Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 19 of 173
Found at i:5269859 original size:418 final size:419
Alignment explanation
Indices: 5268868--5269914 Score: 1624
Period size: 421 Copynumber: 2.5 Consensus size: 419
5268858 TCTAACAGGT
* * *
5268868 ATAACCTTCACAAC-ACTCTATTATTTACTTGAGGCTAAGATAGAACCATTTCATAGGTTTTGTA
1 ATAACATTCACAACTA-TCTATTATTTACTTG-GGTTAAGATAGAACCATTTCATAGTTTTTGTA
* * ** *
5268932 GCCTAACTAAAACCTTCTAACTTTTCGAAGGCTTAACTAAAAACTTATCTAGTTTTTATGGCTCA
64 GCTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCA
* * *
5268997 ATTAGTAATCCTCCGAATATACAAATTGGTGATTTGTATAAACAAATGAAAAACCTCAAAAATGT
129 ATTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAA-AAATGAAAAACCTCTAAAATGT
* *
5269062 TTGAGTGTTTGCAAAGTCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
*
5269127 TCTCACCCTCGCCTAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGAG
258 TCTCACCCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGAG
5269192 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
* * *
5269257 AGTTCAGTAATTGGTATCTTTCAATAACAAGG
388 AGTTCACTAATTGGCATCTTTCAAGAACAAGG
* * *
5269289 TATAACTTTCACAACTCTTTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
1 -ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
5269354 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
65 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
* *
5269419 TTAGTAATCAT-TCGAATATACAAATTGGTGATATGTGTAAGAAAATGAAAAACCTCTAAAATGT
130 TTAGTAATCCTCT-GAATATACAAATTGGTGATTTGTGTAA-AAAATGAAAAACCTCTAAAATGT
*
5269483 ATGAGTGTTTGGAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAAT
* * * *
5269548 TCTCACCCTCGTCGAAGAGTTGGAAAGTGTAATT-GGGTGCTTCAATTATACCCATTTTAATGTG
258 TCTCACCCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGAG
* * *
5269612 ATCCACCAGTTACACCCAAATTCAATTACTAAGTTGCTTTT-CAAACATAGCCTAAAGGTTTTCT
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTG-TTTTCCAAACATAGCCAAAAGGTTTTCC
*
5269676 CAGTTCACTAATTGGCATCTTTCAAGGACAAGG
387 CAGTTCACTAATTGGCATCTTTCAAGAACAAGG
* *
5269709 -TAACATTCACAACTATCTATTATTTACTTGGGTTAAGGTAGAACCATTTCATAATTTTTGTAGC
1 ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
* *
5269773 TTAACTAGAACCTTGTAACTTTTCGAAGGCCCAACTAAAAA-TCTCTCTAGTTTTTATGGTTCAA
66 TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACT-TCTCTAGTTTTTATGGCTCAA
*
5269837 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAAATGAAAATCCTCTAAAATGTA
130 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGT-AAAAAATGAAAAACCTCTAAAATGTA
*
5269902 -G-GTGTTTACAAAG
194 TGAGTGTTTGCAAAG
5269915 TTTAGCTTAT
Statistics
Matches: 576, Mismatches: 42, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
416 10 0.02
417 2 0.00
418 176 0.31
419 3 0.01
420 112 0.19
421 245 0.43
422 28 0.05
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (419 bp):
ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAAT
TAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAATGAAAAACCTCTAAAATGTATG
AGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCGTAATTACTCCAATTCT
CACCCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGAGATC
CACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCCAGT
TCACTAATTGGCATCTTTCAAGAACAAGG
Found at i:5272314 original size:3 final size:3
Alignment explanation
Indices: 5272299--5272346 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
5272289 GCTGTTGTAA
* *
5272299 AAG AAG GAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5272347 CAGAGTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5284913 original size:9 final size:9
Alignment explanation
Indices: 5284895--5284961 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
5284885 TTTGGTTAAA
*
5284895 AATTAACCG
1 AATTACCCG
5284904 AATTACCCG
1 AATTACCCG
* *
5284913 AATTAACTG
1 AATTACCCG
* *
5284922 AATTAACCA
1 AATTACCCG
5284931 AATTACCCG
1 AATTACCCG
*
5284940 AATTACCTG
1 AATTACCCG
5284949 AATTACCCG
1 AATTACCCG
5284958 AATT
1 AATT
5284962 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:5284927 original size:27 final size:27
Alignment explanation
Indices: 5284895--5284961 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
5284885 TTTGGTTAAA
5284895 AATTAACCGAATTACCCGAATTAACTG
1 AATTAACCGAATTACCCGAATTAACTG
* *
5284922 AATTAACCAAATTACCCGAATTACCTG
1 AATTAACCGAATTACCCGAATTAACTG
*
5284949 AATTACCCGAATT
1 AATTAACCGAATT
5284962 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACTG
Found at i:5285134 original size:18 final size:18
Alignment explanation
Indices: 5285111--5285150 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5285101 TTTATGATTA
5285111 GGTTGGGTTCGATAATTG
1 GGTTGGGTTCGATAATTG
* *
5285129 GGTTGGGTTGGATACTTG
1 GGTTGGGTTCGATAATTG
5285147 GGTT
1 GGTT
5285151 TGGATTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.42, T:0.40
Consensus pattern (18 bp):
GGTTGGGTTCGATAATTG
Found at i:5285158 original size:19 final size:18
Alignment explanation
Indices: 5285111--5285158 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5285101 TTTATGATTA
* *
5285111 GGTTGGGTTCGATAATTG
1 GGTTGGATTGGATAATTG
* *
5285129 GGTTGGGTTGGATACTTG
1 GGTTGGATTGGATAATTG
5285147 GGTTTGGATTGG
1 GG-TTGGATTGG
5285159 GTTTAGGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.12, C:0.04, G:0.44, T:0.40
Consensus pattern (18 bp):
GGTTGGATTGGATAATTG
Found at i:5287125 original size:24 final size:24
Alignment explanation
Indices: 5287075--5287127 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5287065 CAAAGAATAG
* * * * *
5287075 AAAAGAATATATTTAAATTGTGTA
1 AAAAGAAAATAATTAAATAGGGAA
5287099 AAAAGAAAATAATTAAATAGGGAA
1 AAAAGAAAATAATTAAATAGGGAA
5287123 AAAAG
1 AAAAG
5287128 GGGAATCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAAGAAAATAATTAAATAGGGAA
Found at i:5289969 original size:22 final size:22
Alignment explanation
Indices: 5289931--5289974 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5289921 GGCCTCGAAG
*
5289931 ATCTAAACTAAACTTTGTCAAA
1 ATCTAAACTAAACTTTGCCAAA
* *
5289953 ATCTAAACTTAATTTTGCCAAA
1 ATCTAAACTAAACTTTGCCAAA
5289975 CAATCAGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (22 bp):
ATCTAAACTAAACTTTGCCAAA
Found at i:5295772 original size:17 final size:17
Alignment explanation
Indices: 5295750--5295786 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5295740 GAAAGGCTAG
5295750 ATGGAATATGTTTATAC
1 ATGGAATATGTTTATAC
5295767 ATGGAATATGTTTATAC
1 ATGGAATATGTTTATAC
5295784 ATG
1 ATG
5295787 AATTGAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (17 bp):
ATGGAATATGTTTATAC
Found at i:5311117 original size:24 final size:24
Alignment explanation
Indices: 5311090--5311208 Score: 175
Period size: 24 Copynumber: 5.0 Consensus size: 24
5311080 TGGTACTCCA
* *
5311090 CCATCATCTGGAGGTGGTAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5311114 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5311138 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
5311162 CCATCATACGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
5311186 CCATCATATGGAGGTGGCAGTCC
1 CCATCATATGGAGGTGGCAGTCC
5311209 ACCAACTACT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 87 1.00
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.19
Consensus pattern (24 bp):
CCATCATATGGAGGTGGCAGTCCC
Found at i:5319020 original size:14 final size:14
Alignment explanation
Indices: 5319003--5319030 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5318993 TATTAAATTG
5319003 TAGAACTAAAATGC
1 TAGAACTAAAATGC
5319017 TAGAACTAAAATGC
1 TAGAACTAAAATGC
5319031 CAAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
TAGAACTAAAATGC
Found at i:5320145 original size:20 final size:18
Alignment explanation
Indices: 5320122--5320178 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
5320112 TTTAGTCATA
5320122 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT--T
*
5320142 TAATATATTTATT-AT-TT
1 TAATA-AATTATTAATATT
5320159 TAATAAATTATTTAATATT
1 TAATAAATTA-TTAATATT
5320178 T
1 T
5320179 TAATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.13
17 8 0.26
18 2 0.06
19 4 0.13
20 7 0.23
21 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATAAATTATTAATATT
Found at i:5320154 original size:21 final size:20
Alignment explanation
Indices: 5320129--5320172 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
5320119 ATATAATAAA
*
5320129 TTATTAATATAATTAATATAT
1 TTATTAATATAATAAAT-TAT
* *
5320150 TTATTATTTTAATAAATTAT
1 TTATTAATATAATAAATTAT
5320170 TTA
1 TTA
5320173 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTAATATAATAAATTAT
Found at i:5320179 original size:20 final size:20
Alignment explanation
Indices: 5320122--5320182 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5320112 TTTAGTCATA
5320122 TAATAAATTA-TTAATA---
1 TAATAAATTATTTAATATTT
* *
5320138 TAATTAATATATTTATTATTT
1 TAATAAAT-TATTTAATATTT
5320159 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
5320179 TAAT
1 TAAT
5320183 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 5 0.14
20 15 0.42
21 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:5320202 original size:13 final size:14
Alignment explanation
Indices: 5320186--5320227 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5320176 TTTTAATTTT
5320186 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
5320199 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
5320214 ATTTTAAATAATAT
1 ATTTT-AATAATAT
5320228 TCTTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:5320212 original size:16 final size:16
Alignment explanation
Indices: 5320190--5320226 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5320180 AATTTTATTT
5320190 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5320207 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5320222 TAATA
1 TAATA
5320227 TTCTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5322761 original size:44 final size:44
Alignment explanation
Indices: 5322666--5323000 Score: 212
Period size: 44 Copynumber: 7.3 Consensus size: 44
5322656 GGTATAGGAA
* * * * *
5322666 TTGTAGTTTCAATCTACTCCGCTGCAACTTCAGGGAGATGAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
** * *
5322710 TCATAGCTTCAATCTGCTCCACTACAACTTCAGTGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* * * *
5322754 TTGTAGCTTGTAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGACT
1 TTGTAGC-T-T--C---AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-T
* * * * * *
5322806 CGCTATGGTAGATTTAATCCGAC-CCACTACAACTTAAGAG-GTATAGGA-
1 ---T-T-GTAGCTTCAATCTG-CTCCACTGCAACTTCAGAGAG-ATAAGAT
* * * *
5322854 TTGTCA-CTTCAATATGCTCCACTACAACTTTAGTGAGATAAGAT
1 TTGT-AGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* *
5322898 TTGTAGCTTTAATCTACTCCACTGCAACTTCAG-GAAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAG-AGATAAGAT
* * *
5322942 TTGTAGCTTCAATCTGCTTCACTGTAACTTCAAAGAGATAAGAT
1 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* *
5322986 TTGTAGTTTTAATCT
1 TTGTAGCTTCAATCT
5323001 ATGCTGCAAC
Statistics
Matches: 225, Mismatches: 44, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
42 1 0.00
43 30 0.13
44 129 0.57
45 3 0.01
46 1 0.00
48 1 0.00
50 23 0.10
51 28 0.12
52 1 0.00
55 2 0.01
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT
Found at i:5323527 original size:36 final size:36
Alignment explanation
Indices: 5323485--5323556 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5323475 AAAATGAGTA
*
5323485 AGATGAAAATAGGTGCCCCAAATATCGCAGCATGAG
1 AGATGAAAATAGGTGCCCCAAATATCGCAACATGAG
5323521 AGATGAAAATAGGTGCCCCAAATATCGCAACATGAG
1 AGATGAAAATAGGTGCCCCAAATATCGCAACATGAG
5323557 CTTCTTTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (36 bp):
AGATGAAAATAGGTGCCCCAAATATCGCAACATGAG
Found at i:5331598 original size:14 final size:15
Alignment explanation
Indices: 5331575--5331607 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5331565 TTTATAGTTT
*
5331575 TTTTTTATTTTT-AA
1 TTTTTAATTTTTAAA
5331589 TTTTTAATTTTTAAA
1 TTTTTAATTTTTAAA
5331604 TTTT
1 TTTT
5331608 CTTTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTAATTTTTAAA
Found at i:5331995 original size:17 final size:17
Alignment explanation
Indices: 5331958--5332009 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
5331948 AATCAAAATT
* *
5331958 TATTTTATGATAAGATAA
1 TATTTTATAATAA-TTAA
5331976 TATTTTATAATAATTAA
1 TATTTTATAATAATTAA
** *
5331993 TATAATATAATATTTAA
1 TATTTTATAATAATTAA
5332010 ACTTAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TATTTTATAATAATTAA
Found at i:5332232 original size:16 final size:16
Alignment explanation
Indices: 5332211--5332241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5332201 ATTTATATTA
5332211 ATTATATTAATAAATT
1 ATTATATTAATAAATT
*
5332227 ATTATATTACTAAAT
1 ATTATATTAATAAAT
5332242 ATAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:5335350 original size:11 final size:11
Alignment explanation
Indices: 5335335--5335403 Score: 81
Period size: 11 Copynumber: 6.4 Consensus size: 11
5335325 AAAATTTAAA
5335335 AAAAAGTATTTT
1 AAAAA-TATTTT
5335347 AAAAATATTTT
1 AAAAATATTTT
5335358 AAAAATATTTT
1 AAAAATATTTT
**
5335369 --AAA-ATTAA
1 AAAAATATTTT
5335377 AAAAAGTATTTT
1 AAAAA-TATTTT
5335389 AAAAATATTTT
1 AAAAATATTTT
5335400 AAAA
1 AAAA
5335404 TTAAAATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 3 0.06
11 27 0.55
12 13 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:5335357 original size:42 final size:41
Alignment explanation
Indices: 5335310--5335420 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 41
5335300 ACCAAAAATT
5335310 TATTTTAAAAATTAAAAAATTTAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTAAAAAA-TTAAAAAAAAGTATTTTAAAAA
**
5335352 TATTTTAAAAATATTTTAAAATT-AAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-ATTAAAAAATTAAAAAAAAGTATTTTAAAAA
5335394 TATTTT-AAAATTAAAATAATTAAAAAA
1 TATTTTAAAAATTAAAA-AATTAAAAAA
5335421 TAAATATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.08
40 7 0.11
41 5 0.08
42 31 0.51
43 6 0.10
44 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAAATTAAAAAATTAAAAAAAAGTATTTTAAAAA
Found at i:5335389 original size:31 final size:30
Alignment explanation
Indices: 5335347--5335409 Score: 117
Period size: 31 Copynumber: 2.1 Consensus size: 30
5335337 AAAGTATTTT
5335347 AAAAATATTTTAAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAAATATTTTAAAATTAA
5335377 AAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAA
5335408 AA
1 AA
5335410 TAATTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:5335411 original size:16 final size:16
Alignment explanation
Indices: 5335390--5335432 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5335380 AAGTATTTTA
* *
5335390 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
5335406 AAAATAATTAAAAAAT
1 AAAATATTTAAAAAAT
5335422 AAATATATTTA
1 AAA-ATATTTA
5335433 GCCCGGGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:5335426 original size:31 final size:31
Alignment explanation
Indices: 5335358--5335432 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
5335348 AAAATATTTT
***
5335358 AAAAATATTTTAAAATTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAGTATAAA
* *
5335389 AAAAATATTTTAAAATTAAAATAATTA-AAA
1 AAAAATATTTTAAAATTAAAAAAAGTATAAA
5335419 AATAAATATATTTA
1 AA-AAATAT-TTTA
5335433 GCCCGGGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 31 0.84
32 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (31 bp):
AAAAATATTTTAAAATTAAAAAAAGTATAAA
Found at i:5340978 original size:3 final size:3
Alignment explanation
Indices: 5340970--5341050 Score: 67
Period size: 3 Copynumber: 26.0 Consensus size: 3
5340960 AAAATAAAAC
* *
5340970 TAA TAA TAA TTAA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
5341017 TGA TAA TACA TTAA -AA TAA TTAA CAA -AA TAA TAA
1 TAA TAA TA-A -TAA TAA TAA -TAA TAA TAA TAA TAA
5341051 GATTGCTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
2 4 0.06
3 47 0.73
4 11 0.17
5 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5341827 original size:14 final size:14
Alignment explanation
Indices: 5341808--5341834 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5341798 ATGTAAAAGA
5341808 TAAAATAAAATAAG
1 TAAAATAAAATAAG
5341822 TAAAATAAAATAA
1 TAAAATAAAATAA
5341835 ACAAGCAGAA
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:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAATAAAATAAG
Found at i:5342989 original size:46 final size:45
Alignment explanation
Indices: 5342937--5343047 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 45
5342927 AAAATTTTAC
* *
5342937 AATATATAATATATAAATAAAAAGTTAAAATTTATAAATTTATG-AA
1 AATATATAATATATAAA-AAAAACTAAAAATTTATAAATTT-TGAAA
5342983 AATATATAA-ATATATAAAAAAACTAAAAATTTATAAATTTTGTAAA
1 AATATATAATATATA-AAAAAAACTAAAAATTTATAAATTTTG-AAA
*
5343029 AAAATATAAATATATAAAA
1 AATATAT-AATATATAAAA
5343048 GAATTAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
44 2 0.04
45 26 0.46
46 19 0.33
47 5 0.09
48 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (45 bp):
AATATATAATATATAAAAAAAACTAAAAATTTATAAATTTTGAAA
Found at i:5342990 original size:18 final size:18
Alignment explanation
Indices: 5342963--5343019 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
5342953 ATAAAAAGTT
* *
5342963 AAAATTTATAAATTTATG
1 AAAATATATAAATTTATA
*
5342981 AAAATATATAAATATATA
1 AAAATATATAAATTTATA
* *
5342999 AAAAAACTAAAAATTTATA
1 AAAATA-TATAAATTTATA
5343018 AA
1 AA
5343020 TTTTGTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATATAAATTTATA
Found at i:5343011 original size:27 final size:27
Alignment explanation
Indices: 5342981--5343046 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5342971 TAAATTTATG
5342981 AAAATATATAAA-TATATAAAAAAACTA
1 AAAATATATAAATTATATAAAAAAA-TA
* * *
5343008 AAAATTTATAAATTTTGTAAAAAAATA
1 AAAATATATAAATTATATAAAAAAATA
*
5343035 TAAATATATAAA
1 AAAATATATAAA
5343047 AGAATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATATATAAATTATATAAAAAAATA
Found at i:5343056 original size:46 final size:45
Alignment explanation
Indices: 5342937--5343058 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 45
5342927 AAAATTTTAC
5342937 AATATATAATATATAAATAAAAAGTT-AAAATTTATAAATTTATGAAAA
1 AATATA-AATATAT-AA-AAAAA-TTAAAAATTTATAAATTTATGAAAA
* *
5342985 TATATAAATATATAAAAAAACTAAAAATTTATAAATTT-TGTAAAAA
1 AATATAAATATATAAAAAAATTAAAAATTTATAAATTTATG--AAAA
*
5343031 AATATAAATATATAAAAGAATTAAAAAT
1 AATATAAATATATAAAAAAATTAAAAAT
5343059 CTCATATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 3 0.05
45 20 0.30
46 31 0.47
47 7 0.11
48 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (45 bp):
AATATAAATATATAAAAAAATTAAAAATTTATAAATTTATGAAAA
Found at i:5346959 original size:27 final size:26
Alignment explanation
Indices: 5346900--5346981 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
5346890 CCCAAATTGA
* * *
5346900 TATAAAATAACTGTTATGCCCCCACGT
1 TATAAAATGACTG-TATGCCCCTATGT
**
5346927 GGTAAAATGACTGTGATGCCCCTATGT
1 TATAAAATGACTGT-ATGCCCCTATGT
* *
5346954 TATAAAATGACTATATG-CTCTATGT
1 TATAAAATGACTGTATGCCCCTATGT
5346979 TAT
1 TAT
5346982 GTATGACTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
25 10 0.22
26 4 0.09
27 31 0.69
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (26 bp):
TATAAAATGACTGTATGCCCCTATGT
Found at i:5351877 original size:13 final size:15
Alignment explanation
Indices: 5351847--5351878 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5351837 ATATTTCATG
5351847 CATTTCATCAATAAT
1 CATTTCATCAATAAT
5351862 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
5351875 CATT
1 CATT
5351879 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:5352402 original size:6 final size:6
Alignment explanation
Indices: 5352365--5352413 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
5352355 CCAAACACAC
* *
5352365 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
5352414 TTCAACACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:5352454 original size:45 final size:45
Alignment explanation
Indices: 5352391--5352574 Score: 228
Period size: 45 Copynumber: 4.1 Consensus size: 45
5352381 GTAACGGTAG
* * * *
5352391 CAGTAACAGTAACAGTAACAGTATTCAACACATAAAGTGCTGAAC
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * * * *
5352436 CTGTAATAGTAACGGTAACAGTATTCGACAGACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
5352481 CGGTAACAGTAAC-GTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* * * *
5352525 CAGTAACAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
5352569 CAGTAA
1 CAGTAA
5352575 GCCGGCAAAT
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
44 57 0.47
45 63 0.52
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:5367264 original size:22 final size:22
Alignment explanation
Indices: 5367222--5367264 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5367212 ATTAACTACA
**
5367222 CATATCTCCAAAATATCTGCAG
1 CATATCTCCAAAATAAATGCAG
5367244 CATATCCTCC-AAATAAATGCA
1 CATAT-CTCCAAAATAAATGCA
5367265 TGATTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (22 bp):
CATATCTCCAAAATAAATGCAG
Found at i:5368274 original size:12 final size:12
Alignment explanation
Indices: 5368257--5368284 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5368247 GTGATTAAGG
5368257 ACATTAATAGTA
1 ACATTAATAGTA
5368269 ACATTAATAGTA
1 ACATTAATAGTA
5368281 ACAT
1 ACAT
5368285 CATGGCTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (12 bp):
ACATTAATAGTA
Found at i:5369141 original size:31 final size:31
Alignment explanation
Indices: 5369103--5369182 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
5369093 CATGGTTGAT
*
5369103 TTAGCAGCAAAAATCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
5369134 TTAGCAGCAAAAACCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
*
5369165 TTAGCTGCAAAAACCAAT
1 TTAGCAGCAAAAACCAAT
5369183 TAAAATCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (31 bp):
TTAGCAGCAAAAACCAATAGAAGGTACCATC
Found at i:5370193 original size:83 final size:83
Alignment explanation
Indices: 5370087--5370515 Score: 714
Period size: 83 Copynumber: 5.2 Consensus size: 83
5370077 ATTTGGAGAT
*
5370087 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTGTATTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
5370152 TTTGCGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* *
5370170 AAAATGCCACTAATATTTAATTCGTCAATGAAACGGCGTCGTTTTGTTCAATTTTTATTATATTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5370235 TTTGCAGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* * *
5370253 AAAACGCCACTAATATTTAATTCTTCAATGAAATGGCGCCGTTTTGTTCAATTTTTATTATTTTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
5370318 TTTGCGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* *
5370336 AAAACGCCACTAATATTTAATTTGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTA
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
5370401 TTTGCGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* * * * *
5370419 AAAATGCCACTAATATTTAATTCATCAATGAAACAGCGTCGTTTTGTTCAATTTTTATTATTTTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5370484 TTTACGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
*
5370502 AAAATGCCACTAAT
1 AAAACGCCACTAAT
5370516 TATTCACTTT
Statistics
Matches: 323, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 323 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (83 bp):
AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
TTTGCGGCGTTTATTGAC
Found at i:5371012 original size:21 final size:21
Alignment explanation
Indices: 5370972--5371013 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5370962 ATCTGTAACA
* **
5370972 CTAAATCCTAAACCTTAAACC
1 CTAAATCCAAAACCCAAAACC
5370993 CTAAATCCAAAACCCAAAACC
1 CTAAATCCAAAACCCAAAACC
5371014 ATGCATTGTA
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:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
CTAAATCCAAAACCCAAAACC
Found at i:5371046 original size:21 final size:21
Alignment explanation
Indices: 5371022--5371062 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5371012 CCATGCATTG
* * *
5371022 TAAACCTTAAATCATTAACAC
1 TAAACCGTAAACCATAAACAC
5371043 TAAACCGTAAACCATAAACA
1 TAAACCGTAAACCATAAACA
5371063 TCAAGCCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCGTAAACCATAAACAC
Found at i:5371144 original size:7 final size:7
Alignment explanation
Indices: 5371134--5371189 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
5371124 CATTAAAACA
5371134 TAAACCC
1 TAAACCC
*
5371141 TAAACCT
1 TAAACCC
5371148 TAAACCC
1 TAAACCC
*
5371155 CAAACCC
1 TAAACCC
* *
5371162 CAAGCCC
1 TAAACCC
5371169 TAAA-CC
1 TAAACCC
* *
5371175 TACACCA
1 TAAACCC
5371182 TAAACCC
1 TAAACCC
5371189 T
1 T
5371190 GAACTCAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.41, C:0.43, G:0.02, T:0.14
Consensus pattern (7 bp):
TAAACCC
Found at i:5371368 original size:41 final size:41
Alignment explanation
Indices: 5371307--5371543 Score: 189
Period size: 41 Copynumber: 5.8 Consensus size: 41
5371297 GCCCCCGACC
*
5371307 ATTAGCGGCGCTTTCT-AAAAACACCGCTAAAGCCTAGAGA
1 ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
* * *
5371347 ATTAACGGCGCTTTCTAAAAAA-ACGCGCTAAAACCCAAAGCA
1 ATTAGCGGCGCTTTCTAAAAAACAC-CGCTAAAGCCCAGAG-A
* * * * *
5371389 A-TAGCGGCACTTTCTTCAAAAACGA-CGCTAATGGCAAGA-A
1 ATTAGCGGCGCTTTC-TAAAAAAC-ACCGCTAAAGCCCAGAGA
* *
5371429 CATTAGCGGCGCTTTCTAGAAAACGCCGCTAAAGCCCAGAGA
1 -ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
* * * * * ** *
5371471 ATTAGTGGCGCTTCCTCAAAAACGCCGCTAAATCCCTCAGC
1 ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
* *
5371512 ATTAGCGACGC-TTCTTCAAAAACACCGCTAAA
1 ATTAGCGGCGCTTTC-TAAAAAACACCGCTAAA
5371544 TCCCCCAACA
Statistics
Matches: 155, Mismatches: 31, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
40 20 0.13
41 104 0.67
42 30 0.19
44 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
Found at i:5371439 original size:83 final size:82
Alignment explanation
Indices: 5371347--5371501 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 82
5371337 AGCCTAGAGA
*
5371347 ATTAACGGCGCTTTCTAAAAAAACG-CGCTAAAACCCAAAGCAA-TAGCGGCACTTTCTTCAAAA
1 ATTAACGGCGCTTTCT-AAAAAACGCCGCTAAAACCCAAAG-AATTAGCGGCAC-TTCCTCAAAA
5371410 ACGACGCTAATGGCAAGAAC
63 ACGACGCTAATGGCAAGAAC
* * * * * *
5371430 ATTAGCGGCGCTTTCTAGAAAACGCCGCTAAAGCCCAGAGAATTAGTGGCGCTTCCTCAAAAACG
1 ATTAACGGCGCTTTCTAAAAAACGCCGCTAAAACCCAAAGAATTAGCGGCACTTCCTCAAAAACG
*
5371495 CCGCTAA
66 ACGCTAA
5371502 ATCCCTCAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
82 27 0.44
83 35 0.56
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (82 bp):
ATTAACGGCGCTTTCTAAAAAACGCCGCTAAAACCCAAAGAATTAGCGGCACTTCCTCAAAAACG
ACGCTAATGGCAAGAAC
Found at i:5371460 original size:124 final size:122
Alignment explanation
Indices: 5371306--5371542 Score: 316
Period size: 124 Copynumber: 1.9 Consensus size: 122
5371296 AGCCCCCGAC
* *
5371306 CATTAGCGGCGCTTTCTAAAAACACCGCTAAAGCCTAGAGAATTAACGGCGCTTTCTAAAAAAAC
1 CATTAGCGGCGCTTTCTAAAAACACCGCTAAAGCCCAGAGAATTAACGGCGCTTCCT-AAAAAAC
*
5371371 G-CGCTAAAACCCAAAGCAATAGCGGCACTTTCTTCAAAAACGA-CGCTAATGGCAAGAA
65 GCCGCTAAAACCCAAAGCAATAGCGACAC-TTCTTCAAAAAC-ACCGCTAATGGCAAGAA
* ** *
5371429 CATTAGCGGCGCTTTCTAGAAAACGCCGCTAAAGCCCAGAGAATTAGTGGCGCTTCCTCAAAAAC
1 CATTAGCGGCGCTTTCTA-AAAACACCGCTAAAGCCCAGAGAATTAACGGCGCTTCCTAAAAAAC
* ** * *
5371494 GCCGCTAAATCCCTCAGCATTAGCGACGCTTCTTCAAAAACACCGCTAA
65 GCCGCTAAAACCCAAAGCAATAGCGACACTTCTTCAAAAACACCGCTAA
5371543 ATCCCCCAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
122 1 0.01
123 43 0.43
124 55 0.56
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (122 bp):
CATTAGCGGCGCTTTCTAAAAACACCGCTAAAGCCCAGAGAATTAACGGCGCTTCCTAAAAAACG
CCGCTAAAACCCAAAGCAATAGCGACACTTCTTCAAAAACACCGCTAATGGCAAGAA
Found at i:5371583 original size:41 final size:41
Alignment explanation
Indices: 5371427--5371590 Score: 163
Period size: 41 Copynumber: 4.0 Consensus size: 41
5371417 TAATGGCAAG
* * **
5371427 AACATTAGCGGCGC-T-TTCTAGAAAACGCCGCTAAAGCCCAG
1 AACATTAGCGACGCTTCTTC-A-AAAACGCCGCTAAATCCCCC
* * * *
5371468 AGA-ATTAGTGGCGCTTCCTCAAAAACGCCGCTAAATCCCTC
1 A-ACATTAGCGACGCTTCTTCAAAAACGCCGCTAAATCCCCC
* *
5371509 AGCATTAGCGACGCTTCTTCAAAAACACCGCTAAATCCCCC
1 AACATTAGCGACGCTTCTTCAAAAACGCCGCTAAATCCCCC
* *
5371550 AACATTAGCGACGCTTCTTCAAAAATGCAGCTAAAGTCCCC
1 AACATTAGCGACGCTTCTTCAAAAACGCCGCTAAA-TCCCC
5371591 AAAGCCTCAG
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
41 93 0.90
42 8 0.08
43 2 0.02
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (41 bp):
AACATTAGCGACGCTTCTTCAAAAACGCCGCTAAATCCCCC
Found at i:5371688 original size:40 final size:41
Alignment explanation
Indices: 5371641--5371733 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
5371631 GCTTCCTTAT
**
5371641 AAACGCCGCTAATGCTCAATTTTTAGCGACGTTT-TTCAAA
1 AAACGCCGCTAATGCTCAATTTTTAGCGACGTTTAGACAAA
* * *
5371681 AAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTAGACAAA
1 AAACGCCGCTAATGCTCAATTTTTAGCGACGTTTAGACAAA
5371722 AAACGCCGCTAA
1 AAACGCCGCTAA
5371734 AAGCCTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 31 0.67
41 15 0.33
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCAATTTTTAGCGACGTTTAGACAAA
Found at i:5374174 original size:25 final size:25
Alignment explanation
Indices: 5374128--5374175 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5374118 TTTATGGAAT
* *
5374128 TTATTTTGAATGAGAAATTGTATTC
1 TTATTATGAATGAGAAAGTGTATTC
5374153 TTATTATGAATTGA-AAAGTGTAT
1 TTATTATGAA-TGAGAAAGTGTAT
5374176 GTGTAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (25 bp):
TTATTATGAATGAGAAAGTGTATTC
Found at i:5388119 original size:20 final size:20
Alignment explanation
Indices: 5388087--5388147 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
5388077 TTTAATATTA
*
5388087 AATTCATTTAATATTAAATT
1 AATTAATTTAATATTAAATT
*
5388107 GATT-ATCTTAATATTAAATTT
1 AATTAAT-TTAATATTAAA-TT
5388128 AATTAATTTAATATTAAATT
1 AATTAATTTAATATTAAATT
5388148 TAATCTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
21 16 0.44
22 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (20 bp):
AATTAATTTAATATTAAATT
Found at i:5388138 original size:21 final size:21
Alignment explanation
Indices: 5388078--5388194 Score: 94
Period size: 21 Copynumber: 5.2 Consensus size: 21
5388068 TTTAATAGAT
* *
5388078 TTAATATTAAATTCATTTAATA
1 TTAA-ATTTAATTAATTTAATA
*
5388100 TTAAA-TTGATT-ATCTTAATA
1 TTAAATTTAATTAAT-TTAATA
5388120 TTAAATTTAATTAATTTAATA
1 TTAAATTTAATTAATTTAATA
* *
5388141 TTAAATTTAATCTAATATTTATC
1 TTAAATTTAAT-TAAT-TTAATA
5388164 TTGATAAGTATTATATTAATTTAATA
1 TT-A-AA-T-TTA-ATTAATTTAATA
5388190 TTAAA
1 TTAAA
5388195 ATGATTAAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.03
20 15 0.19
21 23 0.29
22 10 0.13
23 6 0.08
24 3 0.04
25 3 0.04
26 7 0.09
27 7 0.09
28 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TTAAATTTAATTAATTTAATA
Found at i:5388147 original size:12 final size:12
Alignment explanation
Indices: 5388114--5388151 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5388104 ATTGATTATC
5388114 TTAATATTAAAT
1 TTAATATTAAAT
5388126 TT-A-ATT-AAT
1 TTAATATTAAAT
5388135 TTAATATTAAAT
1 TTAATATTAAAT
5388147 TTAAT
1 TTAAT
5388152 CTAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.22
10 4 0.17
11 4 0.17
12 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATATTAAAT
Found at i:5388147 original size:16 final size:16
Alignment explanation
Indices: 5388076--5388194 Score: 67
Period size: 16 Copynumber: 7.8 Consensus size: 16
5388066 ATTTTAATAG
*
5388076 ATTTAATATTAAATTC
1 ATTTAATATTAAATTA
*
5388092 ATTTAATATTAAATTG
1 ATTTAATATTAAATTA
*
5388108 A-TT-ATCTT-AA-T-
1 ATTTAATATTAAATTA
*
5388119 A-TTAA-ATTTAATTA
1 ATTTAATATTAAATTA
5388133 ATTTAATATTAAATTTA
1 ATTTAATATTAAA-TTA
* ** *
5388150 ATCTAATATTTATCTTG
1 ATTTAATA-TTAAATTA
*
5388167 A--TAAGTATTATATTA
1 ATTTAA-TATTAAATTA
5388182 ATTTAATATTAAA
1 ATTTAATATTAAA
5388195 ATGATTAAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.06
12 4 0.05
13 3 0.04
14 5 0.06
15 16 0.20
16 29 0.36
17 16 0.20
18 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAATATTAAATTA
Found at i:5388315 original size:13 final size:13
Alignment explanation
Indices: 5388283--5388331 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
5388273 TTGAATTCAA
**
5388283 GAGAAAATTGTAGA
1 GAGAAAATTGT-TT
*
5388297 GAGAAAATTTTTT
1 GAGAAAATTGTTT
5388310 GAGAAAATTGTTT
1 GAGAAAATTGTTT
*
5388323 CAGAAAATT
1 GAGAAAATT
5388332 CTCTGAGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (13 bp):
GAGAAAATTGTTT
Found at i:5389590 original size:31 final size:31
Alignment explanation
Indices: 5389538--5389604 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5389528 TAACAGCTTA
*
5389538 GTGACTTAAATAAAGCATTTTGAATAGTTTG
1 GTGACTTAAATAAAACATTTTGAATAGTTTG
*
5389569 GTGATTTAAATGAAAAC-TTTTGAATAGTTTG
1 GTGACTTAAAT-AAAACATTTTGAATAGTTTG
5389600 GTGAC
1 GTGAC
5389605 CAAATTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (31 bp):
GTGACTTAAATAAAACATTTTGAATAGTTTG
Found at i:5395738 original size:11 final size:11
Alignment explanation
Indices: 5395722--5395765 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
5395712 AAAGGGTTTT
5395722 TTATAAAAATA
1 TTATAAAAATA
5395733 TTATAAAAATA
1 TTATAAAAATA
5395744 --ATAAAAAT-
1 TTATAAAAATA
5395752 TTACT-AAAATA
1 TTA-TAAAAATA
5395763 TTA
1 TTA
5395766 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TTATAAAAATA
Found at i:5395847 original size:27 final size:26
Alignment explanation
Indices: 5395750--5395842 Score: 152
Period size: 26 Copynumber: 3.5 Consensus size: 26
5395740 AATAATAAAA
*
5395750 ATTTACTAAAATATTACAATTTTTTT
1 ATTTACCAAAATATTACAATTTTTTT
5395776 ATTTACCAAAATATTACAATTTTTTT
1 ATTTACCAAAATATTACAATTTTTTT
5395802 ATTTACCAAAATATATA-AACTTTTTTT
1 ATTTACCAAAATAT-TACAA-TTTTTTT
5395829 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5395843 ATAAAAAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
26 41 0.64
27 23 0.36
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTACCAAAATATTACAATTTTTTT
Found at i:5396120 original size:19 final size:21
Alignment explanation
Indices: 5396082--5396120 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5396072 AATAATTGAT
*
5396082 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
5396103 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
5396121 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:5396172 original size:3 final size:3
Alignment explanation
Indices: 5396164--5396205 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5396154 TCAAAATAAA
5396164 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5396206 GTTGTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5396210 original size:3 final size:3
Alignment explanation
Indices: 5396204--5396229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5396194 ATTATTATTA
5396204 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
5396230 AGTATGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:5396481 original size:12 final size:12
Alignment explanation
Indices: 5396464--5396494 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5396454 ATAATTTTAG
5396464 TGTGTATTATTT
1 TGTGTATTATTT
5396476 TGTGTATTATTT
1 TGTGTATTATTT
*
5396488 TGAGTAT
1 TGTGTAT
5396495 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:5397091 original size:18 final size:18
Alignment explanation
Indices: 5397048--5397092 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5397038 TTGACATGGT
*
5397048 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAATG
**
5397066 TGCCGGCGAAGAAGAATG
1 TGGTGGCGAAGAAGAATG
5397084 TGGTGGCGA
1 TGGTGGCGA
5397093 TCATTGGGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.44, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAATG
Found at i:5402800 original size:19 final size:19
Alignment explanation
Indices: 5402765--5402802 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5402755 TTTAAACACA
5402765 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
5402784 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
5402803 ACCTTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:5402898 original size:44 final size:42
Alignment explanation
Indices: 5402813--5402965 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 42
5402803 ACCTTTTTTC
* *
5402813 CCTTTCTTCCCTCTTCTTCTTCTTTTTT-TTCTCTTCTCCTTT
1 CCTTTCTTCCTTCTT-TCCTTCTTTTTTCTTCTCTTCTCCTTT
5402855 CCCTTTCTTTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
1 -CCTTTC-TTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
* * *
5402899 TC-TTCTTCTTTCTTTCCTT-TTTTCTCTTCTCCTT-TCCTTGT
1 CCTTTCTTCCTTCTTTCCTTCTTTTTTCTTCT-CTTCTCCTT-T
*
5402940 -CTTTCTTTCCTCTCCTTTCTTTCTTT
1 CCTTTC-TTCCT-T-CTTTCCTTCTTT
5402966 CCCTCCTTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 16
0.80 0.06 0.14
Matches are distributed among these distances:
40 16 0.17
41 20 0.21
42 7 0.07
43 19 0.20
44 29 0.31
45 3 0.03
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.65
Consensus pattern (42 bp):
CCTTTCTTCCTTCTTTCCTTCTTTTTTCTTCTCTTCTCCTTT
Found at i:5402946 original size:38 final size:37
Alignment explanation
Indices: 5402861--5402963 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 37
5402851 CTTTCCCTTT
* *
5402861 CTTTCC-TTCTTTCCTTCTTT--TTTCTTCTCTTCTC
1 CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
*
5402895 CTTTTC-TTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
*
5402930 CTTTCCTTGTCTTTCTTTCCTCTCCTTTCTTTCT
1 CTTTCCTT-TCTTTCTTT-CTTTCCTTT-TTTCT
5402964 TTCCCTCCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
33 9 0.16
34 8 0.14
35 18 0.32
36 1 0.02
37 2 0.04
38 6 0.11
39 8 0.14
40 5 0.09
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.65
Consensus pattern (37 bp):
CTTTCCTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTC
Found at i:5402946 original size:41 final size:39
Alignment explanation
Indices: 5402824--5402963 Score: 130
Period size: 39 Copynumber: 3.5 Consensus size: 39
5402814 CTTTCTTCCC
*
5402824 TCTTCTTC-TTCTTTTTTTTCTCTTCTCCTTTCCCTTTCTT
1 TCTTCTTCTTTC-CTTTTTTCTCTTCTCCTTT-CCTTTCTT
*
5402864 TC--CTTCTTTCCTTCTTTTTTCTTCT-CTTCTCCTTT-TCT
1 TCTTCTTCTTTCCTT-TTTTCTCTTCTCCTT-TCCTTTCT-T
5402902 TCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTGTCTT
1 TCTTC-TTCTTTCCTTTTTTCTCTTCTCCTTTCCTT-TCTT
* *
5402943 TCTT-TCCTCTCCTTTCTTTCT
1 TCTTCTTCTTTCCTTT-TTTCT
5402964 TTCCCTCCTT
Statistics
Matches: 84, Mismatches: 5, Indels: 22
0.76 0.05 0.20
Matches are distributed among these distances:
37 1 0.01
38 17 0.20
39 23 0.27
40 23 0.27
41 19 0.23
42 1 0.01
ACGTcount: A:0.00, C:0.34, G:0.01, T:0.66
Consensus pattern (39 bp):
TCTTCTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTCTT
Found at i:5403039 original size:27 final size:27
Alignment explanation
Indices: 5403007--5403073 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
5402997 TAACACCAAC
* *
5403007 TGGTGCCGCTAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGATATTGGCACCAT
* *
5403034 TGGTGCCGCCAATGATTTTGGCACCTT
1 TGGTGCCGCCAATGATATTGGCACCAT
5403061 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
5403074 ACCATTGGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.30
Consensus pattern (27 bp):
TGGTGCCGCCAATGATATTGGCACCAT
Found at i:5403081 original size:27 final size:27
Alignment explanation
Indices: 5403007--5403082 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
5402997 TAACACCAAC
* **
5403007 TGGTGCCGCTAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGACATTGGCACCAT
** *
5403034 TGGTGCCGCCAATGATTTTGGCACCTT
1 TGGTGCCGCCAATGACATTGGCACCAT
5403061 TGGTGCCGCCAAT-ACCATTGGC
1 TGGTGCCGCCAATGA-CATTGGC
5403083 GTGACCAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAATGACATTGGCACCAT
Found at i:5403185 original size:28 final size:28
Alignment explanation
Indices: 5403145--5403214 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
5403135 TTTTTTTGAT
5403145 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
5403173 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
5403201 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
5403215 TTTTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:5406008 original size:21 final size:20
Alignment explanation
Indices: 5405945--5406009 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
5405935 ATTAATCACC
*
5405945 AAACTCTCAAACCCTAAATCGA
1 AAACTCT-AAACCCTAAAT-GT
* *
5405967 AAACACTAAA-CCTACATTGT
1 AAACTCTAAACCCTA-AATGT
5405987 AAACTCTAAACCCTAAACTGT
1 AAACTCTAAACCCTAAA-TGT
5406008 AA
1 AA
5406010 TCCAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 15 0.43
21 14 0.40
22 6 0.17
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.22
Consensus pattern (20 bp):
AAACTCTAAACCCTAAATGT
Found at i:5406317 original size:75 final size:75
Alignment explanation
Indices: 5406112--5406319 Score: 258
Period size: 76 Copynumber: 2.7 Consensus size: 75
5406102 ATGCATGGTT
* * *
5406112 AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCCCGTAAGCGCCACTAACTC
1 AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCTC-TAAGCGCCACTAACTC
*
5406177 TAGTATACATC
65 TAATATACATC
* * * * *
5406188 AAGACCAAAACAT-TGCGTTTTGGTTAAGATATTTTGCGGTGTTTTTCTTTAAGCGCCACTAATT
1 AAGAACAAAAC-TCTGCGTTTTGGTTAAGATATTTTGCGGCG-CTTTCTCTAAGCGCCACTAACT
*
5406252 CTAATATACCTC
64 CTAATATACATC
* *
5406264 AA-AACAAAACTCTACGTTTTGGTTAAGATATTTTGCGGCGCTTGTCTCAAAGCGCC
1 AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-TCTCTAAGCGCC
5406320 GCGATTACTA
Statistics
Matches: 114, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
74 3 0.03
75 43 0.38
76 64 0.56
77 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (75 bp):
AAGAACAAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCTCTAAGCGCCACTAACTCT
AATATACATC
Found at i:5406817 original size:114 final size:112
Alignment explanation
Indices: 5406486--5406910 Score: 394
Period size: 114 Copynumber: 3.7 Consensus size: 112
5406476 CAAACCATGA
* * * * * * *
5406486 CGGCGTTTTCCATAAGCGTCACTAATTCTAGTATACATTAAGACCAAAAAGCTACGTTTTGTTTT
1 CGGCGTTTTTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCG-TTT-TTTT
* ** * * *
5406551 AAGATATTTTGCGGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTGG
64 AAGATATTTTGCGGCGCTTTTCACAGATCGCCGCTAATAC-TTGCTTTAG
* * * ** *
5406601 CGGCGTTTTTCCATAATCGCCACTAATTATAATATA-ACTCAAAACC-AAACTCTGCATTTTTTT
1 CGGCGTTTTT-CATAAGCGCCACTAATTCTAATATACA-TCAAGACCAAAACGATGCGTTTTTTT
*
5406664 AAGATATTTTACGGCGCTTTTCA-AGACTCGCCGCTAATACATT-CTTTAG
64 AAGATATTTTGCGGCGCTTTTCACAGA-TCGCCGCTAATAC-TTGCTTTAG
*
5406713 CGGCGTGTTTTCTTAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTTCTTT
1 CGGCGT-TTTTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTT-TTT
* * * *
5406778 AAGATTTTTTGCAGCGCTTTTCACGGATCGCCGCTAATACTTGCTTTAA
64 AAGATATTTTGCGGCGCTTTTCACAGATCGCCGCTAATACTTGCTTTAG
* * * * * *
5406827 CGGAGTTTTCCCATAATCGCCACTAATTCTAGTATACATCAACACTAAAAC-ACTGCGTTTTGGT
1 CGGCGTTTT-TCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGA-TGCGTTTT--T
**
5406891 TT-AGGGATTTTGCGGCGCTT
62 TTAAGATATTTTGCGGCGCTT
5406911 GAAGGTAAAC
Statistics
Matches: 255, Mismatches: 43, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
112 42 0.16
113 59 0.23
114 106 0.42
115 21 0.08
116 27 0.11
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (112 bp):
CGGCGTTTTTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTTTTTAA
GATATTTTGCGGCGCTTTTCACAGATCGCCGCTAATACTTGCTTTAG
Found at i:5406909 original size:228 final size:228
Alignment explanation
Indices: 5406498--5406910 Score: 510
Period size: 228 Copynumber: 1.8 Consensus size: 228
5406488 GCGTTTTCCA
* * * * *
5406498 TAAGCGTCACTAATTCTAGTATACATTAAGACCAAAAAGCTACGTTTTGTTTTAAGATATTTTGC
1 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
* ** * *
5406563 GGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTGGCGGCGTTTTTCCATAATCGCCACTAAT
66 AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACGGAGTTTTCCCATAATCGCCACTAAT
* * *
5406628 TATAATATAACTCAAAACCAAACTCTGCATTTTTTTAAGATATTTTACGGCGCTTTTCAAGACTC
131 TATAATATAACTCAAAACAAAACACTGCATTTTTTTAAGAGATTTTACGGCGCTTTTCAAGACTC
5406693 GCCGCTAATACATTCTTTAGCGGCGTGTTTTCT
196 GCCGCTAATACATTCTTTAGCGGCGTGTTTTCT
* * *
5406726 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGATGCGTTTT-CTTTAAGATTTTTTGC
1 TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
* ** ** *
5406790 AGCGCTTTTCACGGATCGCCGCTAATAC-TTGCTTTAACGGAGTTTTCCCATAATCGCCACTAAT
66 AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACGGAGTTTTCCCATAATCGCCACTAAT
* * * * * *
5406854 TCTAGTAT-ACATCAACACTAAAACACTGCGTTTTGGTTT-AGGGATTTTGCGGCGCTT
131 TATAATATAAC-TCAAAAC-AAAACACTGCATTTT--TTTAAGAGATTTTACGGCGCTT
5406911 GAAGGTAAAC
Statistics
Matches: 153, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
225 2 0.01
226 44 0.29
227 47 0.31
228 57 0.37
229 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (228 bp):
TAAGCGCCACTAATTCTAATATACATCAAGACCAAAAAGATACGTTTTGCTTTAAGATATTTTGC
AGCACTTGCCACAAAACGCCGCTAATACTTTGCTTTAACGGAGTTTTCCCATAATCGCCACTAAT
TATAATATAACTCAAAACAAAACACTGCATTTTTTTAAGAGATTTTACGGCGCTTTTCAAGACTC
GCCGCTAATACATTCTTTAGCGGCGTGTTTTCT
Found at i:5409000 original size:145 final size:144
Alignment explanation
Indices: 5408735--5409000 Score: 354
Period size: 145 Copynumber: 1.8 Consensus size: 144
5408725 GAGGATTATT
* * * * * * *
5408735 AATCTAACAAGTTTAATTAATCAATATGGGTTATCAAATTAATTAATTAATTAATAATGTGTTAT
1 AATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATAAATAAATCAATTAATAATGGGTTAT
*
5408800 TAAACTCAAGTAATCAATTTATAAGTATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
66 TAAACTCAAATAATCAATTTATAAGTATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
5408865 CGTGATTGATCATA
131 CGTGATTGATCATA
*** * *
5408879 AATCTAACAAGCTCAATTAATTTTTATGAGTTATCAAAATAAATAAATCAATTTATCATGGGTTA
1 AATCTAACAAGCTCAATTAATCAATATGAGTTATC-AAATAAATAAATCAATTAATAATGGGTTA
* * * *
5408944 TTAAATTCAAATAATCAATTTATAAGTTTATGATGCTT-GAAATTCATAGTAGAATAT
65 TTAAACTCAAATAATCAATTTATAAGTATATGATG-TTCCAAATTCATAGTAAAATAT
5409001 TTAAGTAGAA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
144 29 0.28
145 72 0.70
146 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (144 bp):
AATCTAACAAGCTCAATTAATCAATATGAGTTATCAAATAAATAAATCAATTAATAATGGGTTAT
TAAACTCAAATAATCAATTTATAAGTATATGATGTTCCAAATTCATAGTAAAATATATTCTTACA
CGTGATTGATCATA
Found at i:5409608 original size:28 final size:28
Alignment explanation
Indices: 5409568--5409659 Score: 175
Period size: 28 Copynumber: 3.3 Consensus size: 28
5409558 CTCGACCCCC
*
5409568 TAAAATGAAAATTTTAAATTAGTAAAGG
1 TAAAATTAAAATTTTAAATTAGTAAAGG
5409596 TAAAATTAAAATTTTAAATTAGTAAAGG
1 TAAAATTAAAATTTTAAATTAGTAAAGG
5409624 TAAAATTAAAATTTTAAATTAGTAAAGG
1 TAAAATTAAAATTTTAAATTAGTAAAGG
5409652 TAAAATTA
1 TAAAATTA
5409660 TACTTTGCCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (28 bp):
TAAAATTAAAATTTTAAATTAGTAAAGG
Found at i:5420444 original size:26 final size:26
Alignment explanation
Indices: 5420389--5420442 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
5420379 GCCTTGCTTG
5420389 AAATCGAAAACTTTGATATCGTAAGT
1 AAATCGAAAACTTTGATATCGTAAGT
5420415 AAATCGAAAACTTTGATATC-TAAGT
1 AAATCGAAAACTTTGATATCGTAAGT
5420440 AAA
1 AAA
5420443 ATAATCAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (26 bp):
AAATCGAAAACTTTGATATCGTAAGT
Found at i:5423495 original size:6 final size:6
Alignment explanation
Indices: 5423484--5423538 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
5423474 CATCACTCGT
5423484 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG
5423532 ATATAG A
1 ATATAG A
5423539 GTGTAGGAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:5424347 original size:29 final size:28
Alignment explanation
Indices: 5424302--5424356 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
5424292 GCACTTGCAT
* *
5424302 AAAATGTCTAATATAATCCTTGTACTTTG
1 AAAATGTCCAATATAATACTT-TACTTTG
*
5424331 AAAATGTCCAATGTAATACTTTACTT
1 AAAATGTCCAATATAATACTTTACTT
5424357 GAAGTGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (28 bp):
AAAATGTCCAATATAATACTTTACTTTG
Found at i:5424999 original size:29 final size:29
Alignment explanation
Indices: 5424944--5425000 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
5424934 ACATATATTG
* * *
5424944 ATAGTTCAAATACCACATTAGATATTTTC
1 ATAGTACAAATACCACATTAAACATTTTC
* *
5424973 ATAGTACAATTACTACATTAAACATTTT
1 ATAGTACAAATACCACATTAAACATTTT
5425001 ATAAATAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39
Consensus pattern (29 bp):
ATAGTACAAATACCACATTAAACATTTTC
Found at i:5430067 original size:6 final size:6
Alignment explanation
Indices: 5430027--5430066 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
5430017 GAAAATGTAA
* *
5430027 GCAGCT GCAGTT GCAGTT GCAGTT GCAGTT GCAGGT GCAG
1 GCAGTT GCAGTT GCAGTT GCAGTT GCAGTT GCAGTT GCAG
5430067 GCCATGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (6 bp):
GCAGTT
Found at i:5438041 original size:24 final size:24
Alignment explanation
Indices: 5437950--5438027 Score: 156
Period size: 24 Copynumber: 3.2 Consensus size: 24
5437940 AAACTCATAA
5437950 GAGCCATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
5437974 GAGCCATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
5437998 GAGCCATATTCAGGAAGCTCATGC
1 GAGCCATATTCAGGAAGCTCATGC
5438022 GAGCCA
1 GAGCCA
5438028 ATAACGGGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCCATATTCAGGAAGCTCATGC
Found at i:5438050 original size:48 final size:49
Alignment explanation
Indices: 5437948--5438066 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 49
5437938 GGAAACTCAT
* *
5437948 AAGAGCCATATTCAGGAAGCTCATGCGAGCCATATTCAGGAAGCTCATG
1 AAGAGCCATATTCAGGAAGCTCATGCGAGCCATATACAGGAAGCTCACG
* * *
5437997 -CGAGCCATATTCAGGAAGCTCATGCGAGCCA-ATAACGGGTAGCTC-CG
1 AAGAGCCATATTCAGGAAGCTCATGCGAGCCATAT-ACAGGAAGCTCACG
*
5438044 AAGAGCCATTAATCAGGAAGCTC
1 AAGAGCCA-TATTCAGGAAGCTC
5438067 CAGATAGCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 3 0.05
48 44 0.73
49 13 0.22
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (49 bp):
AAGAGCCATATTCAGGAAGCTCATGCGAGCCATATACAGGAAGCTCACG
Found at i:5438067 original size:25 final size:25
Alignment explanation
Indices: 5438037--5438175 Score: 62
Period size: 26 Copynumber: 5.6 Consensus size: 25
5438027 AATAACGGGT
5438037 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* *
5438062 AGCTCC-AGATAGCCA-TATATCGGGA
1 AGCTCCGA-AGAGCCATTA-ATCAGGA
* *
5438087 AG-TTC-AAGCGAGTCA-T-ATC-GGAA
1 AGCTCCGAA--GAGCCATTAATCAGG-A
*
5438110 AGCTCCG--GAGCTATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * * *
5438133 AGCTCACAAAGAGCCTTTAACCGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
*
5438159 AGCTCATGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
5438176 ATAACGAGAT
Statistics
Matches: 85, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
21 4 0.05
22 3 0.04
23 16 0.19
24 11 0.13
25 25 0.29
26 26 0.31
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:5438152 original size:26 final size:26
Alignment explanation
Indices: 5438123--5438173 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5438113 TCCGGAGCTA
*
5438123 TTAATCAGGAAGCTCACAAAGAGCCT
1 TTAACCAGGAAGCTCACAAAGAGCCT
* **
5438149 TTAACCGGGAAGCTCATGAAGAGCC
1 TTAACCAGGAAGCTCACAAAGAGCC
5438174 ATATAACGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (26 bp):
TTAACCAGGAAGCTCACAAAGAGCCT
Found at i:5438921 original size:21 final size:20
Alignment explanation
Indices: 5438897--5438935 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5438887 AAGTTGTTTA
*
5438897 TCTATCAACAACATTTCATTT
1 TCTA-CAACAAAATTTCATTT
*
5438918 TCTACCACAAAATTTCAT
1 TCTACAACAAAATTTCAT
5438936 AGTTCAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (20 bp):
TCTACAACAAAATTTCATTT
Found at i:5444457 original size:26 final size:26
Alignment explanation
Indices: 5444406--5444457 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5444396 CGGGTAGCTT
* *
5444406 CAAAGAGCCATTAATCAGAAATCTCA
1 CAAAGAACCATTAATCAGAAAGCTCA
* *
5444432 CAAAGAACCTTTAATCAGGAAGCTCA
1 CAAAGAACCATTAATCAGAAAGCTCA
5444458 TGAAGATCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.19
Consensus pattern (26 bp):
CAAAGAACCATTAATCAGAAAGCTCA
Found at i:5448131 original size:25 final size:25
Alignment explanation
Indices: 5448093--5448168 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
5448083 TAAAAATCCG
*
5448093 TTCTCTTTTGCTCTCTTATTTTTTA
1 TTCTCTTTTACTCTCTTATTTTTTA
5448118 TTCTCTTTTACTCT-TATATTTTCTTA
1 TTCTCTTTTACTCTCT-TATTTT-TTA
*
5448144 -T-TC-TTTACTCTCTTTATTATTTA
1 TTCTCTTTTACTCTC-TTATTTTTTA
5448167 TT
1 TT
5448169 TCATAACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
23 11 0.25
24 9 0.20
25 21 0.48
26 3 0.07
ACGTcount: A:0.13, C:0.18, G:0.01, T:0.67
Consensus pattern (25 bp):
TTCTCTTTTACTCTCTTATTTTTTA
Found at i:5448167 original size:23 final size:23
Alignment explanation
Indices: 5448124--5448168 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5448114 TTTATTCTCT
*
5448124 TTTACTCTTATATTTTCTTATTC
1 TTTACTCTTATATTATCTTATTC
*
5448147 TTTACTCTCTTTATTAT-TTATT
1 TTTACTCT-TATATTATCTTATT
5448169 TCATAACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTACTCTTATATTATCTTATTC
Found at i:5456013 original size:31 final size:31
Alignment explanation
Indices: 5455975--5456035 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5455965 TTTAATTGCA
5455975 ATATGAGAACTAGTATGAAACAAAAGCCACC
1 ATATGAGAACTAGTATGAAACAAAAGCCACC
*
5456006 ATATGAGAACTTGTATGAAACAAAAGCCAC
1 ATATGAGAACTAGTATGAAACAAAAGCCAC
5456036 TAAAAGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (31 bp):
ATATGAGAACTAGTATGAAACAAAAGCCACC
Found at i:5465135 original size:24 final size:25
Alignment explanation
Indices: 5465106--5465160 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
5465096 TAATATTTTA
5465106 AAAATTAT-AAAGATAAAAGCTATT
1 AAAATTATAAAAGATAAAAGCTATT
5465130 AAAATTATAAAAGATAAAAGCTATT
1 AAAATTATAAAAGATAAAAGCTATT
5465155 AAAATT
1 AAAATT
5465161 TTATTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (25 bp):
AAAATTATAAAAGATAAAAGCTATT
Found at i:5467306 original size:39 final size:39
Alignment explanation
Indices: 5467256--5467336 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
5467246 ATTACAAAAA
5467256 AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
1 AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
5467295 AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
1 AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
5467334 AAA
1 AAA
5467337 AATTTATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (39 bp):
AAATAAAGTTTAAATATCAAATATTATATTAACCCAAAT
Found at i:5470849 original size:32 final size:32
Alignment explanation
Indices: 5470808--5470872 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5470798 ACGATTTATC
5470808 AAACAATGCTGACAATGGGTCTTTATCATAGG
1 AAACAATGCTGACAATGGGTCTTTATCATAGG
5470840 AAACAATGCTGACAATGGGTCTTTATCATAGG
1 AAACAATGCTGACAATGGGTCTTTATCATAGG
5470872 A
1 A
5470873 TGTTGAGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (32 bp):
AAACAATGCTGACAATGGGTCTTTATCATAGG
Found at i:5472776 original size:16 final size:16
Alignment explanation
Indices: 5472755--5472805 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
5472745 TAGTTTTATT
5472755 TAAAAATTATAAAAAA
1 TAAAAATTATAAAAAA
*
5472771 TAAAAAATATTAAAAATA
1 TAAAAATTA-TAAAAA-A
*
5472789 TATAAAATTCTAAAAAA
1 TA-AAAATTATAAAAAA
5472806 ATTATTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.28
17 7 0.24
18 9 0.31
19 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATTATAAAAAA
Found at i:5473009 original size:45 final size:47
Alignment explanation
Indices: 5472958--5473051 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 47
5472948 ATTCTTCGAT
*
5472958 TTTTATAA-T-TTAGTATGATTGCTTTAAAACATTGAAATTGCACCC
1 TTTTATAATTGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
5473003 TTTTATAATTGAGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
1 TTTTATAATT--GTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
5473052 CAATTAGGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 8 0.18
46 1 0.02
49 35 0.80
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (47 bp):
TTTTATAATTGTTAGTATGATTGCCTTAAAACATTGAAATTGCACCC
Found at i:5473705 original size:11 final size:11
Alignment explanation
Indices: 5473689--5473719 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5473679 TATATATATT
5473689 TAAAAATTATA
1 TAAAAATTATA
*
5473700 TAAAAATAATA
1 TAAAAATTATA
5473711 TAAAAATTA
1 TAAAAATTA
5473720 ATATGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:5473716 original size:12 final size:11
Alignment explanation
Indices: 5473689--5473723 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5473679 TATATATATT
*
5473689 TAAAAATTATA
1 TAAAAATAATA
5473700 TAAAAATAATA
1 TAAAAATAATA
5473711 TAAAAATTAATA
1 TAAAAA-TAATA
5473723 T
1 T
5473724 GGGCGGGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:5476615 original size:24 final size:24
Alignment explanation
Indices: 5476583--5476633 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5476573 ACACTGAAGG
5476583 TGACTTGCTCATCATTAAGTCACA
1 TGACTTGCTCATCATTAAGTCACA
5476607 TGACTTGCTCATCATTAAGTCACA
1 TGACTTGCTCATCATTAAGTCACA
5476631 TGA
1 TGA
5476634 TTAGTTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (24 bp):
TGACTTGCTCATCATTAAGTCACA
Found at i:5503281 original size:14 final size:14
Alignment explanation
Indices: 5503264--5503291 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5503254 GCAGTTACAT
5503264 TAGTATCAATAAGA
1 TAGTATCAATAAGA
5503278 TAGTATCAATAAGA
1 TAGTATCAATAAGA
5503292 GAGAAAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
TAGTATCAATAAGA
Found at i:5505724 original size:25 final size:25
Alignment explanation
Indices: 5505657--5505724 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
5505647 GCTGTAAACA
* *
5505657 GGAAGCTCATCTGAGCTAAATAACG
1 GGAAGCTCATGTGAGCTGAATAACG
5505682 GGAAGCTCATGTGAGCTGAATAACG
1 GGAAGCTCATGTGAGCTGAATAACG
5505707 GGAAGCTCATGTGAGCTG
1 GGAAGCTCATGTGAGCTG
5505725 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATGTGAGCTGAATAACG
Found at i:5506803 original size:13 final size:13
Alignment explanation
Indices: 5506785--5506816 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
5506775 TTAAACAGTA
5506785 AAATTTCTTAACT
1 AAATTTCTTAACT
5506798 AAATTTCTTAACT
1 AAATTTCTTAACT
5506811 AAATTT
1 AAATTT
5506817 TTGTTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTCTTAACT
Found at i:5507896 original size:16 final size:15
Alignment explanation
Indices: 5507870--5507899 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5507860 TTGTATCAAG
5507870 AGAAAATCAATACAC
1 AGAAAATCAATACAC
5507885 AGAAAGATCAATACA
1 AGAAA-ATCAATACA
5507900 AAAAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (15 bp):
AGAAAATCAATACAC
Found at i:5512194 original size:14 final size:15
Alignment explanation
Indices: 5512170--5512200 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5512160 GTGGGAAGAA
5512170 AATGAAAATAGAATC
1 AATGAAAATAGAATC
5512185 AATG-AAATAGAATC
1 AATGAAAATAGAATC
5512199 AA
1 AA
5512201 ATTGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
AATGAAAATAGAATC
Found at i:5527215 original size:20 final size:21
Alignment explanation
Indices: 5527185--5527226 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
5527175 AAATATTTTA
5527185 AAAAAATAAAGATATAAAAAT
1 AAAAAATAAAGATATAAAAAT
*
5527206 AAAAAA-AAAGTTATAAAAAT
1 AAAAAATAAAGATATAAAAAT
5527226 A
1 A
5527227 TTGAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAAAATAAAGATATAAAAAT
Found at i:5527323 original size:10 final size:11
Alignment explanation
Indices: 5527303--5527336 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5527293 AAAAATAGAT
5527303 AAATTATTAAA
1 AAATTATTAAA
*
5527314 AAGTTA-TAAA
1 AAATTATTAAA
5527324 AAATTATTAAA
1 AAATTATTAAA
5527335 AA
1 AA
5527337 TTCCCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:5527337 original size:10 final size:10
Alignment explanation
Indices: 5527303--5527338 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5527293 AAAAATAGAT
5527303 AAATTATTAA
1 AAATTATTAA
*
5527313 AAAGTTATAAA
1 AAA-TTATTAA
5527324 AAATTATTAA
1 AAATTATTAA
5527334 AAATT
1 AAATT
5527339 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
AAATTATTAA
Found at i:5533053 original size:13 final size:13
Alignment explanation
Indices: 5533035--5533064 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5533025 TACTATTTCT
5533035 CTATAAATAGGAA
1 CTATAAATAGGAA
5533048 CTATAAATAGGAA
1 CTATAAATAGGAA
5533061 CTAT
1 CTAT
5533065 GCTGACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (13 bp):
CTATAAATAGGAA
Found at i:5544810 original size:3 final size:3
Alignment explanation
Indices: 5544795--5544862 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
5544785 ATTAGGTTTA
* *
5544795 TAT TAT TAC TAT TAT TAT TAT CT-T TAT TAT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
*
5544840 TAT TAT GTAG TAT TAT TAT TAT T
1 TAT TAT -TAT TAT TAT TAT TAT T
5544863 TACTTTTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 52 0.93
4 3 0.05
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5558990 original size:45 final size:45
Alignment explanation
Indices: 5558923--5559196 Score: 352
Period size: 45 Copynumber: 6.1 Consensus size: 45
5558913 AACAAATCAA
* * * *
5558923 CGAATATAGCAGATCTTATCTTCCTGTATTGGCAGTGAAGCAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * * **
5558968 CAAAGATAGTAGATCTTGTCTTCGTGTATTGGCAGTAAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
*
5559013 CGAAGATAGCAGGA-CTTGTCTTCCTGTATTGGCAGCGCAGTAGAT
1 CGAAGATAGCA-GATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
*
5559058 CGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * *
5559103 CGAAGATAACAGATCTTGTCCTCCTATATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * * * * *
5559148 TGAAGATAGCAGATCATGCCTTCCTGTACTGGCAACGAAGCAGAT
1 CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
5559193 CGAA
1 CGAA
5559197 AAACAACGAA
Statistics
Matches: 198, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
44 2 0.01
45 194 0.98
46 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (45 bp):
CGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
Found at i:5564904 original size:22 final size:23
Alignment explanation
Indices: 5564872--5564914 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5564862 AAGTATCTAC
5564872 AAATCAAATC-TCTAAGATTAGT
1 AAATCAAATCTTCTAAGATTAGT
*
5564894 AAATCATATCTTCTAAGATTA
1 AAATCAAATCTTCTAAGATTA
5564915 CATATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTAGT
Found at i:5564921 original size:22 final size:22
Alignment explanation
Indices: 5564869--5564926 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
5564859 GAAAAGTATC
*
5564869 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
5564890 TAGTAAATCATATCTTCTAAGAT
1 TA-CAAATCATATCTTCTAAGAT
*
5564913 TACATATCATATCT
1 TACAAATCATATCT
5564927 ACGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 2 0.06
22 19 0.61
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5565438 original size:16 final size:16
Alignment explanation
Indices: 5565417--5565448 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5565407 TATTTATTTC
5565417 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
5565433 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
5565449 ATTACTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTGTATCTTTTA
Found at i:5565884 original size:7 final size:7
Alignment explanation
Indices: 5565869--5565943 Score: 69
Period size: 7 Copynumber: 10.7 Consensus size: 7
5565859 TGATTAATTA
*
5565869 TAAATCC
1 TAAACCC
5565876 TAAACCC
1 TAAACCC
**
5565883 TAAACTA
1 TAAACCC
5565890 TAAACCC
1 TAAACCC
*
5565897 TTAACCC
1 TAAACCC
5565904 TAAACCC
1 TAAACCC
*
5565911 CAAACCC
1 TAAACCC
* *
5565918 CAAACCA
1 TAAACCC
* *
5565925 TAAAACT
1 TAAACCC
5565932 TAAACCC
1 TAAACCC
5565939 TAAAC
1 TAAAC
5565944 TCACCAATTA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:5572091 original size:24 final size:24
Alignment explanation
Indices: 5572029--5572080 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5572019 TTTCTAAAAG
* * *
5572029 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
5572053 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
5572077 ATTT
1 ATTT
5572081 GACTTTGATT
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:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:5575891 original size:46 final size:46
Alignment explanation
Indices: 5575813--5576132 Score: 412
Period size: 46 Copynumber: 6.9 Consensus size: 46
5575803 ACATTGTTAT
* * *
5575813 AACTTAGTATGGTTTTCTTCACGGAAATACCATTCCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
5575859 AACTCAGTATGGTTTTCTTCACTAAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * * *
5575905 AATTCAATATGGTTTTCTTCACTAAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
5575951 AACTTAGTATGGTTTTCTTTA-TCGAAATACCATACCTAATTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
5575997 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
5576043 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACATACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* * *
5576089 AACTCAGTACGGTTTTCTTCACTAAAATACCATGCCTACGTTTT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTAC-TTTT
5576133 ACACTTTTCC
Statistics
Matches: 249, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.00
46 243 0.98
47 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:5578022 original size:24 final size:23
Alignment explanation
Indices: 5577990--5578037 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
5577980 TAATCTAAAA
5577990 TATCTCCAACATCATCATTACTTT
1 TATCTCCAACATCATCATTA-TTT
5578014 TATCTCCAACATCATCATTATTT
1 TATCTCCAACATCATCATTATTT
5578037 T
1 T
5578038 CTAGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (23 bp):
TATCTCCAACATCATCATTATTT
Found at i:5581350 original size:8 final size:8
Alignment explanation
Indices: 5581337--5581368 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5581327 AGTAAAATAT
*
5581337 ATATTATC
1 ATATTATA
5581345 ATATTATA
1 ATATTATA
5581353 ATATTATA
1 ATATTATA
5581361 ATATTATA
1 ATATTATA
5581369 TCTTAAGCAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTATA
Found at i:5583972 original size:30 final size:30
Alignment explanation
Indices: 5583938--5583995 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5583928 CATGGGCTGG
5583938 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
1 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
** *
5583968 CACATGGTTGTGTGTCCAGCCCGTGTGG
1 CACATGGGCGTGTGGCCAGCCCGTGTGG
5583996 AAATGCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.24
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:5601924 original size:19 final size:20
Alignment explanation
Indices: 5601884--5601921 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5601874 AGTTTGTTTA
5601884 AAAATAAAATTTTAAAAAAT
1 AAAATAAAATTTTAAAAAAT
5601904 AAAATAAAATTTTAAAAA
1 AAAATAAAATTTTAAAAA
5601922 TAATTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAAATTTTAAAAAAT
Found at i:5609639 original size:17 final size:17
Alignment explanation
Indices: 5609598--5609640 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
5609588 GTAATAGCCC
*
5609598 AAATTTAAT-ATTAAAT
1 AAATTTTATAATTAAAT
**
5609614 AAAAATTATAATTAAAT
1 AAATTTTATAATTAAAT
5609631 AAATTTTATA
1 AAATTTTATA
5609641 GGTATTGGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTTATAATTAAAT
Found at i:5610343 original size:29 final size:29
Alignment explanation
Indices: 5610293--5610348 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5610283 GTTCAACATG
* *
5610293 TAATGTTATATATGAACTTTTATTTTGTA
1 TAATGTTATATATGAACGTTTACTTTGTA
*
5610322 TAATTTTATATATG-ACAGTTTACTTTG
1 TAATGTTATATATGAAC-GTTTACTTTG
5610349 ATTTTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (29 bp):
TAATGTTATATATGAACGTTTACTTTGTA
Done.