Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 10 of 204
Found at i:3158358 original size:14 final size:14
Alignment explanation
Indices: 3158339--3158380 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
3158329 TCACCACTCT
3158339 TAATTATAAAAAAA
1 TAATTATAAAAAAA
3158353 TAATTATAATAAAAA
1 TAATTATAA-AAAAA
*
3158368 TAATAATAAAAAA
1 TAATTATAAAAAA
3158381 TCTTAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATTATAAAAAAA
Found at i:3169574 original size:60 final size:60
Alignment explanation
Indices: 3169496--3169622 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
3169486 CTAAAACTAA
* * ** * *
3169496 AAAAAATCAATAAATTTAGC-CATTAATGTTTACAAAATTTGTCATTTGAGTTTGAATTCT
1 AAAAATTCAATAAATTTAGCGC-TCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
* *
3169556 AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTTAATTTTAATTCT
1 AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
3169616 AAAAATT
1 AAAAATT
3169623 TTTTAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (60 bp):
AAAAATTCAATAAATTTAGCGCTCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
Found at i:3170448 original size:31 final size:30
Alignment explanation
Indices: 3170353--3170450 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 30
3170343 AGAAACAAAA
* *
3170353 CTAAATTAACAAATTTTATAAATGTTGAGGG
1 CTAAATT-ATAAATTTTATAAATATTGAGGG
** * ** **
3170384 CTAAATCTATTGATTTTTTTGA-ATT-AGAA
1 CTAAAT-TATAAATTTTATAAATATTGAGGG
3170413 CTAAATTGATAAATTTTATAAATATTGAGGG
1 CTAAATT-ATAAATTTTATAAATATTGAGGG
3170444 CTAAATT
1 CTAAATT
3170451 TTTTGAATTT
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
28 1 0.02
29 17 0.36
30 5 0.11
31 23 0.49
32 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (30 bp):
CTAAATTATAAATTTTATAAATATTGAGGG
Found at i:3170483 original size:60 final size:60
Alignment explanation
Indices: 3170351--3170467 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
3170341 TTAGAAACAA
* * * * *
3170351 AACTAAATTAACAAATTTTATAAATGTTGAGGGCTAAATCTATTGATTTTTTTGAATTAG
1 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATTAG
* *
3170411 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATTTTTTGA-ATTTTTAAATT
1 AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATT
3170468 TAGGATCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 9 0.18
60 41 0.82
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (60 bp):
AACTAAATTGATAAATTTTATAAATATTGAGGGCTAAATCTATTGATATTTTTAAATTAG
Found at i:3174387 original size:12 final size:12
Alignment explanation
Indices: 3174370--3174398 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3174360 GAGTTGACTC
3174370 TGGTGATGGTGG
1 TGGTGATGGTGG
3174382 TGGTGATGGTGG
1 TGGTGATGGTGG
3174394 TGGTG
1 TGGTG
3174399 GTGAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.59, T:0.34
Consensus pattern (12 bp):
TGGTGATGGTGG
Found at i:3174391 original size:18 final size:18
Alignment explanation
Indices: 3174314--3174401 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 18
3174304 CTTAGATGGG
* * *
3174314 GGTGGTGGTGACGGTGGC
1 GGTGATGGTGATGGTGGT
3174332 GGTGATGGTGATGGTGG-
1 GGTGATGGTGATGGTGGT
* * *
3174349 GG-G-TGGCGATGGAGTT
1 GGTGATGGTGATGGTGGT
* *
3174365 GACT-CTGGTGATGGTGGT
1 G-GTGATGGTGATGGTGGT
*
3174383 GGTGATGGTGGTGGTGGT
1 GGTGATGGTGATGGTGGT
3174401 G
1 G
3174402 AAGAAGAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 9 0.17
16 2 0.04
17 3 0.06
18 39 0.74
ACGTcount: A:0.09, C:0.06, G:0.57, T:0.28
Consensus pattern (18 bp):
GGTGATGGTGATGGTGGT
Found at i:3177971 original size:21 final size:21
Alignment explanation
Indices: 3177930--3177971 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3177920 TGTTGAAGTC
* *
3177930 GTAATTAGTTATTAGTTGATT
1 GTAATTAGTTATCAGTCGATT
3177951 GTAATTA-TTATCAGTACGATT
1 GTAATTAGTTATCAGT-CGATT
3177972 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
GTAATTAGTTATCAGTCGATT
Found at i:3186014 original size:44 final size:43
Alignment explanation
Indices: 3185965--3186333 Score: 231
Period size: 44 Copynumber: 8.6 Consensus size: 43
3185955 ATCTACTCTG
* * * *
3185965 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTTGACTTCAATCTGCTCCA
* * ** * * *
3186009 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGC
1 CTGTAACCTCAGGGAGATAAGATCTTGACTTCAATCTGCTCC-A
* *
3186053 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCT-TGACTTCAATCTGCTCCA
* ** *
3186097 CTGTAACCTCAGGGAGATAAGATC-TGAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCTTG-A--CTTCAATCTGCTCCA
* * * * *
3186142 CTGTAACCTCAGGGAAATAAGA-CCTGA-TGT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTTGACT-TCAATCTGCTCCA
* * * *
3186183 CTGTAACTTC-GAGAGATAAGATC----CTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTTGACTTCAATCTGCTCCA
* * * ** *
3186221 TTGTAATCTCA-GGAGAATAGGAT-TACT-ATCTTTGATCTGCTCCG
1 CTGTAACCTCAGGGAG-ATAAGATCT--TGA-CTTCAATCTGCTCCA
* * *
3186265 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCT-TGACTTCAATCTGCTCCA
3186309 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
3186334 GAAATTCTTT
Statistics
Matches: 253, Mismatches: 51, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.00
38 18 0.07
39 6 0.02
40 9 0.04
41 19 0.08
42 2 0.01
43 12 0.05
44 132 0.52
45 54 0.21
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCTTGACTTCAATCTGCTCCA
Found at i:3186293 original size:212 final size:215
Alignment explanation
Indices: 3185914--3186380 Score: 649
Period size: 212 Copynumber: 2.2 Consensus size: 215
3185904 GTTGTTTTCA
* * * * *
3185914 GTCTATTCCACTGCATCTTCAGGGAAATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* * *
3185979 AGATAAGATCCTTTATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
66 AGATAAGATCC----TTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATACTATCTTCGAT
3186044 CTGCTCCGCCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
127 CTGCTCCGCCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
3186109 GGAGATAAGATCTG-AATTCTCCG
192 GGAGATAAGATCTGAAATTCTCCG
* * * *
3186132 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTC-GAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* *
3186196 AGATAAGATCC-TTTAATCCGCTCCATTGTAA-TCTCA-GGAGAATAGGATTACTATCTTTGATC
66 AGATAAGATCCTTTTAATCCGCTCCACTGTAACT-TCAGGGAG-ATAGGA-TACTATCTTCGATC
*
3186258 TGCTCCG-CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCTCAGG
128 TGCTCCGCCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGG
**
3186322 GAGATAAGATCTGAAATTCTTTG
193 GAGATAAGATCTGAAATTCTCCG
* * *
3186345 GTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTG
3186381 TATAATAAAC
Statistics
Matches: 224, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
211 5 0.02
212 96 0.43
213 57 0.25
217 14 0.06
218 52 0.23
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (215 bp):
GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATACTATCTTCGATCTGC
TCCGCCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
ATAAGATCTGAAATTCTCCG
Found at i:3186376 original size:46 final size:44
Alignment explanation
Indices: 3185954--3186376 Score: 218
Period size: 44 Copynumber: 9.8 Consensus size: 44
3185944 GACTTGATGC
* * * * * *
3185954 GATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAT-TTT
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTATGTCTTT
* * * *
3185998 AATCTGCTCCACTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTC
1 GATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCTA-TGTCTTT
* * *
3186041 GATCTGCTCCGCCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 GATCTGCTCCG-CTGTAATCTCAGGGAGATAAGATCTATGTCTTT
* * * **
3186086 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTCC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--ATGTCTTT
* * * * * *
3186131 GGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATG----T
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-ATGTCTTT
* ** *
3186172 GATCTTCTCTACTGTAA-CTTC-GAGAGATAAGATC-----CTTT
1 GATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCTATGTCTTT
* * ** * *
3186210 AATCCGCTCCATTGTAATCTCA-GGAGAATAGGAT-TACTATCTTT
1 GATCTGCTCCGCTGTAATCTCAGGGAG-ATAAGATCTA-TGTCTTT
* * *
3186254 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTATGTCTTT
* *
3186298 AATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTT
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT---ATGTCTTT
* * *
3186344 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
3186377 CCTGTATAAT
Statistics
Matches: 292, Mismatches: 59, Indels: 54
0.72 0.15 0.13
Matches are distributed among these distances:
38 18 0.06
39 7 0.02
40 11 0.04
41 17 0.06
42 2 0.01
43 12 0.04
44 136 0.47
45 55 0.19
46 33 0.11
47 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTATGTCTTT
Found at i:3217016 original size:3 final size:3
Alignment explanation
Indices: 3216997--3217034 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3216987 TTTAGCAATT
*
3216997 TTA TT- TTA TTG TTA TTA TTA TT- TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3217035 ATCATTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:3217019 original size:17 final size:17
Alignment explanation
Indices: 3216997--3217046 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
3216987 TTTAGCAATT
3216997 TTATTTTATTGTTATTA
1 TTATTTTATTGTTATTA
*
3217014 TTATTTTATTATTATTA
1 TTATTTTATTGTTATTA
* *
3217031 TTATATCATTGTTATT
1 TTATTTTATTGTTATT
3217047 CTCATTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (17 bp):
TTATTTTATTGTTATTA
Found at i:3217140 original size:28 final size:29
Alignment explanation
Indices: 3217076--3217140 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 29
3217066 TATATTTACT
3217076 TATGTA-ATTTTAAATATGTGTCTTATTA
1 TATGTATATTTTAAATATGTGTCTTATTA
* *
3217104 TAT-TAATATTATTATATATTTG-CTTA-TA
1 TATGT-ATATT-TTAAATATGTGTCTTATTA
3217132 TATGTATAT
1 TATGTATAT
3217141 ATGTTTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
27 1 0.03
28 13 0.42
29 8 0.26
30 9 0.29
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (29 bp):
TATGTATATTTTAAATATGTGTCTTATTA
Found at i:3217361 original size:17 final size:17
Alignment explanation
Indices: 3217322--3217361 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3217312 ATGCACATTT
*
3217322 TTTATATGTATATATTA
1 TTTATATGTATATAATA
* *
3217339 TATATATTTATATAATA
1 TTTATATGTATATAATA
3217356 TTTATA
1 TTTATA
3217362 CGCATTTGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATGTATATAATA
Found at i:3227319 original size:17 final size:16
Alignment explanation
Indices: 3227278--3227329 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3227268 AAATTAAAAC
*
3227278 AAAAATAAAAAAATTT
1 AAAATTAAAAAAATTT
** *
3227294 -ATTTTAAAAATATTTT
1 AAAATTAAAAA-AATTT
3227310 AAAATTAAAAAAATTT
1 AAAATTAAAAAAATTT
3227326 AAAA
1 AAAA
3227330 AAAGTATTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAAAAAAATTT
Found at i:3227330 original size:17 final size:17
Alignment explanation
Indices: 3227297--3227330 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3227287 AAAATTTATT
* *
3227297 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
3227314 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
3227331 AAGTATTTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:3227343 original size:11 final size:11
Alignment explanation
Indices: 3227329--3227353 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3227319 AAAATTTAAA
3227329 AAAAGTATTTT
1 AAAAGTATTTT
3227340 AAAAGTATTTT
1 AAAAGTATTTT
3227351 AAA
1 AAA
3227354 TTTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3227369 original size:40 final size:40
Alignment explanation
Indices: 3227260--3227373 Score: 131
Period size: 41 Copynumber: 2.7 Consensus size: 40
3227250 ACCAAAAATT
*
3227260 TATTTTAAAAATTAAAACAAAAATAAAAAAATTTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATAAAAAAATGTATTTTAAAAA
*
3227304 TATTTTAAAATTAAAAAAATTTAAAAAAA-GTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA--TAAAAAAATGTATTTTAAAAA
*
3227345 TATTTTAAATTTTAAAAAAATAAAAAAAT
1 TATTTTAAA-ATTAAAAAAATAAAAAAAT
3227374 AAAAAATTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
40 13 0.21
41 21 0.33
42 17 0.27
43 6 0.10
44 6 0.10
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATAAAAAAATGTATTTTAAAAA
Found at i:3228410 original size:22 final size:20
Alignment explanation
Indices: 3228381--3228420 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3228371 TTAAGAGGTT
*
3228381 TAATAGAAATTTTTAAAAAAG
1 TAATAG-AATTTTCAAAAAAG
3228402 TAATGAGAATTTTCAAAAA
1 TAAT-AGAATTTTCAAAAA
3228421 TTTTGAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATAGAATTTTCAAAAAAG
Found at i:3234921 original size:34 final size:34
Alignment explanation
Indices: 3234846--3234923 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
3234836 ACAATAATAA
* *
3234846 ATATTTTATAAAATAAATTTATATTAATATTTAT
1 ATATTTTATAAAATAAATTTAAATAAATATTTAT
*
3234880 ATATTTTATAAATTAAATTTAAATAAA-ATATTAT
1 ATATTTTATAAAATAAATTTAAATAAATAT-TTAT
3234914 -TATTTT-TAAA
1 ATATTTTATAAA
3234924 CAATAACTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.10
33 8 0.20
34 28 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTTTATAAAATAAATTTAAATAAATATTTAT
Found at i:3235763 original size:24 final size:23
Alignment explanation
Indices: 3235736--3235794 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
3235726 AATTTTAACA
3235736 AATAAAAAATATTAAGTT-AAAATT
1 AATAAAAAATATT--GTTAAAAATT
* *
3235760 AATATAAATATATTTTTAAAAATT
1 AATA-AAAAATATTGTTAAAAATT
3235784 AA-AAAAAATAT
1 AATAAAAAATAT
3235795 ATATGGACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 12 0.40
25 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATAAAAAATATTGTTAAAAATT
Found at i:3236564 original size:11 final size:11
Alignment explanation
Indices: 3236548--3236583 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3236538 TTAAAAATAA
3236548 AAAAGTATTTT
1 AAAAGTATTTT
3236559 AAAAGTATTTT
1 AAAAGTATTTT
*
3236570 AAAA-AATTTT
1 AAAAGTATTTT
3236580 AAAA
1 AAAA
3236584 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3238784 original size:5 final size:5
Alignment explanation
Indices: 3238774--3238801 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3238764 TAATTTTTAA
3238774 TTATT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTA
3238802 ATATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:3245553 original size:15 final size:16
Alignment explanation
Indices: 3245522--3245555 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3245512 TTCCAAAACA
3245522 TAAAATGTGAATCAAG
1 TAAAATGTGAATCAAG
*
3245538 TAAAATGT-ATTCAAG
1 TAAAATGTGAATCAAG
3245553 TAA
1 TAA
3245556 GCTCATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (16 bp):
TAAAATGTGAATCAAG
Found at i:3248553 original size:67 final size:67
Alignment explanation
Indices: 3248445--3248581 Score: 238
Period size: 67 Copynumber: 2.0 Consensus size: 67
3248435 TCCAAGATTT
* * *
3248445 TATTTGTTATACTTCATGAACCTATATAATGGGACATCTATTTAGAATAACTCATGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTATATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
3248510 TC
66 TC
*
3248512 TATTTGTTAAACCTCATGAACCTATATGATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTATATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
3248577 TC
66 TC
3248579 TAT
1 TAT
3248582 AAAATTCGTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (67 bp):
TATTTGTTAAACCTCATGAACCTATATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
TC
Found at i:3253533 original size:13 final size:14
Alignment explanation
Indices: 3253515--3253548 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3253505 TGGAATTCTT
*
3253515 AAAAATTGGGC-TG
1 AAAAATTGGGCAAG
3253528 AAAAATTGGGCAAG
1 AAAAATTGGGCAAG
3253542 AAAAATT
1 AAAAATT
3253549 TTAAAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (14 bp):
AAAAATTGGGCAAG
Found at i:3256917 original size:11 final size:11
Alignment explanation
Indices: 3256901--3256930 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3256891 TGTAGCCCAT
3256901 TTTTTGTTTTA
1 TTTTTGTTTTA
3256912 TTTTTGTTTTA
1 TTTTTGTTTTA
*
3256923 TGTTTGTT
1 TTTTTGTT
3256931 GACAGTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.13, T:0.80
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:3276036 original size:87 final size:88
Alignment explanation
Indices: 3275873--3276036 Score: 188
Period size: 87 Copynumber: 1.9 Consensus size: 88
3275863 ATAAAAAGAT
* ** * * * *
3275873 TGAAATACCCTTAAAAATAAAATTTATTTTAATTATGAAACGATGTTTTTATAATTTCCCTAGCT
1 TGAAATACCCTTAAAAATAAAATTTATTCTAATTACCAAACGATGTGTTCATAAATTCCCTAACT
* *
3275938 AGGTTGGTGTCCAATGAAAAGGC
66 AGATTGATGTCCAATGAAAAGGC
* * * *
3275961 TGAAATGCCCTT-AAAATATAATTTATTCTAATTACCAAAGGATGTGTTCATAAATTCCTTAACT
1 TGAAATACCCTTAAAAATAAAATTTATTCTAATTACCAAACGATGTGTTCATAAATTCCCTAACT
3276025 -GAATTGATGTCC
66 AG-ATTGATGTCC
3276037 GGTTAACTCG
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
86 1 0.02
87 50 0.81
88 11 0.18
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (88 bp):
TGAAATACCCTTAAAAATAAAATTTATTCTAATTACCAAACGATGTGTTCATAAATTCCCTAACT
AGATTGATGTCCAATGAAAAGGC
Found at i:3287307 original size:5 final size:5
Alignment explanation
Indices: 3287297--3287322 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3287287 AAATTTAAAA
3287297 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
3287323 AATAATGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:3297295 original size:2 final size:2
Alignment explanation
Indices: 3297288--3297318 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3297278 ATTGAGCATT
3297288 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3297319 TTTTATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3301548 original size:17 final size:17
Alignment explanation
Indices: 3301528--3301561 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3301518 ATTTTTAATT
3301528 TTTTAATATTT-TTTTAA
1 TTTTAAT-TTTATTTTAA
3301545 TTTTAATTTTATTTTAA
1 TTTTAATTTTATTTTAA
3301562 CCCTCCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTATTTTAA
Found at i:3301792 original size:11 final size:11
Alignment explanation
Indices: 3301776--3301891 Score: 82
Period size: 11 Copynumber: 10.8 Consensus size: 11
3301766 ATTTTTTTAA
3301776 TTTTAAAATAC
1 TTTTAAAATAC
3301787 TTTTAAAATAC
1 TTTTAAAATAC
3301798 TTTTAAAATAC
1 TTTTAAAATAC
*
3301809 TTTTTTAAAA-AT
1 --TTTTAAAATAC
**
3301821 TTTTTTAAT--
1 TTTTAAAATAC
* *
3301830 TTTGAAAAT-T
1 TTTTAAAATAC
3301840 TTTTAAAATAC
1 TTTTAAAATAC
** *
3301851 TTTT--TTTAA
1 TTTTAAAATAC
*
3301860 TTTTAAAATAT
1 TTTTAAAATAC
3301871 TTTTAAAATAC
1 TTTTAAAATAC
3301882 TTTTTAAAAT
1 -TTTTAAAAT
3301892 TTTTATTTTA
Statistics
Matches: 82, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
9 12 0.15
10 14 0.17
11 38 0.46
12 10 0.12
13 8 0.10
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3301875 original size:31 final size:31
Alignment explanation
Indices: 3301798--3301886 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 31
3301788 TTTAAAATAC
3301798 TTTTAAAATACTTTTTTAAAA-A-TTTTTTTAA
1 TTTTAAAATA--TTTTTAAAATACTTTTTTTAA
3301829 TTTTGAAAAT-TTTTTAAAATACTTTTTTTAA
1 TTTT-AAAATATTTTTAAAATACTTTTTTTAA
3301860 TTTTAAAATATTTTTAAAATACTTTTT
1 TTTTAAAATATTTTTAAAATACTTTTT
3301887 AAAATTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.17
30 6 0.11
31 34 0.63
32 5 0.09
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (31 bp):
TTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:3301893 original size:31 final size:31
Alignment explanation
Indices: 3301776--3301894 Score: 127
Period size: 31 Copynumber: 3.8 Consensus size: 31
3301766 ATTTTTTTAA
*
3301776 TTTTAAAATACTTTTAAAATACTTTTAAAATACTT
1 TTTTAAAATACTTTTTAAA-A-TTTTAAAATA--T
**
3301811 TTTTAAAA-A-TTTTTTTAATTTTGAAAAT-T
1 TTTTAAAATACTTTTTAAAATTTT-AAAATAT
**
3301840 TTTTAAAATACTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAAATTTTAAAATAT
3301871 TTTTAAAATACTTTTTAAAATTTT
1 TTTTAAAATACTTTTTAAAATTTT
3301895 TATTTTAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
29 9 0.12
30 6 0.08
31 40 0.53
32 6 0.08
33 5 0.07
34 1 0.01
35 8 0.11
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (31 bp):
TTTTAAAATACTTTTTAAAATTTTAAAATAT
Found at i:3302890 original size:17 final size:17
Alignment explanation
Indices: 3302868--3302921 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3302858 ATTAAATATT
3302868 AAATTATTTAAAAAATA
1 AAATTATTTAAAAAATA
* *
3302885 AAATTATGTAACAAAT-
1 AAATTATTTAAAAAATA
3302901 AAATATATCTATAAAAAATA
1 AAAT-TAT-T-TAAAAAATA
3302921 A
1 A
3302922 TATAAACTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
19 7 0.24
20 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATTATTTAAAAAATA
Found at i:3303655 original size:22 final size:23
Alignment explanation
Indices: 3303626--3303700 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
3303616 TTTAAATTGA
3303626 TTAT-ATAATTTATTAAAAT-AT
1 TTATAATAATTTATTAAAATAAT
**
3303647 TTATAATAAAATATTAGAAGATACAT
1 TTATAATAATTTATTA-AA-ATA-AT
* *
3303673 TT-TAATATTTTATTAAATTAAT
1 TTATAATAATTTATTAAAATAAT
3303695 TTATAA
1 TTATAA
3303701 ATTCACATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 4 0.10
22 13 0.31
23 7 0.17
24 4 0.10
25 10 0.24
26 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (23 bp):
TTATAATAATTTATTAAAATAAT
Found at i:3303766 original size:16 final size:17
Alignment explanation
Indices: 3303745--3303778 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3303735 TAATTTTAAA
*
3303745 AATTCTATTAT-ATATC
1 AATTCTAATATGATATC
3303761 AATTCTAATATGATATC
1 AATTCTAATATGATATC
3303778 A
1 A
3303779 TTAATAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (17 bp):
AATTCTAATATGATATC
Found at i:3303874 original size:21 final size:22
Alignment explanation
Indices: 3303850--3303899 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3303840 CATTATTTTT
*
3303850 AATCTCACT-GCTACAGTATCC
1 AATCTCACTAGCTACAGTAACC
*
3303871 AATCTCA-TAGCTACAGTAACT
1 AATCTCACTAGCTACAGTAACC
3303892 AATCTCAC
1 AATCTCAC
3303900 CGTCACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.34, C:0.30, G:0.08, T:0.28
Consensus pattern (22 bp):
AATCTCACTAGCTACAGTAACC
Found at i:3306253 original size:25 final size:27
Alignment explanation
Indices: 3306224--3306276 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
3306214 TTAAGGCTCC
3306224 ATTTTAGAAAATA-TTTTC-TATTTTT
1 ATTTTAGAAAATAGTTTTCGTATTTTT
* *
3306249 ATTTTAGAATATAGTTTTCGTTTTTTT
1 ATTTTAGAAAATAGTTTTCGTATTTTT
3306276 A
1 A
3306277 AAATTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 5 0.21
27 7 0.29
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (27 bp):
ATTTTAGAAAATAGTTTTCGTATTTTT
Found at i:3307092 original size:14 final size:14
Alignment explanation
Indices: 3307058--3307086 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3307048 TATGCAATAT
3307058 CCAAATAATAACAA
1 CCAAATAATAACAA
3307072 CCAAATAATAACAA
1 CCAAATAATAACAA
3307086 C
1 C
3307087 ATAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (14 bp):
CCAAATAATAACAA
Found at i:3314129 original size:23 final size:23
Alignment explanation
Indices: 3314103--3314224 Score: 147
Period size: 23 Copynumber: 5.3 Consensus size: 23
3314093 ATAAGTGCCA
3314103 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3314126 CACTGATATGAAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
3314149 CACTGAAATGTAGCCAAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
3314172 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* * *
3314195 CACTGAAATTTAGCCGAAGCTGC
1 CACTGATATGTAGCCGAAGCTAC
*
3314218 CATTGAT
1 CACTGAT
3314225 CAATAACACT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.01
23 81 0.98
24 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3314173 original size:46 final size:46
Alignment explanation
Indices: 3314103--3314224 Score: 163
Period size: 46 Copynumber: 2.7 Consensus size: 46
3314093 ATAAGTGCCA
* * *
3314103 CACTGATATGTAGCCGAAGCTACCACTGATATGAAGCCGTAGCTAC
1 CACTGAAATGTAGCCAAAGCTACCACTGATATGAAGCCATAGCTAC
* *
3314149 CACTGAAATGTAGCCAAAGTTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCAAAGCTACCACTGATATGAAGCCATAGCTAC
* * * *
3314195 CACTGAAATTTAGCCGAAGCTGCCATTGAT
1 CACTGAAATGTAGCCAAAGCTACCACTGAT
3314225 CAATAACACT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCAAAGCTACCACTGATATGAAGCCATAGCTAC
Found at i:3316129 original size:21 final size:21
Alignment explanation
Indices: 3316105--3316146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3316095 TTTTTTGTTC
*
3316105 AATTAATTATCGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
**
3316126 AATTTCTTAACGAAACTTTAA
1 AATTAATTAACGAAACTTTAA
3316147 TACTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATTAATTAACGAAACTTTAA
Found at i:3319093 original size:6 final size:6
Alignment explanation
Indices: 3319076--3319136 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
3319066 TTCAACGCAG
* * * * *
3319076 AGAGAG AGAGAA AGAGAA ATATAA ATAG-A ATAGAA AGAGAA AGAGAA
1 AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA AGAGAA
3319123 AGAGAA AGAGAA AG
1 AGAGAA AGAGAA AG
3319137 GCAGAGGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (6 bp):
AGAGAA
Found at i:3319128 original size:23 final size:23
Alignment explanation
Indices: 3319084--3319128 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3319074 AGAGAGAGAG
* * *
3319084 AGAAAGAGAAATATAAATAGAAT
1 AGAAAGAGAAAGAGAAAGAGAAT
3319107 AGAAAGAGAAAGAGAAAGAGAA
1 AGAAAGAGAAAGAGAAAGAGAA
3319129 AGAGAAAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (23 bp):
AGAAAGAGAAAGAGAAAGAGAAT
Found at i:3332466 original size:50 final size:50
Alignment explanation
Indices: 3332408--3332601 Score: 162
Period size: 50 Copynumber: 3.9 Consensus size: 50
3332398 CATTGAGATT
* *
3332408 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCACCAAG
** * * * * * *
3332458 ATGAGAGGTCCCCCGTAAGATCATGTTTGGGACAT-AGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGA-CATTGGCACCAAG
** * * *
3332508 ATGAGAACTCCCATGTAAGACCATATATGGGATATGACATTGGCAGTACAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCA--CCAAG
** * *
3332560 A--A-ACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCA
3332602 TGTTATTATC
Statistics
Matches: 112, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
49 34 0.30
50 74 0.66
51 1 0.01
52 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGACATTGGCACCAAG
Found at i:3337929 original size:56 final size:51
Alignment explanation
Indices: 3337712--3337959 Score: 231
Period size: 50 Copynumber: 4.9 Consensus size: 51
3337702 TGATAATAAC
* * * *
3337712 ATGCCAAAGCCATGTCCCAGAAATGGTCTTACATGGGA-TGT-T--TCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* * * * * *
3337759 TACTGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGT-TCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* * * **
3337811 GTGCCCATGCCATATCCCAGACATGGTCTTACGGGGGAC-CTCTAATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
* *
3337861 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CTCTC-TAATCTC---G
3337917 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCT
3337960 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
48 1 0.01
49 34 0.20
50 75 0.45
51 1 0.01
52 6 0.04
53 8 0.05
54 4 0.02
56 37 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (51 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTCTCTAATCTCG
Found at i:3341095 original size:19 final size:20
Alignment explanation
Indices: 3341046--3341095 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3341036 TAAAATATAA
* *
3341046 ATTTTGGAATTTTTATAAAT
1 ATTTTAGAATTTTGATAAAT
*
3341066 ATTTTAAAATTTTGA-AAATT
1 ATTTTAGAATTTTGATAAA-T
3341086 ATTTT-GAATT
1 ATTTTAGAATT
3341096 ATTTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
ATTTTAGAATTTTGATAAAT
Found at i:3341237 original size:13 final size:13
Alignment explanation
Indices: 3341219--3341253 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3341209 ATTCAACTCG
3341219 ACTTGAACTCGAA
1 ACTTGAACTCGAA
3341232 ACTTGAACTCGAA
1 ACTTGAACTCGAA
3341245 ACTTGAACT
1 ACTTGAACT
3341254 ACTTATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (13 bp):
ACTTGAACTCGAA
Found at i:3342025 original size:20 final size:20
Alignment explanation
Indices: 3341996--3342041 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3341986 TTTACAGGAA
*
3341996 AATT-ATTTTAATTTTTTAT
1 AATTAATTTTAATTATTTAT
*
3342015 AATTAATTTTAGTTATTTAT
1 AATTAATTTTAATTATTTAT
*
3342035 AACTAAT
1 AATTAAT
3342042 ACGAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AATTAATTTTAATTATTTAT
Found at i:3342119 original size:33 final size:33
Alignment explanation
Indices: 3342082--3342155 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 33
3342072 TTATGTTAGT
*
3342082 GTTTTATAAAATTAAATCAAATATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
** *
3342115 G-TTT-TAAAATTGTATTAAAAATATTTATAAA
1 GTTTTATAAAATTAAATCAAAAATATTTATAAA
* *
3342146 ATCTTATAAA
1 GTTTTATAAA
3342156 TTTGAGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 23 0.70
32 5 0.15
33 5 0.15
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (33 bp):
GTTTTATAAAATTAAATCAAAAATATTTATAAA
Found at i:3343012 original size:21 final size:22
Alignment explanation
Indices: 3342988--3343028 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3342978 TTTTTTTAAA
3342988 AAGAATAAAAA-AT-TAAAATTC
1 AAGAA-AAAAATATATAAAATTC
3343009 AAGAAAAAAATATATAAAAT
1 AAGAAAAAAATATATAAAAT
3343029 GTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (22 bp):
AAGAAAAAAATATATAAAATTC
Found at i:3343997 original size:13 final size:13
Alignment explanation
Indices: 3343979--3344025 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3343969 GGTTGGTTTG
3343979 ATTAATTGATTCT
1 ATTAATTGATTCT
3343992 ATTAATTGATT-T
1 ATTAATTGATTCT
* * *
3344004 GATCAACTGATTCC
1 -ATTAATTGATTCT
3344018 ATTAATTG
1 ATTAATTG
3344026 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 1 0.04
13 26 0.96
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (13 bp):
ATTAATTGATTCT
Found at i:3344004 original size:26 final size:26
Alignment explanation
Indices: 3343975--3344025 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3343965 TAGTGGTTGG
* * *
3343975 TTTGATTAATTGATTCTATTAATTGA
1 TTTGATCAACTGATTCCATTAATTGA
3344001 TTTGATCAACTGATTCCATTAATTG
1 TTTGATCAACTGATTCCATTAATTG
3344026 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (26 bp):
TTTGATCAACTGATTCCATTAATTGA
Found at i:3344649 original size:21 final size:20
Alignment explanation
Indices: 3344611--3344658 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
3344601 ATGCATGTTA
* *
3344611 AAAAATTGACTAATAGGGAGG
1 AAAAATTGACTAACAGGG-GC
* *
3344632 AAAAATTGATTTACAGGGGC
1 AAAAATTGACTAACAGGGGC
3344652 AAAAATT
1 AAAAATT
3344659 TTCGACAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (20 bp):
AAAAATTGACTAACAGGGGC
Found at i:3345716 original size:36 final size:36
Alignment explanation
Indices: 3345675--3345747 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
3345665 TTAATGCACT
*
3345675 TTAATTCACCTCATTTTATATTTATAACGATACCAA
1 TTAATTCACCTCATTTTACATTTATAACGATACCAA
* *
3345711 TTAATTCACGTTATTTTACATTTATAACGATACCAA
1 TTAATTCACCTCATTTTACATTTATAACGATACCAA
3345747 T
1 T
3345748 ATCAATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (36 bp):
TTAATTCACCTCATTTTACATTTATAACGATACCAA
Found at i:3348451 original size:14 final size:14
Alignment explanation
Indices: 3348428--3348457 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3348418 TGGGTGTAGT
3348428 TTACCCTTGAAATA
1 TTACCCTTGAAATA
*
3348442 TTACCTTTGAAATA
1 TTACCCTTGAAATA
3348456 TT
1 TT
3348458 TCATAGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (14 bp):
TTACCCTTGAAATA
Found at i:3353472 original size:22 final size:22
Alignment explanation
Indices: 3353414--3353474 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3353404 ATGAGGGTAG
* *
3353414 GATATGATATGATATGAAATGT
1 GATATGATAAGATATGAAATAT
* * *
3353436 GCTACGACATA-ATATGAAATAT
1 GATATGATA-AGATATGAAATAT
3353458 GATATGATAAGATATGA
1 GATATGATAAGATATGA
3353475 TAAAAGATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (22 bp):
GATATGATAAGATATGAAATAT
Found at i:3357315 original size:32 final size:35
Alignment explanation
Indices: 3357239--3357316 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
3357229 CTTTTAATAT
*
3357239 TTAAAAAATAATGATATCATTTTTATATGATAGAAA
1 TTAAAAAA-AATAATATCATTTTTATATGATAGAAA
*
3357275 TTACAAAAAATAATATCATTTATT-T-T-ATA-AAA
1 TTAAAAAAAATAATATCATTT-TTATATGATAGAAA
3357307 TTAAAAAAAA
1 TTAAAAAAAA
3357317 AGTTCAATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 12 0.32
33 3 0.08
34 1 0.03
35 13 0.34
36 9 0.24
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (35 bp):
TTAAAAAAAATAATATCATTTTTATATGATAGAAA
Found at i:3360465 original size:29 final size:30
Alignment explanation
Indices: 3360399--3360465 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
3360389 CTTGATAGAC
* *
3360399 TAAATTTTGGATTAATTGAAATAAATTATT
1 TAAATTTTGAATTAATTGAAATAAATAATT
* *
3360429 T-TATTTTTAATTAATTCG-AATAAATAATT
1 TAAATTTTGAATTAATT-GAAATAAATAATT
3360458 TAAATTTT
1 TAAATTTT
3360466 CATTTTAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (30 bp):
TAAATTTTGAATTAATTGAAATAAATAATT
Found at i:3360608 original size:15 final size:15
Alignment explanation
Indices: 3360577--3360626 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
3360567 TTTTAAGATT
3360577 TTTTTGTAAAGAATATA
1 TTTTT-TAAA-AATATA
3360594 TTTTTTAAAAATATA
1 TTTTTTAAAAATATA
*
3360609 TCTTTTTATAATATATA
1 T-TTTTTA-AAAATATA
3360626 T
1 T
3360627 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 13 0.43
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (15 bp):
TTTTTTAAAAATATA
Found at i:3363258 original size:170 final size:171
Alignment explanation
Indices: 3362963--3363278 Score: 483
Period size: 170 Copynumber: 1.9 Consensus size: 171
3362953 GACCATCAGG
* *
3362963 AACAGTGAGCGGCAGCAACAGAAAGTTCACATCAAAGATAAATGAAATCCATATACGGTAAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
*
3363028 AATCATAATTAAAAATGAAATCCAAATATGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
*
3363093 AAGATTTAATC-TAAATCCAATTAATCTTAAATTGGAAATGC
131 AA-AGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
* * * *
3363134 AACAG-GAGTGGCAGCAACAGAAAGTTAATATCAAAGAAAAATGAAATCCATATATGGTGAGTAT
1 AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
* ** ** *
3363198 AATCATAATTAAAACTGAAATCCGTATACGCTTTTTTGAATGACCAAACCTCACTAAAAGGGAAA
66 AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
3363263 AAAGTTAATCTTAAAT
131 AAAGTTAATCTTAAAT
3363279 TAAGATGTAG
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
169 7 0.05
170 118 0.91
171 5 0.04
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (171 bp):
AACAGTGAGCGGCAGCAACAGAAAGTTAACATCAAAGAAAAATGAAATCCATATACGGTAAGTAT
AATCATAATTAAAAATGAAATCCAAATACGCTTTTTCAAATGACCAAACCTCAATAAAAGGGAAA
AAAGTTAATCTTAAATCCAATTAATCTTAAATTGGAAATGC
Found at i:3364824 original size:133 final size:133
Alignment explanation
Indices: 3364586--3364833 Score: 318
Period size: 133 Copynumber: 1.9 Consensus size: 133
3364576 CTCAGATGTA
* ** * * *
3364586 GTTCTTCATCTTAGTTTCCTTGAGTAAATCTTTATCTTTGATTAAACCACGCACCAAATTAGTAT
1 GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
* * *** * * *
3364651 TAGAGCCTCCTTTTTGGCACTTGTGATGGCGGATAACAATCATTCACATGGTATTACTCTGAATT
66 CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATGGTATTACTCTGAATT
3364716 GTT
131 GTT
* * *
3364719 GTTCTTCATCTCAACTTCCTT-AGTAATTTCTTTATCTTTAATTAAACCGCACACCAAATTGGCA
1 GTTCTTCATCTCAACTTCCTTGAGTAA-ATCTTTATCTTTAATTAAACCACACACCAAATTAGCA
*
3364783 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCCTTCACATG
65 TCAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATG
3364834 ATCTTAGAAG
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
132 5 0.05
133 91 0.95
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (133 bp):
GTTCTTCATCTCAACTTCCTTGAGTAAATCTTTATCTTTAATTAAACCACACACCAAATTAGCAT
CAAAGCCTCCTTTCCAGCACCTATGATGGCAGATAACAATCATTCACATGGTATTACTCTGAATT
GTT
Found at i:3371648 original size:17 final size:18
Alignment explanation
Indices: 3371620--3371674 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
3371610 AAAAAAATTA
*
3371620 ATATAAATAGGTTTATAT
1 ATATACATAGGTTTATAT
3371638 ATAT-CATAGGTTTAT-T
1 ATATACATAGGTTTATAT
* *
3371654 AATATACACAGGTTGATAT
1 -ATATACATAGGTTTATAT
3371673 AT
1 AT
3371675 GTCAATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 14 0.45
18 15 0.48
19 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (18 bp):
ATATACATAGGTTTATAT
Found at i:3372077 original size:15 final size:16
Alignment explanation
Indices: 3372057--3372087 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3372047 TTGGCTCTCC
3372057 TATTTCTA-TTATTTT
1 TATTTCTATTTATTTT
3372072 TATTTCTATTTATTTT
1 TATTTCTATTTATTTT
3372088 ATAACACGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTCTATTTATTTT
Found at i:3373099 original size:21 final size:21
Alignment explanation
Indices: 3373075--3373117 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3373065 TTTTCAATGA
3373075 TAATTATTAAGTAAGTTTTTC
1 TAATTATTAAGTAAGTTTTTC
**
3373096 TAATTATTAAGTTTGTTTTTC
1 TAATTATTAAGTAAGTTTTTC
3373117 T
1 T
3373118 CCAGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (21 bp):
TAATTATTAAGTAAGTTTTTC
Found at i:3373950 original size:224 final size:224
Alignment explanation
Indices: 3373560--3374002 Score: 832
Period size: 224 Copynumber: 2.0 Consensus size: 224
3373550 TCATTGAAGC
*
3373560 TTGTTTTAGCTAACCCATGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
1 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
3373625 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
66 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
****
3373690 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAATTTTTTTTGT
131 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAATTTTGT
3373755 AAAATTTTGGTATAAATAGAGAGTTGTCA
196 AAAATTTTGGTATAAATAGAGAGTTGTCA
3373784 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
1 TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
*
3373849 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGACTAGAT
66 ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
3373914 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAATTTTGT
131 TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAATTTTGT
3373979 AAAATTTTGGTATAAATAGAGAGT
196 AAAATTTTGGTATAAATAGAGAGT
3374003 AGAGGGTTTG
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
224 213 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (224 bp):
TTGTTTTAGCTAACCCACGTACCAATTTGTAAAGCTATTAAAGTTTTTGAAAGTTGTCATTGTTT
ATGTCTTGAAGAAAATGGTGTTAAATTGATAGATTTTAAGCTTAGATTATGAAAATTGAATAGAT
TGTAAAATTAAATTGTTAGTTTTGTACATAAGGACTAAAGTGAATAAAATGTAAAAAAATTTTGT
AAAATTTTGGTATAAATAGAGAGTTGTCA
Found at i:3385925 original size:15 final size:15
Alignment explanation
Indices: 3385905--3385940 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3385895 TCAAAATCAA
3385905 TATTTTTACAATATT
1 TATTTTTACAATATT
*
3385920 TATTTTTATAATATT
1 TATTTTTACAATATT
*
3385935 AATTTT
1 TATTTT
3385941 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTTACAATATT
Found at i:3388709 original size:21 final size:22
Alignment explanation
Indices: 3388657--3388715 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
3388647 CTCATACTAT
*
3388657 GAGTTATTTTCTTTAGATAATTAC
1 GAGTTATTTT-TTTA-ATAATTAA
*
3388681 G-TTTATTTTTTTAA-AATTAA
1 GAGTTATTTTTTTAATAATTAA
3388701 GAGTTATTTTTTTAA
1 GAGTTATTTTTTTAA
3388716 CTTCATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.19
21 13 0.42
22 4 0.13
23 7 0.23
24 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (22 bp):
GAGTTATTTTTTTAATAATTAA
Found at i:3389913 original size:21 final size:20
Alignment explanation
Indices: 3389889--3389933 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3389879 AAGAATATTA
*
3389889 TATTAATAATAATAATAATTT
1 TATTAATAAT-ATAATAATAT
*
3389910 TATTTAATAATTTAATAATAT
1 TA-TTAATAATATAATAATAT
3389931 TAT
1 TAT
3389934 CTTATACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 12 0.57
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATAATATAATAATAT
Found at i:3391042 original size:86 final size:86
Alignment explanation
Indices: 3390941--3391099 Score: 318
Period size: 86 Copynumber: 1.8 Consensus size: 86
3390931 AAATGTTTAT
3390941 CTTTCTCTATTATTTACAATAATACATATATAAAGTGGTATAAGTTCAATAAGGAAATAATAAAA
1 CTTTCTCTATTATTTACAATAATACATATATAAAGTGGTATAAGTTCAATAAGGAAATAATAAAA
3391006 TCTAATCCTAAAGAGATTTGA
66 TCTAATCCTAAAGAGATTTGA
3391027 CTTTCTCTATTATTTACAATAATACATATATAAAGTGGTATAAGTTCAATAAGGAAATAATAAAA
1 CTTTCTCTATTATTTACAATAATACATATATAAAGTGGTATAAGTTCAATAAGGAAATAATAAAA
3391092 TCTAATCC
66 TCTAATCC
3391100 CTAATTACTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (86 bp):
CTTTCTCTATTATTTACAATAATACATATATAAAGTGGTATAAGTTCAATAAGGAAATAATAAAA
TCTAATCCTAAAGAGATTTGA
Found at i:3393452 original size:19 final size:17
Alignment explanation
Indices: 3393428--3393462 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3393418 TATTATATGA
3393428 TGAATTGACGAATTGATGT
1 TGAATTGA-GAA-TGATGT
3393447 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
3393463 GAATGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:3395902 original size:8 final size:8
Alignment explanation
Indices: 3395889--3395920 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3395879 TATCAGTGGA
3395889 GTAATTTC
1 GTAATTTC
3395897 GTAATTTC
1 GTAATTTC
3395905 GTAATTTC
1 GTAATTTC
*
3395913 GCAATTTC
1 GTAATTTC
3395921 TTTAAACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (8 bp):
GTAATTTC
Found at i:3404033 original size:3 final size:3
Alignment explanation
Indices: 3404025--3404054 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3404015 CCGTCATGGA
*
3404025 GAT GAT GAT GTT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3404055 TGGTTCAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (3 bp):
GAT
Found at i:3408584 original size:24 final size:24
Alignment explanation
Indices: 3408556--3408607 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3408546 TTTCTAGAAG
*
3408556 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
3408580 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATTTATTAGTATAATAT
3408604 ATTT
1 ATTT
3408608 GACTTACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:3415590 original size:24 final size:24
Alignment explanation
Indices: 3415554--3415640 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
3415544 AAAAATAATC
* *
3415554 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGCTTATTTG
*
3415578 TTTCAATTTAACTCTGCTTATTTG
1 TTTCAATTAAACTCTGCTTATTTG
*
3415602 TTTCAATTAAACTCTGCTTATTTA
1 TTTCAATTAAACTCTGCTTATTTG
*
3415626 TTTCAATCAAACTCT
1 TTTCAATTAAACTCT
3415641 AATTAGTCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTCAATTAAACTCTGCTTATTTG
Found at i:3416496 original size:14 final size:14
Alignment explanation
Indices: 3416477--3416503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3416467 TGTGCTGTTT
3416477 ACACCATTATCAAA
1 ACACCATTATCAAA
3416491 ACACCATTATCAA
1 ACACCATTATCAA
3416504 GCCACTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
ACACCATTATCAAA
Found at i:3416833 original size:21 final size:21
Alignment explanation
Indices: 3416809--3416849 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3416799 CATATAAAAT
*
3416809 TGACATATTTCTTATTTATCG
1 TGACATATTTATTATTTATCG
*
3416830 TGACGTATTTATTATTTATC
1 TGACATATTTATTATTTATC
3416850 ATGTTCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (21 bp):
TGACATATTTATTATTTATCG
Found at i:3425400 original size:73 final size:73
Alignment explanation
Indices: 3425281--3425424 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
3425271 TCTCGGATTT
* * * * *
3425281 AAAAAATGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCAAGATCATTTAAAA
3425346 CTTGAGAA
66 CTTGAGAA
*
3425354 AAAAAAAGGATCATGCCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCAAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCAAGATCATTTAAAA
3425419 CTTGAG
66 CTTGAG
3425425 TTTGAAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (73 bp):
AAAAAAAGGATCATGCCCAGTAAATTAGGACACAATCTCTTCTTAATTCCCAAGATCATTTAAAA
CTTGAGAA
Found at i:3425841 original size:50 final size:47
Alignment explanation
Indices: 3425780--3425893 Score: 124
Period size: 48 Copynumber: 2.3 Consensus size: 47
3425770 AATAAAATGA
* *
3425780 ATAAAGTTATAAAAATGTAAAA-AGATACATGTATGTACATATATATAAATT
1 ATAAAG-TATAAAAA--AAAAATAGATACAAGTATGT--ATATATATAAATT
*
3425831 AT-AAGATATAATAAAAAAAATATATACAAGTATGTATATATATAAATT
1 ATAAAG-TATAA-AAAAAAAATAGATACAAGTATGTATATATATAAATT
3425879 ATAAAGTATAAAAAA
1 ATAAAGTATAAAAAA
3425894 TAAGTAAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
47 4 0.07
48 20 0.36
49 7 0.12
50 20 0.36
51 5 0.09
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (47 bp):
ATAAAGTATAAAAAAAAAATAGATACAAGTATGTATATATATAAATT
Found at i:3425978 original size:3 final size:3
Alignment explanation
Indices: 3425970--3426012 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3425960 TAAGTGAGTA
3425970 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3426013 CAAGGTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3426453 original size:12 final size:12
Alignment explanation
Indices: 3426436--3426461 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3426426 GGAGCCGGTC
3426436 GGGTCGCACGCG
1 GGGTCGCACGCG
3426448 GGGTCGCACGCG
1 GGGTCGCACGCG
3426460 GG
1 GG
3426462 TCGGCGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.54, T:0.08
Consensus pattern (12 bp):
GGGTCGCACGCG
Found at i:3426462 original size:11 final size:11
Alignment explanation
Indices: 3426435--3426464 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3426425 TGGAGCCGGT
3426435 CGGGTCGCACG
1 CGGGTCGCACG
3426446 CGGGGTCGCACG
1 C-GGGTCGCACG
3426458 CGGGTCG
1 CGGGTCG
3426465 GCGTTAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.07, C:0.33, G:0.50, T:0.10
Consensus pattern (11 bp):
CGGGTCGCACG
Found at i:3428038 original size:10 final size:10
Alignment explanation
Indices: 3427998--3428060 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 10
3427988 AATTTTTCAT
*
3427998 ATTTTCTAAA
1 ATTTTATAAA
*
3428008 ATTTTA-AAT
1 ATTTTATAAA
**
3428017 ATTTT-TTGA
1 ATTTTATAAA
3428026 ATTTTATAAA
1 ATTTTATAAA
3428036 ATTTTA-AAA
1 ATTTTATAAA
* *
3428045 ATATTATATA
1 ATTTTATAAA
3428055 ATTTTA
1 ATTTTA
3428061 GGAATTTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
9 20 0.50
10 20 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:3428248 original size:17 final size:16
Alignment explanation
Indices: 3428211--3428271 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
3428201 AAACTTATCC
3428211 AATTAATTTAAGTTATTTA
1 AATTAATTTAA---ATTTA
*
3428230 AATTAGTTTAAATTTTA
1 AATTAATTTAAA-TTTA
* *
3428247 AAATAATTTAAACTTA
1 AATTAATTTAAATTTA
3428263 AATTAATTT
1 AATTAATTT
3428272 TACCTCAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.33
17 14 0.39
19 10 0.28
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (16 bp):
AATTAATTTAAATTTA
Found at i:3431025 original size:110 final size:107
Alignment explanation
Indices: 3430892--3431181 Score: 372
Period size: 110 Copynumber: 2.7 Consensus size: 107
3430882 AGTGCACTCC
* *
3430892 CCACC-CCACCCGTCCACTCACCACCCCCACCCGTCTTCTCACCACCACCACCAGTGCACTCACC
1 CCACCACCACCAGTCCACTCACCACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACC
3430956 ACCCCCACCCGTCTACTCACCACCCCACCACCCGTCTACTCACCA
66 ACCCCCACCCGTCTACTCACCA--CC-CCACCCGTCTACTCACCA
* *
3431001 CCCCCACCACCAGTGCACTCACCACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACC
1 CCACCACCACCAGTCCACTCACCACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACC
3431066 ACCCCCACCCGTCTACTCACCACCCCACCCGTCTACT--CC-
66 ACCCCCACCCGTCTACTCACCACCCCACCCGTCTACTCACCA
* * * * * * * * *
3431105 CCACCACCACCCGTCTACTCACCACCACCACCACCAGTCCAGTCCCCACCCCCACCCGTCCACTC
1 CCACCACCACCAGTCCACTCACCA-C-CC-CCACCCGTCTACTCACCACCACCACCAGTGCACTC
*
3431170 ACCACCACCACC
63 ACCACCCCCACC
3431182 AGTCCAGTCC
Statistics
Matches: 161, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
104 20 0.12
105 3 0.02
106 2 0.01
107 52 0.32
108 2 0.01
109 4 0.02
110 78 0.48
ACGTcount: A:0.22, C:0.61, G:0.06, T:0.12
Consensus pattern (107 bp):
CCACCACCACCAGTCCACTCACCACCCCCACCCGTCTACTCACCACCACCACCAGTGCACTCACC
ACCCCCACCCGTCTACTCACCACCCCACCCGTCTACTCACCA
Found at i:3431205 original size:21 final size:21
Alignment explanation
Indices: 3430856--3431202 Score: 347
Period size: 21 Copynumber: 16.2 Consensus size: 21
3430846 ACCACCACTA
* *
3430856 CCACCGGTCCACTCCCCACCC
1 CCACCCGTCCACTCACCACCC
* * *
3430877 CCACCAGTGCACTCCCCA-CC
1 CCACCCGTCCACTCACCACCC
3430897 CCACCCGTCCACTCACCACCC
1 CCACCCGTCCACTCACCACCC
** *
3430918 CCACCCGTCTTCTCACCACCA
1 CCACCCGTCCACTCACCACCC
* *
3430939 CCACCAGTGCACTCACCACCC
1 CCACCCGTCCACTCACCACCC
*
3430960 CCACCCGTCTACTCACCACCCC
1 CCACCCGTCCACTCACCA-CCC
*
3430982 ACCACCCGTCTACTCACCACCC
1 -CCACCCGTCCACTCACCACCC
*
3431004 CCACCACCAGTGCACTCACCACCC
1 CCA-C-CC-GTCCACTCACCACCC
* *
3431028 CCACCCGTCTACTCACCACCA
1 CCACCCGTCCACTCACCACCC
* *
3431049 CCACCAGTGCACTCACCACCC
1 CCACCCGTCCACTCACCACCC
*
3431070 CCACCCGTCTACTCACCA-CC
1 CCACCCGTCCACTCACCACCC
* * *
3431090 CCACCCGTCTACTCCCCACCA
1 CCACCCGTCCACTCACCACCC
*
3431111 CCACCCGTCTACTCACCACCACC
1 CCACCCGTCCACTCACCA-C-CC
* * *
3431134 ACCACCAGTCCAGTCCCCACCC
1 -CCACCCGTCCACTCACCACCC
*
3431156 CCACCCGTCCACTCACCACCA
1 CCACCCGTCCACTCACCACCC
* * *
3431177 CCACCAGTCCAGTCCCCACCC
1 CCACCCGTCCACTCACCACCC
3431198 CCACC
1 CCACC
3431203 AGTACAATCT
Statistics
Matches: 272, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
20 36 0.13
21 171 0.63
22 12 0.04
23 23 0.08
24 30 0.11
ACGTcount: A:0.21, C:0.61, G:0.07, T:0.12
Consensus pattern (21 bp):
CCACCCGTCCACTCACCACCC
Found at i:3432270 original size:20 final size:20
Alignment explanation
Indices: 3432234--3432271 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3432224 TCTCCAAACT
*
3432234 CTAAAACTTTTTATTTTCCC
1 CTAAAACTTGTTATTTTCCC
3432254 CTAAAAC-TGTTACTTTTC
1 CTAAAACTTGTTA-TTTTC
3432272 ATCATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (20 bp):
CTAAAACTTGTTATTTTCCC
Found at i:3433064 original size:14 final size:13
Alignment explanation
Indices: 3433032--3433065 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3433022 TAATACTTAA
3433032 TTTTTTATTAAAT
1 TTTTTTATTAAAT
*
3433045 TTTTTTGATTAATT
1 TTTTTT-ATTAAAT
3433059 TTTTTTA
1 TTTTTTA
3433066 GAAAAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTATTAAAT
Found at i:3434821 original size:21 final size:20
Alignment explanation
Indices: 3434785--3435243 Score: 154
Period size: 21 Copynumber: 21.6 Consensus size: 20
3434775 AGCACCGGTT
* *
3434785 CCACCTCCACCAGTCCCTTCC
1 CCACCACCACCCGTCCC-TCC
* *
3434806 CTACCACCACCCGTCCAATCC
1 CCACCACCACCCGTCC-CTCC
*
3434827 CCACCACCACCTGTGCCCTCC
1 CCACCACCACCCGT-CCCTCC
3434848 CCACC-CCACCCGTCCACTCACC
1 CCACCACCACCCGTCC-CT--CC
* *
3434870 ACCACCACCACCGGTTCCTTCAC
1 -CCACCACCACCCG-TCCCTC-C
* ***
3434893 CC-CCACCACCAGTAAAATCC
1 CCACCACCACCCGT-CCCTCC
* * *
3434913 CCACCTCCACCGGTGCCCTCA
1 CCACCACCACCCGT-CCCTCC
*
3434934 CCACCACCACCATCGGTTCCTTCAC
1 CCACCACCACC--C-G-TCCCTC-C
* ***
3434959 CC-CCACCACCAGTAAAATCC
1 CCACCACCACCCGT-CCCTCC
* * * *
3434979 CCACCTCCACCGGTGACCTCA
1 CCACCACCACCCGT-CCCTCC
*
3435000 CCACCACCACCATCGGTTCCTTCAC
1 CCACCACCACC--C-G-TCCCTC-C
* ***
3435025 CC-CCACCACCAGTAAAATCC
1 CCACCACCACCCGT-CCCTCC
* * *
3435045 CCACCTCCACCGGTGCCCTCA
1 CCACCACCACCCGT-CCCTCC
* * *
3435066 CCACCACCACCTGTGCCATCT
1 CCACCACCACCCGT-CCCTCC
*
3435087 CCACCCCCACCCGTCCGCTCC
1 CCACCACCACCCGTCC-CTCC
* *
3435108 CCACC-CCACCTGTGCCCTCT
1 CCACCACCACCCGT-CCCTCC
*
3435128 CCACCCCCACCCGTCCTCTCC
1 CCACCACCACCCGTCC-CTCC
* * * *
3435149 CCACCCCCACCAGTGCACTCA
1 CCACCACCACCCGT-CCCTCC
* *
3435170 CCACCACCACCCGTCCTTTCA
1 CCACCACCACCCGTCC-CTCC
3435191 CCACCACCACCCGTCCTCTCC
1 CCACCACCACCCGTCC-CTCC
* * * *
3435212 CCACCCCCACCAGTGCGCTCA
1 CCACCACCACCCGT-CCCTCC
3435233 CCACCACCACC
1 CCACCACCACC
3435244 ACCACCCGTC
Statistics
Matches: 329, Mismatches: 77, Indels: 64
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.01
20 41 0.12
21 230 0.70
22 9 0.03
23 6 0.02
24 32 0.10
25 9 0.03
ACGTcount: A:0.20, C:0.58, G:0.08, T:0.14
Consensus pattern (20 bp):
CCACCACCACCCGTCCCTCC
Found at i:3434831 original size:42 final size:42
Alignment explanation
Indices: 3434808--3435243 Score: 190
Period size: 42 Copynumber: 10.2 Consensus size: 42
3434798 TCCCTTCCCT
* *
3434808 ACCACCACCCGTCCAATCCCCACCACCACCTGTGCCCTCCCC
1 ACCACCACCCGTCCAATCCCCACCACCACCGGTGCCCTCACC
* * *
3434850 ACC-CCACCCGTCCACTCACCACCACCACCACCGGTTCCTTCACC
1 ACCACCACCCGTCCAAT--CC-CCACCACCACCGGTGCCCTCACC
* * ** *
3434894 CCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACC
1 ACCACCACCCGTCCAATCCCCACCACCACCGGTGCCCTCACC
* * **** *
3434936 ACCACCACCATCGGTTCC-TTCACCC-CCACCACCAGTAAAATCCCC
1 ACCACCACC--C-G-TCCAATC-CCCACCACCACCGGTGCCCTCACC
* * * * * *
3434981 ACCTCCACCGGTGACCTCA-CCACCACCACCATCGGTTCCTTCACC
1 ACCACCACCCGT--CC-AATCC-CCACCACCACCGGTGCCCTCACC
* * ** *
3435026 CCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACC
1 ACCACCACCCGTCCAATCCCCACCACCACCGGTGCCCTCACC
* * * * *
3435068 ACCACCACCTGTGCC-ATCTCCACCCCCACCCGT-CCGCTCCCC
1 ACCACCACCCGT-CCAATCCCCACCACCACCGGTGCC-CTCACC
* * * * * *
3435110 ACC-CCACCTGTGCC-CTCTCCACCCCCACCCGT-CCTCTCCCC
1 ACCACCACCCGT-CCAATCCCCACCACCACCGGTGCC-CTCACC
* * * * * * *
3435151 ACCCCCACCAGTGCACTCACCACCACCACCCGT-CCTTTCACC
1 ACCACCACCCGTCCAATCCCCACCACCACCGGTGCC-CTCACC
** * * *
3435193 ACCACCACCCGTCCTCTCCCCACCCCCACCAGTGCGCTCACC
1 ACCACCACCCGTCCAATCCCCACCACCACCGGTGCCCTCACC
3435235 ACCACCACC
1 ACCACCACC
3435244 ACCACCCGTC
Statistics
Matches: 303, Mismatches: 70, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
41 55 0.18
42 155 0.51
43 10 0.03
44 24 0.08
45 55 0.18
46 4 0.01
ACGTcount: A:0.20, C:0.58, G:0.08, T:0.14
Consensus pattern (42 bp):
ACCACCACCCGTCCAATCCCCACCACCACCGGTGCCCTCACC
Found at i:3434881 original size:86 final size:87
Alignment explanation
Indices: 3434785--3434944 Score: 207
Period size: 86 Copynumber: 1.9 Consensus size: 87
3434775 AGCACCGGTT
* * ** * *
3434785 CCACCTCCACCAGTCCCTTC-CCTACCACCACCCGTCCAATCCCCACCACCACCTGTGCCCTCCC
1 CCACCACCACCAGTCCCTTCACC-ACCACCACCAGTAAAATCCCCACCACCACCGGTGCCCTCAC
3434849 CACC-CCACCCGTCCACTCACCA
65 CACCACCACCCGTCCACTCACCA
* * * *
3434871 CCACCACCACCGGTTCCTTCACCCCCACCACCAGTAAAATCCCCACCTCCACCGGTGCCCTCACC
1 CCACCACCACCAGTCCCTTCACCACCACCACCAGTAAAATCCCCACCACCACCGGTGCCCTCACC
3434936 ACCACCACC
66 ACCACCACC
3434945 ATCGGTTCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
86 55 0.89
87 7 0.11
ACGTcount: A:0.21, C:0.59, G:0.07, T:0.13
Consensus pattern (87 bp):
CCACCACCACCAGTCCCTTCACCACCACCACCAGTAAAATCCCCACCACCACCGGTGCCCTCACC
ACCACCACCCGTCCACTCACCA
Found at i:3434892 original size:24 final size:23
Alignment explanation
Indices: 3434865--3435035 Score: 81
Period size: 24 Copynumber: 7.6 Consensus size: 23
3434855 ACCCGTCCAC
*
3434865 TCACCACCACCACCACCGGTTCCT
1 TCACC-CCACCACCACCGGTACCT
* ***
3434889 TCA-CCC-CCACCACCAGTAAAA
1 TCACCCCACCACCACCGGTACCT
* * *
3434910 T--CCCCACCTCCACCGGTGCCC
1 TCACCCCACCACCACCGGTACCT
* *
3434931 TCACCACCACCACCATCGGTTCCT
1 TCACC-CCACCACCACCGGTACCT
* ***
3434955 TCA-CCC-CCACCACCAGTAAAA
1 TCACCCCACCACCACCGGTACCT
*
3434976 T--CCCCACCTCCACCGGTGACC-
1 TCACCCCACCACCACCGGT-ACCT
* *
3434997 TCACCACCACCACCATCGGTTCCT
1 TCACC-CCACCACCACCGGTACCT
3435021 TCACCCCCACCACCA
1 TCA-CCCCACCACCA
3435036 GTAAAATCCC
Statistics
Matches: 106, Mismatches: 28, Indels: 26
0.66 0.17 0.16
Matches are distributed among these distances:
20 6 0.06
21 41 0.39
22 5 0.05
23 8 0.08
24 44 0.42
25 2 0.02
ACGTcount: A:0.23, C:0.54, G:0.08, T:0.15
Consensus pattern (23 bp):
TCACCCCACCACCACCGGTACCT
Found at i:3434951 original size:66 final size:66
Alignment explanation
Indices: 3434845--3435076 Score: 414
Period size: 66 Copynumber: 3.5 Consensus size: 66
3434835 ACCTGTGCCC
* *
3434845 TCCCCACC-CCACCCGT-CCACTCACCACCACCACCACCGGTTCCTTCACCCCCACCACCAGTAA
1 TCCCCACCTCCACCGGTGCC-CTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAA
3434908 AA
65 AA
3434910 TCCCCACCTCCACCGGTGCCCTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAA
1 TCCCCACCTCCACCGGTGCCCTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAA
3434975 A
66 A
*
3434976 TCCCCACCTCCACCGGTGACCTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAA
1 TCCCCACCTCCACCGGTGCCCTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAA
3435041 A
66 A
3435042 TCCCCACCTCCACCGGTGCCCTCACCACCACCACC
1 TCCCCACCTCCACCGGTGCCCTCACCACCACCACC
3435077 TGTGCCATCT
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
65 8 0.05
66 151 0.94
67 2 0.01
ACGTcount: A:0.23, C:0.55, G:0.08, T:0.14
Consensus pattern (66 bp):
TCCCCACCTCCACCGGTGCCCTCACCACCACCACCATCGGTTCCTTCACCCCCACCACCAGTAAA
A
Found at i:3435261 original size:24 final size:23
Alignment explanation
Indices: 3435168--3435270 Score: 68
Period size: 24 Copynumber: 4.4 Consensus size: 23
3435158 CCAGTGCACT
**
3435168 CACCACCACCACCCGTC-CT-TT
1 CACCACCACCACCCGTCTCTCAC
*
3435189 CACCACCACCACCCGTCCTCTCCC
1 CACCACCACCACCCGT-CTCTCAC
* ** *
3435213 CACCCCCACCAGTGCG-CTCACCAC
1 CACCACCACCA-CCCGTCTC-TCAC
3435237 CACCACCACCACCCGTCTACTCAC
1 CACCACCACCACCCGTCT-CTCAC
* *
3435261 CGCCTCCACC
1 CACCACCACC
3435271 CGTCAAGTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
21 16 0.26
22 1 0.02
23 7 0.11
24 35 0.56
25 3 0.05
ACGTcount: A:0.19, C:0.61, G:0.07, T:0.13
Consensus pattern (23 bp):
CACCACCACCACCCGTCTCTCAC
Found at i:3435290 original size:21 final size:21
Alignment explanation
Indices: 3435062--3435291 Score: 83
Period size: 21 Copynumber: 10.7 Consensus size: 21
3435052 CACCGGTGCC
* *
3435062 CTCACCACCACCACCTGTGCCA
1 CTCACCACCACCACCCGT-CAA
* * **
3435084 -TCTCCACCCCCACCCGTCCG
1 CTCACCACCACCACCCGTCAA
* * *
3435104 CTCCCCACC-CCACCTGTGC-C
1 CTCACCACCACCACCCGT-CAA
* * **
3435124 CTCTCCACCCCCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
* * *
3435145 CTCCCCACCCCCACCAGTGC-A
1 CTCACCACCACCACCCGT-CAA
**
3435166 CTCACCACCACCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
* **
3435187 TTCACCACCACCACCCGTCCT
1 CTCACCACCACCACCCGTCAA
* *
3435208 CTCCCCACCCCCACCAGTGCGCTCACCA
1 CTCACCACCACCACC----CG-TCA--A
*
3435236 C-CACCACCACCACCCGTCTA
1 CTCACCACCACCACCCGTCAA
* *
3435256 CTCACCGCCTCCACCCGTCAA
1 CTCACCACCACCACCCGTCAA
* *
3435277 GTCTCCACCACCACC
1 CTCACCACCACCACC
3435292 AGTAAAATCC
Statistics
Matches: 161, Mismatches: 33, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
20 21 0.13
21 119 0.74
22 3 0.02
23 2 0.01
25 2 0.01
26 2 0.01
27 11 0.07
28 1 0.01
ACGTcount: A:0.17, C:0.61, G:0.08, T:0.14
Consensus pattern (21 bp):
CTCACCACCACCACCCGTCAA
Found at i:3436624 original size:190 final size:191
Alignment explanation
Indices: 3436286--3436634 Score: 515
Period size: 190 Copynumber: 1.8 Consensus size: 191
3436276 AAGTAATAAG
**
3436286 TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
1 TAATGTACTACTATTATATATAACTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
* * * *
3436351 ATGATATTATAATGTTTAATTATATATAAACTATTAATATATTATATAATATGATATAGCATTAC
66 ATAATATTATAATGTTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATTAC
* *
3436416 ATGATACAATAGGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
131 ATAATACAATAAGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
* *
3436477 TAATGTACTACTATTATATATAACTATTATTA-AATTATAGATTATAAT-AAAGGTAT-GGTATT
1 TAATGTACTACTATTATATATAACTATTATTATAA-TATAGATTATAATAAAAGATATAGAT-TT
* * *
3436539 GCATAATATTATAATGTTTAATTATATATAAACTATTAATATATTAAATGATATGACATAACTTT
64 ACATAATATTATAATGTTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATT
* * *
3436604 ATATAATATAGTAAGAGGGTTAACTTTCAAA
129 ACATAATACAATAAGAGGGTTAACTTTCAAA
3436635 GGGATTTAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
189 2 0.01
190 95 0.68
191 43 0.31
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (191 bp):
TAATGTACTACTATTATATATAACTATTATTATAATATAGATTATAATAAAAGATATAGATTTAC
ATAATATTATAATGTTTAATTATATATAAACTATTAATATATTAAATAATATGACATAACATTAC
ATAATACAATAAGAGGGTTAACTTTCAAATGTACGAAAAATATAAAGACTTGGAGCATATT
Found at i:3436677 original size:16 final size:17
Alignment explanation
Indices: 3436658--3436690 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3436648 TATATAATGT
*
3436658 ACTATTGTTAT-ATATA
1 ACTATTATTATAATATA
3436674 ACTATTATTATAATATA
1 ACTATTATTATAATATA
3436691 GATTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
ACTATTATTATAATATA
Found at i:3438810 original size:21 final size:21
Alignment explanation
Indices: 3438786--3438863 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
3438776 TACAGGAGCA
*
3438786 CATAAGTGCTAAACAGAAACC
1 CATAAGGGCTAAACAGAAACC
* * *
3438807 CATAAGGGTTAAACGGAAACT
1 CATAAGGGCTAAACAGAAACC
3438828 CAT-AGGAGCTGTAAA-A-AAACC
1 CATAAGG-GC--TAAACAGAAACC
*
3438849 CATAAGGGTTAAACA
1 CATAAGGGCTAAACA
3438864 AAAGCTCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.09
20 4 0.09
21 29 0.66
22 3 0.07
23 4 0.09
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (21 bp):
CATAAGGGCTAAACAGAAACC
Found at i:3438879 original size:42 final size:41
Alignment explanation
Indices: 3438802--3438908 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
3438792 TGCTAAACAG
* * *
3438802 AAACCCATAAGGGTTAAACGGAAACTCATAGGAGCTGTAA-AA
1 AAACCCATAAGGGTTAAAC-AAAACTCAAAAGAGCTG-AATAA
**
3438844 AAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAATGG
1 AAACCCATAAGGGTTAAACAAAA-CTCAAAAGAGCTGAATAA
* *
3438886 AAACTCATTAGGGTTAAACAAAA
1 AAACCCATAAGGGTTAAACAAAA
3438909 AACTCATATG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 5 0.09
42 51 0.91
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.17
Consensus pattern (41 bp):
AAACCCATAAGGGTTAAACAAAACTCAAAAGAGCTGAATAA
Found at i:3439036 original size:24 final size:24
Alignment explanation
Indices: 3439009--3439072 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
3438999 TAATTTGCCG
* *
3439009 TCAATTCATCTTTTGCATTTTCCA
1 TCAATTCATCCTTTGCATTTACCA
*
3439033 TCAATTCATCCTTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCA
3439057 TCAATTCATCCTTTGC
1 TCAATTCATCCTTTGC
3439073 CACAAAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.20, C:0.28, G:0.06, T:0.45
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATTTACCA
Found at i:3446219 original size:19 final size:21
Alignment explanation
Indices: 3446177--3446225 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
3446167 ATGTTTTACT
*
3446177 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTACAAGC
3446198 TTCTGTTCAGCT-TT-CAAGC
1 TTCTGTTCAGCTCTTACAAGC
3446217 TTCTGTTCA
1 TTCTGTTCA
3446226 CGATGTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTACAAGC
Found at i:3450127 original size:21 final size:21
Alignment explanation
Indices: 3450103--3450155 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3450093 AAATATAATT
3450103 AAATA-TAATAATAACAATAAA
1 AAATAGTAATAA-AACAATAAA
* *
3450124 AAATAGTGATAAAATAAT-AA
1 AAATAGTAATAAAACAATAAA
*
3450144 AAATAGCAATAA
1 AAATAGTAATAA
3450156 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 10 0.37
22 5 0.19
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAGTAATAAAACAATAAA
Found at i:3450139 original size:18 final size:19
Alignment explanation
Indices: 3450112--3450164 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3450102 TAAATATAAT
*
3450112 AATAACAATAAAAAATAGT
1 AATAACAATAAAAAATAGC
*
3450131 GATAA-AATAATAAAAATAGC
1 AATAACAAT-A-AAAAATAGC
*
3450151 AATAATAATAAAAA
1 AATAACAATAAAAA
3450165 TAATTAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 13 0.46
21 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (19 bp):
AATAACAATAAAAAATAGC
Found at i:3451681 original size:44 final size:44
Alignment explanation
Indices: 3451622--3451739 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
3451612 GATGCGATCT
* **
3451622 GCTCTACTGCAACTTCAGAGAGATAAGATCTAT-TTCTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGAT-TATCGACTTTAATCC
* * * *
3451666 GCTCCACTACAACTTCAGGGAGATAGGATTATCGACTTTAATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATCGACTTTAATCC
* *
3451710 GCTCCACTGCAACCTCA-AGGAGAGAAGATT
1 GCTCCACTGCAACTTCAGA-GAGATAAGATT
3451740 TACTTCTTCA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.05
44 57 0.95
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTATCGACTTTAATCC
Found at i:3451795 original size:44 final size:44
Alignment explanation
Indices: 3451711--3451870 Score: 178
Period size: 44 Copynumber: 3.6 Consensus size: 44
3451701 CTTTAATCTG
* * * * * * *
3451711 CTCCACTGCAACCTCAAGGAGAGAAGATTTA-CTTCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCATTTTC-TCAGTCTA
* ** *
3451755 CCCCACTGTGACTTCAGGGGGATAAGACTCATTTTCTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTCATTTTCTCAGTCTA
* * *
3451799 CTCCACTGCAACTTTAGGGAGATAAGACTCGTTTTTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTCATTTTCTCAGTCTA
3451843 CTCCACTGCAACTTCAGGGAGATAAGAC
1 CTCCACTGCAACTTCAGGGAGATAAGAC
3451871 CTGATGGGAT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 93 0.97
45 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCATTTTCTCAGTCTA
Found at i:3452141 original size:87 final size:87
Alignment explanation
Indices: 3452007--3452535 Score: 790
Period size: 87 Copynumber: 6.1 Consensus size: 87
3451997 ACTTGTAATA
* * ** * * *
3452007 TTCGATCTGCTTCACTGTCGACGTAGGAAGGCAAGATCTGCTTTCTTTAACCAACTCCACTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
3452072 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
3452094 TTCGATCTACTTCGCTGTTAACGCAGCAAGGCAAGATATGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
3452159 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
3452181 TTTGATCTGCTTCGCAGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
* **
3452246 CCGATGGAGACAAGGCTTTACT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
3452268 TTCGATCTACTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
3452333 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * *
3452355 TTCGATCTACTTTGCTGTTAATGCTGGAAGACAATATCTG-TATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
3452419 CCGATGGAGGCAAGGTTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
3452441 TTAGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCATTGCAA
1 TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
3452506 CCGATGGAGGCAAGGTTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
3452528 TTCGATCT
1 TTCGATCT
3452536 TCACTGATCT
Statistics
Matches: 398, Mismatches: 43, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
86 76 0.19
87 322 0.81
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (87 bp):
TTCGATCTACTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:3452476 original size:260 final size:261
Alignment explanation
Indices: 3452031--3452535 Score: 823
Period size: 260 Copynumber: 1.9 Consensus size: 261
3452021 CTGTCGACGT
* *
3452031 AGGAAGGCAAGATCTGCTTTCTTTAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
*
3452096 CGATCTACTTCGCTGTTAACGCAGCAAGGCAAGATATGCTATCTTTAACCAGCTCCACTGCAACC
66 CGATCTACTTCGCTGTTAACGCAGCAAGACAAGATATGCTATCTTTAACCAGCTCCACTGCAACC
*
3452161 GATGGAGGCAAGGCTTTGTTTTTGATCTGCTTCGCAGTTAACGCAGGAAGGCAAGATCTGCTATC
131 GATGGAGGCAAGGCTTTGTTTTAGATCTGCTTCGCAGTTAACGCAGGAAGGCAAGATCTGCTATC
*
3452226 TTTAACCAGCTCCACTGCAACCGATGGAGACAAGGCTTTACTTTCGATCTACTTTGCTGTTAACG
196 TTCAACCAGCTCCACTGCAACCGATGGAGACAAGGCTTTACTTTCGATCTACTTTGCTGTTAACG
3452291 C
261 C
* *
3452292 AGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * * * * *
3452357 CGATCTACTTTGCTGTTAATGCTGGAAGACAATATCTG-TATCTTTAACCAGCTCCACTGCAACC
66 CGATCTACTTCGCTGTTAACGCAGCAAGACAAGATATGCTATCTTTAACCAGCTCCACTGCAACC
* *
3452421 GATGGAGGCAAGGTTTTGTTTTAGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATC
131 GATGGAGGCAAGGCTTTGTTTTAGATCTGCTTCGCAGTTAACGCAGGAAGGCAAGATCTGCTATC
* * * **
3452486 TTCAACCAGCTCCATTGCAACCGATGGAGGCAAGGTTTTGTTTTCGATCT
196 TTCAACCAGCTCCACTGCAACCGATGGAGACAAGGCTTTACTTTCGATCT
3452536 TCACTGATCT
Statistics
Matches: 224, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
260 132 0.59
261 92 0.41
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (261 bp):
AGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTACTTCGCTGTTAACGCAGCAAGACAAGATATGCTATCTTTAACCAGCTCCACTGCAACC
GATGGAGGCAAGGCTTTGTTTTAGATCTGCTTCGCAGTTAACGCAGGAAGGCAAGATCTGCTATC
TTCAACCAGCTCCACTGCAACCGATGGAGACAAGGCTTTACTTTCGATCTACTTTGCTGTTAACG
C
Found at i:3459332 original size:21 final size:21
Alignment explanation
Indices: 3459308--3459360 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3459298 AAATATAATT
3459308 AAATA-TAATAATAACAATAAA
1 AAATAGTAATAA-AACAATAAA
* *
3459329 AAATAGTGATAAAATAAT-AA
1 AAATAGTAATAAAACAATAAA
*
3459349 AAATAGCAATAA
1 AAATAGTAATAA
3459361 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 10 0.37
22 5 0.19
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAGTAATAAAACAATAAA
Found at i:3459344 original size:18 final size:19
Alignment explanation
Indices: 3459317--3459369 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3459307 TAAATATAAT
*
3459317 AATAACAATAAAAAATAGT
1 AATAACAATAAAAAATAGC
*
3459336 GATAA-AATAATAAAAATAGC
1 AATAACAAT-A-AAAAATAGC
*
3459356 AATAATAATAAAAA
1 AATAACAATAAAAA
3459370 TAATTAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 13 0.46
21 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (19 bp):
AATAACAATAAAAAATAGC
Found at i:3467163 original size:24 final size:24
Alignment explanation
Indices: 3467136--3467187 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3467126 TTAGTAAGTC
* *
3467136 AAATAAACTATTCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3467160 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3467184 AAAT
1 AAAT
3467188 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3469128 original size:24 final size:24
Alignment explanation
Indices: 3469101--3469152 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3469091 TTAGTAAGTC
*
3469101 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3469125 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3469149 AAAT
1 AAAT
3469153 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3471748 original size:31 final size:31
Alignment explanation
Indices: 3471695--3471757 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3471685 CACATATCAA
* * *
3471695 TTAAGTACCTAATTAAACATTAAAATTAAAC
1 TTAAATACCAAATTAAACATTAAAACTAAAC
*
3471726 TTAAATACCAAATTAAATATTAAAACTAAAC
1 TTAAATACCAAATTAAACATTAAAACTAAAC
3471757 T
1 T
3471758 CATTTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.32
Consensus pattern (31 bp):
TTAAATACCAAATTAAACATTAAAACTAAAC
Found at i:3472753 original size:34 final size:33
Alignment explanation
Indices: 3472697--3472761 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
3472687 ATATATGATT
*
3472697 TTTTATACTTTTTTTCTATTTTA-ATAATTTAGA
1 TTTTATACTTTTTTTATATTTTATAT-ATTTAGA
* *
3472730 TTTTATCCATTTTTTTATTTTTTATATATTTA
1 TTTTATAC-TTTTTTTATATTTTATATATTTA
3472762 ATTATTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.26
34 18 0.67
35 2 0.07
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (33 bp):
TTTTATACTTTTTTTATATTTTATATATTTAGA
Found at i:3475616 original size:87 final size:87
Alignment explanation
Indices: 3475456--3475876 Score: 563
Period size: 87 Copynumber: 4.8 Consensus size: 87
3475446 AGATCAGTGA
* * * *
3475456 AGATCGAAAGCAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTCGC
1 AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGC
*
3475521 CTTCCTGCATGGACAGCGAAGC
66 CTTCCTGCATAGACAGCGAAGC
** * * * * *
3475543 AGATAAAAAACAAAGCCTTGCCTCCATTGGTTGCAGTGGAGCGGGTTAAAGATAGCAAACCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGC
* * *
3475608 CTTTCTGCATTGACAGCGAAGT
66 CTTCCTGCATAGACAGCGAAGC
* *
3475630 AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCGGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGC
* *
3475695 CCTCCTGCATAGACAGTGAAGC
66 CTTCCTGCATAGACAGCGAAGC
* * *
3475717 AGATCGAAGACACAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGC
* *
3475782 CTTCCTGCGTAGACAACGAAGC
66 CTTCCTGCATAGACAGCGAAGC
* * * * *
3475804 AGATCGAAGACACCAGCCTCGCTTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAAACA-AAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTG
*
3475869 TCTTCCTG
65 CCTTCCTG
3475877 TACTGATGGC
Statistics
Matches: 298, Mismatches: 35, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
87 241 0.81
88 57 0.19
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGC
CTTCCTGCATAGACAGCGAAGC
Found at i:3475813 original size:45 final size:45
Alignment explanation
Indices: 3475678--3475813 Score: 127
Period size: 45 Copynumber: 3.1 Consensus size: 45
3475668 GAGCGGGTTA
* * *
3475678 AAGATAGTAGATCTTGCCCTCCTGCATAGACAGTGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGTGAAGCAGATCG
* * * * * * *
3475723 AAGACA-CAG-CCTTGCCTCCCT-CGGTTG-CAGTGGAGCAGGTTG
1 AAGATAGCAGATCTTGCCTTCCTGC-GTAGACAGTGAAGCAGATCG
**
3475765 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAACGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGTGAAGCAGATCG
3475810 AAGA
1 AAGA
3475814 CACCAGCCTC
Statistics
Matches: 67, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
42 18 0.27
43 14 0.21
44 15 0.22
45 20 0.30
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (45 bp):
AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGTGAAGCAGATCG
Found at i:3476101 original size:44 final size:45
Alignment explanation
Indices: 3476033--3476127 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
3476023 ATCGCTTCAG
* * *
3476033 GTCTTATCTCCCTGAGGTTACAATGGAGCAGGCTGAGAA-AGCAA
1 GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
* * *
3476077 GTCTTATCCCCCTGAAGTTGCAATGGGGCAGATTGAGAATAGCAA
1 GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
*
3476122 ATCTTA
1 GTCTTA
3476128 CTGCCCAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 33 0.77
45 10 0.23
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAGTTACAATGGAGCAGACTGAGAATAGCAA
Found at i:3490812 original size:21 final size:19
Alignment explanation
Indices: 3490788--3490835 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
3490778 ATATGGGTGT
3490788 AAGAAAAAAAAATTGATTTGA
1 AAGAAAAAAAAATT-ATTT-A
*
3490809 AAGATTAAAAAAATTATTTA
1 AAGA-AAAAAAAATTATTTA
*
3490829 TAGAAAA
1 AAGAAAA
3490836 TTTTTAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 4 0.17
21 8 0.35
22 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
AAGAAAAAAAAATTATTTA
Found at i:3490837 original size:14 final size:13
Alignment explanation
Indices: 3490813--3490862 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
3490803 ATTTGAAAGA
*
3490813 TTAAAAAAATTAT
1 TTAAGAAAATTAT
3490826 TTATAGAAAATT-T
1 TTA-AGAAAATTAT
3490839 TTAAAGAACAATTAT
1 TT-AAGAA-AATTAT
3490854 TTAAGAAAA
1 TTAAGAAAA
3490863 AAACATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 12 0.38
14 17 0.53
15 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (13 bp):
TTAAGAAAATTAT
Found at i:3494454 original size:23 final size:22
Alignment explanation
Indices: 3494399--3494454 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
3494389 AATAGAAAAC
3494399 ATAAATTAATTTTAAAAATAAA
1 ATAAATTAATTTTAAAAATAAA
* * *
3494421 AGATATTTAATTTTAAAACTAAA
1 ATA-AATTAATTTTAAAAATAAA
3494444 ATAAATGTAAT
1 ATAAAT-TAAT
3494455 CAAAATTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAAATTAATTTTAAAAATAAA
Done.