 5671475--5671602 Score: 97
Period size: 32 Copynumber: 4.2 Consensus size: 32
5671465 AAAAGTTCAA
* *
5671475 GTACCAACTTA-AGAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTTAG
* *
5671506 GTACCAAATTAGAAAAAAAGTGTGAAGTTTTG
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTTAG
* * * * *
5671538 GCACAAAATT-GGACAAAA--G--AAGTTTAC
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTTAG
* * * *
5671565 GTACCAAATTAAAAAAAAAGTATCAAGTTCAA
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTTAG
5671597 GTACCA
1 GTACCA
5671603 TATATTATAT
Statistics
Matches: 73, Mismatches: 18, Indels: 11
0.72 0.18 0.11
Matches are distributed among these distances:
27 14 0.19
28 5 0.07
29 1 0.01
31 16 0.22
32 37 0.51
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.23
Consensus pattern (32 bp):
GTACCAAATTAGAAAAAAAGTGTCAAGTTTAG
Found at i:5671591 original size:91 final size:88
Alignment explanation
Indices: 5671413--5671602 Score: 202
Period size: 91 Copynumber: 2.1 Consensus size: 88
5671403 AAAAAAAAGA
* * * * *
5671413 TTAGGTACCAAATTAGGAATAAAGTCAAGTTTAGGTACTAAATTGGATCCCAAAAAGTTCAAGTA
1 TTAGGTACCAAATTAGAAAAAAAGTCAAGTTTAGGCACAAAATTGGA-CCAAAAAAGTTCAAGTA
* * *
5671478 CCAACTTAAGAAAAAGTGTCAAGT
65 CCAAATTAAAAAAAAGTATCAAGT
* * * *
5671502 TTAGGTACCAAATTAGAAAAAAAGTGTGAAGTTTTGGCACAAAATTGGA-CAAAAGAAGTTTACG
1 TTAGGTACCAAATTAGAAAAAAA--GTCAAGTTTAGGCACAAAATTGGACCAAAA-AAGTTCAAG
5671566 TACCAAATTAAAAAAAAAGTATCAAGT
63 TACCAAATT-AAAAAAAAGTATCAAGT
* *
5671593 TCAAGTACCA
1 TTAGGTACCA
5671603 TATATTATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
89 25 0.30
90 15 0.18
91 43 0.52
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (88 bp):
TTAGGTACCAAATTAGAAAAAAAGTCAAGTTTAGGCACAAAATTGGACCAAAAAAGTTCAAGTAC
CAAATTAAAAAAAAGTATCAAGT
Found at i:5671921 original size:33 final size:35
Alignment explanation
Indices: 5671878--5671942 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
5671868 TAAAGTTGAT
* *
5671878 TTTAAATAAATT-ATT-TGTTATTTTAATATTTTA
1 TTTAAATAAATTAATTATGATATTATAATATTTTA
*
5671911 TTTAATTAAATTAATTATGATATTATAATATT
1 TTTAAATAAATTAATTATGATATTATAATATT
5671943 AAAATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 11 0.41
34 3 0.11
35 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTAAATAAATTAATTATGATATTATAATATTTTA
Found at i:5671977 original size:15 final size:16
Alignment explanation
Indices: 5671937--5671982 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
5671927 ATGATATTAT
5671937 AATATTAAAATTAATA
1 AATATTAAAATTAATA
**
5671953 AATATT-AAATTGTTA
1 AATATTAAAATTAATA
5671968 AAT-TTAAAATATAAT
1 AATATTAAAAT-TAAT
5671983 TTTAAAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 14 0.58
16 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AATATTAAAATTAATA
Found at i:5676941 original size:24 final size:25
Alignment explanation
Indices: 5676914--5676962 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
5676904 TATTTACCAA
5676914 TTTAAAT-ATT-ATTTACTCAATTAG
1 TTTAAATAATTAATTT-CTCAATTAG
5676938 TTTAAATAAATTAATTTCTCAATTA
1 TTTAAAT-AATTAATTTCTCAATTA
5676963 AATTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTAAATAATTAATTTCTCAATTAG
Found at i:5679219 original size:21 final size:21
Alignment explanation
Indices: 5679193--5679266 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
5679183 TAATAGAAGA
5679193 GGACACGGAGGGAACGGAGGT
1 GGACACGGAGGGAACGGAGGT
5679214 GGACACGGAGGGAACGGAGGT
1 GGACACGGAGGGAACGGAGGT
* * *
5679235 GGACACGGAGGGTATGGTGGT
1 GGACACGGAGGGAACGGAGGT
*
5679256 GGCCACGGAGG
1 GGACACGGAGG
5679267 TTATGGTGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.24, C:0.15, G:0.53, T:0.08
Consensus pattern (21 bp):
GGACACGGAGGGAACGGAGGT
Found at i:5679223 original size:12 final size:11
Alignment explanation
Indices: 5679193--5679246 Score: 62
Period size: 12 Copynumber: 5.1 Consensus size: 11
5679183 TAATAGAAGA
5679193 GGACACGGA-G
1 GGACACGGAGG
5679203 GGA-ACGGAGG
1 GGACACGGAGG
5679213 TGGACACGGA-G
1 -GGACACGGAGG
5679224 GGA-ACGGAGG
1 GGACACGGAGG
5679234 TGGACACGGAGG
1 -GGACACGGAGG
5679246 G
1 G
5679247 TATGGTGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 10 0.26
10 8 0.21
11 8 0.21
12 12 0.32
ACGTcount: A:0.28, C:0.15, G:0.54, T:0.04
Consensus pattern (11 bp):
GGACACGGAGG
Found at i:5679271 original size:21 final size:21
Alignment explanation
Indices: 5679193--5679278 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
5679183 TAATAGAAGA
* * *
5679193 GGACACGGAGGGAACGGAGGT
1 GGACACGGAGGGTATGGTGGT
* * *
5679214 GGACACGGAGGGAACGGAGGT
1 GGACACGGAGGGTATGGTGGT
5679235 GGACACGGAGGGTATGGTGGT
1 GGACACGGAGGGTATGGTGGT
* *
5679256 GGCCACGGAGGTTATGGTGGT
1 GGACACGGAGGGTATGGTGGT
5679277 GG
1 GG
5679279 TGGCCACGGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.22, C:0.13, G:0.52, T:0.13
Consensus pattern (21 bp):
GGACACGGAGGGTATGGTGGT
Found at i:5679298 original size:24 final size:24
Alignment explanation
Indices: 5679249--5679299 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5679239 ACGGAGGGTA
* *
5679249 TGGTGGTGGCCACGGAGGTTATGG
1 TGGTGGTGGCCACGGAGGTCACGG
*
5679273 TGGTGGTGGCCACGGCGGTCACGG
1 TGGTGGTGGCCACGGAGGTCACGG
5679297 TGG
1 TGG
5679300 ACATGGAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.18, G:0.51, T:0.22
Consensus pattern (24 bp):
TGGTGGTGGCCACGGAGGTCACGG
Found at i:5684755 original size:22 final size:22
Alignment explanation
Indices: 5684717--5684760 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5684707 AAGAGTATAG
*
5684717 TAATTTATTAATATAATCAATT
1 TAATTTATTAATATAATAAATT
* *
5684739 TAATTTATTATTTTAATAAATT
1 TAATTTATTAATATAATAAATT
5684761 ATTTAAAATT
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:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTATTAATATAATAAATT
Found at i:5684874 original size:24 final size:24
Alignment explanation
Indices: 5684822--5684874 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
5684812 TATTTAATAA
*
5684822 ATTTTTATAGTATAAAATATGAAT
1 ATTTTTATAATATAAAATATGAAT
*
5684846 ATTTTAATAATAT-AAATATGAAT
1 ATTTTTATAATATAAAATATGAAT
5684869 ATTTTT
1 ATTTTT
5684875 TAAATCACGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
ATTTTTATAATATAAAATATGAAT
Found at i:5687395 original size:18 final size:18
Alignment explanation
Indices: 5687372--5687414 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5687362 GAATAAGTTT
5687372 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
5687390 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
5687408 TTAATTA
1 TTAATTA
5687415 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:5696223 original size:28 final size:28
Alignment explanation
Indices: 5696191--5696246 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5696181 CACGCGATAG
*
5696191 CCTCTTAGTATGACACATGACGAACATA
1 CCTCTTAGTATGACACATGAAGAACATA
5696219 CCTCTTAGTATGACACATGAAGAACATA
1 CCTCTTAGTATGACACATGAAGAACATA
5696247 AATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (28 bp):
CCTCTTAGTATGACACATGAAGAACATA
Found at i:5696887 original size:17 final size:16
Alignment explanation
Indices: 5696847--5696888 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5696837 AAATAACCCA
5696847 AAAAATAATTAATTAC
1 AAAAATAATTAATTAC
*
5696863 ATAAATAACTATAATT-C
1 AAAAATAA-T-TAATTAC
5696880 AAAAATAAT
1 AAAAATAAT
5696889 CATCTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 5 0.23
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAATTAATTAC
Found at i:5698113 original size:30 final size:30
Alignment explanation
Indices: 5698018--5698213 Score: 186
Period size: 29 Copynumber: 6.6 Consensus size: 30
5698008 GAGGTTCGAA
* *
5698018 GGTAAAAATGTAATTTTTTTTGAGAAGTTTGGG
1 GGTAAAAATGTAA---TTTTTAAGAAGTTTAGG
* * *
5698051 GGTAAAAATGTAATTTTT-GGAAGTTCAAG
1 GGTAAAAATGTAATTTTTAAGAAGTTTAGG
5698080 GGTAAAAATGTAATTTTTAAGAAGTTTAGG
1 GGTAAAAATGTAATTTTTAAGAAGTTTAGG
** *
5698110 GGT-AAAATGGGATTTTTGA-AAGTTTAGG
1 GGTAAAAATGTAATTTTTAAGAAGTTTAGG
* *
5698138 GGTAAAAATATAATTTTTAAGAAGTTTAGA
1 GGTAAAAATGTAATTTTTAAGAAGTTTAGG
* * * *
5698168 GGCAAAAATGTGA-TTTTAGAAAAATTTAGG
1 GGTAAAAATGTAATTTTTA-AGAAGTTTAGG
*
5698198 GGT-AAAATATAATTTT
1 GGTAAAAATGTAATTTT
5698214 AAAAAGCTTG
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
28 12 0.09
29 62 0.46
30 47 0.35
33 13 0.10
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (30 bp):
GGTAAAAATGTAATTTTTAAGAAGTTTAGG
Found at i:5698141 original size:58 final size:58
Alignment explanation
Indices: 5698034--5698213 Score: 218
Period size: 58 Copynumber: 3.1 Consensus size: 58
5698024 AATGTAATTT
* * * * * * *
5698034 TTTTTGAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTCAAGGGTAAAAATGTAA
1 TTTTTAAGAAGTTTAGGGGT-AAAATGTGATTTTTGAAAGTTTAGGGGTAAAAATATAA
*
5698093 TTTTTAAGAAGTTTAGGGGTAAAATGGGATTTTTGAAAGTTTAGGGGTAAAAATATAA
1 TTTTTAAGAAGTTTAGGGGTAAAATGTGATTTTTGAAAGTTTAGGGGTAAAAATATAA
** * *
5698151 TTTTTAAGAAGTTTAGAGGCAAAAATGTGATTTTAGAAAAATTTAGGGGT-AAAATATAA
1 TTTTTAAGAAGTTTAG-GGGTAAAATGTGATTTTTG-AAAGTTTAGGGGTAAAAATATAA
5698210 TTTT
1 TTTT
5698214 AAAAAGCTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
58 48 0.45
59 46 0.43
60 12 0.11
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (58 bp):
TTTTTAAGAAGTTTAGGGGTAAAATGTGATTTTTGAAAGTTTAGGGGTAAAAATATAA
Found at i:5698233 original size:59 final size:58
Alignment explanation
Indices: 5698079--5698241 Score: 170
Period size: 58 Copynumber: 2.8 Consensus size: 58
5698069 GGAAGTTCAA
* * * * * * * *
5698079 GGGTAAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAATGGGATTTTTGAAAGTTTAG
1 GGGTAAAAATATAATTTTTAAAAAGCTTAGAGGCAAAATGTGATTTTAGAAAATTTAG
* *
5698137 GGGTAAAAATATAATTTTTAAGAAGTTTAGAGGCAAAAATGTGATTTTAGAAAAATTTAG
1 GGGTAAAAATATAATTTTTAAAAAGCTTAGAGGC-AAAATGTGATTTTAG-AAAATTTAG
*
5698197 GGGT-AAAATATAA-TTTTAAAAAGCTT-GAGGTTCAAAATATGATTT
1 GGGTAAAAATATAATTTTTAAAAAGCTTAGAGG--CAAAATGTGATTT
5698242 CTTATAGTAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
57 4 0.04
58 53 0.58
59 23 0.25
60 12 0.13
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (58 bp):
GGGTAAAAATATAATTTTTAAAAAGCTTAGAGGCAAAATGTGATTTTAGAAAATTTAG
Found at i:5699089 original size:13 final size:13
Alignment explanation
Indices: 5699070--5699113 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5699060 TTGTAAAATA
*
5699070 AATTTGGATTTGT
1 AATTTGGACTTGT
*
5699083 GATTTGGACTTGT
1 AATTTGGACTTGT
*
5699096 AATTTTGGACTTTT
1 AA-TTTGGACTTGT
5699110 AATT
1 AATT
5699114 AAACTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (13 bp):
AATTTGGACTTGT
Found at i:5699104 original size:14 final size:14
Alignment explanation
Indices: 5699072--5699113 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5699062 GTAAAATAAA
* *
5699072 TTTGGATTTGTGA-
1 TTTGGACTTGTAAT
5699085 TTTGGACTTGTAAT
1 TTTGGACTTGTAAT
*
5699099 TTTGGACTTTTAAT
1 TTTGGACTTGTAAT
5699113 T
1 T
5699114 AAACTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.55
Consensus pattern (14 bp):
TTTGGACTTGTAAT
Found at i:5699165 original size:34 final size:34
Alignment explanation
Indices: 5699127--5699205 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
5699117 CTTTAAATTT
* *
5699127 AAATTCAAAATAAATTAAAACTCAGAATAAGTTA
1 AAATTTAAAATAAATTAAAACTCAAAATAAGTTA
* * *
5699161 AAATTTAAAATAAATTTAAACTTAAAATAATTTA
1 AAATTTAAAATAAATTAAAACTCAAAATAAGTTA
5699195 AAATTTAAAAT
1 AAATTTAAAAT
5699206 TTAAAATTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (34 bp):
AAATTTAAAATAAATTAAAACTCAAAATAAGTTA
Found at i:5699170 original size:7 final size:7
Alignment explanation
Indices: 5699158--5699213 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
5699148 TCAGAATAAG
5699158 TTAAAAT
1 TTAAAAT
5699165 TTAAAA-
1 TTAAAAT
5699171 -T-AAAT
1 TTAAAAT
*
5699176 TTAAACT
1 TTAAAAT
*
5699183 TAAAATAAT
1 T-TAA-AAT
5699192 TTAAAAT
1 TTAAAAT
5699199 TTAAAAT
1 TTAAAAT
5699206 TTAAAAT
1 TTAAAAT
5699213 T
1 T
5699214 GGGTTCAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
4 3 0.08
5 1 0.03
6 1 0.03
7 28 0.70
8 4 0.10
9 3 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
TTAAAAT
Found at i:5699202 original size:17 final size:17
Alignment explanation
Indices: 5699122--5699205 Score: 82
Period size: 17 Copynumber: 5.0 Consensus size: 17
5699112 TTAAACTTTA
*
5699122 AATTT-AAATTCAAAAT
1 AATTTAAAATTTAAAAT
* * * *
5699138 AAATTAAAACTCAGAAT
1 AATTTAAAATTTAAAAT
*
5699155 AAGTTAAAATTTAAAAT
1 AATTTAAAATTTAAAAT
*
5699172 AAATTT-AAACTTAAAAT
1 -AATTTAAAATTTAAAAT
5699189 AATTTAAAATTTAAAAT
1 AATTTAAAATTTAAAAT
5699206 TTAAAATTGG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.16
17 42 0.76
18 4 0.07
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTAAAATTTAAAAT
Found at i:5699753 original size:78 final size:78
Alignment explanation
Indices: 5699645--5700051 Score: 386
Period size: 78 Copynumber: 5.2 Consensus size: 78
5699635 TCTATCCCAT
* * * *
5699645 GATCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTTAGGGTAAAAGATAGAATGGCTG
1 GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
* *
5699710 TATTTTGCCCTAG
66 TAATCTGCCCTAG
* * * * *
5699723 GCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTA
1 GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
* ** *
5699788 CAATCTTTCCTAT
66 TAATCTGCCCTAG
* * * * *
5699801 AATCGAGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGTTG
1 GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
* * *
5699866 TAATCTACCCCAT
66 TAATCTGCCCTAG
* * * * * *
5699879 GATCGGGGTAAAAGACTGACTGCTGGTGATCTGCCCCAAG-TTCAGGGTAAGAA-ATCGAATAGT
1 GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTT-GGGGTAA-AAGATCGAATGGT
**
5699942 TACAATCTGCCCTAG
64 TGTAATCTGCCCTAG
* * * * * * * *
5699957 GCTCGGAGTAAGAAATTGGCTGATGGTAATTTGCCCCAAGCTTGGGGTAAAAGATCTAGTGGTTA
1 GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
* * *
5700022 CAATCTGCCCCAA
66 TAATCTGCCCTAG
* *
5700035 GCTCGGGATAAGAGATT
1 GATCGGGGTAAGAGATT
5700052 TACCAATGAT
Statistics
Matches: 264, Mismatches: 61, Indels: 8
0.79 0.18 0.02
Matches are distributed among these distances:
77 3 0.01
78 258 0.98
79 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (78 bp):
GATCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
TAATCTGCCCTAG
Found at i:5699850 original size:39 final size:38
Alignment explanation
Indices: 5699647--5700432 Score: 302
Period size: 39 Copynumber: 20.2 Consensus size: 38
5699637 TATCCCATGA
*
5699647 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAAGC
** * * * * * *
5699686 TTAGGGTAAAAGATAG--AATGGCTGTATTTTGCCCTAGGC
1 TCGGGGTAAGAGATTGCTGATGG-TG-A-TCTGCCCCAAGC
* *
5699725 TCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAAGC
* * ** * *
5699764 TCGGGGTAAAAGA-T-C-GAATGGTTACAATCTTTCCTATA-A
1 TCGGGGTAAGAGATTGCTG-ATGG-T--GATCTGCCCCA-AGC
*
5699803 TCGAGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGA-TTGCTGATGGTGATCTGCCCCAAGC
* * * * * * * *
5699842 TCGGGGTAAGAGATCGAATGGTTGTAATCTACCCCATGA
1 TCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAAGC
* * * *
5699881 TCGGGGTAAAAGACTGACTGCTGGTGATCTGCCCCAAGT
1 TCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAAGC
* * * * * *
5699920 TCAGGGTAAGA-AAT-C-GAATAGTTACAATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGCTG-AT-GGT--GATCTGCCCCAAGC
* * * *
5699959 TCGGAGTAAGAAATTGGCTGATGGTAATTTGCCCCAAGC
1 TCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAAGC
* * *
5699998 TTGGGGTAAAAGA-T-CT-AGTGGTTACAATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGCTGA-TGG-T--GATCTGCCCCAAGC
* * ** * * * *
5700037 TCGGGATAAGAGATTTACCAATGATGATTTGCCCCATGA
1 TCGGGGTAAGAGA-TTGCTGATGGTGATCTGCCCCAAGC
* * * * * * * *
5700076 TCGTGGTAAGAGATTGACTAATGGTGATTTACACTAGGT
1 TCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAAGC
* *
5700115 TC-GGGTAAGAGA-T-C-GAATGGCTGCAATCTGCTCCAGGC
1 TCGGGGTAAGAGATTGCTG-ATGG-TG--ATCTGCCCCAAGC
* * * *
5700153 TCGAGGTAACAAATTGACTGATGGTGATCTGCCCCAAGT
1 TCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAAGC
* * * *
5700192 TCGGGGTAAAAGA-T-C-GAATGGTTACAATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGCTG-ATGG-T--GATCTGCCCCAAGC
* * *
5700231 TCGGGGTAAGAGATTTGTTGATGATGATCTACCCCAAGC
1 TCGGGGTAAGAGA-TTGCTGATGGTGATCTGCCCCAAGC
* * *
5700270 TCGGGGTAAGAGA-T-CGGATGGCTGTAATCTGCCCCATGA
1 TCGGGGTAAGAGATTGCTGATGG-TG--ATCTGCCCCAAGC
* *
5700309 TCGGGGTAAGAGATTGGCTGATGGTGATATGCACCAAGC
1 TCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAAGC
* * **
5700348 TCGGGGTAAGAGATCGAATGACT-GCAATCTGCCCCAAGC
1 TCGGGGTAAGAGATTG-CTGA-TGGTGATCTGCCCCAAGC
* *
5700387 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGT
1 TCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAAGC
5700426 TCGGGGT
1 TCGGGGT
5700433 GAAAGATCTA
Statistics
Matches: 547, Mismatches: 139, Indels: 122
0.68 0.17 0.15
Matches are distributed among these distances:
35 8 0.01
36 26 0.05
37 11 0.02
38 33 0.06
39 412 0.75
40 8 0.01
41 14 0.03
42 30 0.05
43 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGCTGATGGTGATCTGCCCCAAGC
Found at i:5700070 original size:156 final size:156
Alignment explanation
Indices: 5699646--5700072 Score: 453
Period size: 156 Copynumber: 2.7 Consensus size: 156
5699636 CTATCCCATG
* * * * *
5699646 ATCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTTAGGGTAAAAGATAGAATGGCTGT
1 ATCGGAGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTGT
* * * * * * *
5699711 ATTTTGCCCTAGGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
66 AATCTGCCCCAAGCTCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCAAGCTCAGGGTAAAAG
* ** *
5699776 ATCGAATGGTTACAATCTTTCCTATA
131 ATCGAATAGTTACAATCTGCCCTAGA
* * *
5699802 ATC-GAGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGAATGGTTG
1 ATCGGA-GTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTG
* * * * * ** *
5699866 TAATCTACCCCATGATCGGGGTAAAAGACTGACTGCTGGTGATCTGCCCCAAGTTCAGGGTAAGA
65 TAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCAAGCTCAGGGTAA-A
*
5699931 A-ATCGAATAGTTACAATCTGCCCTAGG
129 AGATCGAATAGTTACAATCTGCCCTAGA
* * * * * * **
5699958 CTCGGAGTAAGAAATTGGCTGATGGTAATTTGCCCCAAGCTTGGGGTAAAAGATCTAGTGGTTAC
1 ATCGGAGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTGT
* * * * *
5700023 AATCTGCCCCAAGCTCGGGATAAGAGATTTACCAATGATGATTTGCCCCA
66 AATCTGCCCCAAGCTCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCA
5700073 TGATCGTGGT
Statistics
Matches: 218, Mismatches: 50, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
155 1 0.00
156 213 0.98
157 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (156 bp):
ATCGGAGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTGT
AATCTGCCCCAAGCTCGGGGTAAGAGATTGACTAATGGTGATCTGCCCCAAGCTCAGGGTAAAAG
ATCGAATAGTTACAATCTGCCCTAGA
Found at i:5700231 original size:78 final size:78
Alignment explanation
Indices: 5700113--5700440 Score: 399
Period size: 78 Copynumber: 4.2 Consensus size: 78
5700103 TTTACACTAG
* * * *
5700113 GTTC-GGGTAAGAGATCGAATGGCTGCAATCTGCTCCAGGCTCGAGGTAACAAATTGACTGATGG
1 GTTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTGGCTGATGG
5700177 TGATCTGCCCCAA
66 TGATCTGCCCCAA
* * * * * * * *
5700190 GTTCGGGGTAAAAGATCGAATGGTTACAATCTGCCCTAGGCTCGGGGTAAGAGATTTGTTGATGA
1 GTTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTGGCTGATGG
*
5700255 TGATCTACCCCAA
66 TGATCTGCCCCAA
* * * * * *
5700268 GCTCGGGGTAAGAGATCGGATGGCTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGCTGATGG
1 GTTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTGGCTGATGG
* *
5700333 TGATATGCACCAA
66 TGATCTGCCCCAA
* * * *
5700346 GCTCGGGGTAAGAGATCGAATGACTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG
1 GTTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTGGCTGATGG
*
5700411 TGATCTGCCCCAG
66 TGATCTGCCCCAA
5700424 GTTCGGGGTGAA-AGATC
1 GTTCGGGGT-AAGAGATC
5700441 TAATCTTCAA
Statistics
Matches: 212, Mismatches: 37, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
77 4 0.02
78 206 0.97
79 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (78 bp):
GTTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAAATTGGCTGATGG
TGATCTGCCCCAA
Found at i:5700257 original size:194 final size:195
Alignment explanation
Indices: 5699829--5700283 Score: 501
Period size: 194 Copynumber: 2.3 Consensus size: 195
5699819 GCTGATGGTG
* * * *
5699829 ATCTGCCCCAAGCTCGGGGTAAGAGA--T-CGAATGGTTGTAATCTACCCCATGATCGGGGTAAA
1 ATCTGCCCCAAGCTCGGGATAAGAGATTTACCAAT-GATG--ATCTACCCCATGATCGGGGTAAG
* ** * * *
5699891 AGACTGACTGCTGGTGATCTGCCCCAAGTTCAGGGTAAGAAATCGAATAGTTACAATCTGCCCTA
63 AGATTGACTAATGGTGATCTACACCAAGTTCAGGGTAAGAAATCGAATAGCTACAATCTGCCCTA
* * * * *
5699956 GGCTCGGAGTAAGAAATTGGCTGATGGTAATTTGCCCCAAGCTTGGGGTAAAAGATCTAGTGGTT
128 GGCTCGGAGTAACAAATTGACTGATGGTAATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTT
5700021 ACA
193 ACA
* * *
5700024 ATCTGCCCCAAGCTCGGGATAAGAGATTTACCAATGATGATTTGCCCCATGATCGTGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGATAAGAGATTTACCAATGATGATCTACCCCATGATCGGGGTAAGAGA
* * * * * *
5700089 TTGACTAATGGTGATTTACACTAGGTTC-GGGTAAGAGATCGAATGGCTGCAATCTGCTCC-AGG
66 TTGACTAATGGTGATCTACACCAAGTTCAGGGTAAGAAATCGAATAGCTACAATCTGC-CCTAGG
*
5700152 CTC-GAGGTAACAAATTGACTGATGGTGATCTGCCCCAAG-TTCGGGGTAAAAGATCGAATGGTT
130 CTCGGA-GTAACAAATTGACTGATGGTAATCTGCCCCAAGCTT-GGGGTAAAAGATCGAATGGTT
5700215 ACA
193 ACA
* * * **** * *
5700218 ATCTGCCCTAGGCTCGGGGTAAGAGATTTGTTGATGATGATCTACCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGATAAGAGATTTACCAATGATGATCTACCCCATGATCGGGGTAAGAGA
5700283 T
66 T
5700284 CGGATGGCTG
Statistics
Matches: 217, Mismatches: 37, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
193 4 0.02
194 136 0.63
195 69 0.32
197 4 0.02
198 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (195 bp):
ATCTGCCCCAAGCTCGGGATAAGAGATTTACCAATGATGATCTACCCCATGATCGGGGTAAGAGA
TTGACTAATGGTGATCTACACCAAGTTCAGGGTAAGAAATCGAATAGCTACAATCTGCCCTAGGC
TCGGAGTAACAAATTGACTGATGGTAATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGGTTACA
Found at i:5711814 original size:14 final size:14
Alignment explanation
Indices: 5711782--5711833 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
5711772 CACGAACAAT
5711782 TATACGAATGAATAAA
1 TATACGAA--AATAAA
*
5711798 TATACGAAAATAGA
1 TATACGAAAATAAA
*
5711812 TATAAGAAAAATAAA
1 TATACG-AAAATAAA
5711827 -ATACGAA
1 TATACGAA
5711834 TCATGAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 7 0.23
16 8 0.26
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (14 bp):
TATACGAAAATAAA
Found at i:5712023 original size:59 final size:60
Alignment explanation
Indices: 5711967--5712289 Score: 306
Period size: 59 Copynumber: 5.4 Consensus size: 60
5711957 TGAAACTTAA
* * *
5711967 TTTTAAAAAGTTTTAGGGGTAAAAATGTCA-TTTTAGGAAAGTTCG-GGGTAAAAACT-TAAT
1 TTTTGAAAAGTTTGAGGGGTAAAAATGTAATTTTTA-G-AAGTTCGAGGGTAAAAA-TATAAT
* * * *
5712027 TTTT--AAGGTTTGAGGTG-AAAAATATAATTTTTTTGAGAAGTTTGAGGGTAAAAATATAAT
1 TTTTGAAAAGTTTGAGGGGTAAAAATGTAA--TTTTT-AGAAGTTCGAGGGTAAAAATATAAT
* * * *
5712087 TTTTGAGAAGTTTGA-GGGTAAAAAATGTAATCTTTGGAAGTTCGAGGATAAAAATATAAT
1 TTTTGAAAAGTTTGAGGGGT-AAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATATAAT
* ** * * *
5712147 TTTTGAGAAGTTT-AGGGGTAAAAATGGGATTTTTAGAAGTTTGAGGGCAAAAATGTAAT
1 TTTTGAAAAGTTTGAGGGGTAAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATATAAT
* * * *
5712206 TTTTGAGAAGTTTGA-GGGTAAAAATGTGATTTTTAGAAGTTCGAGGGTAAAAATGTGAT
1 TTTTGAAAAGTTTGAGGGGTAAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATATAAT
* *
5712265 TTTAGAAAAGTTT-AGGGGTTAAAAT
1 TTTTGAAAAGTTTGAGGGGTAAAAAT
5712290 TAAAAATGTG
Statistics
Matches: 221, Mismatches: 29, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
57 8 0.04
58 11 0.05
59 113 0.51
60 66 0.30
61 7 0.03
62 7 0.03
63 9 0.04
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (60 bp):
TTTTGAAAAGTTTGAGGGGTAAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATATAAT
Found at i:5712028 original size:29 final size:29
Alignment explanation
Indices: 5711959--5712029 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
5711949 TTCGAGGTTG
5711959 AAACTTAATTTTAAAAAGTTTTAGGGGTAA
1 AAACTTAATTTTAAAAAG-TTTAGGGGTAA
* * *
5711989 AAA-TGTCATTTTAGGAAAG-TTCGGGGTAA
1 AAACT-TAATTTTA-AAAAGTTTAGGGGTAA
5712018 AAACTTAATTTT
1 AAACTTAATTTT
5712030 TAAGGTTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
29 19 0.56
30 11 0.32
31 4 0.12
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (29 bp):
AAACTTAATTTTAAAAAGTTTAGGGGTAA
Found at i:5712151 original size:29 final size:29
Alignment explanation
Indices: 5711974--5712267 Score: 267
Period size: 30 Copynumber: 9.9 Consensus size: 29
5711964 TAATTTTAAA
* * *
5711974 AAGTTTTAGGGGTAAAAATGTCATTTTAGG
1 AAGTTTGA-GGGTAAAAATGTAATTTTTGG
*
5712004 AAAGTTCG-GGGTAAAAACT-TAATTTTT--
1 -AAGTTTGAGGGTAAAAA-TGTAATTTTTGG
*
5712031 AAGGTTTGA-GGTGAAAAATATAATTTTTTTGAG
1 AA-GTTTGAGGGT-AAAAATGTAA--TTTTTG-G
*
5712064 AAGTTTGAGGGTAAAAATATAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
*
5712094 AAGTTTGAGGGTAAAAAATGTAATCTTTGG
1 AAGTTTGAGGGT-AAAAATGTAATTTTTGG
* * *
5712124 AAGTTCGAGGATAAAAATATAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
** *
5712154 AAGTTT-AGGGGTAAAAATGGGATTTTTAG
1 AAGTTTGA-GGGTAAAAATGTAATTTTTGG
*
5712183 AAGTTTGAGGGCAAAAATGTAATTTTTGAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTG-G
* *
5712213 AAGTTTGAGGGTAAAAATGTGATTTTTAG
1 AAGTTTGAGGGTAAAAATGTAATTTTTGG
* *
5712242 AAGTTCGAGGGTAAAAATGTGATTTT
1 AAGTTTGAGGGTAAAAATGTAATTTT
5712268 AGAAAAGTTT
Statistics
Matches: 222, Mismatches: 25, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.01
27 8 0.04
28 8 0.04
29 79 0.36
30 85 0.38
31 19 0.09
32 16 0.07
33 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (29 bp):
AAGTTTGAGGGTAAAAATGTAATTTTTGG
Found at i:5712281 original size:29 final size:29
Alignment explanation
Indices: 5711964--5712356 Score: 169
Period size: 30 Copynumber: 13.0 Consensus size: 29
5711954 GGTTGAAACT
5711964 TAATTTTA-AAAAGTTTTAGGGGTAAAAATG
1 TAATTTTAGAAAAG-TTTA-GGGTAAAAATG
* * **
5711994 TCATTTTAGGAAAGTTCGGGGTAAAAACT-
1 TAATTTTAGAAAAGTTTAGGGTAAAAA-TG
* * *
5712023 TAATTTT--TAAGGTTT-GAGGTGAAAAATA
1 TAATTTTAGAAAAGTTTAG-GGT-AAAAATG
* * *
5712051 TAATTTTTTTGAGAAGTTTGAGGGTAAAAATA
1 TAA--TTTTAGAAAAGTTT-AGGGTAAAAATG
* *
5712083 TAATTTTTGAGAAGTTTGAGGGTAAAAAATG
1 TAATTTTAGAAAAGTTT-AGGGT-AAAAATG
* * * *
5712114 TAATCTTT-G-GAAGTTCGAGGATAAAAATA
1 TAAT-TTTAGAAAAGTT-TAGGGTAAAAATG
* *
5712143 TAATTTTTGAGAAGTTTAGGGGTAAAAATGG
1 TAATTTTAGAAAAGTTTA-GGGTAAAAAT-G
* * *
5712174 GATTTTTAG--AAGTTTGAGGGCAAAAATG
1 TAATTTTAGAAAAGTTT-AGGGTAAAAATG
* *
5712202 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
1 TAATTTTAGAAAAGTTT-AGGGTAAAAATG
* *
5712232 TGATTTTTAG--AAGTTCGAGGGTAAAAATG
1 T-AATTTTAGAAAAGTT-TAGGGTAAAAATG
*
5712261 TGATTTTAGAAAAGTTTAGGGGTTAAAATTAAAAATG
1 TAATTTTAGAAAAGTTTA-GGG-------TAAAAATG
* * *
5712298 TGATTTTAGAAAAGTTTAGGGGTTAAAATA
1 TAATTTTAGAAAAGTTTA-GGGTAAAAATG
* * *
5712328 TAATTTTAAAAAAATTTGAGGGTCAAAAT
1 TAATTTTAGAAAAGTTT-AGGGTAAAAAT
5712357 ATGATTTTTG
Statistics
Matches: 291, Mismatches: 38, Indels: 68
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.00
27 9 0.03
28 24 0.08
29 61 0.21
30 116 0.40
31 28 0.10
32 18 0.06
33 3 0.01
34 1 0.00
37 30 0.10
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (29 bp):
TAATTTTAGAAAAGTTTAGGGTAAAAATG
Found at i:5712294 original size:37 final size:37
Alignment explanation
Indices: 5712253--5712326 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5712243 AGTTCGAGGG
5712253 TAAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
1 TAAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
5712290 TAAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
1 TAAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
5712327 ATAATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (37 bp):
TAAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAAT
Found at i:5714019 original size:17 final size:17
Alignment explanation
Indices: 5713999--5714073 Score: 93
Period size: 16 Copynumber: 4.6 Consensus size: 17
5713989 AATTAAACTT
5713999 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
* *
5714016 TAAATTTAAACTCAGAA
1 TAAATTTAAATTCAAAA
*
5714033 T-AGTTTAAATT-AAAA
1 TAAATTTAAATTCAAAA
*
5714048 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
5714065 T-AATTTAAA
1 TAAATTTAAA
5714074 ATTTAAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
15 4 0.08
16 25 0.50
17 21 0.42
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:5714072 original size:32 final size:32
Alignment explanation
Indices: 5714001--5714082 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
5713991 TTAAACTTTA
*
5714001 AATTTAAATTCAAAATAAATTTAAACTCAGAAT
1 AATTTAAATT-AAAATAAATTTAAACTCAAAAT
* * *
5714034 AGTTTAAATTAAAATAAATTTAAATTTAAAAT
1 AATTTAAATTAAAATAAATTTAAACTCAAAAT
5714066 AATTTAAAATTTAAAAT
1 AATTT-AAA-TTAAAAT
5714083 TGGGTTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 23 0.55
33 12 0.29
34 7 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (32 bp):
AATTTAAATTAAAATAAATTTAAACTCAAAAT
Found at i:5714075 original size:17 final size:17
Alignment explanation
Indices: 5713999--5714082 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
5713989 AATTAAACTT
*
5713999 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
* * *
5714016 TAAATTTAAACTCAGAA
1 TAAATTTAAATTTAAAA
*
5714033 T-AGTTTAAA-TTAAAA
1 TAAATTTAAATTTAAAA
5714048 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
5714065 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
5714082 T
1 T
5714083 TGGGTTCAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
15 5 0.09
16 19 0.33
17 34 0.59
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5732517 original size:14 final size:14
Alignment explanation
Indices: 5732472--5732518 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5732462 ATTGAATAGT
*
5732472 TTATAAAACCTTAT-
1 TTATAAAA-ATTATA
5732486 TTATAAAAATTATAA
1 TTATAAAAATTAT-A
*
5732501 TTATAAAATTTATA
1 TTATAAAAATTATA
5732515 TTAT
1 TTAT
5732519 TGTTTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 4 0.14
14 13 0.45
15 12 0.41
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATAAAAATTATA
Found at i:5733131 original size:20 final size:21
Alignment explanation
Indices: 5733095--5733138 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5733085 GTAAAAACGT
*
5733095 ATAAAAATAACATCC-AAACA
1 ATAAAAACAACATCCAAAACA
5733115 ATAAAAACAACGA-CCAAAACA
1 ATAAAAACAAC-ATCCAAAACA
5733136 ATA
1 ATA
5733139 GCAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.66, C:0.20, G:0.02, T:0.11
Consensus pattern (21 bp):
ATAAAAACAACATCCAAAACA
Found at i:5733367 original size:18 final size:18
Alignment explanation
Indices: 5733344--5733386 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
5733334 ACTCATTTTT
*
5733344 CAAACCTATATTTTTGTC
1 CAAACCTATATTTTTATC
5733362 CAAACCTATATTTTTATC
1 CAAACCTATATTTTTATC
*
5733380 TAAACCT
1 CAAACCT
5733387 TCTCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (18 bp):
CAAACCTATATTTTTATC
Found at i:5735233 original size:30 final size:30
Alignment explanation
Indices: 5735197--5735277 Score: 162
Period size: 30 Copynumber: 2.7 Consensus size: 30
5735187 ACATTACAAG
5735197 TGAATCTAAAATATTATTTCTTTTTTTTAA
1 TGAATCTAAAATATTATTTCTTTTTTTTAA
5735227 TGAATCTAAAATATTATTTCTTTTTTTTAA
1 TGAATCTAAAATATTATTTCTTTTTTTTAA
5735257 TGAATCTAAAATATTATTTCT
1 TGAATCTAAAATATTATTTCT
5735278 AAATAATCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (30 bp):
TGAATCTAAAATATTATTTCTTTTTTTTAA
Found at i:5735629 original size:30 final size:30
Alignment explanation
Indices: 5735593--5735667 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
5735583 ATGTCACACC
* *
5735593 AACAATTAATTAATTTTTAAAAAAATTATA
1 AACAATTAATTAAATTTTAAAAAAAGTATA
**
5735623 AACAATT-ATTAAAATTTTGTAAAAAGTATA
1 AACAATTAATT-AAATTTTAAAAAAAGTATA
5735653 AA-AATTTAATTAAAT
1 AACAA-TTAATTAAAT
5735668 AATAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 5 0.13
30 30 0.79
31 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
AACAATTAATTAAATTTTAAAAAAAGTATA
Found at i:5735958 original size:31 final size:31
Alignment explanation
Indices: 5735901--5735965 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5735891 TTAATAAAAT
* * *
5735901 ATTTGGTACCTGAACTAGAATTTTTTTTTTA
1 ATTTGGTACCTAAACTAGAATCTTTTTTTAA
*
5735932 ATTTGGTACCTAAACTTGACA-CTTTTTTTAA
1 ATTTGGTACCTAAACTAGA-ATCTTTTTTTAA
5735963 ATT
1 ATT
5735966 GATACTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTTGGTACCTAAACTAGAATCTTTTTTTAA
Found at i:5736605 original size:15 final size:14
Alignment explanation
Indices: 5736585--5736633 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
5736575 TTTCAAAACC
5736585 TTAAAAATATAAAGA
1 TTAAAAATATAAA-A
*
5736600 TTAAAAATAATCAAA
1 TTAAAAAT-ATAAAA
5736615 TTAAAAA-ATATAAA
1 TTAAAAATATA-AAA
5736629 TTAAA
1 TTAAA
5736634 TTTATAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
15 16 0.53
16 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
TTAAAAATATAAAA
Found at i:5745952 original size:2 final size:2
Alignment explanation
Indices: 5745945--5745971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5745935 GTAAACCTTA
5745945 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5745972 AACTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5748557 original size:14 final size:13
Alignment explanation
Indices: 5748520--5748559 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5748510 GTATTGAAAG
*
5748520 AAAGAAAGAAAGA
1 AAAGAAAGAAGGA
5748533 AAAGAAAGAAGGA
1 AAAGAAAGAAGGA
*
5748546 AGAAGGAAGAAGGA
1 A-AAGAAAGAAGGA
5748560 GAATGAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGGA
Found at i:5748614 original size:13 final size:12
Alignment explanation
Indices: 5748586--5748610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5748576 AATGTAATGC
5748586 ATTTATTTTTAA
1 ATTTATTTTTAA
5748598 ATTTATTTTTAA
1 ATTTATTTTTAA
5748610 A
1 A
5748611 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:5749288 original size:16 final size:16
Alignment explanation
Indices: 5749244--5749292 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5749234 AAATACTCTA
5749244 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
*
5749260 -A-TAATATA-AAAAAT
1 AATTAAT-TACCAAAAT
5749274 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
5749290 AAT
1 AAT
5749293 ATCCTCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:5749359 original size:30 final size:30
Alignment explanation
Indices: 5749325--5749416 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
5749315 AAATGGTACA
5749325 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
** * * * *
5749355 AAAT-AAT-GGTGTGTGGATACCATTTTGGT
1 AAATAAATATTTATTTTG-TACCATTTTAGT
*
5749384 ATATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
5749414 AAA
1 AAA
5749417 CAACCCATTT
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 20 0.44
31 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:5751328 original size:45 final size:45
Alignment explanation
Indices: 5751254--5751345 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
5751244 ACCTAGCTCA
*
5751254 TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAACCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
5751299 TCAAACCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAACCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
5751344 TC
1 TC
5751346 TACTCCTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.18
Consensus pattern (45 bp):
TCAAACCAAAGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:5754590 original size:19 final size:19
Alignment explanation
Indices: 5754554--5754591 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5754544 ACCTTTTTAA
*
5754554 TTCTCCTCTTTTTCTCTTT
1 TTCTCCTCTTTCTCTCTTT
5754573 TTCTCCTCTGTTCT-TCTTT
1 TTCTCCTCT-TTCTCTCTTT
5754592 CTGTTTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (19 bp):
TTCTCCTCTTTCTCTCTTT
Found at i:5754925 original size:35 final size:36
Alignment explanation
Indices: 5754855--5754927 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
5754845 TATTTTTATT
*
5754855 AAATTAATAATTTTTTAATATTACTTTAGTCAAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
*
5754891 AAATAAATAATTTTTGT-ATATTATTTTAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTTAGTCAAATA
5754926 AA
1 AA
5754928 TACTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 26 0.76
37 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:5758277 original size:30 final size:32
Alignment explanation
Indices: 5758227--5758287 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
5758217 TCAAGAATAA
* * *
5758227 CGAATTAAATTTTGAATAAAAATA-TTAAATT
1 CGAAGTAAATTTTAAATAAAAAAAGTTAAATT
5758258 CGAAGTAAA-TTTAAATAAAAAAAGTTAAAT
1 CGAAGTAAATTTTAAATAAAAAAAGTTAAAT
5758288 CGATATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (32 bp):
CGAAGTAAATTTTAAATAAAAAAAGTTAAATT
Found at i:5758364 original size:2 final size:2
Alignment explanation
Indices: 5758353--5758460 Score: 56
Period size: 2 Copynumber: 57.5 Consensus size: 2
5758343 TTTTTAAGTT
5758353 TA TA -A TA TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5758391 TT TA TA TCA T- TCA -A AA T- TA AA TA TA CTA TA T- TA TA -A AA
1 TA TA TA T-A TA T-A TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
5758429 TA AA TA TA AA GA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5758461 GATAGCAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
1 10 0.12
2 69 0.83
3 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5758371 original size:9 final size:9
Alignment explanation
Indices: 5758357--5758397 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
5758347 TAAGTTTATA
5758357 ATATATATT
1 ATATATATT
5758366 ATATATATAT
1 ATATATAT-T
5758376 ATATATATT
1 ATATATATT
5758385 ATATA-ATT
1 ATATATATT
5758393 -TATAT
1 ATATAT
5758398 CATTCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 4 0.13
8 3 0.10
9 14 0.47
10 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:5762639 original size:17 final size:17
Alignment explanation
Indices: 5762619--5762652 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5762609 TTAGATAAAA
5762619 TTGTATATTATATTTAT
1 TTGTATATTATATTTAT
* *
5762636 TTGTTTATTATTTTTAT
1 TTGTATATTATATTTAT
5762653 CACTAATTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTGTATATTATATTTAT
Found at i:5764172 original size:5 final size:5
Alignment explanation
Indices: 5764162--5764193 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5764152 TATAATCCAG
5764162 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA AC
1 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA AC
5764194 TTATCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:5767542 original size:22 final size:22
Alignment explanation
Indices: 5767514--5767560 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
5767504 TTTTTTAGGG
*
5767514 TTAGAGTTTT-TTAGTTTAGGTT
1 TTAGAGTTTTATT-GTTTAGGAT
5767536 TTAGAGTTTTATTGTTTAGGAT
1 TTAGAGTTTTATTGTTTAGGAT
5767558 TTA
1 TTA
5767561 AGGGTGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (22 bp):
TTAGAGTTTTATTGTTTAGGAT
Found at i:5769128 original size:63 final size:63
Alignment explanation
Indices: 5769034--5769192 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 63
5769024 GACTTCGATG
* * * *
5769034 AAAATGCATTTGCTGAAACGTGTTTTCAAGCACATAAAACCATTTCATTATTATTATTCAATA
1 AAAACGCATCTGCTGAAACGTGTTTTCAAGCACAGAAAACCATTTCATTACTATTATTCAATA
* * * * * *
5769097 AAAAGGTATCTGCTGAAACGTGTTTTCAAGCACAGAAGACCTTTTCATTACTATTATTCGATG
1 AAAACGCATCTGCTGAAACGTGTTTTCAAGCACAGAAAACCATTTCATTACTATTATTCAATA
* ***
5769160 AAAACGCATCTACTGAAACACATTTTCAAGCAC
1 AAAACGCATCTGCTGAAACGTGTTTTCAAGCAC
5769193 GCCTTCCCTC
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (63 bp):
AAAACGCATCTGCTGAAACGTGTTTTCAAGCACAGAAAACCATTTCATTACTATTATTCAATA
Found at i:5769981 original size:12 final size:12
Alignment explanation
Indices: 5769962--5770002 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5769952 TAAAAAGCAT
5769962 AAAAAATAAAAG
1 AAAAAATAAAAG
* *
5769974 AGAAAATAAAAT
1 AAAAAATAAAAG
5769986 AAAAAATAAAAG
1 AAAAAATAAAAG
5769998 CAAAA
1 -AAAA
5770003 TGATTGAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAAAATAAAAG
Found at i:5778808 original size:27 final size:27
Alignment explanation
Indices: 5778766--5778828 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
5778756 CACTATCACT
*
5778766 ATCTCCCTCTGGAACAACTTCCTCCCC
1 ATCTCCCTCTGAAACAACTTCCTCCCC
* *
5778793 ATCTCCTTCTGAAACAACTTCCTCCCT
1 ATCTCCCTCTGAAACAACTTCCTCCCC
5778820 ATCTCCCTC
1 ATCTCCCTC
5778829 CCTATCTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.19, C:0.46, G:0.05, T:0.30
Consensus pattern (27 bp):
ATCTCCCTCTGAAACAACTTCCTCCCC
Found at i:5778828 original size:12 final size:12
Alignment explanation
Indices: 5778813--5778839 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5778803 GAAACAACTT
5778813 CCTCCCTATCTC
1 CCTCCCTATCTC
5778825 CCTCCCTATCTC
1 CCTCCCTATCTC
5778837 CCT
1 CCT
5778840 TTGAAACAAC
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:0.07, C:0.59, G:0.00, T:0.33
Consensus pattern (12 bp):
CCTCCCTATCTC
Found at i:5778837 original size:39 final size:39
Alignment explanation
Indices: 5778786--5778866 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
5778776 GGAACAACTT
5778786 CCTCCCCATCT-CCTTCTGAAACAACTTCCTCCCTATCTC
1 CCTCCCCATCTCCCTT-TGAAACAACTTCCTCCCTATCTC
* *
5778825 CCTCCCTATCTCCCTTTGAAACAACTTCCTCCTTATCTC
1 CCTCCCCATCTCCCTTTGAAACAACTTCCTCCCTATCTC
5778864 CCT
1 CCT
5778867 TTGAAACAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 35 0.90
40 4 0.10
ACGTcount: A:0.17, C:0.47, G:0.02, T:0.33
Consensus pattern (39 bp):
CCTCCCCATCTCCCTTTGAAACAACTTCCTCCCTATCTC
Found at i:5778863 original size:27 final size:27
Alignment explanation
Indices: 5778825--5778916 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
5778815 TCCCTATCTC
* *
5778825 CCTCCCTATCTCCCTTTGAAACAACTT
1 CCTCCTTATCTCCCTTTGAAACAGCTT
5778852 CCTCCTTATCTCCCTTTGAAACAGCTT
1 CCTCCTTATCTCCCTTTGAAACAGCTT
* * * * *
5778879 CCTCATTGTCTCCCTCTGGAATAGCTT
1 CCTCCTTATCTCCCTTTGAAACAGCTT
5778906 CCTCCTTATCT
1 CCTCCTTATCT
5778917 TCCAAGTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.17, C:0.38, G:0.08, T:0.37
Consensus pattern (27 bp):
CCTCCTTATCTCCCTTTGAAACAGCTT
Found at i:5778891 original size:66 final size:66
Alignment explanation
Indices: 5778764--5778894 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
5778754 GTCACTATCA
* *
5778764 CTATCTCCCTCTGGAACAACTTCCTCCCCATCTCCTTCTGAAACAACTTCCTCCCTATCTCCCTC
1 CTATCTCCCTCTGAAACAACTTCCTCCCCATCTCCTTCTGAAACAACTTCCTCACTATCTCCCTC
5778829 C
66 C
* ** * * *
5778830 CTATCTCCCTTTGAAACAACTTCCTCCTTATCTCCCTT-TGAAACAGCTTCCTCATTGTCTCCCT
1 CTATCTCCCTCTGAAACAACTTCCTCCCCATCT-CCTTCTGAAACAACTTCCTCACTATCTCCCT
5778894 C
65 C
5778895 TGGAATAGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 52 0.93
67 4 0.07
ACGTcount: A:0.18, C:0.43, G:0.05, T:0.34
Consensus pattern (66 bp):
CTATCTCCCTCTGAAACAACTTCCTCCCCATCTCCTTCTGAAACAACTTCCTCACTATCTCCCTC
C
Found at i:5780278 original size:18 final size:18
Alignment explanation
Indices: 5780252--5780286 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5780242 AATGGTGAAT
*
5780252 AATTTTGTTTTCAAATTA
1 AATTATGTTTTCAAATTA
*
5780270 AATTATGTTTTTAAATT
1 AATTATGTTTTCAAATT
5780287 GCGATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTATGTTTTCAAATTA
Found at i:5781074 original size:22 final size:19
Alignment explanation
Indices: 5781044--5781093 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
5781034 CTTTAATTTC
*
5781044 TTTT-TTTCTTTATATTTTG
1 TTTTCTTTCTTT-GATTTTG
5781063 CTTCTTCTTTCTTTGATTTTG
1 -TT-TTCTTTCTTTGATTTTG
5781084 TTTTCTTTCT
1 TTTTCTTTCT
5781094 CCGGCTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.30
20 4 0.15
21 8 0.30
22 7 0.26
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTTCTTTCTTTGATTTTG
Found at i:5800772 original size:52 final size:52
Alignment explanation
Indices: 5800687--5800880 Score: 280
Period size: 52 Copynumber: 3.7 Consensus size: 52
5800677 TAAATGCAAA
* * *
5800687 AAGGTCTGATGACTATGTGTCATAGTGATTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
*
5800739 AAGGTCCGATGACTATGTGTCATCGCGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * * *
5800791 GAGGTCTGATGGCTATGTCTCATCGTGAGCATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
5800843 GAGGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
5800881 GAAATGAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 128 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:5804837 original size:88 final size:89
Alignment explanation
Indices: 5804686--5804855 Score: 204
Period size: 89 Copynumber: 1.9 Consensus size: 89
5804676 TTTTTTATGA
* * * * *
5804686 TTTTTTTTGCACTCACTTGGGTATTTGAATTTTTAAAATGCATACAAAAATCCTCAAACTTTTTT
1 TTTTTTTCGCACTCAATTGGGTACTTGAACTTTTAAAATGCATACAAAAACCCTCAAACTTTTTT
5804751 -AAACAAAA-CAATTAAGTCTCTAC
66 CAAA-AAAAGCAATTAAGTCTCTAC
** *
5804774 TTTTATTTCGCACTCAATTGGG-ACTTGAACTTTTAAAATGCATTA-AGAAGGCCCTCAAATTTT
1 TTTT-TTTCGCACTCAATTGGGTACTTGAACTTTTAAAATGCA-TACA-AAAACCCTCAAACTTT
5804837 TTTCAAAAAAAGCAATTAA
63 TTTCAAAAAAAGCAATTAA
5804856 TGTAATACCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 23 0.33
89 36 0.52
90 10 0.14
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (89 bp):
TTTTTTTCGCACTCAATTGGGTACTTGAACTTTTAAAATGCATACAAAAACCCTCAAACTTTTTT
CAAAAAAAGCAATTAAGTCTCTAC
Found at i:5806285 original size:80 final size:80
Alignment explanation
Indices: 5806143--5806300 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 80
5806133 ACTTGTATCC
* * *
5806143 AAATTCGTCAATTCATGGCACCAGGTGCCTAGCGGATAAATCGCGATAAGTGAGCCTAGCTCTAG
1 AAATCCGTAAATTCATGGCACCAGGTGCCTAGCGGATAAATCGCGATAAGTGAGCCCAGCTCTAG
5806208 TTGGATTAACCAACA
66 TTGGATTAACCAACA
5806223 AAATCCGTAAATTCATGGCACCCA-GTGCCTAGCGGATAAA-CTGCGATAAGTGAGCCCAGCTCT
1 AAATCCGTAAATTCATGGCA-CCAGGTGCCTAGCGGATAAATC-GCGATAAGTGAGCCCAGCTCT
5806286 AGTTGGATTAACCAA
64 AGTTGGATTAACCAA
5806301 TGGTTTTGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
79 1 0.01
80 69 0.95
81 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (80 bp):
AAATCCGTAAATTCATGGCACCAGGTGCCTAGCGGATAAATCGCGATAAGTGAGCCCAGCTCTAG
TTGGATTAACCAACA
Found at i:5812442 original size:14 final size:15
Alignment explanation
Indices: 5812412--5812445 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5812402 CTTTTATACT
*
5812412 TTAATTATAAGTTAA
1 TTAATCATAAGTTAA
5812427 TTAATCATAA-TTAA
1 TTAATCATAAGTTAA
5812441 TTAAT
1 TTAAT
5812446 TTAAGTTTAA
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:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATCATAAGTTAA
Found at i:5814216 original size:23 final size:23
Alignment explanation
Indices: 5814185--5814275 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
5814175 ACCGAACAAA
* * *
5814185 CATACATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
5814208 CATAAATCACAATAAAACTTAAG
1 CATAAATCACATTAATATTTAAG
*
5814231 TATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
5814254 CACAAATCACATTAATATTTAA
1 CATAAATCACATTAATATTTAA
5814276 CACATTTATT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.32
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:5814823 original size:36 final size:36
Alignment explanation
Indices: 5814773--5814850 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
5814763 AATATAACCA
** *
5814773 ATCACATGGTATGAAAAACATACCCACATATTTACT
1 ATCACATGACATGAAAAACATACCCACATATTCACT
* *
5814809 ATCACATGACATGAATAACATACCCTCATATTCACT
1 ATCACATGACATGAAAAACATACCCACATATTCACT
*
5814845 TTCACA
1 ATCACA
5814851 ATAGTCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.28
Consensus pattern (36 bp):
ATCACATGACATGAAAAACATACCCACATATTCACT
Found at i:5827908 original size:17 final size:18
Alignment explanation
Indices: 5827886--5827919 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5827876 TATAATTTTA
*
5827886 TTTTTATTAATT-TAAAT
1 TTTTTATAAATTATAAAT
5827903 TTTTTATAAATTATAAA
1 TTTTTATAAATTATAAA
5827920 GAGGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTATAAATTATAAAT
Found at i:5830565 original size:25 final size:25
Alignment explanation
Indices: 5830531--5830581 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5830521 AACTTGTCTA
5830531 ACTTGTCAAAGAGTTAAAGTAAAAC
1 ACTTGTCAAAGAGTTAAAGTAAAAC
5830556 ACTTGTCAAAGAGTTAAAGTAAAAC
1 ACTTGTCAAAGAGTTAAAGTAAAAC
5830581 A
1 A
5830582 TCATGTTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
ACTTGTCAAAGAGTTAAAGTAAAAC
Found at i:5835201 original size:14 final size:15
Alignment explanation
Indices: 5835182--5835210 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5835172 AATGCTTTTA
5835182 ATATGAA-TGATATG
1 ATATGAATTGATATG
5835196 ATATGAATTGATATG
1 ATATGAATTGATATG
5835211 TGGAAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
ATATGAATTGATATG
Found at i:5841968 original size:17 final size:16
Alignment explanation
Indices: 5841913--5841971 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
5841903 TAGGTTTTCA
*
5841913 TGTAATTGGGCTTGTTGG
1 TGTAATTAGGCTTG--GG
5841931 -GTAATTAGGCTTGGG
1 TGTAATTAGGCTTGGG
*
5841946 TGTAATTAGGTTTGGG
1 TGTAATTAGGCTTGGG
5841962 TTGTAATTAG
1 -TGTAATTAG
5841972 AAATTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.05
16 14 0.38
17 21 0.57
ACGTcount: A:0.19, C:0.03, G:0.36, T:0.42
Consensus pattern (16 bp):
TGTAATTAGGCTTGGG
Found at i:5842533 original size:47 final size:48
Alignment explanation
Indices: 5842457--5842550 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
5842447 GCATTAAGCT
* *
5842457 TCGCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGA
1 TCGCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGA
* *
5842505 TCGCTTCGTTG-TTTGATCCACTTCTTTGTTTCTCATCAAGAAGATG
1 TCGCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATG
5842551 GGGTTTGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 32 0.76
48 10 0.24
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (48 bp):
TCGCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGA
Found at i:5842726 original size:124 final size:123
Alignment explanation
Indices: 5842386--5842817 Score: 598
Period size: 122 Copynumber: 3.5 Consensus size: 123
5842376 GTGTTTGTAA
* * * * *
5842386 CTTCATC-TTTTGGTACACTTCTCTATATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCGCA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACA
* * * *
5842450 TTAAGCTTCGCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGATCG
66 TTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCG
* * * * * *
5842508 CTTCGTTG-TTTGATCCACTTCTTTGTTTCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCATA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACA
*
5842572 TTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTATATCTCATCAGGAAGCTGACCG
66 TTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCG
*
5842630 CTTCATCGTTTTGATCCACTTCTCTGTATCTGATCAGGAAGATGGGGGTTTGAAGTTTCACTCAC
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCAC
* * * *
5842695 ATTGAGCTTTGCTTCATTGTTTTGGTCCACTTCTCTACATCTCATTAGGAAGATGACTG
65 ATTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCG
* * * *
5842754 TTTCATCGTTTTTATCCACTTTTTTTGTATCTCATCAGGAAGATGGAGGTTTGAAGTTTCACTC
1 CTTCATCGTTTTGATCCAC-TTCTCTGTATCTCATCAGGAAGATGG-GGTTTGAAGTTTCACTC
5842818 TACTCCACTG
Statistics
Matches: 272, Mismatches: 33, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
122 111 0.41
123 30 0.11
124 93 0.34
125 38 0.14
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (123 bp):
CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACA
TTGAGCTTCGCTTCATTGTTTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCG
Found at i:5842911 original size:48 final size:48
Alignment explanation
Indices: 5842849--5842943 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
5842839 ATGTTAAGCC
* * * * *
5842849 CTGCTTTATTGTTTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGA
1 CTGCTTCATCGTTTTGATCCACTTATCTGTATCTCATCAAGAAGATGA
*
5842897 CTGCTTCATCGTTTTGATCCACTTATTTGTATCTCATCAAGAAGATG
1 CTGCTTCATCGTTTTGATCCACTTATCTGTATCTCATCAAGAAGATG
5842944 GGGGTTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (48 bp):
CTGCTTCATCGTTTTGATCCACTTATCTGTATCTCATCAAGAAGATGA
Found at i:5842986 original size:145 final size:145
Alignment explanation
Indices: 5842696--5843147 Score: 629
Period size: 145 Copynumber: 3.1 Consensus size: 145
5842686 TTCACTCACA
* * ** * *
5842696 TTGAGCTTTGCTTCATTGTTTTGGTCCACTTCTCTACATCTCATTAGGAAGATGACTGTTTCATC
1 TTGAGCTCTGCTTCATTGTTTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATC
* * *
5842761 GTTTTTATCCACTTTTTTTGTATCTCATCAGGAAGATGGAGGTTTGAAGTTTCACTCTACTCCAC
66 GTTTTGATCCAC-TTATTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCTACTCCAC
5842826 TGTAACCTCAGGGATG
130 TGTAACCTCAGGGATG
* * * *
5842842 TTAAGCCCTGCTTTATTGTTTTGGTTCACTTCTCTGTATCTCATCAAGAAGATGACTGCTTCATC
1 TTGAGCTCTGCTTCATTGTTTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATC
*
5842907 GTTTTGATCCACTTATTTGTATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACT
66 GTTTTGATCCACTTATTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACT
*
5842972 GTAACCTTAGGGATG
131 GTAACCTCAGGGATG
* * * *
5842987 TTGAGCTCTACTTCATTGTTTT-GATCAATTTCTCTGTATCTCATCAGGAAGATGA-TCGCTTAA
1 TTGAGCTCTGCTTCATTGTTTTGGTTC-ACTTCTCTGTATCTCATCAGGAAGATGACT-GCTTCA
* * * * * **
5843050 TTGTGTTGATCCACTTCTCTGTATCTCATCAGGAAGATGAGGGTTTGAAGTTTCACTCTGTTCCA
64 TCGTTTTGATCCACTTATTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCTACTCCA
5843115 CTGTAACCTCAGGGATG
129 CTGTAACCTCAGGGATG
5843132 TTGAGCTCTGCTTCAT
1 TTGAGCTCTGCTTCAT
5843148 GTAAAGCATG
Statistics
Matches: 271, Mismatches: 33, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
144 4 0.01
145 201 0.74
146 66 0.24
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (145 bp):
TTGAGCTCTGCTTCATTGTTTTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACTGCTTCATC
GTTTTGATCCACTTATTTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACT
GTAACCTCAGGGATG
Found at i:5848690 original size:28 final size:28
Alignment explanation
Indices: 5848650--5848703 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
5848640 GTTATCCGAT
* *
5848650 TTACTCCCTGTTGACCCGAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGCTCATGC
5848678 TTACTCCCTGTTGACCCAAAGCTCAT
1 TTACTCCCTGTTGACCCAAAGCTCAT
5848704 ACTTGTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGCTCATGC
Done.