Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008441.1 Hibiscus syriacus cultivar Beakdansim tig00111242_pilon, whole genome shotgun sequence
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: 151049
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3229 original size:9 final size:9
Alignment explanation
Indices: 3204--3246 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
3194 CACGTGAGGA
3204 TTATTTTATT
1 TTATTTTA-T
3214 CTTATTTTAT
1 -TTATTTTAT
3224 TTATTTTAT
1 TTATTTTAT
*
3233 TTATCTT-T
1 TTATTTTAT
3241 TTATTT
1 TTATTT
3247 ACTGTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 6 0.20
9 15 0.50
10 1 0.03
11 8 0.27
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTTTAT
Found at i:3241 original size:20 final size:21
Alignment explanation
Indices: 3204--3247 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3194 CACGTGAGGA
3204 TTATTTTATTCTTA-TTTTAT
1 TTATTTTATTCTTATTTTTAT
*
3224 TTATTTTATT-TATCTTTTTAT
1 TTATTTTATTCT-TATTTTTAT
3245 TTA
1 TTA
3248 CTGTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.52
21 9 0.43
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTATTCTTATTTTTAT
Found at i:3263 original size:21 final size:21
Alignment explanation
Indices: 3217--3263 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3207 TTTTATTCTT
* *
3217 ATTTTATTTATTTTATTTATC
1 ATTTTATTTATGTTATTTACC
*
3238 TTTTTATTTACTGTT-TTTACC
1 ATTTTATTTA-TGTTATTTACC
3259 ATTTT
1 ATTTT
3264 TCATTGCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTATTTATGTTATTTACC
Found at i:3992 original size:2 final size:2
Alignment explanation
Indices: 3985--4011 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3975 TCTAATTCTC
3985 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4012 CCTTGGGCTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10780 original size:15 final size:15
Alignment explanation
Indices: 10760--10826 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
10750 TATCCTTTAC
*
10760 TCACATATAACACAT
1 TCACATAGAACACAT
* * *
10775 TCACATAGCATATAT
1 TCACATAGAACACAT
* *
10790 TCACGTAGAAC-CTTT
1 TCACATAGAACAC-AT
*
10805 TCACATAAAACACAT
1 TCACATAGAACACAT
10820 TCACATA
1 TCACATA
10827 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
15 37 0.97
16 1 0.03
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.28
Consensus pattern (15 bp):
TCACATAGAACACAT
Found at i:14438 original size:33 final size:31
Alignment explanation
Indices: 14371--14446 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 31
14361 GTAAAAAGTT
14371 ATAATAAAAATTTAGGTGTGAAATTAAAAAATA
1 ATAATAAAAATTTAGGTGTGAAATT--AAAATA
*
14404 ATAATAAAAATTTAGGTAGTGTAAAATT-AGATA
1 ATAATAAAAATTTAGGT-GTG--AAATTAAAATA
14437 ATTAATAAAA
1 A-TAATAAAA
14447 TATATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 22 0.58
34 11 0.29
36 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.32
Consensus pattern (31 bp):
ATAATAAAAATTTAGGTGTGAAATTAAAATA
Found at i:24150 original size:60 final size:60
Alignment explanation
Indices: 24057--24203 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
24047 TTAAATGGAT
* * ** *
24057 AAAG-TACACAAATAGTCCCTCGACTATAGGATGATGTTTTGTTGAGT-TTCTCAACTATTA
1 AAAGTTACA-AAATGGTCCCTCAACTATAGGATGATACTTTGTTGAGTCCTC-CAACTATTA
* *
24117 AAAGTTACAAAATGGTCCTTCAACTATAGGATGATACTTTGTTGAGTCCTCCGACTATTA
1 AAAGTTACAAAATGGTCCCTCAACTATAGGATGATACTTTGTTGAGTCCTCCAACTATTA
*
24177 AAAGTTATAAAATGGTCACC-CAACTAT
1 AAAGTTACAAAATGGTC-CCTCAACTAT
24204 TTAGTATGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
60 68 0.91
61 7 0.09
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCAACTATAGGATGATACTTTGTTGAGTCCTCCAACTATTA
Found at i:35647 original size:31 final size:31
Alignment explanation
Indices: 35606--35671 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
35596 TTTAAGGATA
*
35606 AAATTGATATTTTATCTTAAAAT-TATAT-ATC
1 AAATTAATATTTTATC-TAAAATCTA-ATGATC
35637 AAATTAATATTTTATCTAAAATCTAATGATC
1 AAATTAATATTTTATCTAAAATCTAATGATC
35668 AAAT
1 AAAT
35672 ATAAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
AAATTAATATTTTATCTAAAATCTAATGATC
Found at i:35658 original size:18 final size:18
Alignment explanation
Indices: 35604--35663 Score: 51
Period size: 19 Copynumber: 3.6 Consensus size: 18
35594 AGTTTAAGGA
*
35604 TAAAATTGATATTTTATC
1 TAAAATTAATATTTTATC
35622 TTAAAATT-ATA---TATC
1 -TAAAATTAATATTTTATC
35637 --AAATTAATATTTTATC
1 TAAAATTAATATTTTATC
35653 TAAAATCTAAT
1 TAAAAT-TAAT
35664 GATCAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
12 5 0.15
13 3 0.09
15 4 0.12
16 4 0.12
18 7 0.21
19 11 0.32
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (18 bp):
TAAAATTAATATTTTATC
Found at i:36084 original size:24 final size:22
Alignment explanation
Indices: 36057--36110 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
36047 TGTTGTTGGT
36057 GATCAAGCTACCGATAACACAACC
1 GATCAAGCTACCGATAAC-CAA-C
36081 GATC-A---ACCGATAACCAAC
1 GATCAAGCTACCGATAACCAAC
36099 GATCAAGCTACC
1 GATCAAGCTACC
36111 AATCAAGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 9 0.35
22 3 0.12
23 1 0.04
24 4 0.15
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (22 bp):
GATCAAGCTACCGATAACCAAC
Found at i:36103 original size:18 final size:20
Alignment explanation
Indices: 36066--36104 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
36056 TGATCAAGCT
36066 ACCGATAACACAACCGATCA
1 ACCGATAACACAACCGATCA
36086 ACCGATAAC-CAA-CGATCA
1 ACCGATAACACAACCGATCA
36104 A
1 A
36105 GCTACCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.10
Consensus pattern (20 bp):
ACCGATAACACAACCGATCA
Found at i:39324 original size:26 final size:23
Alignment explanation
Indices: 39286--39341 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 23
39276 CATAATTCGA
39286 TTTTATTTATTTTTTATTTTTTCTTG
1 TTTTA-TTATTTTTTA-TTTTT-TTG
39312 TTTTATTATTTTTTATTTTTTTG
1 TTTTATTATTTTTTATTTTTTTG
39335 TTTTATT
1 TTTTATT
39342 CATTATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.33
24 5 0.17
25 10 0.33
26 5 0.17
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTTATTATTTTTTATTTTTTTG
Found at i:39350 original size:23 final size:23
Alignment explanation
Indices: 39291--39350 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
39281 TTCGATTTTA
*
39291 TTTATTTTTTATT-TTTTCTTGT
1 TTTATTATTTATTATTTTCTTGT
* *
39313 TTTATTATTTTTTATTTTTTTGT
1 TTTATTATTTATTATTTTCTTGT
39336 TTTATTCA-TTATTAT
1 TTTATT-ATTTATTAT
39351 CACGTTTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 11 0.34
23 20 0.62
24 1 0.03
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.78
Consensus pattern (23 bp):
TTTATTATTTATTATTTTCTTGT
Found at i:42438 original size:15 final size:14
Alignment explanation
Indices: 42417--42450 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
42407 AAAAAGAGAA
42417 AAAAAAAAGCAAAGAG
1 AAAAAAAA-CAAAG-G
42433 AAAAAAAACAAAGG
1 AAAAAAAACAAAGG
42447 AAAA
1 AAAA
42451 TTGAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 5 0.28
16 8 0.44
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAGG
Found at i:42641 original size:69 final size:69
Alignment explanation
Indices: 42523--42660 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
42513 GGTTCAAACT
* *
42523 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACTACTTCACTCAAAGATCATAGAGCA
1 ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACTACTCCACTCAAAGATCATAGAGCA
42588 TCAA
66 TCAA
* *
42592 ATGAGACTGATCAAGCACAATCATTTCTGAATCACTGAA-TCACTCCACTCGAAGATCATAGAGC
1 ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACT-ACTCCACTCAAAGATCATAGAGC
42656 ATCAA
65 ATCAA
42661 GAGAGAGAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (69 bp):
ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACTACTCCACTCAAAGATCATAGAGCA
TCAA
Found at i:44252 original size:36 final size:32
Alignment explanation
Indices: 44205--44289 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 32
44195 ATTGAAAACA
44205 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-AAATTT-G--TCTCTTGAGACAG
* *
44241 TTTCCCTTGAAACAA-TTGTCTCTTGAGATAG
1 TTTCCCTTGAAAAAATTTGTCTCTTGAGACAG
44272 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAA-AAATT
44290 ATTTGAAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 24 0.55
32 2 0.05
33 2 0.05
34 2 0.05
35 2 0.05
36 12 0.27
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (32 bp):
TTTCCCTTGAAAAAATTTGTCTCTTGAGACAG
Found at i:44265 original size:31 final size:31
Alignment explanation
Indices: 44228--44286 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
44218 AAATTTCGTC
44228 TCTCTTGAGACAGTTTCCCTTGAAACAATTG
1 TCTCTTGAGACAGTTTCCCTTGAAACAATTG
*
44259 TCTCTTGAGATAGTTTCCCTTGAAACAA
1 TCTCTTGAGACAGTTTCCCTTGAAACAA
44287 ATTATTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (31 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAATTG
Found at i:44391 original size:36 final size:36
Alignment explanation
Indices: 44292--44406 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 36
44282 AACAAATTAT
* * *
44292 TTGAAACAAATTTCATCTCCCTTGAGACATTTTCTT
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
* * *
44328 TTGGAACTAAGTCTT-GTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAAT-TTCATCTCTCTTGAGACAGTTTCTC
*
44365 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
44401 TTGAAA
1 TTGAAA
44407 AAAAATCTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
35 2 0.03
36 35 0.53
37 27 0.41
38 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
Found at i:44442 original size:118 final size:114
Alignment explanation
Indices: 44225--44442 Score: 242
Period size: 118 Copynumber: 1.8 Consensus size: 114
44215 AATAAATTTC
* * * *
44225 GTCTCTCTTGAGACAGTTTCCCTTGAAACAATTGTCTCTTGAGATAGTTTCCCTTGAAACAAATT
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAATTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAT
* * *
44290 ATTTGAAACAAATTTCATCTCCCTTGAGACATTTTCTTTTGGAACTAAGTCTT
66 ATTTG----AAATTTCATCTCCCCTAAAACATTTTCTTTTGGAACTAAGTCTT
*
44343 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAA
1 GTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA--T--TCTCTCTTGAGACAGTTTCCCTTGAAAA
* *
44408 AAAATCTTTG-AATTT-ATTTCCCCTAAAACAATTTT
61 AAAATATTTGAAATTTCATCTCCCCTAAAAC-ATTTT
44443 GTCTCCCTTG
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
117 10 0.12
118 38 0.45
119 2 0.02
121 1 0.01
123 33 0.39
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (114 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAATTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAT
ATTTGAAATTTCATCTCCCCTAAAACATTTTCTTTTGGAACTAAGTCTT
Found at i:44475 original size:63 final size:64
Alignment explanation
Indices: 44368--44521 Score: 188
Period size: 63 Copynumber: 2.4 Consensus size: 64
44358 GTTTCTCTTG
** * **
44368 AAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAAAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTT-CCTTGAAAAAAAATCTTCAAATTTATTTCCCCTA
*
44433 AAAC-AATTTTGTCTCCCTTGAG-CAGTTT-CTTGAAACACAAAATCTTCAAATTTATTTCCCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTGAAA-A-AAAATCTTCAAATTTATTTCCCCT
44495 A
64 A
*
44496 AAACAAAATTTTGTTTCCCTTGAGAC
1 AAAC-AAATTTTGTCTCCCTTGAGAC
44522 CATTTTCATG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
61 7 0.09
62 1 0.01
63 32 0.42
64 15 0.19
65 21 0.27
66 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37
Consensus pattern (64 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTGAAAAAAAATCTTCAAATTTATTTCCCCTA
Found at i:45446 original size:110 final size:109
Alignment explanation
Indices: 45180--45546 Score: 485
Period size: 110 Copynumber: 3.4 Consensus size: 109
45170 GCTTCCTAGT
* * * *
45180 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAATACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
45245 CAACGAAGGGGCAACTAATTGTCAACAAACAACTTTCAGTTTCA
66 CAACGAAGAGGCGACTGATTGTCAACAAACAACTTTCAGTTTCA
*
45289 TTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
45354 CAACGAAGTGGCGATTGATTGTCAACAAACAACTTTTCAGTTTTA
66 CAACGAAGAGGCGACTGATTGTCAACAAACAAC-TTTCAGTTTCA
*
45399 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * **
45464 CACCGAAGAGGCGGCTGGCTGTCAACAAACAA-TTTCCCAG-TTC-
66 CAACGAAGAGGCGACTGATTGTCAACAAACAACTTT--CAGTTTCA
* * *
45507 --CAGATCCAATTTCAACTTCACGA-CGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCAC-ATCGAAGGATATTGAACTC
45547 GGAACAATAC
Statistics
Matches: 232, Mismatches: 22, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
106 35 0.15
107 1 0.00
108 3 0.01
109 91 0.39
110 102 0.44
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (109 bp):
TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGAGGCGACTGATTGTCAACAAACAACTTTCAGTTTCA
Found at i:46841 original size:2 final size:2
Alignment explanation
Indices: 46834--47115 Score: 76
Period size: 2 Copynumber: 146.5 Consensus size: 2
46824 TTTCATCCCC
* *
46834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
46876 TA TT TA TT TA TT TA CTA TA T- TCC TT TT TT TA TT TA TA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * * *
46918 T- TA TT TT TA T- TA TA TA TA TC T- TA TA TCA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * * * * * *
46958 TA TG TA TGA GTA T- TA -A T- TT TC TC CA TT TA CTA TG TA TA TA
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * **
46998 TA TA TA TA T- TT TA -A TA T- TA -A TT TA TA CG T- 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
* * * *
47035 TA TA TA TG TA TA TA TA TA TA TA TA TC T- TA -A TA T- TC TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
47074 TT TG TT TT TA TT TA TT TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47115 T
1 T
47116 TTTTACTTTA
Statistics
Matches: 210, Mismatches: 47, Indels: 46
0.69 0.16 0.15
Matches are distributed among these distances:
1 17 0.08
2 183 0.87
3 9 0.04
4 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Found at i:47131 original size:43 final size:45
Alignment explanation
Indices: 47045--47133 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
47035 TATATATGTA
* * * *
47045 TATATATATATATATCTTAATATTCTATTTTTGTTTTTATTTATT
1 TATATATATATATATCATAATATTATATTTTTCTTTATATTTATT
47090 TATATATATATATAT-AT-ATATTATATTTTTACTTTAT-TTTATT
1 TATATATATATATATCATAATATTATATTTTT-CTTTATATTTATT
47133 T
1 T
47134 TTTTCTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 19 0.49
44 5 0.13
45 15 0.38
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (45 bp):
TATATATATATATATCATAATATTATATTTTTCTTTATATTTATT
Found at i:47375 original size:19 final size:19
Alignment explanation
Indices: 47353--47414 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
47343 TTCATTTTGG
47353 TTTTTTTTGTTTTTTTTTA
1 TTTTTTTTGTTTTTTTTTA
* * *
47372 TTTTTTATGTGTTTTGTTA
1 TTTTTTTTGTTTTTTTTTA
* *
47391 TTTTCTCTTTATTTTATTTTA
1 TTTT-T-TTTGTTTTTTTTTA
47412 TTT
1 TTT
47415 ATTATTCTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
19 20 0.61
20 1 0.03
21 12 0.36
ACGTcount: A:0.10, C:0.03, G:0.06, T:0.81
Consensus pattern (19 bp):
TTTTTTTTGTTTTTTTTTA
Found at i:48724 original size:79 final size:79
Alignment explanation
Indices: 48640--48787 Score: 224
Period size: 79 Copynumber: 1.9 Consensus size: 79
48630 AGAAAAAAAT
* * * * *
48640 AACATTTTAGGTAACGCCCAATATTAAGATTTTCGATAAAAATAATAATGCTTTAAGTATTAATT
1 AACATTTTAAGTAACGCCCAATATTAACATTTCCGATAAAAAAAATAATACTTTAAGTATTAATT
48705 TACCGAAAATGTTA
66 TACCGAAAATGTTA
* * *
48719 AACATTTTAAGTAACGCCCAATATTAACATTTCCGATAAAAAAAATAATATTTTAGGTATTATTT
1 AACATTTTAAGTAACGCCCAATATTAACATTTCCGATAAAAAAAATAATACTTTAAGTATTAATT
48784 TACC
66 TACC
48788 ATAAATATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (79 bp):
AACATTTTAAGTAACGCCCAATATTAACATTTCCGATAAAAAAAATAATACTTTAAGTATTAATT
TACCGAAAATGTTA
Found at i:49915 original size:66 final size:61
Alignment explanation
Indices: 49791--49917 Score: 209
Period size: 66 Copynumber: 2.0 Consensus size: 61
49781 TTCAAGTCGA
49791 GGGTCTAAAATTCGGAAGAACTTCTTGTCTCCAGATGCGTCTTGCCCATTCCACTAGATTG
1 GGGTCTAAAATTCGGAAGAACTTCTTGTCTCCAGATGCGTCTTGCCCATTCCACTAGATTG
49852 GGGTCTAAAATTCGGAAGAACCTTCTCTTGTCTCCTAGATGCGGTCTTGCCCATTCCACTAGATT
1 GGGTCTAAAATTCGGAAGAA-C-T-TCTTGTCTCC-AGATGC-GTCTTGCCCATTCCACTAGATT
49917 G
61 G
49918 TGCTCCCCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
61 20 0.33
62 1 0.02
63 1 0.02
64 10 0.16
65 6 0.10
66 23 0.38
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.31
Consensus pattern (61 bp):
GGGTCTAAAATTCGGAAGAACTTCTTGTCTCCAGATGCGTCTTGCCCATTCCACTAGATTG
Found at i:52828 original size:42 final size:43
Alignment explanation
Indices: 52776--52860 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
52766 TTATATAATT
52776 ATTTAATTCCATTTTGATCTTAAATGATTTATA-CTTTTAAAA
1 ATTTAATTCCATTTTGATCTTAAATGATTTATACCTTTTAAAA
52818 ATTTAATTCCATTTTGATCTTAAATGATTTATACCTTTTAAAA
1 ATTTAATTCCATTTTGATCTTAAATGATTTATACCTTTTAAAA
52861 TTAATCTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 33 0.79
43 9 0.21
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (43 bp):
ATTTAATTCCATTTTGATCTTAAATGATTTATACCTTTTAAAA
Found at i:53180 original size:45 final size:45
Alignment explanation
Indices: 53041--53180 Score: 112
Period size: 45 Copynumber: 3.1 Consensus size: 45
53031 GGAGTATAAA
53041 ATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTT
1 ATATTTATTATCAAAAAGTTAAAAGCATTTCAAC-AATATTACCTT
** * * * * * *
53087 ATATTCGTT-TCAAATTA-TT-AAA-CATTGCATATATAGGAGTA--TAA
1 ATATTTATTATCAAA-AAGTTAAAAGCATTTCA-ACA-A-TATTACCT-T
53131 ATATTTATTATCAAAAAGTTAAAAGCATTTCAACAATATTACCTT
1 ATATTTATTATCAAAAAGTTAAAAGCATTTCAACAATATTACCTT
53176 ATATT
1 ATATT
53181 CGTTTCAAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 23
0.63 0.15 0.22
Matches are distributed among these distances:
43 8 0.12
44 16 0.24
45 23 0.34
46 14 0.21
47 6 0.09
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (45 bp):
ATATTTATTATCAAAAAGTTAAAAGCATTTCAACAATATTACCTT
Found at i:53186 original size:89 final size:91
Alignment explanation
Indices: 53026--53197 Score: 330
Period size: 90 Copynumber: 1.9 Consensus size: 91
53016 TGAGCATTGC
53026 ATATAGGAGTATAAAATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATAT
1 ATATAGGAGTATAAAATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATAT
53091 TCGTTTCAAATTATTAAACATTGCAT
66 TCGTTTCAAATTATTAAACATTGCAT
53117 ATATAGGAGTAT-AAATATTTATTATCAAAAAGTTAAAAGCATTTCAAC-AATATTACCTTATAT
1 ATATAGGAGTATAAAATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATAT
53180 TCGTTTCAAATTATTAAA
66 TCGTTTCAAATTATTAAA
53198 AAAATTAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 33 0.41
90 36 0.44
91 12 0.15
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (91 bp):
ATATAGGAGTATAAAATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATAT
TCGTTTCAAATTATTAAACATTGCAT
Found at i:53236 original size:89 final size:89
Alignment explanation
Indices: 53040--53218 Score: 225
Period size: 90 Copynumber: 2.0 Consensus size: 89
53030 AGGAGTATAA
* *
53040 AATATTTATTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATATTCGTTTCAAATTAT
1 AATACTTACTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATATTCGTTTCAAATTAT
* ** * *
53105 TAAACATTGCATATATAGGAGTAT
66 TAAAAATTAAATAAATAAGAGTAT
* *
53129 AAATATTTATTATCAAAAAGTTAAAAGCATTTCAAC-AATATTACCTTATATTCGTTTCAAATTA
1 -AATACTTACTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATATTCGTTTCAAATTA
53193 TTAAAAAAATTAAATTCAAATAAGAG
65 TT--AAAAATTAAA-T-AAATAAGAG
53219 ATATGACTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
89 30 0.38
90 35 0.44
91 7 0.09
92 1 0.01
93 7 0.09
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (89 bp):
AATACTTACTATCAAAAAGTTAAAAGCATTTCAACAAATATTACCTTATATTCGTTTCAAATTAT
TAAAAATTAAATAAATAAGAGTAT
Found at i:54216 original size:31 final size:26
Alignment explanation
Indices: 54160--54209 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
54150 AAATTTAGAA
54160 TGGTAGTCATAATCTAAAGATGAAAT
1 TGGTAGTCATAATCTAAAGATGAAAT
54186 TGGTAGTCATAATCTAAAGATGAA
1 TGGTAGTCATAATCTAAAGATGAA
54210 TTGAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (26 bp):
TGGTAGTCATAATCTAAAGATGAAAT
Found at i:56695 original size:60 final size:60
Alignment explanation
Indices: 56575--56710 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 60
56565 AAAGTCGGGT
* * * * ** *
56575 GACCATTTTGTAAC-TTTAATAGTCGAGGGACTCAACAAAGCAACTCCTTATAGTCGAGG
1 GACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACACCATATAACCAAGG
* *
56634 GACCATTTTGTAACTTTTAATAATCTG-GGGATTCAACAAAACTACACCATATAACCAAGG
1 GACCATTTTGTAACTTTTAATAATC-GAGGGACTCAACAAAACAACACCATATAACCAAGG
*
56694 GATCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
56711 ATCCATTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 14 0.22
60 46 0.72
61 4 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACACCATATAACCAAGG
Found at i:56763 original size:22 final size:22
Alignment explanation
Indices: 56738--56787 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
56728 TTTGAATTTT
56738 ATCTCTTAAATTTTATTACTTC
1 ATCTCTTAAATTTTATTACTTC
*
56760 ATCTCTTAAATTTTATTAGTTC
1 ATCTCTTAAATTTTATTACTTC
56782 ATCTCT
1 ATCTCT
56788 AACGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.02, T:0.54
Consensus pattern (22 bp):
ATCTCTTAAATTTTATTACTTC
Found at i:57392 original size:6 final size:6
Alignment explanation
Indices: 57383--57414 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
57373 AAAAGAGGAC
57383 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GA
57415 ATTTTACTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:61493 original size:60 final size:58
Alignment explanation
Indices: 61383--61536 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 58
61373 AAATTAGACT
* * * *
61383 TTAAAGTTTTGCATATTTTAATTTTATCCCTAAACTATGATTCTCATTCTAAATTAATCC
1 TTAAACTTTTGAATATTCT-ATTTTATCCCTAAACTATCATTCT-ATTCTAAATTAATCC
* *
61443 TTAAACTTTTGAATATTCTGATTTCATCCCTAAACTATTACATTCT-TTCTAAATTAGTCC
1 TTAAACTTTTGAATATTCT-ATTTTATCCCTAAACTA-T-CATTCTATTCTAAATTAATCC
* *
61503 TCAAACTTTTGAACATTCTACTTTTATCCCTAAA
1 TTAAACTTTTGAATATTCTA-TTTTATCCCTAAA
61537 TTCATCCAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 1 0.01
60 74 0.91
61 1 0.01
62 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (58 bp):
TTAAACTTTTGAATATTCTATTTTATCCCTAAACTATCATTCTATTCTAAATTAATCC
Found at i:61778 original size:60 final size:59
Alignment explanation
Indices: 61667--61802 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
61657 TTATAGATTG
*
61667 GGATGAAATTGAAATGTTGAAAAATTAGGGACTAATTTAGAATGAATGTCATAATTT-A
1 GGATGAAATTGAAATATTGAAAAATTAGGGACTAATTTAGAATGAATGTCATAATTTAA
* * * * * *
61725 GAGATGAAATTGAAATATTTAAAAGTTTGATGACTAATTTAGAATG-CTAGTCATAGTTTAA
1 G-GATGAAATTGAAATATTGAAAAATTAG-GGACTAATTTAGAATGAAT-GTCATAATTTAA
61786 GGAT-AAAGTTGAAATAT
1 GGATGAAA-TTGAAATAT
61803 ATATATATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 1 0.02
59 27 0.41
60 36 0.55
61 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.34
Consensus pattern (59 bp):
GGATGAAATTGAAATATTGAAAAATTAGGGACTAATTTAGAATGAATGTCATAATTTAA
Found at i:74062 original size:296 final size:295
Alignment explanation
Indices: 73513--74099 Score: 723
Period size: 296 Copynumber: 2.0 Consensus size: 295
73503 AGAAAAAAAA
* * * *
73513 TATTGTTTTAAATAAATATAAAAAAAAAGGTTGTAGTAAAATAAAAATGATTAAGTTATTTTAAC
1 TATTGTTTTAAATAAACAT--AAAAAAAGGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAAC
*
73578 ATTAACCATAGAATTAGAATAGAATGACGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATG
64 ATTAACCATAGAATTAGAATAGAATGACGGATGTAGCTCAAATGATAGAGCGCTCGCTTTGCATG
* ** * ** * * * * * *
73643 CAAGAAGCACGGTGATTGATACCCCGCATCTTGACATTGGAAGTACATGGACTCATATTATTTCT
129 CAAGAAGCACGGGGATCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTATTACT
* * * *
73708 AGCAAAACACGTGAATTCAATTTAATATAAACTATTAAAAGTGATCTATTAGTATCTTAATTTAA
194 AGCAAAACACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAATATCTTAATTAAA
* *
73773 ATTGTTTTGCGGCGATAATTATTCTTTTAAAAATATC
259 ATTGTTTTGCGGCGATAACTATTATTTTAAAAATATC
*
73810 TATTGTTTTAAATAAACAT-AAAAAAGTGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAACG
1 TATTGTTTTAAATAAACATAAAAAAAG-GTTGCAGTAAAATAAAAATAATTAAGCTATTTTAACA
* * * * * * * *
73874 TTAACCATAGACTTATAATAGAATGAGGGTATGTAG-TACAAATTATTGAGTGCTTGTTTTGCAT
65 TTAACCATAGAATTAGAATAGAATGACGG-ATGTAGCT-CAAATGATAGAGCGCTCGCTTTGCAT
* *
73938 GCGAA-AAGTACGGGGATCAATACCCCACATCTCCACATTAGAAATGCAAGGACTCACAGTATTA
128 GC-AAGAAGCACGGGGATCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTATTA
* * ** *
74002 CTAGCAAAACAAC-TTATTTAAATTTAATATGCACTATTAAAAGCGATTTATTAATATCTTAATT
192 CTAGCAAAAC-ACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAATATCTTAATT
*
74066 AAAATTGTTTTGTGGCGATAACTATTATTTTAAA
256 AAAATTGTTTTGCGGCGATAACTATTATTTTAAA
74100 TAATGATAAA
Statistics
Matches: 245, Mismatches: 40, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
294 7 0.03
295 60 0.24
296 156 0.64
297 22 0.09
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (295 bp):
TATTGTTTTAAATAAACATAAAAAAAGGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAACAT
TAACCATAGAATTAGAATAGAATGACGGATGTAGCTCAAATGATAGAGCGCTCGCTTTGCATGCA
AGAAGCACGGGGATCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTATTACTAG
CAAAACACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAATATCTTAATTAAAAT
TGTTTTGCGGCGATAACTATTATTTTAAAAATATC
Found at i:76106 original size:139 final size:139
Alignment explanation
Indices: 75851--76126 Score: 417
Period size: 139 Copynumber: 2.0 Consensus size: 139
75841 AATATAATAA
* *
75851 AAATGATTAAGCTATTTTAACGTTAATCATGATCTTAGAATAAAATGAGGGAATGTAGCTCAAAT
1 AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGTAGCTCAAAT
** ** * * *
75916 GGTAGAGCGATTGCTTTGCATGTGAGATGTACAGGATTGATACCTCACATCTCTACATTACAAAT
66 GGTAGAGCGACCGCTTTGCATGCAAGAAGTACAGGATCGATACCTCACATCTCCACATTACAAAT
*
75981 GTAAGGAGT
131 GCAAGGAGT
75990 AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGTAGCTCAAAT
1 AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGTAGCTCAAAT
* * * * *
76055 GGTAGAGCGCCCGCTTTGTATGCAAGAAGTACGGGATCGATACCTCGCATCTCCATATTACAAAT
66 GGTAGAGCGACCGCTTTGCATGCAAGAAGTACAGGATCGATACCTCACATCTCCACATTACAAAT
76120 GCAAGGA
131 GCAAGGA
76127 TTCATAATAT
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
139 122 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (139 bp):
AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGTAGCTCAAAT
GGTAGAGCGACCGCTTTGCATGCAAGAAGTACAGGATCGATACCTCACATCTCCACATTACAAAT
GCAAGGAGT
Found at i:82029 original size:19 final size:19
Alignment explanation
Indices: 82005--82043 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
81995 TCGAATGCAT
82005 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
82024 TCCATGCATCGATGCGCTC
1 TCCATGCACCGATGCACTC
82043 T
1 T
82044 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.18, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:90264 original size:20 final size:21
Alignment explanation
Indices: 90235--90290 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
90225 TTTGTGCTTC
*
90235 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
90255 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
90277 ATGCATCGATGCAT
1 ATGCATCGATGCAT
90291 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:91858 original size:21 final size:21
Alignment explanation
Indices: 91816--91859 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
91806 AACCCCGGAG
*
91816 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
91837 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
91858 CT
1 CT
91860 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:92913 original size:19 final size:19
Alignment explanation
Indices: 92889--92927 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
92879 TCGAATGCAT
92889 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
92908 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
92927 T
1 T
92928 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:92944 original size:65 final size:64
Alignment explanation
Indices: 92826--93035 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
92816 TATTCAAAGG
* ** *
92826 CATGCACCGATGCATC-AGTACATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCATCGATGCA-CAAG-ACATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCA
*
92888 TTC
62 TTT
* **** *
92891 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATT
1 CATGCATCGATGCACAAGACATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATT
92955 T
64 T
* **
92956 GATGCATCGATGCACAAGACATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGACATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
93020 CATGCATCGATGCACA
1 CATGCATCGATGCACA
93036 CTTGGTGCAC
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
63 6 0.05
64 52 0.43
65 63 0.52
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAAGACATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:93050 original size:64 final size:64
Alignment explanation
Indices: 92826--93055 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
92816 TATTCAAAGG
* * * *
92826 CATGCACCGATGCATCAGTACATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTACATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
92888 TTC
62 TTT
* * * *
92891 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTACATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
92956 GATGCATCGATGCACAAGACATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTACATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
93020 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTACATGCATCGATGCATCA
93056 AGTGTTCCAA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 68 0.50
65 63 0.46
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTACATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:95602 original size:12 final size:13
Alignment explanation
Indices: 95585--95623 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
95575 TTATTTTTCT
95585 TTTATATTTA-TA
1 TTTATATTTATTA
95597 TTTATA-TTATTA
1 TTTATATTTATTA
95609 TTTATA-TTATTA
1 TTTATATTTATTA
95621 TTT
1 TTT
95624 TTGGATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTTATTA
Found at i:100323 original size:770 final size:779
Alignment explanation
Indices: 99102--100547 Score: 2029
Period size: 770 Copynumber: 1.9 Consensus size: 779
99092 AAAAATTGAA
* * * *
99102 TATAAACTATTAAAAGTGATCTATTAGTATCTTAATAAAAATTGTTTTATAGCGATAACTATTTT
1 TATAAACTATTAAAAGTGATATATTAGTATCTTAATAAAAATTATTTTATAGCGATAACTATATC
**
99167 TTTTAAAGAATGATAAATGAAATTATTGTATATATTTCAAATGTTTCTTATCAGTAACAATTGCA
66 TTTTAAAGAATGATAAATGAAATTATTGTATATATTTCAAATGTTTCTTATCAGTAACAATCACA
* *
99232 TCCATTGCTACAAAAGATATTTACTTATTTGCAATTTTTCATGTCTTTTACATAGCATAGACATA
131 TCCATTGCTACAAAAGAAATTTAC-TATTTGCAATTTTTCATGTCTTTTACATAGCAAAGACATA
* * * *
99297 CTGAAAACCTAATCTAGCATCCCAATGAATCGATAATCATAATCCATATTTTCAAACCAAAATCG
195 CCGAAAACCTAATATACCATCCCAATGAATCGATAATCAAAATCCATATTTTCAAACCAAAATCG
* * *
99362 AGCAACCCATTCACCTTCTTTACCATGTGTTTTGCAATACTTGCCATAGGGTTGTGTTTTAAGTA
260 AGCAACCCATTCACCTTCTTTA-CATGTGTTCTACAATACTTGCCATAGGATTGTGTTTTAAGTA
* * *
99427 GTATATATTTCATTGGGCACATACATTTCAAGTTAAGGTTAAGGACATAACATATCATGATACAT
324 GTATATATTTCATTGGACACATACATTTCAAGTGAAGATTAAGGACATAACATATCATGATACAT
* * * *
99492 GTTTTGAAAAGAGAAAACAACCTTTAGAGATACCAAGAAGCAGAATAATGACATCTTTGATATTT
389 GATTTGAAAAGAGAAAACAACATTTAGAGAGACCAAGAAGCAGAATAATGACATATTTGATATTT
*
99557 A-TTGTATATTAATTTTACTAGAGGAATGAGAGATTACAAGATAATAAGAAAACGTAGAAAAATG
454 ATTTGTATATTAATTTTACTAGAGGAATGAGAGATTACAAGATAAGAAGAAAACGTAGAAAAATG
* * * *
99621 ATATTGCATTAGTAA-TG-GAAAAGAAGCT-AT-TGTATTTGACTATCTTACCATAAAAGGAGAT
519 ATATTGCATTAGTAACGGAGAAAAGAAGCTAATATCT-TTTGACTATCTTACCATAAAAGAAGAA
* * *
99682 GTATGTGGTTGTTATAAACATGAAAATGTGTCGTACTGCATTCAAGATAAC-G-TCCAGTGTTAA
583 ATATGTGGATGTTATAAACATGAAAATGTGTCGTACTGCATTCAAGATAACGGTTCCAGTGTGAA
**
99745 ACATGAAAGTCATAAAATGTGAGTGGACGTATATCATATGGTAGAGTGCTCACTTAGCATGCGAG
648 ACATGAAAACCATAAAATGTGAGTGGACGTATATCATATGGTAGAGTGCTCACTTAGCATGCGAG
99810 AGGTATAGGGATCGTTACCCCTTATCTCCACATTAGAAATGCAAGGTCTCATATTTATTAAATGT
713 AGGTATAGGGATCGTTACCCCTTATCTCCACATTAGAAATGCAAGGTCTCATATTTATTAAATGT
99875 AG
778 AG
* * *
99877 TATAAACTATTAAAAGTGATATATTATTATCTTAATTAAAATTATTTTGTCA-CGATAACTA-AT
1 TATAAACTATTAAAAGTGATATATTAGTATCTTAATAAAAATTATTTTAT-AGCGATAACTATAT
* *
99940 CTTTTAAATAATGATAAATGAAATTATTGTATATATTTCAAATGTTTCTTCTCAGTAACAATCAC
65 CTTTTAAAGAATGATAAATGAAATTATTGTATATATTTCAAATGTTTCTTATCAGTAACAATCAC
* * *
100005 ATCCATTGCTATAAAAGAAATTTA-T-TTT-CAATTTTTCGTGTCTTTTACATAGCAAAGACTTA
130 ATCCATTGCTACAAAAGAAATTTACTATTTGCAATTTTTCATGTCTTTTACATAGCAAAGACATA
* * *
100067 CCGAAAACCTAATATACCATCCCAATGAATTGATGATCAAAATCCATGTTTTCAAACCAAAATCG
195 CCGAAAACCTAATATACCATCCCAATGAATCGATAATCAAAATCCATATTTTCAAACCAAAATCG
** ** * * * *
100132 AGCAATTCATTTGCCTTGCTTCT-CATGTGTTCTACGATACTTGTCATAGTATTGTGTTTTAGGT
260 AGCAACCCATTCACCTT-CTT-TACATGTGTTCTACAATACTTGCCATAGGATTGTGTTTTAAGT
* * *
100196 TGTATATATTTCATTGGATACATACATTTTAAGTGAAGATTAAGGACATAACATATCATGATA-A
323 AGTATATATTTCATTGGACACATACATTTCAAGTGAAGATTAAGGACATAACATATCATGATACA
* * * * * *
100260 TTGATTTGGAAAGAGAATACAACATTTGGAGAGACTAAGAAGCTGGATAATGACATATTTGATAT
388 -TGATTTGAAAAGAGAAAACAACATTTAGAGAGACCAAGAAGCAGAATAATGACATATTTGATAT
* * * * * * * *
100325 TTATTTTTTTGTTAATTTTGCTAGAGGAATGAGAGCTTGCAAGATCAGAAGAAAATGTAGAAAAA
452 TTATTTGTATATTAATTTTACTAGAGGAATGAGAGATTACAAGATAAGAAGAAAACGTAGAAAAA
* ***
100390 TGATCTTGCATTAGTAACGGAAAAGAAAAGAAGCTAATATCTTTTGACTATCTTACCATGCGAGA
517 TGATATTGCATTAGTAACGG---AGAAAAGAAGCTAATATCTTTTGACTATCTTACCATAAAAGA
* *
100455 AGAAATATGTGGATGTTATAAACATGAAAATGTTTCGTACTGCATTCAAGATAACGTGTTCCATT
579 AGAAATATGTGGATGTTATAAACATGAAAATGTGTCGTACTGCATTCAAGATAACG-GTTCCAGT
100520 GTGAAACATGAAAACCATAAAATGTGAG
643 GTGAAACATGAAAACCATAAAATGTGAG
100548 GGGATGTAGC
Statistics
Matches: 582, Mismatches: 74, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
769 1 0.00
770 250 0.43
771 74 0.13
772 3 0.01
774 83 0.14
775 54 0.09
776 12 0.02
777 72 0.12
778 2 0.00
779 1 0.00
780 30 0.05
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (779 bp):
TATAAACTATTAAAAGTGATATATTAGTATCTTAATAAAAATTATTTTATAGCGATAACTATATC
TTTTAAAGAATGATAAATGAAATTATTGTATATATTTCAAATGTTTCTTATCAGTAACAATCACA
TCCATTGCTACAAAAGAAATTTACTATTTGCAATTTTTCATGTCTTTTACATAGCAAAGACATAC
CGAAAACCTAATATACCATCCCAATGAATCGATAATCAAAATCCATATTTTCAAACCAAAATCGA
GCAACCCATTCACCTTCTTTACATGTGTTCTACAATACTTGCCATAGGATTGTGTTTTAAGTAGT
ATATATTTCATTGGACACATACATTTCAAGTGAAGATTAAGGACATAACATATCATGATACATGA
TTTGAAAAGAGAAAACAACATTTAGAGAGACCAAGAAGCAGAATAATGACATATTTGATATTTAT
TTGTATATTAATTTTACTAGAGGAATGAGAGATTACAAGATAAGAAGAAAACGTAGAAAAATGAT
ATTGCATTAGTAACGGAGAAAAGAAGCTAATATCTTTTGACTATCTTACCATAAAAGAAGAAATA
TGTGGATGTTATAAACATGAAAATGTGTCGTACTGCATTCAAGATAACGGTTCCAGTGTGAAACA
TGAAAACCATAAAATGTGAGTGGACGTATATCATATGGTAGAGTGCTCACTTAGCATGCGAGAGG
TATAGGGATCGTTACCCCTTATCTCCACATTAGAAATGCAAGGTCTCATATTTATTAAATGTAG
Found at i:101647 original size:3 final size:3
Alignment explanation
Indices: 101635--101695 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
101625 AAAAAACCTT
* *
101635 TTA TTA -TA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
101682 TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TT
101696 TTTTGGTAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:102649 original size:23 final size:23
Alignment explanation
Indices: 102623--102668 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
102613 AAGAACCAAT
*
102623 ATAAA-CTTAAATATACCATTAAA
1 ATAAAGCTTAAACAT-CCATTAAA
*
102646 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
102669 CTAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAGCTTAAACATCCATTAAA
Found at i:112829 original size:23 final size:23
Alignment explanation
Indices: 112803--112851 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
112793 ATAAAAAACC
*
112803 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
112826 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
112849 AAA
1 AAA
112852 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:114477 original size:25 final size:23
Alignment explanation
Indices: 114442--114560 Score: 86
Period size: 25 Copynumber: 5.1 Consensus size: 23
114432 ATTTATTCAA
*
114442 TTTATTATTATTATTATTATTTT
1 TTTATTTTTATTATTATTATTTT
114465 GGTTTATTTTTATTATTATT-TTTT
1 --TTTATTTTTATTATTATTATTTT
*
114489 TTCTATTTTT-TTATCTTTTATTTT
1 TT-TATTTTTATTAT-TATTATTTT
* *
114513 ATTTTTTTTCTATGATTTATT-TTTT
1 -TTTATTTT-TATTA-TTATTATTTT
* *
114538 TTTAATTTT-TT-TTATGATTTT
1 TTTATTTTTATTATTATTATTTT
114559 TT
1 TT
114561 ACTTCGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.05
21 6 0.08
22 7 0.09
23 11 0.14
24 19 0.25
25 24 0.31
26 5 0.06
27 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (23 bp):
TTTATTTTTATTATTATTATTTT
Found at i:114485 original size:12 final size:12
Alignment explanation
Indices: 114443--114559 Score: 52
Period size: 12 Copynumber: 9.9 Consensus size: 12
114433 TTTATTCAAT
*
114443 TTATTATTATTA
1 TTATTATTTTTA
*
114455 TTATTA-TTTTG
1 TTATTATTTTTA
*
114466 GT-TTATTTTTA
1 TTATTATTTTTA
*
114477 TTATTATTTTTTT
1 TTATTA-TTTTTA
114490 TCTATT-TTTTTA
1 T-TATTATTTTTA
*
114502 TCTTTTA-TTTTA
1 T-TATTATTTTTA
114514 TT-TT-TTTTCTA
1 TTATTATTTT-TA
*
114525 TGATTTATTTTT-
1 TTA-TTATTTTTA
*
114537 TT-TTAATTTTTT
1 TTATT-ATTTTTA
*
114549 TTATGATTTTT
1 TTATTATTTTT
114560 TACTTCGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
10 10 0.12
11 19 0.23
12 34 0.42
13 10 0.12
14 8 0.10
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:114502 original size:22 final size:21
Alignment explanation
Indices: 114446--114520 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
114436 ATTCAATTTA
* **
114446 TTATTATTATTATTATTTTGGT
1 TTATT-TTTTTATTATTTTATT
*
114468 TTATTTTTATTATTATTTTTTT
1 TTATTTTT-TTATTATTTTATT
*
114490 TCTATTTTTTTA-TCTTTTATT
1 T-TATTTTTTTATTATTTTATT
114511 TTATTTTTTT
1 TTATTTTTTT
114521 TCTATGATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 9 0.20
21 10 0.22
22 20 0.43
23 7 0.15
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (21 bp):
TTATTTTTTTATTATTTTATT
Found at i:114540 original size:19 final size:19
Alignment explanation
Indices: 114492--114540 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
114482 ATTTTTTTTC
* * *
114492 TATTTTTTTATCTTTTATT
1 TATTTTTTTTTCTATGATT
114511 T-TATTTTTTTTCTATGATT
1 TAT-TTTTTTTTCTATGATT
114530 TATTTTTTTTT
1 TATTTTTTTTT
114541 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (19 bp):
TATTTTTTTTTCTATGATT
Found at i:114559 original size:40 final size:40
Alignment explanation
Indices: 114494--114574 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
114484 TTTTTTTCTA
* *
114494 TTTTTTTATCTTTTATTTTATTTTTTTTCTAT-GATTTATT
1 TTTTTTTATATTTTATTTTATTTTTTTACT-TCGATTTATT
114534 TTTTTTTA-ATTTT-TTTTATGATTTTTTACTTCGATTTATT
1 TTTTTTTATATTTTATTTTAT--TTTTTTACTTCGATTTATT
114574 T
1 T
114575 AACGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 6 0.17
39 5 0.14
40 25 0.69
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (40 bp):
TTTTTTTATATTTTATTTTATTTTTTTACTTCGATTTATT
Found at i:114560 original size:12 final size:11
Alignment explanation
Indices: 114469--114560 Score: 61
Period size: 10 Copynumber: 8.7 Consensus size: 11
114459 TATTTTGGTT
*
114469 TATTTTTATTA
1 TATTTTTTTTA
*
114480 TTATTTTTTTTC
1 -TATTTTTTTTA
114492 TA-TTTTTTTA
1 TATTTTTTTTA
* *
114502 TCTTTTATTT-
1 TATTTTTTTTA
*
114512 TATTTTTTTTC
1 TATTTTTTTTA
**
114523 TA--TGATTTA
1 TATTTTTTTTA
114532 T-TTTTTTTTA
1 TATTTTTTTTA
114542 -ATTTTTTTTA
1 TATTTTTTTTA
114552 TGATTTTTT
1 T-ATTTTTT
114561 ACTTCGATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
9 5 0.08
10 30 0.49
11 10 0.16
12 16 0.26
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.78
Consensus pattern (11 bp):
TATTTTTTTTA
Found at i:119038 original size:12 final size:11
Alignment explanation
Indices: 119021--119068 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
119011 CATATTGAAT
119021 TTTCTTTTAAA
1 TTTCTTTTAAA
119032 CTTTCTTTTTAAA
1 -TTTC-TTTTAAA
*
119045 TTTCTTTTTAA
1 TTTCTTTTAAA
119056 TCTTCTTTTAAA
1 T-TTCTTTTAAA
119068 T
1 T
119069 CTTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 7 0.22
12 18 0.56
13 7 0.22
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTCTTTTAAA
Found at i:119071 original size:21 final size:22
Alignment explanation
Indices: 119038--119084 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
119028 TAAACTTTCT
119038 TTTTAAATTTCTTTTTAATCTTC
1 TTTTAAA-TTCTTTTTAATCTTC
* *
119061 TTTTAAA-TCTTTTTATTTTTC
1 TTTTAAATTCTTTTTAATCTTC
119082 TTT
1 TTT
119085 CTTCTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAAATTCTTTTTAATCTTC
Found at i:137330 original size:20 final size:21
Alignment explanation
Indices: 137305--137353 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
137295 TAATTTCTAT
137305 TAATAATAATATAAAT-AAAA
1 TAATAATAATATAAATGAAAA
* * *
137325 TAATAAAAATATGAATGAAAT
1 TAATAATAATATAAATGAAAA
137346 TAATAATA
1 TAATAATA
137354 GCAATAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TAATAATAATATAAATGAAAA
Found at i:138198 original size:39 final size:39
Alignment explanation
Indices: 138149--138223 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
138139 AGCACCACGG
*
138149 TCACTCAGACGTAAAACTCGTGCTCAATATAATGCACCA
1 TCACACAGACGTAAAACTCGTGCTCAATATAATGCACCA
*
138188 TCACACAGACGTCAAACTCGTGCTCAATATAATGCA
1 TCACACAGACGTAAAACTCGTGCTCAATATAATGCA
138224 GCTGCTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (39 bp):
TCACACAGACGTAAAACTCGTGCTCAATATAATGCACCA
Found at i:141949 original size:21 final size:20
Alignment explanation
Indices: 141863--142020 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
141853 AAATGACCAA
**
141863 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
141882 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
141902 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
141922 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
141943 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
141964 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
141984 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
142005 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
142021 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:142013 original size:20 final size:20
Alignment explanation
Indices: 141988--142181 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
141978 GATTTTCAAT
* *
141988 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
142008 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
142028 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
142048 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
142068 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
142088 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
142108 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
142128 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
142149 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
142169 AATCGCAACGCGA
1 AATCGCAACGCGA
142182 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:142033 original size:40 final size:39
Alignment explanation
Indices: 141988--142181 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
141978 GATTTTCAAT
* ** *
141988 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
142028 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
142068 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
142108 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
142149 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
142182 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:142071 original size:60 final size:60
Alignment explanation
Indices: 141988--142180 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
141978 GATTTTCAAT
* ** * *
141988 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
142048 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
142108 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
142169 AATCGCAACGCG
1 AATCGCAACGCG
142181 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:142350 original size:20 final size:21
Alignment explanation
Indices: 142325--142366 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
142315 CTCTCTACGG
142325 CGAAGAAATCCGT-CCCATCT
1 CGAAGAAATCCGTCCCCATCT
**
142345 CGAAGATTTCCGTCCCCATCT
1 CGAAGAAATCCGTCCCCATCT
142366 C
1 C
142367 CGGCGAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (21 bp):
CGAAGAAATCCGTCCCCATCT
Found at i:142598 original size:33 final size:33
Alignment explanation
Indices: 142559--142629 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
142549 TTCACTTAGA
*
142559 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
142592 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
142625 TTTCA
1 TTTCA
142630 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:142769 original size:14 final size:14
Alignment explanation
Indices: 142750--142804 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
142740 AGAATGACTG
142750 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
142764 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
142783 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
142797 TCGCAACG
1 TCGCAACG
142805 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:142787 original size:33 final size:33
Alignment explanation
Indices: 142750--142820 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
142740 AGAATGACTG
**
142750 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
142783 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
142816 TCGCA
1 TCGCA
142821 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:142838 original size:19 final size:19
Alignment explanation
Indices: 142816--142913 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
142806 GAAACCAAAA
*
142816 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
142835 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
142849 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
142868 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
142882 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
142901 TCGCGTTGCGATT
1 TCGCGTTGCGATT
142914 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:142857 original size:14 final size:14
Alignment explanation
Indices: 142838--142927 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
142828 TTTCATTTCG
142838 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
142852 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
142871 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
142885 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
142902 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
142918 CGTTGCGATT
1 CGTTGCGATT
142928 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:142863 original size:33 final size:33
Alignment explanation
Indices: 142821--142935 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
142811 CAAAATCGCA
142821 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
142854 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
142887 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
142920 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
142936 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:144864 original size:91 final size:93
Alignment explanation
Indices: 144622--144996 Score: 706
Period size: 91 Copynumber: 4.1 Consensus size: 93
144612 TAGATTGCTT
*
144622 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144687 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144715 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144779 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144807 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144870 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144897 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144961 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144989 AGTAAATT
1 AGTAAATT
144997 ATCCATTCAA
Statistics
Matches: 278, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 37 0.13
91 109 0.39
92 71 0.26
93 61 0.22
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:145080 original size:19 final size:19
Alignment explanation
Indices: 145040--145168 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
145030 TAGTTTACTT
* *
145040 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
145060 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
145079 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
145098 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
145112 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
145131 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
145145 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
145164 TCGCA
1 TCGCA
145169 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:145119 original size:33 final size:32
Alignment explanation
Indices: 145076--145168 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
145066 CGCGAAACCA
**
145076 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
145108 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
145141 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
145169 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:145166 original size:52 final size:52
Alignment explanation
Indices: 145040--145168 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
145030 TAGTTTACTT
**
145040 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
145092 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
145145 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
145169 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:145186 original size:19 final size:19
Alignment explanation
Indices: 145164--145295 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
145154 GAAACCAAAA
*
145164 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
145183 TCGCGTTGCGA--TTC--T
1 TCGCGTTGCGATTTTCATT
145198 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
145214 TCGC-ATGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
145229 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
145246 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
145265 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
145285 TCGTGTTGCGA
1 TCGCGTTGCGA
145296 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 9 0.10
14 8 0.09
15 4 0.04
16 8 0.09
17 10 0.11
18 1 0.01
19 39 0.43
20 12 0.13
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:145214 original size:31 final size:33
Alignment explanation
Indices: 145169--145258 Score: 150
Period size: 31 Copynumber: 2.8 Consensus size: 33
145159 CAAAATCGCA
145169 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
145201 TTGCGA-TTTCATTTCGC-ATGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
145232 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
145259 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
30 9 0.17
31 20 0.38
32 17 0.32
33 7 0.13
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:147200 original size:14 final size:14
Alignment explanation
Indices: 147181--147216 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
147171 GATTGTTAAT
147181 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
147195 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
147209 TGATTTGT
1 TGATTTGT
147217 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:147390 original size:20 final size:19
Alignment explanation
Indices: 147322--147404 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
147312 AAAAATGACT
147322 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
147341 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
147355 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
147374 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
147394 ATCGCAATGCG
1 ATCGCAATGCG
147405 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:147428 original size:19 final size:18
Alignment explanation
Indices: 147411--147671 Score: 311
Period size: 19 Copynumber: 14.9 Consensus size: 18
147401 TGCGTTTATA
147411 ATTTCGCATTGCGA-TT-
1 ATTTCGCATTGCGATTTC
*
147427 ATCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147444 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147463 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
147480 -TTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147496 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147515 ATTTCGCATTGCGATTTCC
1 ATTTCGCATTGCGATTT-C
147534 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
147552 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
147570 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
147587 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147603 ATTTCGCATTGCGATTTC
1 ATTTCGCATTGCGATTTC
147621 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
147638 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
147654 ATTTCCGCATTGCGATTT
1 ATTT-CGCATTGCGATTT
147672 TCATGTTGGG
Statistics
Matches: 217, Mismatches: 6, Indels: 41
0.82 0.02 0.16
Matches are distributed among these distances:
14 24 0.11
16 29 0.13
17 25 0.12
18 56 0.26
19 77 0.35
20 6 0.03
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:147473 original size:52 final size:52
Alignment explanation
Indices: 147411--147675 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
147401 TGCGTTTATA
*
147411 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
147463 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
147515 ATTTCGCATTGCGATTTCCATTTCGCATTGCGA-TTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
147570 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
147621 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
147674 AT
1 AT
147676 GTTGGGATTT
Statistics
Matches: 202, Mismatches: 3, Indels: 15
0.92 0.01 0.07
Matches are distributed among these distances:
50 6 0.03
51 59 0.29
52 78 0.39
53 9 0.04
54 3 0.01
55 23 0.11
56 18 0.09
57 6 0.03
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:149975 original size:12 final size:12
Alignment explanation
Indices: 149958--149982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
149948 TTCTTCGGGA
149958 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149970 CTTTTTCTTCTT
1 CTTTTTCTTCTT
149982 C
1 C
149983 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:150190 original size:24 final size:24
Alignment explanation
Indices: 150156--150202 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
150146 CTGAAACATC
150156 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
150180 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
150203 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:150897 original size:20 final size:20
Alignment explanation
Indices: 150869--151043 Score: 226
Period size: 20 Copynumber: 8.8 Consensus size: 20
150859 AAATTTCAGT
* *
150869 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
150889 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
150909 GTTGCGA-TTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
150928 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
150948 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
150968 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
150988 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
151008 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
151028 ATTGCGATTTACGGAT
1 GTTGCGATTTACGGAT
151044 ACGCGT
Statistics
Matches: 137, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
19 17 0.12
20 120 0.88
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:150982 original size:40 final size:40
Alignment explanation
Indices: 150869--151049 Score: 260
Period size: 40 Copynumber: 4.5 Consensus size: 40
150859 AAATTTCAGT
* * * *
150869 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
* * *
150909 GTTGCGA-TTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
150948 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
150988 GTTGCGATTTACGGATACGCGTTGCGATTTACGGA-TA-C
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
151026 GCATTGCGATTTACGGATACGCGT
1 G--TTGCGATTTACGGATACGCGT
Statistics
Matches: 134, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
38 2 0.01
39 41 0.31
40 91 0.68
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
Done.