Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 55 of 66
Found at i:20175875 original size:16 final size:15
Alignment explanation
Indices: 20175838--20175904 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
20175828 CAAGTATATT
* *
20175838 TATATTTTTTTATTA
1 TATATTTTTATATAA
20175853 T-TAATTTTTATATAA
1 TAT-ATTTTTATATAA
*
20175868 TATCATTTCT-TA-AA
1 TAT-ATTTTTATATAA
*
20175882 TATATTTTTAATATCA
1 TATATTTTT-ATATAA
20175898 TATATTT
1 TATATTT
20175905 CATTTTCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.12
14 6 0.15
15 16 0.39
16 14 0.34
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTTTATATAA
Found at i:20175943 original size:33 final size:32
Alignment explanation
Indices: 20175880--20175945 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
20175870 TCATTTCTTA
20175880 AATATATTTTTAATATCATATATTTCATTTTC
1 AATATATTTTTAATATCATATATTTCATTTTC
* * * *
20175912 AATATTTTTTATAATCTTATATATTTTATTTTC
1 AATATATTTT-TAATATCATATATTTCATTTTC
20175945 A
1 A
20175946 TTTCTGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (32 bp):
AATATATTTTTAATATCATATATTTCATTTTC
Found at i:20180208 original size:13 final size:13
Alignment explanation
Indices: 20180190--20180223 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
20180180 AGATGGCTCC
20180190 CTTTGCTTCCGCA
1 CTTTGCTTCCGCA
20180203 CTTTGCTTCCGCA
1 CTTTGCTTCCGCA
20180216 CTTTGCTT
1 CTTTGCTT
20180224 ACAACTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.35, G:0.15, T:0.44
Consensus pattern (13 bp):
CTTTGCTTCCGCA
Found at i:20180520 original size:13 final size:13
Alignment explanation
Indices: 20180497--20180535 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
20180487 ATTAAAAATC
20180497 CAAACAATAATTCT
1 CAAAC-ATAATTCT
20180511 -AAACATTAATTCT
1 CAAACA-TAATTCT
20180524 CAAACATAATTC
1 CAAACATAATTC
20180536 CTAATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 17 0.74
14 5 0.22
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAACATAATTCT
Found at i:20180529 original size:85 final size:84
Alignment explanation
Indices: 20180423--20180678 Score: 288
Period size: 85 Copynumber: 3.1 Consensus size: 84
20180413 TAATTAAAAA
* * * * *
20180423 TCTAAAAAATAATTCCCAAACATAATTTTGAATATTTAATTCTAGCATATTACCAATAATTTTAA
1 TCTAAAAATTAATTCTCAAACATAATTTT-AATGTTTAATTCTAGCATATTACAAATCATTTTAA
20180488 TTAAAAATCCAAACAATAAT
65 TTAAAAATCCAAACAATAAT
* * * *
20180508 TCTAAACATTAATTCTCAAACATAATTCCTAATGTTTAATTCTAACATATTACTAATCATTTTAA
1 TCTAAAAATTAATTCTCAAACATAATT-TTAATGTTTAATTCTAGCATATTACAAATCATTTTAA
***
20180573 TTAAAAATTTGAACAATAAT
65 TTAAAAATCCAAACAATAAT
* *
20180593 TCTAAATATTAATT-TCTAAACATATTTCTTAATGTTTAATTCTAGC--A-T-CAAATCATTTTA
1 TCTAAAAATTAATTCTC-AAACATAATT-TTAATGTTTAATTCTAGCATATTACAAATCATTTTA
** *
20180653 ATTAATTATCCAAATAATAAT
64 ATTAAAAATCCAAACAATAAT
20180674 TCTAA
1 TCTAA
20180679 CTATTAAAGT
Statistics
Matches: 147, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
81 31 0.21
82 1 0.01
83 1 0.01
84 2 0.01
85 111 0.76
86 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (84 bp):
TCTAAAAATTAATTCTCAAACATAATTTTAATGTTTAATTCTAGCATATTACAAATCATTTTAAT
TAAAAATCCAAACAATAAT
Found at i:20182808 original size:18 final size:18
Alignment explanation
Indices: 20182762--20182815 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
20182752 TTATAAACAA
* *
20182762 GAAAAATTAAAAG-ATAT
1 GAAAAATGAAAAGAAAAT
*
20182779 GAAAAAAAGAAAAGAAAAT
1 G-AAAAATGAAAAGAAAAT
20182798 GAAAAATGAAAAAGAAAA
1 GAAAAATG-AAAAGAAAA
20182816 AAAAGAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 13 0.43
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (18 bp):
GAAAAATGAAAAGAAAAT
Found at i:20183338 original size:129 final size:129
Alignment explanation
Indices: 20183108--20183367 Score: 439
Period size: 129 Copynumber: 2.0 Consensus size: 129
20183098 AACGTGTTCA
* * * * *
20183108 GGGAGAGCCGGCTTTAGCGACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGGAACCAGACCATTG
1 GGGAGAGCCGACTTGACCCACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGGAACCAGACCATCG
*
20183173 ACGCCGCCAGATCTGCAGCTGGAAGGAAGAGCCGATCCAGGACAGCTGCGATGCCACCGGTTGG
66 ACGCCGCCAGATCTGCAGCTGGAAGGAAGAGCCGATCCAGGACAGCTGCGACGCCACCGGTTGG
20183237 GGGAGAGCCGACTTGACCCACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGGAACCAGACCATCG
1 GGGAGAGCCGACTTGACCCACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGGAACCAGACCATCG
* * *
20183302 ATGCCGCCAGATCTGCCGCTGGAAGGAAGAGCCGATCCAGGACAGCTGCGACGTCACCGGTTGG
66 ACGCCGCCAGATCTGCAGCTGGAAGGAAGAGCCGATCCAGGACAGCTGCGACGCCACCGGTTGG
20183366 GG
1 GG
20183368 AAGTCGACCG
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.24, C:0.29, G:0.37, T:0.10
Consensus pattern (129 bp):
GGGAGAGCCGACTTGACCCACGCCGCAAGGAGGAGCTCGCCGGCGGAGAAGGAACCAGACCATCG
ACGCCGCCAGATCTGCAGCTGGAAGGAAGAGCCGATCCAGGACAGCTGCGACGCCACCGGTTGG
Found at i:20206973 original size:15 final size:15
Alignment explanation
Indices: 20206953--20206984 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20206943 TAACATTACC
*
20206953 AAAATTATTATTTAT
1 AAAATTATTAATTAT
20206968 AAAATTATTAATTAT
1 AAAATTATTAATTAT
20206983 AA
1 AA
20206985 TATATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTATTAATTAT
Found at i:20207220 original size:26 final size:26
Alignment explanation
Indices: 20207191--20207250 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
20207181 AATTTATAAG
20207191 AAATATAATTACTATTATATATAC-TA
1 AAATATAATTACTA-TATATATACTTA
** * *
20207217 AAATATTTTTAGTATATATATACTTT
1 AAATATAATTACTATATATATACTTA
20207243 AAATATAA
1 AAATATAA
20207251 ATATATTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATATAATTACTATATATATACTTA
Found at i:20207928 original size:272 final size:272
Alignment explanation
Indices: 20207433--20207948 Score: 747
Period size: 272 Copynumber: 1.9 Consensus size: 272
20207423 AAAAAAATAA
* *
20207433 CTTTGTTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAAGTTAGAATAATTTTGA
1 CTTTATTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAAGTTAGAACAATTTTGA
20207498 AACCTAATTATTTTATTTAATTATATGTAATCAAAGACAAATCCATATAGTTAATTAAATTAATT
66 AACCTAATTATTTTATTTAATTATATGTAATCAAAGACAAATCCATATAGTTAATTAAATTAATT
* * *
20207563 CATAAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATATTTTATATATATTAGG
131 AATAAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATACTTTATATACATTAGG
* * *
20207628 TTGATTTATAAGGAATATAATTACTATTATATATATTAAAATACTTTTAATGTGTGTGTGTGTAT
196 TTCATTTATAAGAAATATAATTACTATTATATATATTAAAACACTTTTAATGTGTGTGTGTGTAT
20207693 ATATATATATAT
261 ATATATATATAT
* * *
20207705 CTTTATTTGTATAAACTTATAATATATAAATCTAAAG-GCAAGTTGTG-AGATTAGAACAGTTTT
1 CTTTATTTATATAAACTTATAATATATAAACCTAAAGAG-AAGTTGTGAAG-TTAGAACAATTTT
* * * * *
20207768 GAAATCTAGTTACTTTT-TTTAATT-TCATGTAATTAAGGATAAA-CTCATATAGTTAATTAAAT
64 GAAACCTAATTA-TTTTATTTAATTAT-ATGTAATCAAAGACAAATC-CATATAGTTAATTAAAT
* * * * *
20207830 TAATTAATGAAATTATGATTATTAATTGACTTGTAATGTCTTTTAATATTTATACTTTATATACA
126 TAATTAATAAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATACTTTATATACA
20207895 TT-GAGTTCATTTATAAGAAATATAATTACTATTATATATATTAAAACACTTTTA
191 TTAG-GTTCATTTATAAGAAATATAATTACTATTATATATATTAAAACACTTTTA
20207949 GTATATATAC
Statistics
Matches: 217, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
271 6 0.03
272 207 0.95
273 4 0.02
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (272 bp):
CTTTATTTATATAAACTTATAATATATAAACCTAAAGAGAAGTTGTGAAGTTAGAACAATTTTGA
AACCTAATTATTTTATTTAATTATATGTAATCAAAGACAAATCCATATAGTTAATTAAATTAATT
AATAAAACTATAATTATTAATTAACTTGTAATGTCTTTTAATATATATACTTTATATACATTAGG
TTCATTTATAAGAAATATAATTACTATTATATATATTAAAACACTTTTAATGTGTGTGTGTGTAT
ATATATATATAT
Found at i:20209181 original size:19 final size:19
Alignment explanation
Indices: 20209143--20209179 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
20209133 AAAAACTTAC
20209143 ATATTAAATATTTTAATTT
1 ATATTAAATATTTTAATTT
20209162 ATATTAAA-ATTTTAATTT
1 ATATTAAATATTTTAATTT
20209180 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTAAATATTTTAATTT
Found at i:20222908 original size:2 final size:2
Alignment explanation
Indices: 20222899--20222928 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20222889 TTTCATGGTT
20222899 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20222929 TGTGGATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20252132 original size:15 final size:15
Alignment explanation
Indices: 20252112--20252159 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
20252102 TTTTTATTAA
20252112 AAATAATTTTAAATT
1 AAATAATTTTAAATT
* *
20252127 ACATAATATTATAAATAA
1 AAATAAT-TT-TAAAT-T
20252145 AAATAATTTTAAATT
1 AAATAATTTTAAATT
20252160 TAAAAACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.23
16 7 0.27
17 7 0.27
18 6 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATAATTTTAAATT
Found at i:20252149 original size:33 final size:33
Alignment explanation
Indices: 20252109--20252177 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
20252099 TATTTTTTAT
* *
20252109 TAAAAATAATTTTAAA-TTACATAATATTATAAA
1 TAAAAATAATTTTAAATTTA-AAAACATTATAAA
20252142 TAAAAATAATTTTAAATTTAAAAACATTATAAA
1 TAAAAATAATTTTAAATTTAAAAACATTATAAA
20252175 TAA
1 TAA
20252178 TAGTAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAATAATTTTAAATTTAAAAACATTATAAA
Found at i:20254351 original size:18 final size:19
Alignment explanation
Indices: 20254328--20254364 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
20254318 ATAGACAAGA
20254328 TATTTAAAAAAA-TTAAAT
1 TATTTAAAAAAATTTAAAT
20254346 TATTTAAAAAAATTTAAAT
1 TATTTAAAAAAATTTAAAT
20254365 GAACCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTTAAAAAAATTTAAAT
Found at i:20255239 original size:30 final size:30
Alignment explanation
Indices: 20255203--20255263 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
20255193 TTACATCCAG
20255203 TGTATGTACATTCCTATCTACTAAGTTCAT
1 TGTATGTACATTCCTATCTACTAAGTTCAT
20255233 TGTATGTACATTCCTATCTACTAAGTTCAT
1 TGTATGTACATTCCTATCTACTAAGTTCAT
20255263 T
1 T
20255264 CTCTCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (30 bp):
TGTATGTACATTCCTATCTACTAAGTTCAT
Found at i:20260002 original size:3 final size:3
Alignment explanation
Indices: 20259939--20260014 Score: 50
Period size: 3 Copynumber: 25.0 Consensus size: 3
20259929 AATACATATA
* * * *
20259939 TAT T-T TAT TAAT TAT T-T TAAT TTT TAT ATAT TTT TAA TAT AAT TAAT
1 TAT TAT TAT T-AT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT T-AT
*
20259986 TA- TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20260015 AAAATTATGA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
2 6 0.11
3 39 0.70
4 11 0.20
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:20260484 original size:2 final size:2
Alignment explanation
Indices: 20260479--20260507 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20260469 CCTCCTCTCT
20260479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20260508 TTTGTTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20262292 original size:24 final size:22
Alignment explanation
Indices: 20262265--20262321 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
20262255 CGTTTAAAAT
* *
20262265 TTTTAATTTAAACATATAATATTA
1 TTTTAATTTAAAAAAATAATA--A
20262289 TTTTAATTTAAAAAAATAATAA
1 TTTTAATTTAAAAAAATAATAA
*
20262311 TTTAAATTTAA
1 TTTTAATTTAA
20262322 CTCTTTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 11 0.37
24 19 0.63
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAATTTAAAAAAATAATAA
Found at i:20282439 original size:63 final size:62
Alignment explanation
Indices: 20282366--20282490 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 62
20282356 GTTTGATAAA
20282366 TTTATATAATATATGTTCTTTTCTACATTGACTGGAAAAGGAAAAAGTATGCAATACCCGAC
1 TTTATATAATATATGTTCTTTTCTACATTGACTGGAAAAGGAAAAAGTATGCAATACCCGAC
20282428 NTTTATATAATATATGTTCTTTTCTACATTGACTGGAAAAGGAAAAAGTATGCAATACCCGAC
1 -TTTATATAATATATGTTCTTTTCTACATTGACTGGAAAAGGAAAAAGTATGCAATACCCGAC
20282491 AATTCTATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (62 bp):
TTTATATAATATATGTTCTTTTCTACATTGACTGGAAAAGGAAAAAGTATGCAATACCCGAC
Found at i:20284046 original size:11 final size:11
Alignment explanation
Indices: 20284030--20284089 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
20284020 CTGCTATTCT
20284030 TGCTGCTGATC
1 TGCTGCTGATC
20284041 TGCTGCCATG-TC
1 TGCTG-C-TGATC
* *
20284053 TGTTGCTGATT
1 TGCTGCTGATC
* *
20284064 TGCTGCTGGTT
1 TGCTGCTGATC
*
20284075 TGGTGCTGATC
1 TGCTGCTGATC
20284086 TGCT
1 TGCT
20284090 ACCATGTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.05
11 27 0.71
12 7 0.18
13 2 0.05
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.42
Consensus pattern (11 bp):
TGCTGCTGATC
Found at i:20284059 original size:23 final size:23
Alignment explanation
Indices: 20284033--20284196 Score: 99
Period size: 23 Copynumber: 7.3 Consensus size: 23
20284023 CTATTCTTGC
*
20284033 TGCTGATCTGCTGCCATGTCTGT
1 TGCTGATCTGCTGCCATGTTTGT
* *
20284056 TGCTGATTTGCTG-C-TGGTTTGG
1 TGCTGATCTGCTGCCAT-GTTTGT
*
20284078 TGCTGATCTGCTACCATGTTTGT
1 TGCTGATCTGCTGCCATGTTTGT
** * *
20284101 TGCTGAAT-TAATG--TTGGTTTGA
1 TGCTG-ATCTGCTGCCAT-GTTTGT
* *
20284123 TGTTGATTTGCTGCCATGTTTGT
1 TGCTGATCTGCTGCCATGTTTGT
* * * *
20284146 TGCTGATTTGTTG--TTGGTTTGG
1 TGCTGATCTGCTGCCAT-GTTTGT
* *
20284168 TGCTAATCTGTTGCCATGTTTGT
1 TGCTGATCTGCTGCCATGTTTGT
20284191 TGCTGA
1 TGCTGA
20284197 ATTACTGTTG
Statistics
Matches: 105, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
21 5 0.05
22 44 0.42
23 51 0.49
24 5 0.05
ACGTcount: A:0.11, C:0.15, G:0.28, T:0.46
Consensus pattern (23 bp):
TGCTGATCTGCTGCCATGTTTGT
Found at i:20284084 original size:45 final size:45
Alignment explanation
Indices: 20284033--20284214 Score: 238
Period size: 45 Copynumber: 4.0 Consensus size: 45
20284023 CTATTCTTGC
* * * *
20284033 TGCTGATCTGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGG
1 TGCTGATCTGCTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
* * *
20284078 TGCTGATCTGCTACCATGTTTGTTGCTGAATTAATGTTGGTTTGA
1 TGCTGATCTGCTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
* * * **
20284123 TGTTGATTTGCTGCCATGTTTGTTGCTGATTTGTTGTTGGTTTGG
1 TGCTGATCTGCTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
* *
20284168 TGCTAATCTGTTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
1 TGCTGATCTGCTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
20284213 TG
1 TG
20284215 AGTAATTTGT
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 116 1.00
ACGTcount: A:0.11, C:0.14, G:0.29, T:0.47
Consensus pattern (45 bp):
TGCTGATCTGCTGCCATGTTTGTTGCTGAATTACTGTTGGTTTGG
Found at i:20284153 original size:90 final size:90
Alignment explanation
Indices: 20284036--20284211 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
20284026 TTCTTGCTGC
*
20284036 TGATCTGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGGTGCTGATCTGCTACCATGTTTGT
1 TGATCTGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGGTGCTAATCTGCTACCATGTTTGT
20284101 TGCTGAATTAATGTTGGTTTGATGT
66 TGCTGAATTAATGTTGGTTTGATGT
* * * * * *
20284126 TGATTTGCTGCCATGTTTGTTGCTGATTTGTTGTTGGTTTGGTGCTAATCTGTTGCCATGTTTGT
1 TGATCTGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGGTGCTAATCTGCTACCATGTTTGT
*
20284191 TGCTGAATTACTGTTGGTTTG
66 TGCTGAATTAATGTTGGTTTG
20284212 GTGAGTAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.11, C:0.14, G:0.28, T:0.47
Consensus pattern (90 bp):
TGATCTGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGGTGCTAATCTGCTACCATGTTTGT
TGCTGAATTAATGTTGGTTTGATGT
Found at i:20284244 original size:90 final size:90
Alignment explanation
Indices: 20284041--20284251 Score: 219
Period size: 90 Copynumber: 2.3 Consensus size: 90
20284031 GCTGCTGATC
* * * * * * *
20284041 TGCTGCCATGTCTGTTGCTGATTTGCTGCTGGTTTGGTGCTGATCTGCTACCATGTTTGTTGCTG
1 TGCTGCCATGTTTATGGCAGATTTGTTGTTGGTTTGGTGCTAATCTGCTACCATGTTTGTTGCTG
* *
20284106 AATTAATGTTGGTTTGATGTTGATT
66 AATTAATGTTGGTTTGATGGTAATT
* * * * *
20284131 TGCTGCCATGTTTGTTGCTGATTTGTTGTTGGTTTGGTGCTAATCTGTTGCCATGTTTGTTGCTG
1 TGCTGCCATGTTTATGGCAGATTTGTTGTTGGTTTGGTGCTAATCTGCTACCATGTTTGTTGCTG
* *
20284196 AATTACTGTTGGTTTGGTGAGTAATT
66 AATTAATGTTGGTTTGATG-GTAATT
* * *
20284222 TGTTG-C-TGGTTTATGGGAGATTTATTGTTG
1 TGCTGCCAT-GTTTATGGCAGATTTGTTGTTG
20284252 ATCTGTAGGA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
89 1 0.01
90 94 0.91
91 8 0.08
ACGTcount: A:0.12, C:0.11, G:0.29, T:0.47
Consensus pattern (90 bp):
TGCTGCCATGTTTATGGCAGATTTGTTGTTGGTTTGGTGCTAATCTGCTACCATGTTTGTTGCTG
AATTAATGTTGGTTTGATGGTAATT
Found at i:20289374 original size:34 final size:34
Alignment explanation
Indices: 20289330--20289406 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
20289320 GCTGCTATTC
* * *
20289330 TTGCTACTGATCTGCTGCCATGTCTGTTGCTGAT
1 TTGCTGCTGATCTGCTACCATGTCTGTTGCTGAA
* *
20289364 TTGGTGCTGATCTGCTACCATGTTTGTTGCTGAA
1 TTGCTGCTGATCTGCTACCATGTCTGTTGCTGAA
20289398 TTGCTGCTG
1 TTGCTGCTG
20289407 GTTTGGTGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (34 bp):
TTGCTGCTGATCTGCTACCATGTCTGTTGCTGAA
Found at i:20289416 original size:22 final size:22
Alignment explanation
Indices: 20289352--20289426 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
20289342 TGCTGCCATG
* *
20289352 TCTGTTGCTGATTTGGTGCTGA
1 TCTGCTGCTGGTTTGGTGCTGA
* *
20289374 TCTGCTACCAT-GTTTGTTGCTGAA
1 TCTGCT-GC-TGGTTTGGTGCTG-A
20289398 T-TGCTGCTGGTTTGGTGCTGA
1 TCTGCTGCTGGTTTGGTGCTGA
20289419 TCTGCTGC
1 TCTGCTGC
20289427 CATGTATGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 3 0.07
22 22 0.52
23 14 0.33
24 3 0.07
ACGTcount: A:0.09, C:0.19, G:0.29, T:0.43
Consensus pattern (22 bp):
TCTGCTGCTGGTTTGGTGCTGA
Found at i:20289459 original size:23 final size:23
Alignment explanation
Indices: 20289433--20289479 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20289423 CTGCCATGTA
*
20289433 TGGTGAGTAATTTGTTGCTGGTT
1 TGGTGAGTAATTTGTTGCTCGTT
20289456 TGGTGAGTAATTTGTTGCTCGTT
1 TGGTGAGTAATTTGTTGCTCGTT
20289479 T
1 T
20289480 ATGGGAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.06, G:0.32, T:0.49
Consensus pattern (23 bp):
TGGTGAGTAATTTGTTGCTCGTT
Found at i:20297542 original size:27 final size:28
Alignment explanation
Indices: 20297485--20297542 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20297475 AAAAAAATGT
*
20297485 CCTGATGGTGGAAAATTACAATTTTGCC
1 CCTGATGGTGGAAAATTACAATTTTGAC
20297513 CCTGA-GGTGGTAAAATTATC-ATTTT-AC
1 CCTGATGGTGG-AAAATTA-CAATTTTGAC
20297540 CCT
1 CCT
20297543 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 9 0.33
28 17 0.63
29 1 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (28 bp):
CCTGATGGTGGAAAATTACAATTTTGAC
Found at i:20297613 original size:20 final size:20
Alignment explanation
Indices: 20297588--20297633 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
20297578 CTTCTAAACC
20297588 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
20297608 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
20297628 TCAAAT
1 TCAAAT
20297634 GGGATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:20300965 original size:35 final size:35
Alignment explanation
Indices: 20300921--20300993 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
20300911 GAAATACATG
* *
20300921 TGATGATATTGAAATGTGCGTGTAAGGAGTGCACA
1 TGATGATATTGAAATATGCGTATAAGGAGTGCACA
*
20300956 TGATGATATTGAAATATGCGTATAGGGAGTGCACA
1 TGATGATATTGAAATATGCGTATAAGGAGTGCACA
20300991 TGA
1 TGA
20300994 GCTGAGCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (35 bp):
TGATGATATTGAAATATGCGTATAAGGAGTGCACA
Found at i:20305792 original size:13 final size:13
Alignment explanation
Indices: 20305774--20305798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20305764 AGACTCAATC
20305774 TTTTAGACAACTA
1 TTTTAGACAACTA
20305787 TTTTAGACAACT
1 TTTTAGACAACT
20305799 CTATCCTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTAGACAACTA
Found at i:20309280 original size:29 final size:29
Alignment explanation
Indices: 20309248--20309325 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
20309238 TATTGAAAAA
20309248 TTTAAATAAATTTTTATTTTTTTATTATG
1 TTTAAATAAATTTTTATTTTTTTATTATG
* * * *
20309277 TTT-AATCGAATTATTATACTTTTTATTTTG
1 TTTAAAT-AAATTTTTAT-TTTTTTATTATG
* *
20309307 TGTCAAATAAGTTTTTATT
1 T-TTAAATAAATTTTTATT
20309326 ATTAGTGCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
28 3 0.08
29 11 0.31
30 11 0.31
31 8 0.22
32 3 0.08
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (29 bp):
TTTAAATAAATTTTTATTTTTTTATTATG
Found at i:20317348 original size:15 final size:15
Alignment explanation
Indices: 20317336--20317374 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20317326 CGTTGTTAGA
20317336 AATGTAATTGTTAAG
1 AATGTAATTGTTAAG
* *
20317351 AATGTAATTATTGAG
1 AATGTAATTGTTAAG
*
20317366 AATATAATT
1 AATGTAATT
20317375 TTGTAGCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (15 bp):
AATGTAATTGTTAAG
Found at i:20317613 original size:22 final size:21
Alignment explanation
Indices: 20317575--20317615 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
20317565 ATTTTAAGTA
20317575 ATTAAAATAATAAATAATAAC
1 ATTAAAATAATAAATAATAAC
20317596 ATTAAAA-AAGTAATATAATA
1 ATTAAAATAA-TAA-ATAATA
20317616 TTTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTAAAATAATAAATAATAAC
Found at i:20319030 original size:21 final size:21
Alignment explanation
Indices: 20319006--20319048 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20318996 ATATTAACGA
20319006 CGTATGGTGCTATCACTTAAT
1 CGTATGGTGCTATCACTTAAT
20319027 CGTATGGTGCTATCACTTAAT
1 CGTATGGTGCTATCACTTAAT
20319048 C
1 C
20319049 ATAAAAGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
CGTATGGTGCTATCACTTAAT
Found at i:20319838 original size:27 final size:27
Alignment explanation
Indices: 20319783--20319840 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20319773 AAATTTAAAT
* * *
20319783 AAATTTTTATATTTTTTATGTTTACTC
1 AAATTATTATACTTTTTATGTTGACTC
* *
20319810 AAATTATTATACTTTTTATTTTGAGTC
1 AAATTATTATACTTTTTATGTTGACTC
20319837 AAAT
1 AAAT
20319841 AGGTATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (27 bp):
AAATTATTATACTTTTTATGTTGACTC
Found at i:20319904 original size:140 final size:139
Alignment explanation
Indices: 20319749--20320028 Score: 551
Period size: 140 Copynumber: 2.0 Consensus size: 139
20319739 ATGATATCTT
20319749 AAAAAACTCTTAAATTATTGAAAAAAATTTAAATAAATTTTTATATTTTTTATGTTTACTCAAAT
1 AAAAAACTCTTAAATTATTGAAAAAAATTTAAATAAATTTTTATATTTTTTATGTTTACTCAAAT
20319814 TATTATACTTTTTATTTTGAGTCAAATAGGTATTTATTACTAATACTTAATTAATTGTTATTAGT
66 TATTATACTTTTTATTTTGAGTCAAATAGGTATTTATTACTAATACTTAATTAATTGTTATTAGT
20319879 TAAAATGTA
131 TAAAATGTA
20319888 NAAAAAACTCTTAAATTATTGAAAAAAATTTAAATAAATTTTTATATTTTTTATGTTTACTCAAA
1 -AAAAAACTCTTAAATTATTGAAAAAAATTTAAATAAATTTTTATATTTTTTATGTTTACTCAAA
20319953 TTATTATACTTTTTATTTTGAGTCAAATAGGTATTTATTACTAATACTTAATTAATTGTTATTAG
65 TTATTATACTTTTTATTTTGAGTCAAATAGGTATTTATTACTAATACTTAATTAATTGTTATTAG
20320018 TTAAAATGTA
130 TTAAAATGTA
20320028 A
1 A
20320029 TTTAGATATT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 1 0.01
140 139 0.99
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (139 bp):
AAAAAACTCTTAAATTATTGAAAAAAATTTAAATAAATTTTTATATTTTTTATGTTTACTCAAAT
TATTATACTTTTTATTTTGAGTCAAATAGGTATTTATTACTAATACTTAATTAATTGTTATTAGT
TAAAATGTA
Found at i:20319978 original size:27 final size:27
Alignment explanation
Indices: 20319923--20319980 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
20319913 AAATTTAAAT
* * *
20319923 AAATTTTTATATTTTTTATGTTTACTC
1 AAATTATTATACTTTTTATGTTGACTC
* *
20319950 AAATTATTATACTTTTTATTTTGAGTC
1 AAATTATTATACTTTTTATGTTGACTC
20319977 AAAT
1 AAAT
20319981 AGGTATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (27 bp):
AAATTATTATACTTTTTATGTTGACTC
Found at i:20321372 original size:11 final size:10
Alignment explanation
Indices: 20321347--20321371 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20321337 TAGAAAACGC
20321347 AAAAAGAAAA
1 AAAAAGAAAA
20321357 AAAAAGAAAA
1 AAAAAGAAAA
20321367 AAAAA
1 AAAAA
20321372 AAGGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:20335153 original size:2 final size:2
Alignment explanation
Indices: 20335146--20335175 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20335136 CAAGGTTGGA
*
20335146 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20335176 TCTGTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20342431 original size:6 final size:6
Alignment explanation
Indices: 20342420--20342445 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20342410 ACCTGCACTT
20342420 CAGCCA CAGCCA CAGCCA CAGCCA CA
1 CAGCCA CAGCCA CAGCCA CAGCCA CA
20342446 ACAAGCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
CAGCCA
Found at i:20342474 original size:3 final size:3
Alignment explanation
Indices: 20342468--20342514 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
20342458 GCAACAAGCT
* * *
20342468 CAG CAG CAA CAAG CAT CA- CAG CAG CAG CAG CAG CAG CAG CAT CAG
1 CAG CAG CAG C-AG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
20342513 CA
1 CA
20342515 AAGTCAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.38, C:0.34, G:0.23, T:0.04
Consensus pattern (3 bp):
CAG
Found at i:20342493 original size:18 final size:15
Alignment explanation
Indices: 20342444--20342490 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
20342434 GCCACAGCCA
20342444 CAACAAGCTCAGCAG
1 CAACAAGCTCAGCAG
20342459 CAACAAGCTCAGCAG
1 CAACAAGCTCAGCAG
20342474 CAACAAGCATCA-CAG
1 CAACAAGC-TCAGCAG
20342489 CA
1 CA
20342491 GCAGCAGCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 28 0.90
16 3 0.10
ACGTcount: A:0.43, C:0.34, G:0.17, T:0.06
Consensus pattern (15 bp):
CAACAAGCTCAGCAG
Found at i:20342689 original size:3 final size:3
Alignment explanation
Indices: 20342681--20342749 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
20342671 TCAGATGTTA
* * * * *
20342681 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAA CAG CAT CAA CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
20342729 CAG CAG CAG CCA- CAG CAG CAG
1 CAG CAG CAG -CAG CAG CAG CAG
20342750 AGGAAATTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.39, C:0.35, G:0.25, T:0.01
Consensus pattern (3 bp):
CAG
Found at i:20342698 original size:12 final size:12
Alignment explanation
Indices: 20342680--20342749 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
20342670 TTCAGATGTT
20342680 ACAGCAGCAGCA
1 ACAGCAGCAGCA
*
20342692 GCAGCAGCAGCA
1 ACAGCAGCAGCA
* *
20342704 GCAGCAGCAACA
1 ACAGCAGCAGCA
* *
20342716 ACAGCATCAACA
1 ACAGCAGCAGCA
*
20342728 ACAGCAGCAGCC
1 ACAGCAGCAGCA
20342740 ACAGCAGCAG
1 ACAGCAGCAG
20342750 AGGAAATTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.40, C:0.34, G:0.24, T:0.01
Consensus pattern (12 bp):
ACAGCAGCAGCA
Found at i:20343269 original size:24 final size:24
Alignment explanation
Indices: 20343242--20343310 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
20343232 TTACATGAAC
*** *
20343242 CAGCATCAGCAACAGTTTCAGTTG
1 CAGCATCAGCAACAGCAGCAATTG
*
20343266 CAGCATCAGCAGCAGCAGCAATTG
1 CAGCATCAGCAACAGCAGCAATTG
* *
20343290 CAGCATCAGCAGCAACAGCAA
1 CAGCATCAGCAACAGCAGCAA
20343311 CAACAGCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (24 bp):
CAGCATCAGCAACAGCAGCAATTG
Found at i:20343332 original size:24 final size:24
Alignment explanation
Indices: 20343305--20343387 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
20343295 TCAGCAGCAA
* *
20343305 CAGCAACAACAGCAACACTTACAG
1 CAGCAGCAGCAGCAACACTTACAG
* * * *
20343329 CAGCTGCAGCATCAGCAATTACAG
1 CAGCAGCAGCAGCAACACTTACAG
*
20343353 CAACAGCAGCAGCAACAGC-TACAG
1 CAGCAGCAGCAGCAACA-CTTACAG
20343377 CAGCAGCAGCA
1 CAGCAGCAGCA
20343388 ACAAGAAACA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.40, C:0.33, G:0.19, T:0.08
Consensus pattern (24 bp):
CAGCAGCAGCAGCAACACTTACAG
Found at i:20343338 original size:21 final size:21
Alignment explanation
Indices: 20343304--20343390 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 21
20343294 ATCAGCAGCA
* *
20343304 ACAGCAACAACAGCAACACTT
1 ACAGCAGCAGCAGCAACACTT
* *
20343325 ACAGCAGCTGCAGCATCAGCAATT
1 ACAGCAGCAGCAGCA--A-CACTT
20343349 ACAGCAACAGCAGCAGCAACAGC-T
1 ACAG---CAGCAGCAGCAACA-CTT
20343373 ACAGCAGCAGCAGCAACA
1 ACAGCAGCAGCAGCAACA
20343391 AGAAACAACC
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
21 26 0.49
23 1 0.02
24 15 0.28
25 1 0.02
27 10 0.19
ACGTcount: A:0.41, C:0.32, G:0.18, T:0.08
Consensus pattern (21 bp):
ACAGCAGCAGCAGCAACACTT
Found at i:20343367 original size:12 final size:12
Alignment explanation
Indices: 20343350--20343387 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20343340 TCAGCAATTA
20343350 CAGCAACAGCAG
1 CAGCAACAGCAG
20343362 CAGCAACAGCTA-
1 CAGCAACAGC-AG
*
20343374 CAGCAGCAGCAG
1 CAGCAACAGCAG
20343386 CA
1 CA
20343388 ACAAGAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.39, C:0.34, G:0.24, T:0.03
Consensus pattern (12 bp):
CAGCAACAGCAG
Found at i:20343370 original size:18 final size:18
Alignment explanation
Indices: 20343349--20343384 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20343339 ATCAGCAATT
20343349 ACAGCAACAGCAGCAGCA
1 ACAGCAACAGCAGCAGCA
*
20343367 ACAGCTACAGCAGCAGCA
1 ACAGCAACAGCAGCAGCA
20343385 GCAACAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.22, T:0.03
Consensus pattern (18 bp):
ACAGCAACAGCAGCAGCA
Found at i:20343502 original size:15 final size:15
Alignment explanation
Indices: 20343482--20343520 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
20343472 CCAACAATCT
20343482 CAGCAACAGCAAGCC
1 CAGCAACAGCAAGCC
20343497 CAGCAACAGCAAGCC
1 CAGCAACAGCAAGCC
20343512 CAGCAACAG
1 CAGCAACAG
20343521 ACCAGTCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.41, C:0.38, G:0.21, T:0.00
Consensus pattern (15 bp):
CAGCAACAGCAAGCC
Found at i:20356197 original size:144 final size:144
Alignment explanation
Indices: 20355949--20356234 Score: 509
Period size: 144 Copynumber: 2.0 Consensus size: 144
20355939 AACCTTCCCA
20355949 TACATGAACATTTTTATACTCTGATTGAAAACTTCTAGCCTTGAAATTAGGAGAAAAGCCTGACT
1 TACATGAACATTTTTATACTCTGATTGAAAACTTCTAGCCTTGAAATTAGGAGAAAAGCCTGACT
* * *
20356014 GTTCAGGGAGTTGAATCCTTTTTTCTCTAGGAGCGACTGATAAACCTGATTGCTTAGGTTGATTT
66 GTTCAGGGAGTTGAATCCTTTTTTCTCTAGGAGCAACTGATAAACCTGACTGCTTAGATTGATTT
20356079 GCAAGCTGCTGAAG
131 GCAAGCTGCTGAAG
*
20356093 TACATGAACATTTTTATACTCTGATTGAAAACTTTTAGCCTTGAAATTAGGAGAAAAGCCTGACT
1 TACATGAACATTTTTATACTCTGATTGAAAACTTCTAGCCTTGAAATTAGGAGAAAAGCCTGACT
* * *
20356158 GTTCAGGGAGTTGAATCCTTTTTTCTCTGGGAGTAACTGATAAACCTGACTGCTTAGATTGGTTT
66 GTTCAGGGAGTTGAATCCTTTTTTCTCTAGGAGCAACTGATAAACCTGACTGCTTAGATTGATTT
20356223 GCAAGCTGCTGA
131 GCAAGCTGCTGA
20356235 GGTTCAGCTA
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 135 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (144 bp):
TACATGAACATTTTTATACTCTGATTGAAAACTTCTAGCCTTGAAATTAGGAGAAAAGCCTGACT
GTTCAGGGAGTTGAATCCTTTTTTCTCTAGGAGCAACTGATAAACCTGACTGCTTAGATTGATTT
GCAAGCTGCTGAAG
Found at i:20363087 original size:21 final size:21
Alignment explanation
Indices: 20363048--20363087 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20363038 AAAAGAAAAT
*
20363048 TCATATTAACACTTATCAATG
1 TCATATCAACACTTATCAATG
* *
20363069 TCATATCAACGCTTTTCAA
1 TCATATCAACACTTATCAA
20363088 AATCAGGTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (21 bp):
TCATATCAACACTTATCAATG
Found at i:20363273 original size:31 final size:30
Alignment explanation
Indices: 20363238--20363345 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
20363228 GTGCATGAAT
20363238 TAAATTAAACATTTTGATAAAATATACAGAC
1 TAAATT-AACATTTTGATAAAATATACAGAC
* *
20363269 TAAATTCAACATTTTGATAAAA-GTACATGGAT
1 TAAATT-AACATTTTGATAAAATATACA--GAC
* *
20363301 TAAATCTAATA-TTTGATAAAATATAAAGAC
1 TAAAT-TAACATTTTGATAAAATATACAGAC
*
20363331 TAAATCTAATATTTT
1 TAAAT-TAACATTTT
20363346 TGTATAATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
30 17 0.26
31 34 0.52
32 13 0.20
33 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAATTAACATTTTGATAAAATATACAGAC
Found at i:20363283 original size:62 final size:62
Alignment explanation
Indices: 20363207--20363335 Score: 172
Period size: 62 Copynumber: 2.1 Consensus size: 62
20363197 ACTACTTGAT
* * * *
20363207 TAAATTTAACATTTTGAT-AGAGTGCATGAATTAAAT-TAAACATTTTGATAAAATATACAGAC
1 TAAATTCAACATTTTGATAAAAGTACATGAATTAAATCT-AACA-TTTGATAAAATATAAAGAC
* *
20363269 TAAATTCAACATTTTGATAAAAGTACATGGATTAAATCTAATATTTGATAAAATATAAAGAC
1 TAAATTCAACATTTTGATAAAAGTACATGAATTAAATCTAACATTTGATAAAATATAAAGAC
20363331 TAAAT
1 TAAAT
20363336 CTAATATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
62 40 0.68
63 18 0.31
64 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (62 bp):
TAAATTCAACATTTTGATAAAAGTACATGAATTAAATCTAACATTTGATAAAATATAAAGAC
Found at i:20378987 original size:14 final size:14
Alignment explanation
Indices: 20378968--20379009 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
20378958 AATAGTTATA
*
20378968 AAAATAATTATAAC
1 AAAATAATAATAAC
20378982 AAAATAATAATAAC
1 AAAATAATAATAAC
20378996 ATCAAAT-ATAATAA
1 A--AAATAATAATAA
20379010 AATTTATCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 14 0.56
15 7 0.28
16 4 0.16
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAATAATAAC
Found at i:20380977 original size:40 final size:40
Alignment explanation
Indices: 20380919--20381016 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
20380909 TTTATCCACT
* * *
20380919 TCTAGTGGATAAATGTATCCATCTACTTTTACTTGGTAAA
1 TCTAATGGGTAAAGGTATCCATCTACTTTTACTTGGTAAA
20380959 TCTAATGGGTAAAGGTATCCATCTACTTTTACTTGGTAAA
1 TCTAATGGGTAAAGGTATCCATCTACTTTTACTTGGTAAA
20380999 TCTAATGGGTAAAGGTAT
1 TCTAATGGGTAAAGGTAT
20381017 TTATCAACTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (40 bp):
TCTAATGGGTAAAGGTATCCATCTACTTTTACTTGGTAAA
Found at i:20381027 original size:40 final size:40
Alignment explanation
Indices: 20380919--20381038 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 40
20380909 TTTATCCACT
* * * *
20380919 TCTAGTGGATAAATGTATCCATCTACTTTTACTTGGTAAA
1 TCTAATGGGTAAAGGTATCCATCAACTTTTACTTGGTAAA
*
20380959 TCTAATGGGTAAAGGTATCCATCTACTTTTACTTGGTAAA
1 TCTAATGGGTAAAGGTATCCATCAACTTTTACTTGGTAAA
** * *
20380999 TCTAATGGGTAAAGGTATTTATCAACTTTTAGTGGGTAAA
1 TCTAATGGGTAAAGGTATCCATCAACTTTTACTTGGTAAA
20381039 GATATCCATC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (40 bp):
TCTAATGGGTAAAGGTATCCATCAACTTTTACTTGGTAAA
Found at i:20381100 original size:77 final size:77
Alignment explanation
Indices: 20381007--20381159 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 77
20380997 AATCTAATGG
** * * * *
20381007 GTAAAGGTATTTATCAACTTTTAGTGGGTAAAGATATCCATCAATTTTTTATGGGTATAGGTAGC
1 GTAAAGGTATACATCAACTTCTAGTGGGTAAAGATATCCATCAACTTTTGATGGGTAAAGGTAGC
20381072 CATCAACTTCTA
66 CATCAACTTCTA
* * * * *
20381084 GTAAAGGTATACATCAACTTCTGGTGGGTATAGGTATCCATCAACTTTTGGTGGGTAAAGGTATC
1 GTAAAGGTATACATCAACTTCTAGTGGGTAAAGATATCCATCAACTTTTGATGGGTAAAGGTAGC
20381149 CATCAACTTCT
66 CATCAACTTCT
20381160 GGTGGGTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (77 bp):
GTAAAGGTATACATCAACTTCTAGTGGGTAAAGATATCCATCAACTTTTGATGGGTAAAGGTAGC
CATCAACTTCTA
Found at i:20381187 original size:27 final size:27
Alignment explanation
Indices: 20381004--20381189 Score: 191
Period size: 27 Copynumber: 7.0 Consensus size: 27
20380994 GTAAATCTAA
** * *
20381004 TGGGTAAAGGTATTTATCAACTTTTAG
1 TGGGTAAAGGTATCCATCAACTTCTGG
* * * **
20381031 TGGGTAAAGATATCCATCAATTTTTTA
1 TGGGTAAAGGTATCCATCAACTTCTGG
* *
20381058 TGGGTATAGGTAGCCATCAACTTC---
1 TGGGTAAAGGTATCCATCAACTTCTGG
* *
20381082 T-AGTAAAGGTATACATCAACTTCTGG
1 TGGGTAAAGGTATCCATCAACTTCTGG
* *
20381108 TGGGTATAGGTATCCATCAACTTTTGG
1 TGGGTAAAGGTATCCATCAACTTCTGG
20381135 TGGGTAAAGGTATCCATCAACTTCTGG
1 TGGGTAAAGGTATCCATCAACTTCTGG
* *
20381162 TGGGTAAATGTATTCATCAACTTCTGG
1 TGGGTAAAGGTATCCATCAACTTCTGG
20381189 T
1 T
20381190 ATCCATCCAT
Statistics
Matches: 132, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.14
24 1 0.01
26 1 0.01
27 112 0.85
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (27 bp):
TGGGTAAAGGTATCCATCAACTTCTGG
Found at i:20382114 original size:16 final size:16
Alignment explanation
Indices: 20382093--20382126 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20382083 TTTCACTAGT
20382093 TACAAAATAAATATCA
1 TACAAAATAAATATCA
* *
20382109 TACAAAATCAATTTCA
1 TACAAAATAAATATCA
20382125 TA
1 TA
20382127 TGTTCAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (16 bp):
TACAAAATAAATATCA
Found at i:20382869 original size:2 final size:2
Alignment explanation
Indices: 20382864--20382903 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20382854 CACACACACA
20382864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20382904 TAATATGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20383027 original size:2 final size:2
Alignment explanation
Indices: 20383020--20383045 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20383010 NNNNNNNNNN
20383020 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20383046 TCATAACACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20383756 original size:15 final size:15
Alignment explanation
Indices: 20383733--20383762 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20383723 TGCATGTTTG
*
20383733 GTTGTAATTTTTGGT
1 GTTGCAATTTTTGGT
20383748 GTTGCAATTTTTGGT
1 GTTGCAATTTTTGGT
20383763 TTTTGTTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.27, T:0.57
Consensus pattern (15 bp):
GTTGCAATTTTTGGT
Found at i:20383829 original size:17 final size:17
Alignment explanation
Indices: 20383807--20383839 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20383797 AGTTTTCAAG
20383807 TTCTATCCAATTAGAAC
1 TTCTATCCAATTAGAAC
20383824 TTCTATCCAATTAGAA
1 TTCTATCCAATTAGAA
20383840 ATGCTGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
TTCTATCCAATTAGAAC
Found at i:20384058 original size:24 final size:24
Alignment explanation
Indices: 20384031--20384371 Score: 319
Period size: 24 Copynumber: 14.2 Consensus size: 24
20384021 CTTTTTTAAC
* *
20384031 CATGACGTGTAACATGTTTTTGTA
1 CATGGCGTGTCACATGTTTTTGTA
20384055 CATGGCGTGTCACATGTTTTTGTA
1 CATGGCGTGTCACATGTTTTTGTA
* * * *
20384079 CATAGCATGTCACATGCTTCTGTA
1 CATGGCGTGTCACATGTTTTTGTA
20384103 CATGGCGTGTCACATGTTTTTTGTA
1 CATGGCGTGTCACATG-TTTTTGTA
* * * *
20384128 TATGGTGTGTCACATGTTCCTT-CA
1 CATGGCGTGTCACATGTT-TTTGTA
* *
20384152 CATGGCGTATCACATGTTTCTGTA
1 CATGGCGTGTCACATGTTTTTGTA
*
20384176 CATGGCATGTCACATGTTTTTGTA
1 CATGGCGTGTCACATGTTTTTGTA
* * *
20384200 CGTGGAGTGTCACATGTTTCTGTA
1 CATGGCGTGTCACATGTTTTTGTA
* *
20384224 CATGACGTGTCACATGTTCCTT-TA
1 CATGGCGTGTCACATGTT-TTTGTA
* *
20384248 CATGGTGTGTCACATATTTTTGTA
1 CATGGCGTGTCACATGTTTTTGTA
* * **
20384272 CATGGTGTGTCATATGTTTCAGTA
1 CATGGCGTGTCACATGTTTTTGTA
*
20384296 CATGGCGTGTCACATGTTCCTT-TA
1 CATGGCGTGTCACATGTT-TTTGTA
* * * *
20384320 CATGGTGTATTACATATTTTTGTA
1 CATGGCGTGTCACATGTTTTTGTA
* ** * *
20384344 TATGGCACGTCATATGTTTTTTTA
1 CATGGCGTGTCACATGTTTTTGTA
20384368 CATG
1 CATG
20384372 TAAGAGTTAT
Statistics
Matches: 250, Mismatches: 60, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
23 5 0.02
24 222 0.89
25 23 0.09
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (24 bp):
CATGGCGTGTCACATGTTTTTGTA
Found at i:20384118 original size:72 final size:72
Alignment explanation
Indices: 20384031--20384371 Score: 353
Period size: 72 Copynumber: 4.7 Consensus size: 72
20384021 CTTTTTTAAC
* * * *
20384031 CATGACGTGTAACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATAGCATGTCACATGC
1 CATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATG-
20384096 TT-CTGTA
65 TTCCTGTA
* * * * *
20384103 CATGGCGTGTCACATGTTTTTTGTATATGGTGTGTCACATGTTCCTT-CACATGGCGTATCACAT
1 CATGGCGTGTCACATG-TTTTTGTACATGGCGTGTCACATGTT-TTTGTACATGGCGTGTCACAT
*
20384167 GTTTCTGTA
64 GTTCCTGTA
* * * * *
20384176 CATGGCATGTCACATGTTTTTGTACGTGGAGTGTCACATGTTTCTGTACATGACGTGTCACATGT
1 CATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGT
*
20384241 TCCTTTA
66 TCCTGTA
* * * * **
20384248 CATGGTGTGTCACATATTTTTGTACATGGTGTGTCATATGTTTCAGTACATGGCGTGTCACATGT
1 CATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGT
*
20384313 TCCTTTA
66 TCCTGTA
* * * * * ** * *
20384320 CATGGTGTATTACATATTTTTGTATATGGCACGTCATATGTTTTTTTACATG
1 CATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATG
20384372 TAAGAGTTAT
Statistics
Matches: 228, Mismatches: 37, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
71 1 0.00
72 167 0.73
73 58 0.25
74 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (72 bp):
CATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGTTTTTGTACATGGCGTGTCACATGT
TCCTGTA
Found at i:20385493 original size:32 final size:32
Alignment explanation
Indices: 20385453--20385576 Score: 101
Period size: 32 Copynumber: 3.6 Consensus size: 32
20385443 ATTATATTAA
20385453 AAAT-AAAAATAAAATATATACTTGTAATAAG
1 AAATGAAAAATAAAATATATACTTGTAATAAG
**
20385484 AAATGAAAAATAAAATATAT--TTAAAAANTAAG
1 AAATGAAAAATAAAATATATACTT-GTAA-TAAG
*
20385516 AAATTATATTAAAATAAAATAAAATATATACTTGTAATAAG
1 --A--A-A-T--GA-AAAATAAAATATATACTTGTAATAAG
20385557 AAATGAAAAATAAAATATAT
1 AAATGAAAAATAAAATATAT
20385577 TTAAAAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
30 2 0.03
31 6 0.08
32 33 0.45
33 1 0.01
34 1 0.01
35 1 0.01
36 2 0.03
37 2 0.03
38 1 0.01
39 1 0.01
40 1 0.01
41 18 0.25
42 2 0.03
43 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (32 bp):
AAATGAAAAATAAAATATATACTTGTAATAAG
Found at i:20385543 original size:20 final size:19
Alignment explanation
Indices: 20385489--20385544 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
20385479 ATAAGAAATG
20385489 AAAAATAAAATATATTTAAA
1 AAAAATAAAATATA-TTAAA
* * *
20385509 AANTAAGAAATTATATTAAA
1 AA-AAATAAAATATATTAAA
20385529 ATAAAATAAAATATAT
1 A-AAAATAAAATATAT
20385545 ACTTGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATAAAATATATTAAA
Found at i:20385553 original size:73 final size:74
Alignment explanation
Indices: 20385436--20385611 Score: 281
Period size: 73 Copynumber: 2.4 Consensus size: 74
20385426 AATATACAAT
20385436 ATAAGAAATTATATTAAAAATAAAAATAAAATATATACTTGTAATAAGAAATGAAAAATAAAATA
1 ATAAGAAATTATATTAAAAATAAAAATAAAATATATACTTGTAATAAGAAATGAAAAATAAAATA
20385501 TATTTAAAA
66 TATTTAAAA
20385510 ANTAAGAAATTATATT-AAAAT-AAAATAAAATATATACTTGTAATAAGAAATGAAAAATAAAAT
1 A-TAAGAAATTATATTAAAAATAAAAATAAAATATATACTTGTAATAAGAAATGAAAAATAAAAT
20385573 ATATTTAAAA
65 ATATTTAAAA
* *
20385583 AT--GACATTATA-TAAAAATTAATAATAAAA
1 ATAAGAAATTATATTAAAAA-TAAAAATAAAA
20385612 AAATACATAT
Statistics
Matches: 96, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
69 1 0.01
70 12 0.12
71 1 0.01
72 9 0.09
73 53 0.55
74 6 0.06
75 14 0.15
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (74 bp):
ATAAGAAATTATATTAAAAATAAAAATAAAATATATACTTGTAATAAGAAATGAAAAATAAAATA
TATTTAAAA
Found at i:20385790 original size:15 final size:15
Alignment explanation
Indices: 20385764--20385827 Score: 92
Period size: 15 Copynumber: 4.3 Consensus size: 15
20385754 CTGCAATGTT
*
20385764 ATATTTCCTGCAATC
1 ATATTACCTGCAATC
*
20385779 ATATTACTTGCAATC
1 ATATTACCTGCAATC
*
20385794 ACATTACCTGCAATC
1 ATATTACCTGCAATC
*
20385809 ACATTACCTGCAATC
1 ATATTACCTGCAATC
20385824 ATAT
1 ATAT
20385828 CACTTGTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (15 bp):
ATATTACCTGCAATC
Found at i:20386710 original size:12 final size:10
Alignment explanation
Indices: 20386682--20386719 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
20386672 GCCCCCAAAA
20386682 TTTAATTTTT
1 TTTAATTTTT
20386692 TTTAATTTTT
1 TTTAATTTTT
20386702 TTATAAATTTTT
1 TT-T-AATTTTT
20386714 TTTAAT
1 TTTAAT
20386720 GATCCTCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:20386832 original size:17 final size:16
Alignment explanation
Indices: 20386811--20386848 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
20386801 TAAAGTTTTT
20386811 TTTATTT-TTTAATTTA
1 TTTATTTGTTT-ATTTA
20386827 TATTATTTGTTTATTTA
1 T-TTATTTGTTTATTTA
20386844 TTTAT
1 TTTAT
20386849 CTATTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 12 0.60
18 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATTTGTTTATTTA
Found at i:20387775 original size:19 final size:20
Alignment explanation
Indices: 20387753--20387794 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
20387743 GTCTAATATC
*
20387753 TTTTGAATTTTATTTAAT-T
1 TTTTGAATTTGATTTAATCT
20387772 TTTTGAATTTGATTTAATCT
1 TTTTGAATTTGATTTAATCT
20387792 TTT
1 TTT
20387795 AAATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTGAATTTGATTTAATCT
Found at i:20398419 original size:20 final size:20
Alignment explanation
Indices: 20398372--20398421 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20398362 AAGTTTCTAA
* *
20398372 CAACTTCTTCAAATTTCCAG
1 CAACTTTTTCAAACTTCCAG
*
20398392 CAGA-TTTTTCAAGCTTCCAG
1 CA-ACTTTTTCAAACTTCCAG
20398412 CAACTTTTTC
1 CAACTTTTTC
20398422 TTCTTCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (20 bp):
CAACTTTTTCAAACTTCCAG
Found at i:20399272 original size:38 final size:39
Alignment explanation
Indices: 20399219--20399305 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
20399209 NNNNNNNNNN
* *
20399219 GGATGCACACGATGGCACTAAC-TGTGCACGATGTGGGG
1 GGATGCACACAATGGCACTAACATGTGCACGATGTGGGA
* **
20399257 GGATGCACACAATGGCTCTGGCTATGTGCACGATGTGGGA
1 GGATGCACACAATGGCACTAAC-ATGTGCACGATGTGGGA
*
20399297 GGATACACA
1 GGATGCACA
20399306 TGAGTCGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 18 0.44
40 23 0.56
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.20
Consensus pattern (39 bp):
GGATGCACACAATGGCACTAACATGTGCACGATGTGGGA
Found at i:20403306 original size:9 final size:9
Alignment explanation
Indices: 20403286--20403324 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
20403276 ACACGATTAA
*
20403286 TAACACGTT
1 TAACACGAT
*
20403295 TAACATGAT
1 TAACACGAT
*
20403304 TAACACGTT
1 TAACACGAT
20403313 TAACACGAT
1 TAACACGAT
20403322 TAA
1 TAA
20403325 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:20403309 original size:18 final size:18
Alignment explanation
Indices: 20403286--20403324 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20403276 ACACGATTAA
*
20403286 TAACACGTTTAACATGAT
1 TAACACGTTTAACACGAT
20403304 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
20403322 TAA
1 TAA
20403325 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:20403375 original size:80 final size:79
Alignment explanation
Indices: 20403284--20403445 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 79
20403274 TGACACGATT
20403284 AATAACACGTTTAACATGATTAACACGTTTAACACGATTAAATAAAAATATTTATAATTAAGTAT
1 AATAACACGTTTAACATGATTAACACGTTTAACACGATTAAATAAAAATATTTATAATTAAGTAT
20403349 AATTTTATTATTTA
66 AATTTTATTATTTA
*
20403363 ANATAACACGTTTAACATGATTAACATGTTTAACACGATTAAATAAAAATATTTATAATTAAGTA
1 A-ATAACACGTTTAACATGATTAACACGTTTAACACGATTAAATAAAAATATTTATAATTAAGTA
20403428 TAATTTTATTATTTA
65 TAATTTTATTATTTA
20403443 AAT
1 AAT
20403446 TTAAAATCTA
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
79 3 0.04
80 78 0.96
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (79 bp):
AATAACACGTTTAACATGATTAACACGTTTAACACGATTAAATAAAAATATTTATAATTAAGTAT
AATTTTATTATTTA
Found at i:20403387 original size:18 final size:18
Alignment explanation
Indices: 20403366--20403404 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20403356 TTATTTAANA
*
20403366 TAACACGTTTAACATGAT
1 TAACACGTTTAACACGAT
*
20403384 TAACATGTTTAACACGAT
1 TAACACGTTTAACACGAT
20403402 TAA
1 TAA
20403405 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:20403688 original size:18 final size:18
Alignment explanation
Indices: 20403667--20403712 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
20403657 TGTCACGTAT
*
20403667 ACACGTTTAAACACGATA
1 ACACGATTAAACACGATA
20403685 ACACGATTAAACACGATA
1 ACACGATTAAACACGATA
*
20403703 ACATGATTAA
1 ACACGATTAA
20403713 GTAAACGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:20414809 original size:3 final size:3
Alignment explanation
Indices: 20414801--20414825 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20414791 ACCGAATTTG
20414801 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
20414826 CTTTTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20431051 original size:19 final size:18
Alignment explanation
Indices: 20430987--20431053 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
20430977 TTTTTTTCAC
*
20430987 AAACATAACTTTTTGAAAT
1 AAACATAATTTTTTG-AAT
* * *
20431006 AAATATAATTATTTAAAT
1 AAACATAATTTTTTGAAT
*
20431024 AAAATATAATTTTTTTGAAT
1 -AAACATAA-TTTTTTGAAT
20431044 AAACATAATT
1 AAACATAATT
20431054 GATCAAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.13
19 26 0.67
20 8 0.21
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
AAACATAATTTTTTGAAT
Found at i:20444341 original size:16 final size:15
Alignment explanation
Indices: 20444308--20444341 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20444298 TTTGTATTTT
*
20444308 TTTTTATTTTTTTGG
1 TTTTTATTTTTTTAG
20444323 TTTTTATTTTTTTAAG
1 TTTTTATTTTTTT-AG
20444339 TTT
1 TTT
20444342 GAAGAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTTATTTTTTTAG
Found at i:20445933 original size:32 final size:30
Alignment explanation
Indices: 20445889--20445972 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 30
20445879 ATGATAGATC
*
20445889 TTTGTTC-ATTTAGTCTTTATGCTTTACAAT
1 TTTGTTCAATTTAGTCTTTATG-TCTACAAT
* *
20445919 TTTGTTTCAATTTAGCACTTGTAT-TCTACATT
1 TTTG-TTCAATTTAG-TCTT-TATGTCTACAAT
*
20445951 TTTGTTCAATTTAGTATTTATG
1 TTTGTTCAATTTAGTCTTTATG
20445973 ATATATTACC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
29 3 0.07
30 6 0.14
31 13 0.30
32 16 0.36
33 3 0.07
34 3 0.07
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (30 bp):
TTTGTTCAATTTAGTCTTTATGTCTACAAT
Found at i:20450216 original size:13 final size:13
Alignment explanation
Indices: 20450198--20450222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20450188 GATAAATTTC
20450198 TTTTTATAAGTTT
1 TTTTTATAAGTTT
20450211 TTTTTATAAGTT
1 TTTTTATAAGTT
20450223 ATAATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTTTATAAGTTT
Found at i:20450242 original size:18 final size:20
Alignment explanation
Indices: 20450201--20450242 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
20450191 AAATTTCTTT
* *
20450201 TTATAAGTTTTTTTTATAAG
1 TTATAAGTTTTTGTTATAAA
20450221 TTATAA-TTTTTGTTA-AAA
1 TTATAAGTTTTTGTTATAAA
20450239 TTAT
1 TTAT
20450243 CAAAAAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
TTATAAGTTTTTGTTATAAA
Found at i:20451013 original size:2 final size:2
Alignment explanation
Indices: 20451006--20451051 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
20450996 CAACGAAATC
* * *
20451006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20451048 AT AT
1 AT AT
20451052 TAGTATTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20452634 original size:60 final size:60
Alignment explanation
Indices: 20452560--20452672 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
20452550 GAGTCTCATA
* * * **
20452560 TACTTTTATTGTTCAATGTCCACATCAAAGTCTATTAGTTTTAAGTTTACAAACCCTATG
1 TACTTGTATTGTTCAATATCCACATCAAAGTCCACAAGTTTTAAGTTTACAAACCCTATG
*
20452620 TACTTGTATTGTTCAATATCCATATCAAAGTCCACAAGTTTTAAGTTTACAAA
1 TACTTGTATTGTTCAATATCCACATCAAAGTCCACAAGTTTTAAGTTTACAAA
20452673 AGCCTAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (60 bp):
TACTTGTATTGTTCAATATCCACATCAAAGTCCACAAGTTTTAAGTTTACAAACCCTATG
Found at i:20455491 original size:3 final size:3
Alignment explanation
Indices: 20455483--20455515 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
20455473 CGAATCCGCT
*
20455483 TCC TCC TCC TCC TCC TCC TCC TCT TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
20455516 GAATCGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:20458588 original size:22 final size:22
Alignment explanation
Indices: 20458560--20458616 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
20458550 TTCTAAAAGT
20458560 AAAAATCTGTAAATTAAAGTAA
1 AAAAATCTGTAAATTAAAGTAA
*
20458582 AAAAATCTGTAAATTAAAGTGA
1 AAAAATCTGTAAATTAAAGTAA
*
20458604 AAAAATATGTAAA
1 AAAAATCTGTAAA
20458617 GATTAGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.26
Consensus pattern (22 bp):
AAAAATCTGTAAATTAAAGTAA
Found at i:20460408 original size:14 final size:14
Alignment explanation
Indices: 20460389--20460417 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20460379 CATTGAAGGA
20460389 GAAGACTAAAGGGC
1 GAAGACTAAAGGGC
20460403 GAAGACTAAAGGGC
1 GAAGACTAAAGGGC
20460417 G
1 G
20460418 TTATACGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.38, T:0.07
Consensus pattern (14 bp):
GAAGACTAAAGGGC
Found at i:20461896 original size:15 final size:15
Alignment explanation
Indices: 20461876--20461906 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20461866 GGAAAAGTGC
20461876 CCCGGAAAATTGGAT
1 CCCGGAAAATTGGAT
20461891 CCCGGAAAATTGGAT
1 CCCGGAAAATTGGAT
20461906 C
1 C
20461907 AACTCTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (15 bp):
CCCGGAAAATTGGAT
Found at i:20466049 original size:13 final size:13
Alignment explanation
Indices: 20466021--20466069 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
20466011 TGATTATGTC
20466021 TATAGTATATAT-A
1 TATA-TATATATAA
20466034 TATATATATATAA
1 TATATATATATAA
*
20466047 TATATATATATAG
1 TATATATATATAA
20466060 TATATATATA
1 TATATATATA
20466070 GTTTCAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 7 0.21
13 27 0.79
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (13 bp):
TATATATATATAA
Found at i:20466082 original size:2 final size:2
Alignment explanation
Indices: 20466021--20466069 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
20466011 TGATTATGTC
20466021 TA TA GTA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
20466064 TA TA TA
1 TA TA TA
20466070 GTTTCAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.02
2 39 0.89
3 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:20472385 original size:2 final size:2
Alignment explanation
Indices: 20472378--20472417 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
20472368 ATCATGTTAG
20472378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20472418 AGTTAATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20478251 original size:55 final size:55
Alignment explanation
Indices: 20478130--20478348 Score: 196
Period size: 55 Copynumber: 4.0 Consensus size: 55
20478120 AAAAATTAAG
* * *
20478130 TTGAAAA-TATAATTATTATACATTATGTTAAAAATTTAGTTATTACATG-CTATG
1 TTGAAAACTATAATTATTATACATTATGTTGAAAATTTAGTTATTACACGTC-ATA
* * * * * * *
20478184 TTTAAAAATATAATTATTATACGTTATATTGAAGATTTAGTTGTTATACGTCATA
1 TTGAAAACTATAATTATTATACATTATGTTGAAAATTTAGTTATTACACGTCATA
* * * *
20478239 TTGAAAACTATAATTGTTGTATATTATGTTGAAAATTTAGTTATTACACGTTATA
1 TTGAAAACTATAATTATTATACATTATGTTGAAAATTTAGTTATTACACGTCATA
* * * *
20478294 TTGAAAAACTGTAATT-GT-TACATGTCATGAT-AAAATTTTTGTTATTACACGTCAT
1 TTG-AAAACTATAATTATTATACAT-T-ATGTTGAAAA-TTTAGTTATTACACGTCAT
20478349 GTTAAAAAAA
Statistics
Matches: 133, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
54 10 0.08
55 90 0.68
56 33 0.25
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (55 bp):
TTGAAAACTATAATTATTATACATTATGTTGAAAATTTAGTTATTACACGTCATA
Found at i:20478297 original size:27 final size:27
Alignment explanation
Indices: 20478130--20478300 Score: 117
Period size: 27 Copynumber: 6.3 Consensus size: 27
20478120 AAAAATTAAG
* *
20478130 TTGAAAATATAATTATTATACATTATG
1 TTGAAAATATAATTATTATACGTTATA
* * * * * * *
20478157 TTAAAAATTTAGTTATTACATGCTATGT
1 TTGAAAATATAATTATTATACGTTAT-A
*
20478185 TTAAAAATATAATTATTATACGTTATA
1 TTGAAAATATAATTATTATACGTTATA
* * * * *
20478212 TTGAAGATTTAGTTGTTATACGTCATA
1 TTGAAAATATAATTATTATACGTTATA
* * ** *
20478239 TTGAAAACTATAATTGTTGTATATTATG
1 TTGAAAA-TATAATTATTATACGTTATA
* * *
20478267 TTGAAAATTTAGTTATTACACGTTATA
1 TTGAAAATATAATTATTATACGTTATA
20478294 TTGAAAA
1 TTGAAAA
20478301 ACTGTAATTG
Statistics
Matches: 106, Mismatches: 36, Indels: 4
0.73 0.25 0.03
Matches are distributed among these distances:
27 65 0.61
28 41 0.39
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (27 bp):
TTGAAAATATAATTATTATACGTTATA
Found at i:20478364 original size:55 final size:55
Alignment explanation
Indices: 20478270--20478376 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 55
20478260 TATTATGTTG
* * *
20478270 AAAATTTAGTTATTACACGTTATATTGAAAAACTGTAATT-GTTACATGTCATGAT
1 AAAATTTAGTTATTACACGTCATATTAAAAAAATGTAATTAG-TACATGTCATGAT
* *
20478325 AAAATTTTTGTTATTACACGTCATGTTAAAAAAAT-TAATTAGTACATGTCAT
1 AAAA-TTTAGTTATTACACGTCATATTAAAAAAATGTAATTAGTACATGTCAT
20478377 AATGAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 19 0.42
56 26 0.58
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (55 bp):
AAAATTTAGTTATTACACGTCATATTAAAAAAATGTAATTAGTACATGTCATGAT
Found at i:20488398 original size:15 final size:16
Alignment explanation
Indices: 20488378--20488408 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20488368 GGAGACAAAT
20488378 AAGAGC-AGAAAAGTG
1 AAGAGCAAGAAAAGTG
20488393 AAGAGCAAGAAAAGTG
1 AAGAGCAAGAAAAGTG
20488409 TTGTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGCAAGAAAAGTG
Found at i:20493695 original size:15 final size:16
Alignment explanation
Indices: 20493675--20493705 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20493665 AGAGATAAAT
20493675 AAGAGC-AGAAAAGTG
1 AAGAGCAAGAAAAGTG
20493690 AAGAGCAAGAAAAGTG
1 AAGAGCAAGAAAAGTG
20493706 TTTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGCAAGAAAAGTG
Found at i:20497928 original size:2 final size:2
Alignment explanation
Indices: 20497921--20497959 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20497911 CTGATTGCGC
20497921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20497960 GACTTCCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20503009 original size:3 final size:3
Alignment explanation
Indices: 20503003--20503028 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20502993 CTCTGCGCCT
20503003 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
20503029 TGGTTTCTTT
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:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20506269 original size:70 final size:70
Alignment explanation
Indices: 20506156--20506291 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
20506146 ATCAATCAAT
* *
20506156 AAAATGAATCATATCACAAGTTAGAGTGATTGAGCTCAAAACAGTGACTCTGACAGAACTTAAAA
1 AAAATGAATCACATCACAAGTTAGAGTGATTGAGCTCAAAACAGCGACTCTGACAGAACTTAAAA
20506221 AAAAA
66 AAAAA
* *
20506226 AAAATGAATCACATCACAAGTTTGAGTGATTGAGTTCAAAACAGCGACTCTGACAGAACTTAAAA
1 AAAATGAATCACATCACAAGTTAGAGTGATTGAGCTCAAAACAGCGACTCTGACAGAACTTAAAA
20506291 A
66 A
20506292 TAAGACACAG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22
Consensus pattern (70 bp):
AAAATGAATCACATCACAAGTTAGAGTGATTGAGCTCAAAACAGCGACTCTGACAGAACTTAAAA
AAAAA
Found at i:20512854 original size:6 final size:6
Alignment explanation
Indices: 20512835--20512870 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
20512825 TCGACGAGAG
*
20512835 TGCTCC TGCACC TGCTCC TGCTCC TGCTCC TGCTCC
1 TGCTCC TGCTCC TGCTCC TGCTCC TGCTCC TGCTCC
20512871 CACTGGCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.50, G:0.17, T:0.31
Consensus pattern (6 bp):
TGCTCC
Found at i:20523719 original size:18 final size:19
Alignment explanation
Indices: 20523685--20523720 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20523675 ATGCTCTGTA
*
20523685 AAATTATTTTTATAATTAG
1 AAATTATTTTGATAATTAG
20523704 AAATTATTTTGA-AATTA
1 AAATTATTTTGATAATTA
20523721 ACAAGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
AAATTATTTTGATAATTAG
Found at i:20524530 original size:22 final size:22
Alignment explanation
Indices: 20524502--20524576 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
20524492 GCCACGCAAA
*
20524502 ACTTAAAAATTAGTCACATAAT
1 ACTTAAAAATTAGTCACGTAAT
*
20524524 ACTTAAAAATTAGTCACGCAAT
1 ACTTAAAAATTAGTCACGTAAT
** *
20524546 A-TCTAAAAATCGGTTACGTAAT
1 ACT-TAAAAATTAGTCACGTAAT
20524568 ACTTAAAAA
1 ACTTAAAAA
20524577 CCACAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.96
23 1 0.02
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (22 bp):
ACTTAAAAATTAGTCACGTAAT
Found at i:20528298 original size:2 final size:2
Alignment explanation
Indices: 20528286--20528356 Score: 94
Period size: 2 Copynumber: 37.0 Consensus size: 2
20528276 ATAAATCTAC
20528286 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* **
20528327 TA -A GA -A GN TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20528357 AAAGAGAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:20545554 original size:21 final size:21
Alignment explanation
Indices: 20545524--20545580 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
20545514 TAGTTTTTAG
* *
20545524 ACATTGCGTGACTGACTTTGA
1 ACATTACGTGACTGAATTTGA
* * *
20545545 ATATTACGTGACTAAATTTGG
1 ACATTACGTGACTGAATTTGA
*
20545566 GCATTACGTGACTGA
1 ACATTACGTGACTGA
20545581 TTTTTGATAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (21 bp):
ACATTACGTGACTGAATTTGA
Found at i:20545676 original size:74 final size:70
Alignment explanation
Indices: 20545565--20545856 Score: 282
Period size: 69 Copynumber: 4.0 Consensus size: 70
20545555 ACTAAATTTG
* *
20545565 GGCATTACGTGACTGATTTTTGATAAAGCATTGCGTGACTAGTTTTTGATAAAGCATTGCGTGAC
1 GGCATTACGTGACT-A--GTTGAT-AGGCATTGCGTGACTA--TTTT--TAAAGCATTGCGTGAC
20545630 TAGTTTTTGATAA
58 TAGTTTTTGATAA
* * * * *
20545643 GGAATTACGTGACTATTTAATAGGCATTGCGTGACTAGTTTTTGATAAGGTATTGCATGACTAGT
1 GGCATTACGTGACTAGTTGATAGGCATTGCGTGACTA-TTTTT-A-AA-GCATTGCGTGACTAGT
*
20545708 TTATGATAA
62 TTTTGATAA
* ** * * *
20545717 AGCATTACGTGACTAGTTGATAGGCATTGCGTGACTA-ACTTAAGGCATTGTGTGACTAGTTTCT
1 GGCATTACGTGACTAGTTGATAGGCATTGCGTGACTATTTTTAAAGCATTGCGTGACTAGTTTTT
20545781 GATAA
66 GATAA
* * * ** *
20545786 GGCATTATGTGACTAGTTGATAGGTATTACGTGACTAACTTTAGA-CATTGCGTGACTAGTTTTT
1 GGCATTACGTGACTAGTTGATAGGCATTGCGTGACTATTTTTAAAGCATTGCGTGACTAGTTTTT
20545850 GATAA
66 GATAA
20545855 GG
1 GG
20545857 TATTGTGTGA
Statistics
Matches: 182, Mismatches: 28, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
69 78 0.43
70 4 0.02
71 2 0.01
72 3 0.02
73 6 0.03
74 70 0.38
75 5 0.03
77 1 0.01
78 13 0.07
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.37
Consensus pattern (70 bp):
GGCATTACGTGACTAGTTGATAGGCATTGCGTGACTATTTTTAAAGCATTGCGTGACTAGTTTTT
GATAA
Found at i:20545683 original size:48 final size:48
Alignment explanation
Indices: 20545565--20545822 Score: 206
Period size: 48 Copynumber: 5.3 Consensus size: 48
20545555 ACTAAATTTG
* *
20545565 GGCATTACGTGACT-GATTTTTGATAAAGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTACGTGACTAG-TTTTTGATAAGGCATTGCGTGACTA---TTTAAT-A
* * * *
20545617 AGCATTGCGTGACTAGTTTTTGATAAGGAATTACGTGACTATTTAATA
1 GGCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACTATTTAATA
* * *
20545665 GGCATTGCGTGACTAGTTTTTGATAAGGTATTGCATGACTAGTTTATGATAA
1 GGCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACTA-TTTA--AT-A
* *
20545717 AGCATTACGTGACTAG---TTGAT-AGGCATTGCGTGACTAACTT-A-A
1 GGCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACT-ATTTAATA
** * ** * *
20545760 GGCATTGTGTGACTAGTTTCTGATAAGGCATTATGTGACTAGTTGATA
1 GGCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACTATTTAATA
*
20545808 GGTATTACGTGACTA
1 GGCATTACGTGACTA
20545823 ACTTTAGACA
Statistics
Matches: 169, Mismatches: 25, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
43 14 0.08
45 1 0.01
46 7 0.04
47 14 0.08
48 66 0.39
49 15 0.09
51 2 0.01
52 49 0.29
53 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (48 bp):
GGCATTACGTGACTAGTTTTTGATAAGGCATTGCGTGACTATTTAATA
Found at i:20545796 original size:26 final size:26
Alignment explanation
Indices: 20545565--20545898 Score: 228
Period size: 26 Copynumber: 13.7 Consensus size: 26
20545555 ACTAAATTTG
*
20545565 GGCATTACGTGACT-GATTTTTGATAA
1 GGCATTGCGTGACTAG-TTTTTGATAA
*
20545591 AGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
*
20545617 AGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * *
20545643 GGAATTACGTGACTA---TTTAAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
20545665 GGCATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * *
20545691 GGTATTGCATGACTAGTTTATGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* *
20545717 AGCATTACGTGACTAG---TTGAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
**
20545739 GGCATTGCGTGACTA---ACT--TAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* *
20545760 GGCATTGTGTGACTAGTTTCTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
**
20545786 GGCATTATGTGACTAG---TTGAT-A
1 GGCATTGCGTGACTAGTTTTTGATAA
* * **
20545808 GGTATTACGTGACTA--ACTT--T-A
1 GGCATTGCGTGACTAGTTTTTGATAA
*
20545829 GACATTGCGTGACTAGTTTTTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * * * *
20545855 GGTATTGTGTGATTAATTTCTGATAA
1 GGCATTGCGTGACTAGTTTTTGATAA
* * *
20545881 GACATTGCATAACTAGTT
1 GGCATTGCGTGACTAGTT
20545899 GATGGGCATT
Statistics
Matches: 245, Mismatches: 44, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.00
21 29 0.12
22 43 0.18
23 17 0.07
24 2 0.01
25 6 0.02
26 146 0.60
27 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.37
Consensus pattern (26 bp):
GGCATTGCGTGACTAGTTTTTGATAA
Found at i:20545866 original size:69 final size:69
Alignment explanation
Indices: 20545618--20545856 Score: 289
Period size: 69 Copynumber: 3.4 Consensus size: 69
20545608 TTTTGATAAA
* * * *
20545618 GCATTGCGTGACTAGTTTTTGATAAGGAATTACGTGACTATTTAATAGGCATTGCGTGACTAGTT
1 GCATTGCGTGACTAGTTTTTGATAAGGCATTACGTGACTAGTTGATAGGCATTGCGTGACTA--A
*
20545683 TTTGATAAG
64 CTT--T-AG
* * * *
20545692 GTATTGCATGACTAGTTTATGATAAAGCATTACGTGACTAGTTGATAGGCATTGCGTGACTAACT
1 GCATTGCGTGACTAGTTTTTGATAAGGCATTACGTGACTAGTTGATAGGCATTGCGTGACTAACT
*
20545757 TAAG
66 TTAG
* * * * *
20545761 GCATTGTGTGACTAGTTTCTGATAAGGCATTATGTGACTAGTTGATAGGTATTACGTGACTAACT
1 GCATTGCGTGACTAGTTTTTGATAAGGCATTACGTGACTAGTTGATAGGCATTGCGTGACTAACT
20545826 TTAG
66 TTAG
*
20545830 ACATTGCGTGACTAGTTTTTGATAAGG
1 GCATTGCGTGACTAGTTTTTGATAAGG
20545857 TATTGTGTGA
Statistics
Matches: 143, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
69 86 0.60
72 2 0.01
74 55 0.38
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (69 bp):
GCATTGCGTGACTAGTTTTTGATAAGGCATTACGTGACTAGTTGATAGGCATTGCGTGACTAACT
TTAG
Found at i:20545932 original size:23 final size:23
Alignment explanation
Indices: 20545904--20546055 Score: 223
Period size: 23 Copynumber: 6.6 Consensus size: 23
20545894 TAGTTGATGG
20545904 GCATTGCGTGACTTGTTAGTAAA
1 GCATTGCGTGACTTGTTAGTAAA
*
20545927 GTATTGCGTGACTTGTTAGTAAA
1 GCATTGCGTGACTTGTTAGTAAA
* * *
20545950 GTATTGCGTAACTTGTTAGCAAA
1 GCATTGCGTGACTTGTTAGTAAA
* *
20545973 ACATTGTGTGACTTGTTAGTAAA
1 GCATTGCGTGACTTGTTAGTAAA
*
20545996 GCATTGCGCGACTTGTTAGTAAA
1 GCATTGCGTGACTTGTTAGTAAA
*
20546019 GCATTGCGCGACTTGTTAGTAAA
1 GCATTGCGTGACTTGTTAGTAAA
*
20546042 GCATTACGTGACTT
1 GCATTGCGTGACTT
20546056 AGGCATTGCT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 116 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (23 bp):
GCATTGCGTGACTTGTTAGTAAA
Found at i:20546122 original size:22 final size:22
Alignment explanation
Indices: 20546066--20546122 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
20546056 AGGCATTGCT
*
20546066 TAAAAA-TCAGTCACGTAATGCC
1 TAAAAACT-AGTCACGTAATGAC
* *
20546088 T-AAAACCAATCACGTAATGAC
1 TAAAAACTAGTCACGTAATGAC
20546109 TAAAAACTAGTCAC
1 TAAAAACTAGTCAC
20546123 ACGATGATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.21
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGAC
Found at i:20548848 original size:15 final size:16
Alignment explanation
Indices: 20548814--20548848 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
20548804 ATGATTTGGC
*
20548814 TTCTGCATCACCTAGT
1 TTCTGCATCAACTAGT
20548830 TTCTGCATCAACT-GT
1 TTCTGCATCAACTAGT
20548845 TTCT
1 TTCT
20548849 CTACATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (16 bp):
TTCTGCATCAACTAGT
Found at i:20568478 original size:21 final size:23
Alignment explanation
Indices: 20568431--20568479 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
20568421 TTAATTATAA
20568431 ATTTTATATTATATAAAAATACT
1 ATTTTATATTATATAAAAATACT
* *
20568454 -TTTTATATT-TTTAAAAAT-TT
1 ATTTTATATTATATAAAAATACT
20568474 ATTTTA
1 ATTTTA
20568480 ATGAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 13 0.57
22 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTATATTATATAAAAATACT
Found at i:20585187 original size:23 final size:24
Alignment explanation
Indices: 20585158--20585212 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
20585148 TATAATTTAT
20585158 TTTTATTTT-TAAAAATTTTAAAA
1 TTTTATTTTATAAAAATTTTAAAA
*
20585181 TTTTATTTTGATAAAACTTTTAAAA
1 TTTTATTTT-ATAAAAATTTTAAAA
20585206 TTCTTAT
1 TT-TTAT
20585213 AACATACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 9 0.32
25 15 0.54
26 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTATTTTATAAAAATTTTAAAA
Found at i:20586395 original size:74 final size:74
Alignment explanation
Indices: 20586235--20586385 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
20586225 AAACTTTGCC
20586235 GCAAAAACAAAAGCAAAGACTACAAGTAGAAAGCAACCCAAGCTAGACAGCATAAGAAATAGGAA
1 GCAAAAACAAAAGCAAAGACTACAAGTAGAAAGCAACCCAAGCTAGACAGCATAAGAAATAGGAA
20586300 TCCAAAAAA
66 TCCAAAAAA
20586309 GCAAAAACAAAAGCAAAGACTACAAGTAGAAAGCAACCCAAGCTAGACAGCATAAGAAATAGGAA
1 GCAAAAACAAAAGCAAAGACTACAAGTAGAAAGCAACCCAAGCTAGACAGCATAAGAAATAGGAA
20586374 TCCAAAAAA
66 TCCAAAAAA
20586383 GCA
1 GCA
20586386 TGCAGAAAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.56, C:0.19, G:0.17, T:0.08
Consensus pattern (74 bp):
GCAAAAACAAAAGCAAAGACTACAAGTAGAAAGCAACCCAAGCTAGACAGCATAAGAAATAGGAA
TCCAAAAAA
Done.