Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 123 of 125
Found at i:38931600 original size:2 final size:2
Alignment explanation
Indices: 38931576--38931637 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
38931566 AACACTATCG
* *
38931576 TA TA TT TA TA -A TC TA TA -A 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
38931616 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
38931638 AATGTATGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38931923 original size:26 final size:27
Alignment explanation
Indices: 38931873--38931925 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
38931863 TATGATATAA
38931873 TGTCAAATTTAGTTTTAATATTTTTTT
1 TGTCAAATTTAGTTTTAATATTTTTTT
*
38931900 TGTC-AATTTAGCTTTTATTATTTTTT
1 TGTCAAATTTAG-TTTTAATATTTTTT
38931926 AGCTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.64
Consensus pattern (27 bp):
TGTCAAATTTAGTTTTAATATTTTTTT
Found at i:38931934 original size:27 final size:26
Alignment explanation
Indices: 38931877--38931935 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
38931867 ATATAATGTC
*
38931877 AAATTTAGTTTTAATATTTTTTTTGT
1 AAATTTAGTTTTAATATTTTTTTAGT
* *
38931903 CAATTTAGCTTTTATTA-TTTTTTAGCT
1 AAATTTAG-TTTTAATATTTTTTTAG-T
38931930 AAATTT
1 AAATTT
38931936 GATATTCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (26 bp):
AAATTTAGTTTTAATATTTTTTTAGT
Found at i:38932303 original size:46 final size:46
Alignment explanation
Indices: 38932252--38932341 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
38932242 TTTTTTCTAA
38932252 ATTTTACATAAAATAAAATAAATAATCTTATAGTGATGATTGTTAG
1 ATTTTACATAAAATAAAATAAATAATCTTATAGTGATGATTGTTAG
38932298 ATTTTACATAAAATAAAATAAATAATCTTATAGTGATGATTGTT
1 ATTTTACATAAAATAAAATAAATAATCTTATAGTGATGATTGTT
38932342 GTTTTATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (46 bp):
ATTTTACATAAAATAAAATAAATAATCTTATAGTGATGATTGTTAG
Found at i:38932993 original size:2 final size:2
Alignment explanation
Indices: 38932986--38933012 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38932976 TATTAAATTG
38932986 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38933013 AACATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38937844 original size:23 final size:21
Alignment explanation
Indices: 38937792--38937845 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
38937782 TTAATCTATG
38937792 ATAAATTTATATTTAACTTTT
1 ATAAATTTATATTTAACTTTT
* *
38937813 AAAATATTTATAATTTAATTTTTT
1 ATAA-ATTTAT-ATTTAA-CTTTT
*
38937837 TTAAATTTA
1 ATAAATTTA
38937846 CCCCTAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 11 0.42
24 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAAATTTATATTTAACTTTT
Found at i:38941690 original size:11 final size:11
Alignment explanation
Indices: 38941641--38941690 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
38941631 TTTAAAAACA
38941641 TAATTTAAATT
1 TAATTTAAATT
38941652 TAAATTTAAATT
1 T-AATTTAAATT
*
38941664 T-ATTTAACAGT
1 TAATTTAA-ATT
*
38941675 T-ATTTAATTT
1 TAATTTAAATT
38941685 TAATTT
1 TAATTT
38941691 TTAAATTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.24
11 14 0.42
12 11 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:38942539 original size:22 final size:21
Alignment explanation
Indices: 38942514--38942558 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
38942504 AATTGAACTT
38942514 AAATTTTAAAAATAAAAAAATA
1 AAATTTTAAAAA-AAAAAAATA
*
38942536 AAATTTTAAAAAATAAAAATA
1 AAATTTTAAAAAAAAAAAATA
38942557 AA
1 AA
38942559 TAAACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATTTTAAAAAAAAAAAATA
Found at i:38942544 original size:29 final size:29
Alignment explanation
Indices: 38942512--38942584 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
38942502 ACAATTGAAC
38942512 TTAAATTTTAAAAATAAA-AAAATAAAATT
1 TTAAATTTTAAAAATAAATAAAAT-AAATT
*** *
38942541 TTAAAAAATAAAAATAAATAAACTAAATT
1 TTAAATTTTAAAAATAAATAAAATAAATT
38942570 TTAAATTTATAAAAA
1 TTAAATTT-TAAAAA
38942585 GTATCAAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
TTAAATTTTAAAAATAAATAAAATAAATT
Found at i:38943258 original size:7 final size:7
Alignment explanation
Indices: 38943246--38943282 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
38943236 ATATTTTACC
38943246 ATTTTAA
1 ATTTTAA
38943253 ATTTTAA
1 ATTTTAA
*
38943260 ACTTTAA
1 ATTTTAA
38943267 ATTTTAA
1 ATTTTAA
*
38943274 ATTCTAA
1 ATTTTAA
38943281 AT
1 AT
38943283 GCGGGAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (7 bp):
ATTTTAA
Found at i:38946392 original size:14 final size:14
Alignment explanation
Indices: 38946350--38946392 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
38946340 GTATATGATT
*
38946350 TTAAAATT-ATTTT
1 TTAAAATTAATTTA
38946363 TTAAAATATAAATTTA
1 TTAAAAT-T-AATTTA
38946379 TTAAAATTAATTTA
1 TTAAAATTAATTTA
38946393 AAATTCATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 1 0.04
16 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAAATTAATTTA
Found at i:38947208 original size:22 final size:20
Alignment explanation
Indices: 38947149--38947209 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 20
38947139 AAATTAAAAA
* *
38947149 TTAAAATTATTTAATAATATTT
1 TTAAAA-TATTT-TTAATAATT
*
38947171 TTAAAAATAATTTTAATAATT
1 TT-AAAATATTTTTAATAATT
38947192 TTAAAATCATTTGTTAAT
1 TTAAAAT-ATTT-TTAAT
38947210 GTGATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 11 0.34
23 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAAATATTTTTAATAATT
Found at i:38948494 original size:24 final size:23
Alignment explanation
Indices: 38948459--38948503 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
38948449 TATAGATTTA
38948459 AACTTAAAGTTTAATTGATATAT
1 AACTTAAAGTTTAATTGATATAT
* * *
38948482 AACTCTAATGTTTTATTTATAT
1 AACT-TAAAGTTTAATTGATAT
38948504 TATATTTAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
AACTTAAAGTTTAATTGATATAT
Found at i:38953153 original size:32 final size:32
Alignment explanation
Indices: 38953117--38953180 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
38953107 TCATATATGC
*
38953117 AAACTGTTGCGTAATCAATCACTAGAAAACAG
1 AAACTGTTGCATAATCAATCACTAGAAAACAG
38953149 AAACTGTTGCATAATCAATCACTAGAAAACAG
1 AAACTGTTGCATAATCAATCACTAGAAAACAG
38953181 CAAAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (32 bp):
AAACTGTTGCATAATCAATCACTAGAAAACAG
Found at i:38956607 original size:31 final size:31
Alignment explanation
Indices: 38956572--38956639 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
38956562 CACATAATGG
38956572 TCACTAAACTATTCAAAAATATTCATTTAAA
1 TCACTAAACTATTCAAAAATATTCATTTAAA
* * * *
38956603 TCACTAAACTATTCAAAAGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAATATTCATTTAAA
38956634 TCACTA
1 TCACTA
38956640 GACTGTTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAATATTCATTTAAA
Found at i:38957730 original size:161 final size:160
Alignment explanation
Indices: 38957534--38958176 Score: 729
Period size: 161 Copynumber: 4.0 Consensus size: 160
38957524 ATCCGGACCC
* * * **
38957534 GGGACTTATTTCGATTGATTCATTCAGTTACCTTTAAAAGATGGCATCGGACATATACGGGGTTC
1 GGGACTTATTTCGATTGATTCATCCAATCACCTTTAAAAGATGGCATCCAACATATACGGGGTTC
* * * *
38957599 GGATACCAATATCTATACCAAAA-GCTAAACTTTTAATCATTTGAGGTGTATTGAAAATTCAAAG
66 GAATCCCAATATCTATACCAAAAGGGT-AACTTTTAATCATTTG-GGTGTATTGAAAATTCAGAG
* * *
38957663 AATGTGTCGTGGTGCTAAGAATATGCTCGGAT
129 AATGTGTCATGGTGCTAAAAATGTGCTCGGAT
* * * * * *
38957695 GGGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATTCGACATATATGGGGTTT
1 GGGACTTATTTCGATTGATTCATCCAATCACCTTTAAAAGATGGCATCCAACATATACGGGGTTC
* * *
38957760 GAATCCCAATATCTATA-CAATAAGGGTAAGTTTTAATCATTTGGGTGTATCGAAAACTCAGAGA
66 GAATCCCAATATCTATACCAA-AAGGGTAACTTTTAATCATTTGGGTGTATTGAAAATTCAGAGA
* * * *
38957824 ATGTGTCGTCGTGCAAAAAAATGTGCTCGTAT
130 ATGTGTCATGGTGC-TAAAAATGTGCTCGGAT
* * ** * * * **
38957856 GGGACTTATTTCGAGTGATTCGTTTAATCACCTTTAAAAGATGACACCCAACAGATTTGGGGTT-
1 GGGACTTATTTCGATTGATTCATCCAATCACCTTTAAAAGATGGCATCCAACATATACGGGGTTC
* * * *
38957920 GAATCCCAATATCTGTACCAAAAGGGAAACTTTTAATCATTTGGGTGCAATGAAAATTCAGAGAA
66 GAATCCCAATATCTATACCAAAAGGGTAACTTTTAATCATTTGGGTGTATTGAAAATTCAGAGAA
* * * *
38957985 TGTGTCACGGCGCTAAAAATGTGCTCGAAA
131 TGTGTCATGGTGCTAAAAATGTGCTCGGAT
* * * * *
38958015 GGGACTTCTTTCGATTGATTCATCCAATTATCTTTAAAAGGATGGTATCCAACATATTTC-GGGT
1 GGGACTTATTTCGATTGATTCATCCAATCACCTTTAAAA-GATGGCATCCAACATA-TACGGGGT
* * *
38958079 TCGAGTCCCAATATCTATACCAAAAGGGTAACTTCTAATCATTTGGGTGTATTG-AAAGTCTAGA
64 TCGAATCCCAATATCTATACCAAAAGGGTAACTTTTAATCATTTGGGTGTATTGAAAATTC-AGA
*
38958143 GAATGTGTCATGGTGATAAAAATGTGCTCGGAT
128 GAATGTGTCATGGTGCTAAAAATGTGCTCGGAT
38958176 G
1 G
38958177 ACAATGAATA
Statistics
Matches: 405, Mismatches: 69, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
159 46 0.11
160 119 0.29
161 238 0.59
162 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (160 bp):
GGGACTTATTTCGATTGATTCATCCAATCACCTTTAAAAGATGGCATCCAACATATACGGGGTTC
GAATCCCAATATCTATACCAAAAGGGTAACTTTTAATCATTTGGGTGTATTGAAAATTCAGAGAA
TGTGTCATGGTGCTAAAAATGTGCTCGGAT
Found at i:38958120 original size:321 final size:321
Alignment explanation
Indices: 38957534--38958172 Score: 800
Period size: 321 Copynumber: 2.0 Consensus size: 321
38957524 ATCCGGACCC
* * * * * ** *
38957534 GGGACTTATTTCGATTGATTCATTCAGTTACCTTTAAAAGATGGCATCGGACATATACGGGGTTC
1 GGGACTTATTTCGAGTGATTCATTCAATCACCTTTAAAAGATGACACCCAACAGATACGGGGTTC
* * * *
38957599 GGATACCAATATCTATACCAAAAGCTAAACTTTTAATCATTTGAGGTGTATTGAAAATTCAAAGA
66 GAATACCAATATCTATACCAAAAGCGAAACTTTTAATCATTTGAGGTGCAATGAAAATTCAAAGA
** * * * * * *
38957664 ATGTGTCGTGGTGCTAAGAATATGCTCGGATGGGATTTATTTCGATTGATTCATCCAGTCACCTT
131 ATGTGTCACGGCGCTAAAAATATGCTCGAAAGGGACTTATTTCGATTGATTCATCCAATCACCTT
* * * * * *
38957729 TAAAAGATGGCATTCGACATATATGGGGTTTGAATCCCAATATCTATACAATAAGGGTAAGTTTT
196 TAAAAGATGGCATCCAACATATATCGGGTTCGAATCCCAATATCTATACAATAAGGGTAACTTCT
*
38957794 AATCATTTGGGTGTATCGAAAACTC-AGAGAATGTGTCGTCGTGCAAAAAAATGTGCTCGTAT
261 AATCATTTGGGTGTATCG-AAACTCTAGAGAATGTGTCATCGTG-AAAAAAATGTGCTCGTAT
* * **
38957856 GGGACTTATTTCGAGTGATTCGTTTAATCACCTTTAAAAGATGACACCCAACAGATTTGGGGTT-
1 GGGACTTATTTCGAGTGATTCATTCAATCACCTTTAAAAGATGACACCCAACAGATACGGGGTTC
* * * *
38957920 GAATCCCAATATCTGTACCAAAAGGGAAACTTTTAATCATTTG-GGTGCAATGAAAATTCAGAGA
66 GAATACCAATATCTATACCAAAAGCGAAACTTTTAATCATTTGAGGTGCAATGAAAATTCAAAGA
* * * *
38957984 ATGTGTCACGGCGCTAAAAATGTGCTCGAAAGGGACTTCTTTCGATTGATTCATCCAATTATCTT
131 ATGTGTCACGGCGCTAAAAATATGCTCGAAAGGGACTTATTTCGATTGATTCATCCAATCACCTT
* * *
38958049 TAAAAGGATGGTATCCAACATATTTCGGGTTCGAGTCCCAATATCTATACCAA-AAGGGTAACTT
196 TAAAA-GATGGCATCCAACATATATCGGGTTCGAATCCCAATATCTATA-CAATAAGGGTAACTT
* * * *
38958113 CTAATCATTTGGGTGTATTGAAAGTCTAGAGAATGTGTCATGGTGATAAAAATGTGCTCG
259 CTAATCATTTGGGTGTATCGAAACTCTAGAGAATGTGTCATCGTGAAAAAAATGTGCTCG
38958173 GATGACAATG
Statistics
Matches: 268, Mismatches: 46, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
320 95 0.35
321 118 0.44
322 55 0.21
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (321 bp):
GGGACTTATTTCGAGTGATTCATTCAATCACCTTTAAAAGATGACACCCAACAGATACGGGGTTC
GAATACCAATATCTATACCAAAAGCGAAACTTTTAATCATTTGAGGTGCAATGAAAATTCAAAGA
ATGTGTCACGGCGCTAAAAATATGCTCGAAAGGGACTTATTTCGATTGATTCATCCAATCACCTT
TAAAAGATGGCATCCAACATATATCGGGTTCGAATCCCAATATCTATACAATAAGGGTAACTTCT
AATCATTTGGGTGTATCGAAACTCTAGAGAATGTGTCATCGTGAAAAAAATGTGCTCGTAT
Found at i:38969349 original size:22 final size:21
Alignment explanation
Indices: 38969309--38969358 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
38969299 ATATTTGTAA
* *
38969309 TTTTTAAATTGATCCAATATAT
1 TTTTTATATTGATCAAATAT-T
*
38969331 TTTTTATATTGATTAAATATT
1 TTTTTATATTGATCAAATATT
*
38969352 TATTTAT
1 TTTTTAT
38969359 TGCTTTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTTATATTGATCAAATATT
Found at i:38972362 original size:19 final size:20
Alignment explanation
Indices: 38972322--38972365 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
38972312 AGAAAATAGT
38972322 TTTTATTAATATTTATATAA
1 TTTTATTAATATTTATATAA
38972342 TTTTATT-AT-TTTATAATAA
1 TTTTATTAATATTTAT-ATAA
38972361 TTTTA
1 TTTTA
38972366 AATAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 11 0.48
20 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTAATATTTATATAA
Found at i:38972365 original size:11 final size:10
Alignment explanation
Indices: 38972322--38972370 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
38972312 AGAAAATAGT
38972322 TTTTAT-TAA
1 TTTTATATAA
38972331 TATTTATATAA
1 T-TTTATATAA
38972342 TTTTAT-T-A
1 TTTTATATAA
38972350 TTTTATAATAA
1 TTTTAT-ATAA
*
38972361 TTTTAAATAA
1 TTTTATATAA
38972371 AAATCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 15 0.44
11 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTATATAA
Found at i:38976184 original size:19 final size:20
Alignment explanation
Indices: 38976157--38976195 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
38976147 AAAGCTCTTT
*
38976157 TTTATTTTTTCTTTT-ATAA
1 TTTAGTTTTTCTTTTCATAA
*
38976176 TTTAGTTTTTTTTTTCATAA
1 TTTAGTTTTTCTTTTCATAA
38976196 AACAACTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTAGTTTTTCTTTTCATAA
Found at i:38976186 original size:20 final size:19
Alignment explanation
Indices: 38976157--38976195 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
38976147 AAAGCTCTTT
38976157 TTTATTTTTTCTTTT-ATAA
1 TTTATTTTTT-TTTTCATAA
38976176 TTTAGTTTTTTTTTTCATAA
1 TTTA-TTTTTTTTTTCATAA
38976196 AACAACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTTTTTTTTTCATAA
Found at i:38981612 original size:2 final size:2
Alignment explanation
Indices: 38981605--38981652 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
38981595 CAAGCAAATA
38981605 AT 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 AT
38981647 AT AT AT
1 AT AT AT
38981653 TATTTTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38984044 original size:222 final size:216
Alignment explanation
Indices: 38983601--38984052 Score: 568
Period size: 227 Copynumber: 2.0 Consensus size: 216
38983591 TTCAAAATCT
* * *
38983601 TATATATATGAACTAGAAGATCAAACATCACCAGAACTCCTTCACTATGTATGCACTATGAACTT
1 TATATATATGAACTAGAAGATCAAACATCACCAGAACTCCATCACTATGCATGAACTATGAACTT
* * **
38983666 ACCATTGTTATATTTTGCTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTTCAAATTTT
66 ACCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTCCAAATTCA
* * *
38983731 AAACTTTCTCAAATAGTTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAAAATTAGCCA
131 AAACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACTAATCAAGTT-AAAAATTAGCAA
*
38983796 AAAAACTTCAAAACATTATATA
195 AAAAACATCAAAACATTATATA
* * *
38983818 TATATATATGAACTAGAAGATCAATAAAGCATCACTAGCACTCCATCACTATGCATGAATTATGA
1 TATATATATGAACTAGAAGATC---AAA-CATCACCAGAACTCCATCACTATGCATGAACTATGA
* *
38983883 ACTTAACCATTGTTATATTTTACTACTAAAATCTACACCTGAACCTGATATAAATTACAGTTTTA
62 ACTT-ACCATTGTTATATTTTACTACTAAAATCTACACCTG-A----A-ACAAATTACAGTTTCA
* * *
38983948 TTCCAAGTTCAAAAC-TTCTCAAATAGGTTCCATTAAAACTCTCATATTATA-TCAATCAAGTT-
120 TTCCAAATTCAAAACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACT-AATCAAGTTA
* *
38984010 AAATTTAGCAAAAGAAACATCAAAATATTATATA
184 AAAATTAGCAAAA-AAACATCAAAACATTATATA
38984044 TATATATAT
1 TATATATAT
38984053 ATATATGAAC
Statistics
Matches: 201, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
217 22 0.11
220 3 0.01
221 34 0.17
222 35 0.17
223 1 0.00
225 11 0.05
226 28 0.14
227 42 0.21
228 25 0.12
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.33
Consensus pattern (216 bp):
TATATATATGAACTAGAAGATCAAACATCACCAGAACTCCATCACTATGCATGAACTATGAACTT
ACCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTCCAAATTCA
AAACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACTAATCAAGTTAAAAATTAGCAAA
AAAACATCAAAACATTATATA
Found at i:38984106 original size:222 final size:215
Alignment explanation
Indices: 38983601--38984241 Score: 528
Period size: 201 Copynumber: 3.0 Consensus size: 215
38983591 TTCAAAATCT
* * * *
38983601 TATATATATGAACTAGAAGAT---C-AAACATCACCAGAACTCCTTCACTATGTATGCACTATGA
1 TATATATATGAACTAGAAGATCAACAAAACATCACTAGCACTCC-ACACTA--CATG-A-TATGA
* *
38983662 ACTTACCATTGTTATATTTTGCTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTTCAAA
61 ACTTACCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTCCAAA
** * *
38983727 TTTTAAACTTTCTCAAATAGTTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAAAATTA
126 TTCAAAACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACTAATCAAGTT-AAAAATTA
* *
38983792 GCCAAAAAACTTCAAAACATTATATA
190 GCAAAAAAACATCAAAACATTATATA
* *
38983818 TATATATATGAACTAGAAGATCAATAAAGCATCACTAGCACTCCATCACTATGCATGAATTATGA
1 TATATATATGAACTAGAAGATCAACAAAACATCACTAGCACTCCA-CACTA--CATG-A-TATGA
* *
38983883 ACTTAACCATTGTTATATTTTACTACTAAAATCTACACCTGAACCTGATATAAATTACAGTTTTA
61 ACTT-ACCATTGTTATATTTTACTACTAAAATCTACACCTG-A----A-ACAAATTACAGTTTCA
* * *
38983948 TTCCAAGTTCAAAAC-TTCTCAAATAGGTTCCATTAAAACTCTCATATTATA-TCAATCAAGTT-
119 TTCCAAATTCAAAACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACT-AATCAAGTTA
* *
38984010 AAATTTAGCAAAAGAAACATCAAAATATTATATATATATA
183 AAAATTAGCAAAA-AAACATC--AA-A--ACAT-TATATA
*
38984050 TATATATATGAACTAGAAGATCAACAAAACATCACTATCACT-C-CACTA-A-G-TATGAAC-T-
1 TATATATATGAACTAGAAGATCAACAAAACATCACTAGCACTCCACACTACATGATATGAACTTA
* * * * * *
38984108 --A-TG---------ACTGCTAAAATCTACATCTGATATAATTTACAGTTTCATTTCAAATTCAA
66 CCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTCCAAATTCAA
* * * * *
38984161 AAC-TTCTTAAATAGGTTCCATTCAAACTCTTATATGATACCAATCAAGTT-AAAATTAGCAAAA
131 AACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACTAATCAAGTTAAAAATTAGCAAAA
* *
38984224 GAAACTTCAAAATATTAT
196 -AAACATCAAAACATTAT
38984242 CAAGTTAAAA
Statistics
Matches: 363, Mismatches: 40, Indels: 64
0.78 0.09 0.14
Matches are distributed among these distances:
195 3 0.01
196 4 0.01
198 1 0.00
199 2 0.01
201 87 0.24
206 1 0.00
207 18 0.05
216 2 0.01
217 22 0.06
221 36 0.10
222 42 0.12
223 1 0.00
225 12 0.03
226 8 0.02
227 42 0.12
228 27 0.07
229 6 0.02
231 4 0.01
232 45 0.12
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (215 bp):
TATATATATGAACTAGAAGATCAACAAAACATCACTAGCACTCCACACTACATGATATGAACTTA
CCATTGTTATATTTTACTACTAAAATCTACACCTGAAACAAATTACAGTTTCATTCCAAATTCAA
AACTTTCTCAAATAGGTTCCATTAAAACACTCATATGATACTAATCAAGTTAAAAATTAGCAAAA
AAACATCAAAACATTATATA
Found at i:38988776 original size:23 final size:23
Alignment explanation
Indices: 38988746--38988799 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
38988736 ACGCTAGCGC
38988746 GCTTACTGTTTCGCACTTCATGT
1 GCTTACTGTTTCGCACTTCATGT
* *
38988769 GCTTACTGTTTTGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCATGT
*
38988792 GCCTACTG
1 GCTTACTG
38988800 ATTTGCGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCATGT
Found at i:38988862 original size:23 final size:22
Alignment explanation
Indices: 38988766--38988864 Score: 101
Period size: 23 Copynumber: 4.4 Consensus size: 22
38988756 TCGCACTTCA
*
38988766 TGTGCTTACTGTTTTGCACT-TCG
1 TGTGCTTACTG-ATTGCACTGT-G
* * *
38988789 TGTGCCTACTGATTTGCGCTATG
1 TGTGCTTACTGA-TTGCACTGTG
* *
38988812 TGCGCCTACTGATTGCACTGTG
1 TGTGCTTACTGATTGCACTGTG
38988834 TGTGCTTACTGGATTGCACTGTG
1 TGTGCTTACT-GATTGCACTGTG
38988857 TGTGCTTA
1 TGTGCTTA
38988865 TTGTTTCCTC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 16 0.25
23 48 0.74
24 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.40
Consensus pattern (22 bp):
TGTGCTTACTGATTGCACTGTG
Found at i:38989802 original size:9 final size:9
Alignment explanation
Indices: 38989790--38989979 Score: 93
Period size: 10 Copynumber: 20.0 Consensus size: 9
38989780 TTTATGATTT
38989790 TTTTTATAA
1 TTTTTATAA
38989799 TTTTTATAAA
1 TTTTTAT-AA
* *
38989809 TTTATATCA
1 TTTTTATAA
*
38989818 TTTTTAATAT
1 TTTTT-ATAA
38989828 TTTTTCCATAA
1 TTTTT--ATAA
38989839 TTTTTTATAA
1 -TTTTTATAA
*
38989849 TTTTTCATTAT
1 TTTTT-A-TAA
*
38989860 TTTTTAAGAA
1 TTTTT-ATAA
* *
38989870 TTCTAATATA
1 TTTTTATA-A
38989880 TTTTT-TAA
1 TTTTTATAA
**
38989888 TTTAAAT-A
1 TTTTTATAA
*
38989896 TTTTAAGTAA
1 TTTTTA-TAA
38989906 TTTTTATTAA
1 TTTTTA-TAA
38989916 -TTTTATAA
1 TTTTTATAA
38989924 TTTTTTTATAA
1 --TTTTTATAA
* *
38989935 CTTATTAGAA
1 -TTTTTATAA
38989945 TTTATTATAA
1 TTT-TTATAA
38989955 -TTTTATAA
1 TTTTTATAA
*
38989963 -TATTATAA
1 TTTTTATAA
38989971 TTTTTATAA
1 TTTTTATAA
38989980 CTTATTAGTG
Statistics
Matches: 138, Mismatches: 28, Indels: 30
0.70 0.14 0.15
Matches are distributed among these distances:
8 26 0.19
9 39 0.28
10 49 0.36
11 19 0.14
12 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38989843 original size:21 final size:20
Alignment explanation
Indices: 38989789--38989863 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 20
38989779 TTTTATGATT
*
38989789 TTTTTTATAATTTTT-ATAAA
1 TTTTTCATAATTTTTAAT-AA
* * *
38989809 TTTAT-ATCATTTTTAATAT
1 TTTTTCATAATTTTTAATAA
*
38989828 TTTTTCCATAATTTTTTATAA
1 TTTTT-CATAATTTTTAATAA
*
38989849 TTTTTCATTATTTTT
1 TTTTTCATAATTTTT
38989864 TAAGAATTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 13 0.30
20 15 0.34
21 16 0.36
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTCATAATTTTTAATAA
Found at i:38989871 original size:21 final size:22
Alignment explanation
Indices: 38989818--38989871 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
38989808 ATTTATATCA
*
38989818 TTTTTAATATTTTTTCCATAAT
1 TTTTTAATAATTTTTCCATAAT
*
38989840 TTTTT-ATAATTTTT-CATTAT
1 TTTTTAATAATTTTTCCATAAT
*
38989860 TTTTTAAGAATT
1 TTTTTAATAATT
38989872 CTAATATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAATAATTTTTCCATAAT
Found at i:38989916 original size:10 final size:9
Alignment explanation
Indices: 38989903--38989979 Score: 61
Period size: 8 Copynumber: 8.3 Consensus size: 9
38989893 ATATTTTAAG
38989903 TAATTTTTA
1 TAATTTTTA
38989912 TTAA-TTTTA
1 -TAATTTTTA
38989921 TAATTTTTTTA
1 TAA--TTTTTA
*
38989932 TAACTTATTA
1 TAA-TTTTTA
*
38989942 GAATTTATTA
1 TAATTT-TTA
38989952 TAA-TTTTA
1 TAATTTTTA
*
38989960 TAA-TATTA
1 TAATTTTTA
38989968 TAATTTTTA
1 TAATTTTTA
38989977 TAA
1 TAA
38989980 CTTATTAGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
8 16 0.29
9 16 0.29
10 15 0.27
11 8 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (9 bp):
TAATTTTTA
Found at i:38989924 original size:18 final size:18
Alignment explanation
Indices: 38989903--38989963 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
38989893 ATATTTTAAG
38989903 TAATTTTTATTAATTTTA
1 TAATTTTTATTAATTTTA
*
38989921 TAATTTTTTTATAACTTATTA
1 TAATTTTTAT-TAA-TT-TTA
*
38989942 GAATTTATTA-TAATTTTA
1 TAATTT-TTATTAATTTTA
38989960 TAAT
1 TAAT
38989964 ATTATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 15 0.43
19 5 0.14
20 5 0.14
21 8 0.23
22 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TAATTTTTATTAATTTTA
Found at i:38989958 original size:28 final size:25
Alignment explanation
Indices: 38989927--38989979 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
38989917 TTTATAATTT
38989927 TTTTATAACTTATTAGAATTTATTATAA
1 TTTTATAA--TATTAGAATTT-TTATAA
*
38989955 TTTTATAATATTATAATTTTTATAA
1 TTTTATAATATTAGAATTTTTATAA
38989980 CTTATTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 10 0.42
28 8 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTTATAATATTAGAATTTTTATAA
Found at i:38989995 original size:47 final size:48
Alignment explanation
Indices: 38989907--38990001 Score: 124
Period size: 47 Copynumber: 2.0 Consensus size: 48
38989897 TTTAAGTAAT
*
38989907 TTTTATTAATTTTATAATTTTTTTATAACTTATTAGAATTTAT-TATAA
1 TTTTATTAATATTATAA-TTTTTTATAACTTATTAGAATTTATATATAA
*
38989955 TTTTA-TAATATTATAA-TTTTTATAACTTATTAGTGTATTTATATATA
1 TTTTATTAATATTATAATTTTTTATAACTTATTA--GAATTTATATATA
38990002 TATATATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
45 16 0.38
47 17 0.40
48 9 0.21
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (48 bp):
TTTTATTAATATTATAATTTTTTATAACTTATTAGAATTTATATATAA
Found at i:38992690 original size:46 final size:48
Alignment explanation
Indices: 38992637--38992734 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 48
38992627 TCTATCGATG
* * *
38992637 ATTTTATTTAAATCAAAATAA-TTTAACTGAATTTTAAAGATTAA-TA
1 ATTTTATTTAAATAAAAAAAAGTTTAACTAAATTTTAAAGATTAATTA
*
38992683 ATTTTATTTAAATAAAAAAAAGTTTAACTAAATTTTAAAGTTTAATTA
1 ATTTTATTTAAATAAAAAAAAGTTTAACTAAATTTTAAAGATTAATTA
38992731 ATTT
1 ATTT
38992735 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 19 0.41
47 21 0.46
48 6 0.13
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (48 bp):
ATTTTATTTAAATAAAAAAAAGTTTAACTAAATTTTAAAGATTAATTA
Found at i:38993793 original size:17 final size:15
Alignment explanation
Indices: 38993760--38993789 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38993750 ACCCTATAAA
38993760 ATACTTATTAATTTT
1 ATACTTATTAATTTT
38993775 ATACTTATTAATTTT
1 ATACTTATTAATTTT
38993790 TTATTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
ATACTTATTAATTTT
Found at i:39000770 original size:2 final size:2
Alignment explanation
Indices: 39000763--39000789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39000753 TGGAGATGAA
39000763 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39000790 AACAAGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39008285 original size:23 final size:22
Alignment explanation
Indices: 39008254--39008311 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
39008244 TTTATTTAAA
* *
39008254 TGTACTTTAATTATTAGTTTGAT
1 TGTAATTTAATTATGAGTTT-AT
*
39008277 TGTAATTT-ATAATGAGTTTAT
1 TGTAATTTAATTATGAGTTTAT
*
39008298 TTTAATTATAATTA
1 TGTAATT-TAATTA
39008312 CTCAAACATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 8 0.29
22 10 0.36
23 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (22 bp):
TGTAATTTAATTATGAGTTTAT
Found at i:39008304 original size:21 final size:21
Alignment explanation
Indices: 39008269--39008309 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39008259 TTTAATTATT
39008269 AGTTTGATTGTAATTTATAATG
1 AGTTTGATTGTAA-TTATAATG
*
39008291 AGTTT-ATTTTAATTATAAT
1 AGTTTGATTGTAATTATAAT
39008310 TACTCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (21 bp):
AGTTTGATTGTAATTATAATG
Found at i:39009060 original size:21 final size:21
Alignment explanation
Indices: 39009034--39009083 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
39009024 AAATATGAAA
39009034 TTAATTCAAACTCGAAGTAAC
1 TTAATTCAAACTCGAAGTAAC
39009055 TTAATTCAAACTCGAAGTAAC
1 TTAATTCAAACTCGAAGTAAC
39009076 TTAATTCA
1 TTAATTCA
39009084 GAACCACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (21 bp):
TTAATTCAAACTCGAAGTAAC
Found at i:39014844 original size:30 final size:30
Alignment explanation
Indices: 39014783--39014853 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
39014773 ACAACAAGAG
* * * *
39014783 GACTATTTTATCACTTTTCGAAATTTTAGT
1 GACTGTTTTGTCACTTTTCGAAAGTTGAGT
*
39014813 GATTGTTTTGTCACATTTTC-AAAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGAAAGTTGAGT
39014843 GACTGTTTTGT
1 GACTGTTTTGT
39014854 TAAATTTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (30 bp):
GACTGTTTTGTCACTTTTCGAAAGTTGAGT
Found at i:39018030 original size:42 final size:42
Alignment explanation
Indices: 39017958--39018108 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
39017948 GAGCTTGAAC
* * * *
39017958 GAGCCTAT-GGGAACTGACCGGAGGGGCACCAATAACCTGCCT
1 GAGCCTATAGGG-ACTGACCAGAGGGTCACCAAGAACTTGCCT
* *
39018000 GAGTCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGACT
1 GAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCT
* * * * * *
39018042 GAGCCTATGGGGAATGACCAAAGTGTCACAAAGAGCTTGCCT
1 GAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCT
39018084 GAGCCTATAGGGACTGACCAGAGGG
1 GAGCCTATAGGGACTGACCAGAGGG
39018109 ACTTGCCTGA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 87 0.97
43 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (42 bp):
GAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCT
Found at i:39018178 original size:75 final size:75
Alignment explanation
Indices: 39018034--39018178 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 75
39018024 GTCACCAAGA
* * * *
39018034 ACTTGACTGAGCCTATGGGGAATGACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACT
1 ACTTGACTGAGCCTATGGGGAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATAGGGACC
39018099 GACCAGAGGG
66 GACCAGAGGG
* * * *
39018109 ACTTGCCTGAGCCTATGGGGACTGACCAAAGTGTCCCAAGGACCTTGCCTAAGCCAAT-GGAGAC
1 ACTTGACTGAGCCTATGGGGAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATAGG-GAC
39018173 CGACCA
65 CGACCA
39018179 ACGTATCACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.03
75 59 0.97
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (75 bp):
ACTTGACTGAGCCTATGGGGAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATAGGGACC
GACCAGAGGG
Found at i:39018199 original size:42 final size:42
Alignment explanation
Indices: 39018110--39018199 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
39018100 ACCAGAGGGA
* * * * * * *
39018110 CTTGCCTGAGCCTATGGGGACTGACCAAAGTGTCCCAAGGAC
1 CTTGCCTAAGCCAATGGAGACCGACCAAAGTATCACAAAGAC
*
39018152 CTTGCCTAAGCCAATGGAGACCGACCAACGTATCACAAAGAC
1 CTTGCCTAAGCCAATGGAGACCGACCAAAGTATCACAAAGAC
*
39018194 TTTGCC
1 CTTGCC
39018200 CGAGCCTACA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (42 bp):
CTTGCCTAAGCCAATGGAGACCGACCAAAGTATCACAAAGAC
Found at i:39018205 original size:117 final size:117
Alignment explanation
Indices: 39017995--39018207 Score: 268
Period size: 117 Copynumber: 1.8 Consensus size: 117
39017985 ACCAATAACC
* * * * * *
39017995 TGCCTGAGTCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGACTGAGCCTATGGGGAATGAC
1 TGCCTGAGCCTATAGGGACTGACCAAAGGGTCACCAAGAACTTGACTAAGCCAATGGAGAACGAC
* *
39018060 CAAAGTGTCACAAAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGGGACT
66 CAAAGTATCACAAAGAGCTTGCCCGAGCCTATAGGGACTGACCAGAGGGACT
* * * * *
39018112 TGCCTGAGCCTATGGGGACTGACCAAAGTGTC-CCAAGGACCTTGCCTAAGCCAATGGAGACCGA
1 TGCCTGAGCCTATAGGGACTGACCAAAGGGTCACCAA-GAACTTGACTAAGCCAATGGAGAACGA
*
39018176 CCAACGTATCACAAAGA-CTTTGCCCGAGCCTA
65 CCAAAGTATCACAAAGAGC-TTGCCCGAGCCTA
39018208 CAGAGATTGG
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
116 5 0.06
117 75 0.94
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (117 bp):
TGCCTGAGCCTATAGGGACTGACCAAAGGGTCACCAAGAACTTGACTAAGCCAATGGAGAACGAC
CAAAGTATCACAAAGAGCTTGCCCGAGCCTATAGGGACTGACCAGAGGGACT
Found at i:39027923 original size:19 final size:19
Alignment explanation
Indices: 39027901--39027955 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
39027891 TGAATCAAAA
*
39027901 TTAACATTTAAAATCATAT
1 TTAAAATTTAAAATCATAT
* *
39027920 TTAATATTT--AGTCAATAT
1 TTAAAATTTAAAATC-ATAT
*
39027938 TAAAAATTTAAAATCATA
1 TTAAAATTTAAAATCATA
39027956 CATATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 11 0.39
20 3 0.11
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAAATTTAAAATCATAT
Found at i:39039004 original size:13 final size:14
Alignment explanation
Indices: 39038981--39039012 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
39038971 TTAAATGCTA
39038981 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
39038995 AAAAAA-TAAAAAT
1 AAAAAATTAAAAAT
39039008 AAAAA
1 AAAAA
39039013 TTACCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Found at i:39041027 original size:141 final size:141
Alignment explanation
Indices: 39040769--39041058 Score: 481
Period size: 141 Copynumber: 2.1 Consensus size: 141
39040759 ACCACCGCCG
* * * * **
39040769 CCACCTCCGCCTCCTGCAGCTGCATTTCGTAAACCAAGGCGAAGTTATCAAGTTGTTGGCCGGAA
1 CCACCGCCGCCTCCTGCACCTGAATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGGAA
*
39040834 AGACAATGTGAATAATACTCAGAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCCTC
66 AGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCCTC
39040899 AGCCAGTAACA
131 AGCCAGTAACA
39040910 CCACCGCCGCCTCCTGCACCTGAATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGGAA
1 CCACCGCCGCCTCCTGCACCTGAATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGGAA
** *
39040975 AGGGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAACTGAGTCTCCGGCTCCTC
66 AGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCCTC
*
39041040 AGCCAGTAACG
131 AGCCAGTAACA
39041051 CCACCGCC
1 CCACCGCC
39041059 ACCGCCGCCT
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (141 bp):
CCACCGCCGCCTCCTGCACCTGAATATCGTAAACCAAGGCGAAGTTATCAAACTGTTGGCCGGAA
AGACAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAATGAGTCTCCGGCTCCTC
AGCCAGTAACA
Found at i:39050072 original size:18 final size:19
Alignment explanation
Indices: 39050030--39050072 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
39050020 AATTATAAAT
39050030 TTTAAAAATTAAAACAATA
1 TTTAAAAATTAAAACAATA
*
39050049 TATAAAAA-TAAAA-AAGTA
1 TTTAAAAATTAAAACAA-TA
39050067 TTTAAA
1 TTTAAA
39050073 TTTTTGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TTTAAAAATTAAAACAATA
Found at i:39053721 original size:56 final size:56
Alignment explanation
Indices: 39053635--39053747 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
39053625 AAAGTTCAAA
39053635 TTACAATTTATCTTTAGATAAAAATATGTTTTTACCATTACACTTATTTATAATTT
1 TTACAATTTATCTTTAGATAAAAATATGTTTTTACCATTACACTTATTTATAATTT
39053691 TTACAATTTATCTTTAGATAAAAATATGTTTTTACCATTACACTTATTTATAATTT
1 TTACAATTTATCTTTAGATAAAAATATGTTTTTACCATTACACTTATTTATAATTT
39053747 T
1 T
39053748 AAAAACTTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (56 bp):
TTACAATTTATCTTTAGATAAAAATATGTTTTTACCATTACACTTATTTATAATTT
Found at i:39054891 original size:30 final size:31
Alignment explanation
Indices: 39054808--39054896 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
39054798 ATATTTAATG
*
39054808 TATCATTATATTAAATTATTTAAATATCATT
1 TATCATTATGTTAAATTATTTAAATATCATT
* *
39054839 TATCATTATGTTAAATTGTTTAAATGTCATT
1 TATCATTATGTTAAATTATTTAAATATCATT
* * *
39054870 TATTA-TATGTTTAATTTTTTAAGATAT
1 TATCATTATGTTAAATTATTTAA-ATAT
39054897 TTTATACAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.30
31 35 0.70
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (31 bp):
TATCATTATGTTAAATTATTTAAATATCATT
Found at i:39055746 original size:21 final size:21
Alignment explanation
Indices: 39055722--39055765 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
39055712 CAAAAAAAAG
39055722 GAGAATAATAATAACAATAAA
1 GAGAATAATAATAACAATAAA
39055743 GAGAATAATAATAACAATAAA
1 GAGAATAATAATAACAATAAA
39055764 GA
1 GA
39055766 AAAGGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (21 bp):
GAGAATAATAATAACAATAAA
Found at i:39056281 original size:2 final size:2
Alignment explanation
Indices: 39056276--39056302 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39056266 ATATATATAT
39056276 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39056303 ACAAGAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39057206 original size:31 final size:31
Alignment explanation
Indices: 39057171--39057239 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
39057161 CATAGCAGGC
*
39057171 CAATGACTTAAATAAAAAATTGTAAATAGTT
1 CAATGACTTAAATAAAAAATTGTAAATAATT
* * * *
39057202 CAATGACTTAAATGAAAACTTTTGAATAATT
1 CAATGACTTAAATAAAAAATTGTAAATAATT
39057233 CAATGAC
1 CAATGAC
39057240 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAAATTGTAAATAATT
Found at i:39059090 original size:6 final size:6
Alignment explanation
Indices: 39059079--39059119 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
39059069 GGGTAATATA
39059079 ACCCGG ACCCGG A-CCGG ACCCGG ACCCGG ACCCGG ACCCGG
1 ACCCGG ACCCGG ACCCGG ACCCGG ACCCGG ACCCGG ACCCGG
39059120 TTACCTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.17, C:0.49, G:0.34, T:0.00
Consensus pattern (6 bp):
ACCCGG
Found at i:39059097 original size:11 final size:11
Alignment explanation
Indices: 39059081--39059116 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
39059071 GTAATATAAC
39059081 CCGGACCCGGA
1 CCGGACCCGGA
39059092 CCGGACCCGGA
1 CCGGACCCGGA
39059103 CCCGGACCCGGA
1 -CCGGACCCGGA
39059115 CC
1 CC
39059117 CGGTTACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.17, C:0.50, G:0.33, T:0.00
Consensus pattern (11 bp):
CCGGACCCGGA
Found at i:39059101 original size:17 final size:18
Alignment explanation
Indices: 39059079--39059119 Score: 75
Period size: 17 Copynumber: 2.3 Consensus size: 18
39059069 GGGTAATATA
39059079 ACCCGGACCCGGA-CCGG
1 ACCCGGACCCGGACCCGG
39059096 ACCCGGACCCGGACCCGG
1 ACCCGGACCCGGACCCGG
39059114 ACCCGG
1 ACCCGG
39059120 TTACCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.17, C:0.49, G:0.34, T:0.00
Consensus pattern (18 bp):
ACCCGGACCCGGACCCGG
Found at i:39078278 original size:15 final size:16
Alignment explanation
Indices: 39078258--39078287 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39078248 GTTCTTTGGG
39078258 TTGTTTTTTT-TTTGT
1 TTGTTTTTTTCTTTGT
39078273 TTGTTTTTTTCTTTG
1 TTGTTTTTTTCTTTG
39078288 GGTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.83
Consensus pattern (16 bp):
TTGTTTTTTTCTTTGT
Found at i:39082600 original size:13 final size:14
Alignment explanation
Indices: 39082582--39082616 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39082572 CTGGTATTTC
39082582 TTTTTATAT-TTAT
1 TTTTTATATATTAT
39082595 TTTTTATATATTAT
1 TTTTTATATATTAT
39082609 TTTTTATA
1 TTTTTATA
39082617 GTATAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTATATATTAT
Found at i:39082626 original size:19 final size:19
Alignment explanation
Indices: 39082599--39082635 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39082589 ATTTATTTTT
* *
39082599 TATATATTATTTTTTATAG
1 TATAAATTATATTTTATAG
39082618 TATAAATTATATTTTATA
1 TATAAATTATATTTTATA
39082636 CAATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TATAAATTATATTTTATAG
Found at i:39095809 original size:13 final size:14
Alignment explanation
Indices: 39095769--39095809 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
39095759 TTAATTCAAC
39095769 TTAAAATTGAATAA
1 TTAAAATTGAATAA
39095783 TT--AATTGAATTAA
1 TTAAAATTGAA-TAA
39095796 TTAAAATT-AATAA
1 TTAAAATTGAATAA
39095809 T
1 T
39095810 ATATTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.29
13 9 0.38
14 4 0.17
15 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
TTAAAATTGAATAA
Found at i:39101166 original size:19 final size:20
Alignment explanation
Indices: 39101128--39101166 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
39101118 AAAAGAAGAA
*
39101128 AATTCCAATTTTTACGATAT
1 AATTCCAATGTTTACGATAT
*
39101148 AATTCCAA-GTTTACTATAT
1 AATTCCAATGTTTACGATAT
39101167 GTCTGAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTCCAATGTTTACGATAT
Found at i:39103819 original size:23 final size:24
Alignment explanation
Indices: 39103766--39103812 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
39103756 TACTAGCCTC
39103766 TTTATTTTAATCCATGTTTTAATAA
1 TTTATTTTAATCCA-GTTTTAATAA
*
39103791 TTTATTTTAATCGA-TTTTAATA
1 TTTATTTTAATCCAGTTTTAATA
39103813 TATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTATTTTAATCCAGTTTTAATAA
Found at i:39103884 original size:13 final size:15
Alignment explanation
Indices: 39103829--39103887 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
39103819 TAAAAACTCT
*
39103829 TATATTA-TTAAATTA
1 TATATTATTTTAA-TA
39103844 TATTATTATTCTTAATA
1 TA-TATTATT-TTAATA
*
39103861 TATATTGTTTTAATA
1 TATATTATTTTAATA
39103876 -AT-TTATTTTAAT
1 TATATTATTTTAAT
39103888 CGATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 8 0.21
16 11 0.29
17 5 0.13
18 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATTATTTTAATA
Found at i:39103921 original size:86 final size:86
Alignment explanation
Indices: 39103780--39103952 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
39103770 TTTTAATCCA
39103780 TGTTTTAATAATTTATTTTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTAT
1 TGTTTTAATAATTTATTTTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTAT
39103845 ATTATTATTCTTAATATATAT
66 ATTATTATTCTTAATATATAT
39103866 TGTTTTAATAATTTATTTTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTAT
1 TGTTTTAATAATTTATTTTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTAT
39103931 ATTATTATTCTTAATATATAT
66 ATTATTATTCTTAATATATAT
39103952 T
1 T
39103953 TTTAATCGTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (86 bp):
TGTTTTAATAATTTATTTTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTAT
ATTATTATTCTTAATATATAT
Found at i:39103996 original size:86 final size:86
Alignment explanation
Indices: 39103797--39103970 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 86
39103787 ATAATTTATT
* * *
39103797 TTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTATATTATTATTCTTAATAT
1 TTAATCGATTTGAAAAAATTATTAAAAACTCTTATATTATTAAATTATATTATTATTCTTAATAT
* * **
39103862 ATATTGTTTTAATAATTTATT
66 ATATTGTTTTAATAAGTAAGC
* * *
39103883 TTAATCGATTTTAATATATTATTAAAAACTCTTATATTATTAAATTATATTATTATTCTTAATAT
1 TTAATCGATTTGAAAAAATTATTAAAAACTCTTATATTATTAAATTATATTATTATTCTTAATAT
*
39103948 ATA-T-TTTTAAT-CGTAAGC
66 ATATTGTTTTAATAAGTAAGC
39103966 TTAAT
1 TTAAT
39103971 TATTGAACCA
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
83 7 0.08
84 7 0.08
85 1 0.01
86 68 0.82
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (86 bp):
TTAATCGATTTGAAAAAATTATTAAAAACTCTTATATTATTAAATTATATTATTATTCTTAATAT
ATATTGTTTTAATAAGTAAGC
Found at i:39108367 original size:15 final size:15
Alignment explanation
Indices: 39108339--39108368 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39108329 TTACGAAATA
39108339 AATATATTATTTTTT
1 AATATATTATTTTTT
39108354 AATATCATTATTTTT
1 AATAT-ATTATTTTT
39108369 GGATACTATA
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:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
AATATATTATTTTTT
Found at i:39109392 original size:18 final size:19
Alignment explanation
Indices: 39109371--39109406 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
39109361 TTTAAAAAAT
39109371 TATAATTTTTT-AATTTTA
1 TATAATTTTTTAAATTTTA
39109389 TATAATTTTTTAAATTTT
1 TATAATTTTTTAAATTTT
39109407 TTAGGTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATAATTTTTTAAATTTTA
Found at i:39109398 original size:19 final size:18
Alignment explanation
Indices: 39109371--39109406 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39109361 TTTAAAAAAT
*
39109371 TATAATTTTTTAATTTTA
1 TATAATTTTTAAATTTTA
39109389 TATAATTTTTTAAATTTT
1 TATAA-TTTTTAAATTTT
39109407 TTAGGTGATG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATAATTTTTAAATTTTA
Found at i:39110237 original size:19 final size:19
Alignment explanation
Indices: 39110197--39110253 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
39110187 TACAAAATAA
*
39110197 TCAAAATAATTTTAAAAAAAT
1 TCAAAATAATTTT--TAAAAT
*
39110218 TGAAAATAATTTTTAAAAT
1 TCAAAATAATTTTTAAAAT
*
39110237 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTTTAAAA
39110254 ATTCTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.28
19 11 0.34
21 12 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
TCAAAATAATTTTTAAAAT
Found at i:39110254 original size:19 final size:20
Alignment explanation
Indices: 39110197--39110262 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
39110187 TACAAAATAA
*
39110197 TCAAAATAATTTTAAAAAAAT
1 TCAAAATAA-TTTATAAAAAT
* *
39110218 TGAAAATAATTT-TTAAAAT
1 TCAAAATAATTTATAAAAAT
39110237 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTTATAAAAAT
*
39110256 TCTAAAT
1 TCAAAAT
39110263 TTTGTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 4 0.11
19 23 0.61
20 3 0.08
21 8 0.21
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (20 bp):
TCAAAATAATTTATAAAAAT
Found at i:39111093 original size:30 final size:32
Alignment explanation
Indices: 39111044--39111111 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
39111034 TTGACAGCAT
39111044 AGTGACTTAAATAAAAAC-TTTCGAAT-AGTTC
1 AGTGACTTAAATAAAAACTTTTCGAATCA-TTC
*
39111075 AGTGACTTAAAT-AAAACTTTTTGAATCATTC
1 AGTGACTTAAATAAAAACTTTTCGAATCATTC
39111106 AGTGAC
1 AGTGAC
39111112 CAATTTGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.15
31 28 0.82
32 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (32 bp):
AGTGACTTAAATAAAAACTTTTCGAATCATTC
Found at i:39111432 original size:21 final size:21
Alignment explanation
Indices: 39111406--39111454 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
39111396 CTAAAATTGT
* *
39111406 GTCACATAGTGCAATCTTTGA
1 GTCACACAGTACAATCTTTGA
39111427 GTCACACAGTACAATCTTTGA
1 GTCACACAGTACAATCTTTGA
39111448 GTCACAC
1 GTCACAC
39111455 GTCACCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (21 bp):
GTCACACAGTACAATCTTTGA
Found at i:39113184 original size:22 final size:22
Alignment explanation
Indices: 39113138--39113185 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
39113128 AAATTCAAAT
*
39113138 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAACATA
39113160 TAAATATTAA-TATATAAAACA-A
1 TAAAT-TTAATTATA-AAAACATA
39113182 TAAA
1 TAAA
39113186 ACGAGCGTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATTTAATTATAAAAACATA
Found at i:39118617 original size:2 final size:2
Alignment explanation
Indices: 39118610--39118646 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39118600 GACTTTCATA
39118610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39118647 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39118651 original size:2 final size:2
Alignment explanation
Indices: 39118646--39118719 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
39118636 ATATATATAT
39118646 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39118688 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39118720 GAACATAGTG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39120185 original size:33 final size:34
Alignment explanation
Indices: 39120131--39120208 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
39120121 TTTTGGTTTA
*
39120131 ATTTATTTA-TATGTATAATATTATAT-TCAATTT
1 ATTTATATATTATGTATAATATTATATCT-AATTT
* *
39120164 ATTTATATATTATTTAT-ATATTATATCTATTTT
1 ATTTATATATTATGTATAATATTATATCTAATTT
39120197 ATTTTATATATT
1 A-TTTATATATT
39120209 CTAAATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
33 22 0.56
34 17 0.44
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (34 bp):
ATTTATATATTATGTATAATATTATATCTAATTT
Found at i:39120189 original size:18 final size:17
Alignment explanation
Indices: 39120163--39120271 Score: 84
Period size: 17 Copynumber: 6.4 Consensus size: 17
39120153 ATATTCAATT
39120163 TATTTATATATTATTTA
1 TATTTATATATTATTTA
*
39120180 TATATTATAT-CTATTT-
1 TAT-TTATATATTATTTA
* **
39120196 TATTTTATATATTCTAAA
1 TA-TTTATATATTATTTA
39120214 TATTTGATATATT-TTTA
1 TATTT-ATATATTATTTA
*
39120231 TATTTATACATTA-TTA
1 TATTTATATATTATTTA
39120247 TTATTATATATATT-TTTA
1 -TATT-TATATATTATTTA
*
39120265 TTTTTAT
1 TATTTAT
39120272 TTTTTGTATA
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
16 20 0.27
17 28 0.38
18 25 0.34
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (17 bp):
TATTTATATATTATTTA
Found at i:39120203 original size:16 final size:15
Alignment explanation
Indices: 39120151--39120205 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
39120141 ATGTATAATA
*
39120151 TTATATTCAATTTATT
1 TTATATT-ATTTTATT
*
39120167 TATATATTATTTATATA
1 T-TATATTATTT-TATT
39120184 TTATATCTATTTTATT
1 TTATAT-TATTTTATT
39120200 TTATAT
1 TTATAT
39120206 ATTCTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATATTATTTTATT
Found at i:39120208 original size:34 final size:34
Alignment explanation
Indices: 39120148--39120290 Score: 113
Period size: 34 Copynumber: 4.3 Consensus size: 34
39120138 TATATGTATA
*
39120148 ATATTATAT-TCAATTTA-TTTATATATTATTTAT
1 ATATTATATAT-ATTTTATTTTATATATTATTTAT
* * **
39120181 ATATTATATCTATTTTATTTTATATATTCTAAAT
1 ATATTATATATATTTTATTTTATATATTATTTAT
*
39120215 AT-TTGATATAT-TTTTATATTTATACATTA-TTAT
1 ATATT-ATATATATTTTAT-TTTATATATTATTTAT
*
39120248 -TATTATATATATTTTTATTTT-TAT-TTTTTGTAT
1 ATATTATATATA-TTTTATTTTATATATTATT-TAT
*
39120281 ACATTATATA
1 ATATTATATA
39120291 CAATACAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
31 2 0.02
32 10 0.11
33 32 0.36
34 44 0.50
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (34 bp):
ATATTATATATATTTTATTTTATATATTATTTAT
Found at i:39120217 original size:23 final size:22
Alignment explanation
Indices: 39120168--39120218 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
39120158 CAATTTATTT
* *
39120168 ATATATTATTTATATATTATAT
1 ATATTTTATTTATATATTATAA
* *
39120190 CTATTTTATTTTATATATTCTAA
1 ATATTTTA-TTTATATATTATAA
39120213 ATATTT
1 ATATTT
39120219 GATATATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTTATTTATATATTATAA
Found at i:39122619 original size:17 final size:16
Alignment explanation
Indices: 39122597--39122631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
39122587 TATTGTTGAT
*
39122597 AAAAAAAAATAAAGGAC
1 AAAAAAAAA-AAAAGAC
39122614 AAAAAAAAAAAAAGAC
1 AAAAAAAAAAAAAGAC
39122630 AA
1 AA
39122632 CATTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAC
Found at i:39129820 original size:16 final size:18
Alignment explanation
Indices: 39129799--39129835 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
39129789 TTAGAGTCTG
39129799 TTAATAATT-TT-ATATA
1 TTAATAATTATTAATATA
39129815 TTAATAATTATTAATATA
1 TTAATAATTATTAATATA
39129833 TTA
1 TTA
39129836 TACTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 2 0.11
18 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATAATTATTAATATA
Found at i:39134670 original size:26 final size:27
Alignment explanation
Indices: 39134641--39134691 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39134631 AGAGAGGATG
*
39134641 ACGACAAAAG-CAAGATTAAAACTTGC
1 ACGACAAAAGACAAGATAAAAACTTGC
* *
39134667 ACGATACAAGACAAGATAAAAACTT
1 ACGACAAAAGACAAGATAAAAACTT
39134692 TTAAAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.53, C:0.18, G:0.14, T:0.16
Consensus pattern (27 bp):
ACGACAAAAGACAAGATAAAAACTTGC
Found at i:39137012 original size:30 final size:30
Alignment explanation
Indices: 39136975--39137056 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 30
39136965 TTTATAAGTT
*
39136975 AAATTTTTTTTTACCAACTTTTAAGGGCTC
1 AAATTTTTTTTTACCAACTTTTAAGGGCCC
* ** **
39137005 TAATTTTTTTTT-TTAGTTTTTAAGGGCCC
1 AAATTTTTTTTTACCAACTTTTAAGGGCCC
*
39137034 AAAATTTTTTTTACCAACTTTTA
1 AAATTTTTTTTTACCAACTTTTA
39137057 GAAGACTTAA
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (30 bp):
AAATTTTTTTTTACCAACTTTTAAGGGCCC
Found at i:39139473 original size:18 final size:19
Alignment explanation
Indices: 39139446--39139484 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
39139436 TTTAAGTTTT
*
39139446 TTTTTTGTTA-ATTTTTAA
1 TTTTTAGTTATATTTTTAA
*
39139464 TTTTTAGTTATTTTTTTAA
1 TTTTTAGTTATATTTTTAA
39139483 TT
1 TT
39139485 AAGAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTAGTTATATTTTTAA
Found at i:39139527 original size:26 final size:26
Alignment explanation
Indices: 39139489--39139540 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39139479 TTAATTAAGA
* *
39139489 AATTTGTCATTTTTAATT-TTAATTTT
1 AATTTATC-TTTTTAATTAATAATTTT
39139515 AATTTATCTTTTTAATTAATAATTTT
1 AATTTATCTTTTTAATTAATAATTTT
39139541 TTATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
AATTTATCTTTTTAATTAATAATTTT
Found at i:39139612 original size:76 final size:78
Alignment explanation
Indices: 39139523--39139669 Score: 235
Period size: 78 Copynumber: 1.9 Consensus size: 78
39139513 TTAATTTATC
* * * * *
39139523 TTTTTAATTAATAATT-TTTTATTTATATAAATAAAATAA-AAATATGTAATTATATAATGAAAA
1 TTTTTAATCAATAATTCATTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAA
39139586 TATATTTTACATA
66 TATATTTTACATA
39139599 TTTTTAATCAATAATTCATTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAA
1 TTTTTAATCAATAATTCATTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAA
39139664 TATATT
66 TATATT
39139670 ATATATAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 15 0.23
77 21 0.33
78 28 0.44
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (78 bp):
TTTTTAATCAATAATTCATTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAA
TATATTTTACATA
Found at i:39139699 original size:78 final size:75
Alignment explanation
Indices: 39139526--39139701 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 75
39139516 ATTTATCTTT
* * *
39139526 TTAATTAATAATTTTTTATTTATATAAATAAAATAAAAATATGTAATTATATAATGAAAATATAT
1 TTAATTAATAA-TTTTTATTTATATAAACAAAATAAAAATATGTAATTATACAACGAAAATATAT
* * *
39139591 TTTACATATTT
65 TATACATAATA
*
39139602 TTAATCAATAATTCATTTATTTATATAAACAAAATAATAAATATGTAATTATACAACGAAAATAT
1 TTAATTAATAATT--TTTATTTATATAAACAAAATAA-AAATATGTAATTATACAACGAAAATAT
*
39139667 ATTATATATAATA
63 ATTATACATAATA
*
39139680 TTATATTAAAAATATTTTATTT
1 TTA-ATTAATAAT-TTTTATTT
39139702 TTTTAAGAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
75 2 0.02
76 10 0.12
77 21 0.25
78 44 0.52
79 7 0.08
80 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (75 bp):
TTAATTAATAATTTTTATTTATATAAACAAAATAAAAATATGTAATTATACAACGAAAATATATT
ATACATAATA
Found at i:39142093 original size:7 final size:7
Alignment explanation
Indices: 39142045--39142089 Score: 81
Period size: 7 Copynumber: 6.3 Consensus size: 7
39142035 CGTATACCCT
39142045 TGGCTGG
1 TGGCTGG
39142052 TGGCTGG
1 TGGCTGG
39142059 TGGCTGG
1 TGGCTGG
39142066 TGGCTGG
1 TGGCTGG
39142073 TGGCTGG
1 TGGCTGG
39142080 TGGTCTGG
1 TGG-CTGG
39142088 TG
1 TG
39142090 TCTGCTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 31 0.84
8 6 0.16
ACGTcount: A:0.00, C:0.13, G:0.56, T:0.31
Consensus pattern (7 bp):
TGGCTGG
Found at i:39143149 original size:2 final size:2
Alignment explanation
Indices: 39143142--39143171 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39143132 AAAGACAGTT
39143142 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39143172 CCTTGTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39149885 original size:21 final size:22
Alignment explanation
Indices: 39149861--39149906 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39149851 GATTTTTGTG
*
39149861 AAATT-ATGAGAATTTTAAAAA
1 AAATTAATGAAAATTTTAAAAA
*
39149882 AAATTAATTAAAATTTTAAAAA
1 AAATTAATGAAAATTTTAAAAA
39149904 AAA
1 AAA
39149907 AGGTATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTAATGAAAATTTTAAAAA
Found at i:39150045 original size:55 final size:57
Alignment explanation
Indices: 39149942--39150054 Score: 142
Period size: 56 Copynumber: 2.0 Consensus size: 57
39149932 TTGGAGGTGT
*
39149942 CTAAATAAATTTTTCTAAAAACTTTAAGAAAAAAATGAAAATTTCC-AAATTGGGGC
1 CTAAATAAATTTTTCTAAAAAATTTAAGAAAAAAATGAAAATTTCCAAAATTGGGGC
* ** * *
39149998 CTAATTAAATTTTT-TAAAAAATTTAAG-GGAAAATGAAATTTTCCCAAAATTTGGGC
1 CTAAATAAATTTTTCTAAAAAATTTAAGAAAAAAATGAAAATTT-CCAAAATTGGGGC
39150054 C
1 C
39150055 CATTGGTCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 12 0.24
55 14 0.29
56 23 0.47
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (57 bp):
CTAAATAAATTTTTCTAAAAAATTTAAGAAAAAAATGAAAATTTCCAAAATTGGGGC
Found at i:39156600 original size:32 final size:30
Alignment explanation
Indices: 39156540--39156619 Score: 81
Period size: 32 Copynumber: 2.6 Consensus size: 30
39156530 ATTGTAACAA
* * * *
39156540 AATTGAAACAACAATTAATATTTTATGGTATTG
1 AATTGAAA-AAAAATTAAGAATTGATGGTA--G
39156573 AATTGAAAAAAAATTAAGAATTGATGGTAG
1 AATTGAAAAAAAATTAAGAATTGATGGTAG
39156603 ATATTG-AAAAAAATTAA
1 A-ATTGAAAAAAAATTAA
39156620 AAAGAACCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 13 0.31
31 4 0.10
32 17 0.40
33 8 0.19
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.33
Consensus pattern (30 bp):
AATTGAAAAAAAATTAAGAATTGATGGTAG
Found at i:39156903 original size:28 final size:29
Alignment explanation
Indices: 39156865--39156919 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
39156855 TTCCACTAAA
39156865 AAATAATTAG-TTTAATTTTAGTCAAAAT
1 AAATAATTAGTTTTAATTTTAGTCAAAAT
39156893 AAATAATTAGTTTTAATTTTAGTCAAA
1 AAATAATTAGTTTTAATTTTAGTCAAA
39156920 TAATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (29 bp):
AAATAATTAGTTTTAATTTTAGTCAAAAT
Found at i:39156920 original size:28 final size:28
Alignment explanation
Indices: 39156839--39156922 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 28
39156829 CTTAGATTTA
* ** *
39156839 AAATAATTAATTTTAATTCCACT-AAA-
1 AAATAATTAGTTTTAATTTTAGTCAAAT
39156865 AAATAATTAG-TTTAATTTTAGTCAAAAT
1 AAATAATTAGTTTTAATTTTAGTC-AAAT
39156893 AAATAATTAGTTTTAATTTTAGTCAAAT
1 AAATAATTAGTTTTAATTTTAGTCAAAT
39156921 AA
1 AA
39156923 TTTTTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.18
26 9 0.18
27 3 0.06
28 16 0.32
29 13 0.26
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (28 bp):
AAATAATTAGTTTTAATTTTAGTCAAAT
Found at i:39160327 original size:102 final size:102
Alignment explanation
Indices: 39160122--39160334 Score: 266
Period size: 102 Copynumber: 2.1 Consensus size: 102
39160112 GAATTTGAGT
* * * * **
39160122 GGAAATGAAATCCCGGAACCCGTTCCCCTGCAATTACCGACGAACGATGAAGTTCCTTTTGATAT
1 GGAAATGAAATCCCGGAACCAGTTCCCCGGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
* ** *
39160187 CGATAGTCTTTTAGTGGACCCGAGTGAAAATAAGTTG
66 CGATAGTCTTTTAGCGGACCAAAGAGAAAATAAGTTG
* * *
39160224 GGAAATGAAATCCCGGAACCAGTTTCCCGGAAATTACCGATGAACGATGAATTTCCTATCAATAT
1 GGAAATGAAATCCCGGAACCAGTTCCCCGGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
* * *
39160289 TGATAGTCTTTTAGCGGATCAAAGAG-AAATGAATTTG
66 CGATAGTCTTTTAGCGGACCAAAGAGAAAAT-AAGTTG
39160326 GGAAATGAA
1 GGAAATGAA
39160335 TTCCGTGTAC
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 4 0.04
102 90 0.96
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (102 bp):
GGAAATGAAATCCCGGAACCAGTTCCCCGGAAATTACCGACGAACGATGAAGTTCCTATCAATAT
CGATAGTCTTTTAGCGGACCAAAGAGAAAATAAGTTG
Found at i:39161910 original size:56 final size:58
Alignment explanation
Indices: 39161757--39161928 Score: 222
Period size: 56 Copynumber: 2.9 Consensus size: 58
39161747 CACCCACATT
* *
39161757 ATTATTTTTGGGATTTGTTTGAAATGTAGTAAAAACTACATATCCACAGTATTACTTTTGGG
1 ATTA-TTTT-GGATTTGTTTGAAATGTAGTAAAAACTAC--ATCCACACTATTATTTTTGGG
* *
39161819 ATTATTTTGGATTTGTTTGAAATGTAGTATAAACTACATCCACACTATCATTTTTGGG
1 ATTATTTTGGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTATTTTTGGG
* * * *
39161877 ATT-TTTT-TATTTGTTTGAATTGTTGTAAAAACTACATCCACATTATTATTTT
1 ATTATTTTGGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTATTTT
39161929 GGATTAATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
56 39 0.39
57 4 0.04
58 21 0.21
60 28 0.28
61 4 0.04
62 4 0.04
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (58 bp):
ATTATTTTGGATTTGTTTGAAATGTAGTAAAAACTACATCCACACTATTATTTTTGGG
Found at i:39162258 original size:67 final size:67
Alignment explanation
Indices: 39162174--39162312 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 67
39162164 TTTAAGTTTC
*
39162174 TTTTTTAAATGCAGTAAAAT-CTACATCCACATTATTATTTTTGGGATTATTTTTGTAATTTTCT
1 TTTTTTAAATACAGTAAAATAC-ACATCCACATTATTATTTTTGGGATTATTTTTGTAATTTTCT
39162238 TAT
65 TAT
39162241 TTTTTTAAATACAGTAAAATACACATCCACATTATTATTTTTGGGATTATTTTTGTAATTTTCTT
1 TTTTTTAAATACAGTAAAATACACATCCACATTATTATTTTTGGGATTATTTTTGTAATTTTCTT
39162306 AT
66 AT
39162308 TTTTT
1 TTTTT
39162313 GCAGTATTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 69 0.99
68 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (67 bp):
TTTTTTAAATACAGTAAAATACACATCCACATTATTATTTTTGGGATTATTTTTGTAATTTTCTT
AT
Found at i:39173224 original size:6 final size:6
Alignment explanation
Indices: 39173213--39173249 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
39173203 CATTGTTGAT
*
39173213 AAAGAG AAAGAG AAAGAG AAAGAG CAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
39173250 TAACAAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:39173328 original size:35 final size:31
Alignment explanation
Indices: 39173289--39173381 Score: 141
Period size: 32 Copynumber: 2.8 Consensus size: 31
39173279 TTTTCCGAAG
39173289 GAAATGAAATTCAATTATTATTTTTTAAATGAAAT
1 GAAATGAAATTCAATTATTATTTTTT---T-AAAT
39173324 GAAATGAAATTCAATTATTATTTTTTTAAAT
1 GAAATGAAATTCAATTATTATTTTTTTAAAT
39173355 GAAAATGAAATTCAATTATTATTTTTT
1 G-AAATGAAATTCAATTATTATTTTTT
39173382 GAAGTGTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
31 5 0.09
32 26 0.46
35 26 0.46
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (31 bp):
GAAATGAAATTCAATTATTATTTTTTTAAAT
Found at i:39175480 original size:57 final size:57
Alignment explanation
Indices: 39175419--39175602 Score: 185
Period size: 57 Copynumber: 3.1 Consensus size: 57
39175409 ATTTTTTGTT
* *
39175419 TTGGCCATCAAATGACCGGCACTCTCTTTTCTCGAAAAAAAATTGCATTTTTGGGTG
1 TTGGCCATCAAATGGCCGACACTCTCTTTTCTCGAAAAAAAATTGCATTTTTGGGTG
* * * * * *
39175476 TTGGCTATCAAATGGCCGACA-TCCACTGTTT-TAGAAAAAAAATTTCAAATTTTTTTGGTT
1 TTGGCCATCAAATGGCCGACACT-CTCT-TTTCTCGAAAAAAAATTGC--A-TTTTTGGGTG
*
39175536 TTGGCCATCAAATGGTCGACAC-CTCCTTTTCTCGAGAAAAAAAATTGCATTTTTGGGTG
1 TTGGCCATCAAATGGCCGACACTCT-CTTTTCTC--GAAAAAAAATTGCATTTTTGGGTG
*
39175595 TTGACCAT
1 TTGGCCAT
39175603 TGCATGGTCG
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
56 1 0.01
57 34 0.34
58 3 0.03
59 20 0.20
60 31 0.31
62 12 0.12
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (57 bp):
TTGGCCATCAAATGGCCGACACTCTCTTTTCTCGAAAAAAAATTGCATTTTTGGGTG
Found at i:39175704 original size:42 final size:45
Alignment explanation
Indices: 39175618--39175705 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 45
39175608 GGTCGACACC
* *
39175618 TCCTATTTCTTGAGAAAAAAATTCAAATTTTTTTGGTGTCGGCCA
1 TCCTATTTCTCGAGAAAAAAATTCAAATTTTTTTGATGTCGGCCA
* *
39175663 TCCT-TTTCTCGAG-AAAAAATTC-AATTTTTTTTATGTTGGCCA
1 TCCTATTTCTCGAGAAAAAAATTCAAATTTTTTTGATGTCGGCCA
39175705 T
1 T
39175706 TGCATGGCCG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 18 0.46
43 9 0.23
44 8 0.21
45 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (45 bp):
TCCTATTTCTCGAGAAAAAAATTCAAATTTTTTTGATGTCGGCCA
Found at i:39175709 original size:103 final size:104
Alignment explanation
Indices: 39175559--39175768 Score: 293
Period size: 104 Copynumber: 2.0 Consensus size: 104
39175549 GGTCGACACC
* *
39175559 TCCTTTTCTCGAGAAAAAAAATTGCATTTTTGGGTGTTGACCATTGCATGGTCGACACCT-CCTA
1 TCCTTTTCTCGAG-AAAAAAATTGCATTTTTGGATGTTGACCATTGCATGGCCGACACCTCCCT-
*
39175623 TTTCTTGAG-AAAAAAATTCAAATTTTTTTGGTGTCGGCCA
64 TTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTCGGCCA
** *
39175663 TCCTTTTCTCGAG-AAAAAATT-CAATTTTTTTTATGTTGGCCATTGCATGGCCGACACCTCCCT
1 TCCTTTTCTCGAGAAAAAAATTGC-A-TTTTTGGATGTTGACCATTGCATGGCCGACACCTCCCT
*
39175726 TTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCA
64 TTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTCGGCCA
39175767 TC
1 TC
39175769 AAATGGCCGA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
101 1 0.01
102 9 0.09
103 37 0.39
104 48 0.51
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (104 bp):
TCCTTTTCTCGAGAAAAAAATTGCATTTTTGGATGTTGACCATTGCATGGCCGACACCTCCCTTT
TCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTCGGCCA
Found at i:39175766 original size:62 final size:59
Alignment explanation
Indices: 39175664--39175782 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 59
39175654 TGTCGGCCAT
* ***
39175664 CCTTTTCTCGAGAAAAAATTCAATTTTTTTTATGTTGGCCATTGCATGGCCGACACCTC
1 CCTTTTCTCGAGAAAAAATTCAATTTTTTTGATGTTGGCCATCAAATGGCCGACACCTC
*
39175723 CCTTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
1 CCTTTTCTCGAG--AAAAAATTC-AATTTTTTTGATGTTGGCCATCAAATGGCCGACACC
39175783 AACTTCTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 12 0.23
61 9 0.17
62 31 0.60
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (59 bp):
CCTTTTCTCGAGAAAAAATTCAATTTTTTTGATGTTGGCCATCAAATGGCCGACACCTC
Found at i:39179495 original size:12 final size:12
Alignment explanation
Indices: 39179453--39179500 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
39179443 ATTTGTGTAA
*
39179453 AAATTAATTTGA
1 AAATTAATTTGG
39179465 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
39179481 AAATTAATTTGG
1 AAATTAATTTGG
39179493 AAATTAAT
1 AAATTAAT
39179501 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:39179776 original size:45 final size:44
Alignment explanation
Indices: 39179709--39179865 Score: 107
Period size: 45 Copynumber: 3.6 Consensus size: 44
39179699 ATTTAAGTAC
*
39179709 AAATTATTATTATATTACAATTTT-TATCATATAATGTGTTGATTTG
1 AAATAATTATT-TATT--AATTTTATATCATATAATGTGTTGATTTG
* * ****
39179755 ACAATACATTATTTATTAATTTTATATC-TTTAA-ATAAAAATTT-
1 A-AATA-ATTATTTATTAATTTTATATCATATAATGTGTTGATTTG
*
39179798 ---TAATTATATTA-CAATTTT-TATCATATAATGTGTTGATTTG
1 AAATAATTAT-TTATTAATTTTATATCATATAATGTGTTGATTTG
39179838 ATAATATATTATTTATTAATTTTATATC
1 A-AATA-ATTATTTATTAATTTTATATC
39179866 TTTAAATAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
37 4 0.05
38 15 0.18
39 10 0.12
44 10 0.12
45 21 0.26
46 9 0.11
47 7 0.09
48 6 0.07
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (44 bp):
AAATAATTATTTATTAATTTTATATCATATAATGTGTTGATTTG
Found at i:39179814 original size:38 final size:37
Alignment explanation
Indices: 39179772--39179902 Score: 93
Period size: 38 Copynumber: 3.3 Consensus size: 37
39179762 ATTATTTATT
39179772 AATTTTATATCTTTAAATAAAAATTTTAATTATATTAC
1 AATTTT-TATCTTTAAATAAAAATTTTAATTATATTAC
* * **** *
39179810 AATTTTTATCATATAATGTGTTGATTTGATAATATATTATTTATT
1 AATTTTTATC-TTTAA-ATAAAAATTT--TAAT-TA-TA-TTA-C
39179855 AATTTTATATCTTTAAATAAAAAATTTT-ATTATATTAC
1 AATTTT-TATCTTTAAAT-AAAAATTTTAATTATATTAC
39179893 AATTTTTATC
1 AATTTTTATC
39179903 ATATTTTAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 21
0.66 0.13 0.20
Matches are distributed among these distances:
37 8 0.12
38 16 0.23
39 8 0.12
40 2 0.03
41 6 0.09
42 4 0.06
43 3 0.04
44 4 0.06
45 14 0.20
46 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (37 bp):
AATTTTTATCTTTAAATAAAAATTTTAATTATATTAC
Found at i:39179815 original size:83 final size:82
Alignment explanation
Indices: 39179631--39179906 Score: 394
Period size: 83 Copynumber: 3.3 Consensus size: 82
39179621 AAAAAGATAG
* * * * * *
39179631 TTATTATATTACAATTTATATCAAATATTGTATTAATTTGACAATACATTATTTATCAAAATTTT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT--TAATTTT
* *
39179696 CATA--TTTAAGTACAAATT
64 -ATATCTTTAAATAAAAATT
39179714 ATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTA
1 -TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTA
39179779 TATCTTTAAATAAAAATT
65 TATCTTTAAATAAAAATT
* *
39179797 TTAATTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATATATTATTTATTAATTTTA
1 TT-ATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTA
39179862 TATCTTTAAATAAAAAATT
65 TATCTTTAAAT-AAAAATT
39179881 TTATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
39179907 TTTAAATTTC
Statistics
Matches: 178, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
81 3 0.02
82 8 0.04
83 107 0.60
84 60 0.34
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (82 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAAATT
Found at i:39180087 original size:10 final size:10
Alignment explanation
Indices: 39180070--39180109 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
39180060 ATCCCGAAAT
39180070 CGCCGTTGAC
1 CGCCGTTGAC
* *
39180080 CACCGTTGAT
1 CGCCGTTGAC
*
39180090 CGCTGTTGAC
1 CGCCGTTGAC
39180100 CGCCGTTGAC
1 CGCCGTTGAC
39180110 TGACTTTATC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (10 bp):
CGCCGTTGAC
Found at i:39180097 original size:20 final size:20
Alignment explanation
Indices: 39180068--39180108 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39180058 ACATCCCGAA
39180068 ATCGCCGTTGACCACCGTTG
1 ATCGCCGTTGACCACCGTTG
* *
39180088 ATCGCTGTTGACCGCCGTTG
1 ATCGCCGTTGACCACCGTTG
39180108 A
1 A
39180109 CTGACTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCCGTTGACCACCGTTG
Found at i:39181849 original size:12 final size:12
Alignment explanation
Indices: 39181832--39181865 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39181822 GAGCCTCAAG
* *
39181832 ACCAACCCGAGT
1 ACCAACCAGAGC
39181844 ACCAACCAGAGC
1 ACCAACCAGAGC
39181856 ACCAACCAGA
1 ACCAACCAGA
39181866 TCCCCAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.41, G:0.15, T:0.03
Consensus pattern (12 bp):
ACCAACCAGAGC
Found at i:39182003 original size:61 final size:60
Alignment explanation
Indices: 39181931--39182440 Score: 419
Period size: 61 Copynumber: 8.5 Consensus size: 60
39181921 TTTCTTAAGA
* * *
39181931 ATGGCCGATACCAAAAAAATTTGAATTTTTTTTTTCGAGAAAAGGGGGGTGTCCGCCATTTG
1 ATGGCCAACACCAAAAAAATTTGAA-TTTTTTTCTCGAGAAAAGGGGGGTGT-CGCCATTTG
* * *
39181993 AT-GCCAATACCAAAAAATTTTGAATTTTTTTCTCGAGAAAAGAGGGGATGTCGACCATTTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAG-GGGGGTGTCG-CCATTTG
* * ***
39182054 ATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTTGAGAAAA-GGGGGTGTCGACCATGCA
1 ATGGCCAACACCAAAAAAATTTGAA-TTTTTTTCTCGAGAAAAGGGGGGTGTCG-CCATTTG
* * * * ***
39182115 ATGACCAACATCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGGGGGCGTCGGCCATGCA
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTC-GCCATTTG
* * * * *
39182176 ATGGCCAACACAAAAAAAATTTGAA-ATTTTTCTTGAGAAAAAAAGAGGGGTTTCTGCCA-TTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAG---AAAAGGGGGGTGTC-GCCATTTG
* ** * * * *
39182238 CATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAAATA-AAGGATGTTG----GTC
1 -ATGGCCAACACCAAAAAAATTT-GAATTTTTTTCTCGAGAAA-AGGGGGGTGTCGCCATTTG
* *
39182296 AT---CAACACC-CAAAAATGT-AATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTC-GCCATTTG
* * *
39182351 ATGGCCAACACCAAAAAAATTTAAATTTTTTT-T-GTG-AAACGGGGGTGTCGACCATTTG
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCG-CCATTTG
39182409 ATGGCCAACACC-AAAAAATTTGGAATTTTTTT
1 ATGGCCAACACCAAAAAAATTT-GAATTTTTTT
39182441 TAAAACAGGG
Statistics
Matches: 371, Mismatches: 51, Indels: 56
0.78 0.11 0.12
Matches are distributed among these distances:
50 6 0.02
51 19 0.05
53 7 0.02
54 7 0.02
55 3 0.01
57 15 0.04
58 47 0.13
59 8 0.02
60 54 0.15
61 110 0.30
62 30 0.08
63 53 0.14
64 2 0.01
65 10 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (60 bp):
ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGGTGTCGCCATTTG
Found at i:39182130 original size:123 final size:120
Alignment explanation
Indices: 39181931--39182477 Score: 447
Period size: 123 Copynumber: 4.6 Consensus size: 120
39181921 TTTCTTAAGA
* * * * ***
39181931 ATGGCCGATACCAAAAAAATTTGAATTTTTTTTTTCGAGAAAAGGGGGGTGTCCGCCATTTGAT-
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTT-GAGAAAA-GGGGGTGT-CGCCATGCAATG
* * * *
39181995 GCCAATACCAAAAAATTTTGAATTTTTTTCTCGAGAAAAGAGGGGATGTCGACCATTTG
63 GCCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAG-GGGGATGTCGACCATGTG
*
39182054 ATGGCCAACACCAAAAAAATTTAAATTTTTTTTCTTGAGAAAAGGGGGTGTCGACCATGCAATGA
1 ATGGCCAACACCAAAAAAATTTAAA-TTTTTTTCTTGAGAAAAGGGGGTGTCG-CCATGCAATGG
* ** * **
39182119 CCAACATCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGGGGGCGTCGGCCATGCA
64 CCAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGGGGATGTCGACCATGTG
* *
39182176 ATGGCCAACACAAAAAAAATTTGAAA--TTTTTCTTGAGAAAAAAAGAGGGGTTTCTGCCATTGC
1 ATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTTGAG---AAAAG-GGGGTGTC-GCCA-TGC
** * *
39182239 -ATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCGAGAAATA-AAGGATGTTG-----GTC
59 AATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTCGAGAAA-AGGGGGATGTCGACCATGTG
* * * ***
39182296 AT---CAACACC-CAAAAATGT-AATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGGC
1 ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTTGAGAAAAGGGGGTGTC-GCCATGCAATGGC
* * *
39182356 CAACACCAAAAAAATTTAAATTTTTTT-T-GTGAAACGGGGG-TGTCGACCATTTG
65 CAACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGGGGATGTCGACCATGTG
*
39182409 ATGGCCAACACC-AAAAAATTTGGAA-TTTTTT-TT-A-AAACAGGGGGTGTCGACCATGCAATG
1 ATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTTGAGAAA-AGGGGGTGTCG-CCATGCAATG
*
39182469 GCTAACACC
63 GCCAACACC
39182478 TCAATTTTTT
Statistics
Matches: 345, Mismatches: 51, Indels: 64
0.75 0.11 0.14
Matches are distributed among these distances:
108 4 0.01
109 7 0.02
110 1 0.00
111 11 0.03
112 33 0.10
113 8 0.02
114 6 0.02
115 26 0.08
116 32 0.09
117 12 0.03
118 2 0.01
120 14 0.04
121 2 0.01
122 47 0.14
123 72 0.21
124 39 0.11
125 28 0.08
126 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (120 bp):
ATGGCCAACACCAAAAAAATTTAAATTTTTTTCTTGAGAAAAGGGGGTGTCGCCATGCAATGGCC
AACACCAAAAAAATTTAAATTTTTTTCTCGAGAAAAGGGGGATGTCGACCATGTG
Found at i:39182535 original size:17 final size:18
Alignment explanation
Indices: 39182508--39182541 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39182498 TCGTATTTTC
39182508 GTATATTAAAAAAATACT
1 GTATATTAAAAAAATACT
39182526 GTAT-TTAAAAAAATAC
1 GTATATTAAAAAAATAC
39182542 ACACGTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (18 bp):
GTATATTAAAAAAATACT
Found at i:39189632 original size:29 final size:31
Alignment explanation
Indices: 39189585--39189650 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
39189575 ATCACAATTG
* *
39189585 AAGTGTAAATTTCCCATTTTCTTTGGGTT-A
1 AAGTGTAAATTTCCAATTTCCTTTGGGTTAA
39189615 AAGTGT-AATTTCCAATTTCCTTTGGGTTAA
1 AAGTGTAAATTTCCAATTTCCTTTGGGTTAA
39189645 AAGTGT
1 AAGTGT
39189651 GAACTCGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (31 bp):
AAGTGTAAATTTCCAATTTCCTTTGGGTTAA
Found at i:39190999 original size:2 final size:2
Alignment explanation
Indices: 39190994--39191038 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
39190984 TCTGGGTATG
* *
39190994 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AC AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39191034 AT AT A
1 AT AT A
39191039 ATTATTATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39197783 original size:6 final size:6
Alignment explanation
Indices: 39197774--39197812 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
39197764 ATTTTATGAA
39197774 TATGCT TATGCT TATGCT TATGCT TATGCT TATGCT TAT
1 TATGCT TATGCT TATGCT TATGCT TATGCT TATGCT TAT
39197813 TATTATTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
TATGCT
Found at i:39197818 original size:18 final size:18
Alignment explanation
Indices: 39197767--39197812 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
39197757 GACTACTATT
*
39197767 TTATGAATATGCTTATGC
1 TTATGATTATGCTTATGC
*
39197785 TTATGCTTATGCTTATGC
1 TTATGATTATGCTTATGC
*
39197803 TTATGCTTAT
1 TTATGATTAT
39197813 TATTATTGTT
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:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGATTATGCTTATGC
Found at i:39213788 original size:82 final size:82
Alignment explanation
Indices: 39213505--39213792 Score: 280
Period size: 82 Copynumber: 3.4 Consensus size: 82
39213495 TTTTTCCTCT
* * * * * *
39213505 TTTTG-TTGAATATGAATTACATGG-CTTAAAGATCTTGTTTCTGTTTAATGTGTTGTG--ATTT
1 TTTTGATTGAATATGCATTACATGGACTTAAAGATCTTGTTTTTATTTTATGTATGGTGATATTT
39213566 TTTCTGGGTTTTGCTTG
66 TTTCTGGGTTTTGCTTG
* * * * * *
39213583 TCTTGATTGAATATGCATTACAAGGAGTTAAA-ATCGTGTTTTTTTTTTAAAAATTTAAAGTCTG
1 TTTTGATTGAATATGCATTACATGGACTTAAAGATCTTGTTTTTATTTT----A--T---GTATG
* *
39213647 TTATGATACTTTTTCTGGGTTTTGCTTG
57 --GTGATATTTTTTCTGGGTTTTGCTTG
*
39213675 TTTTGATTGAATATGCATTACTTGGACTTAAAGATCTTGTTTTTATTTTATGTATGGTGATATTT
1 TTTTGATTGAATATGCATTACATGGACTTAAAGATCTTGTTTTTATTTTATGTATGGTGATATTT
*
39213740 TTTCTGGGTCTTGCTTG
66 TTTCTGGGTTTTGCTTG
**
39213757 TTTTGATTGAATATGCATTACATGGTGTTAAAGATC
1 TTTTGATTGAATATGCATTACATGGACTTAAAGATC
39213793 AAGTTTTTTT
Statistics
Matches: 169, Mismatches: 25, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
78 4 0.02
79 29 0.17
80 5 0.03
82 56 0.33
83 1 0.01
84 4 0.02
85 1 0.01
87 1 0.01
88 3 0.02
89 1 0.01
90 2 0.01
92 48 0.28
93 14 0.08
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (82 bp):
TTTTGATTGAATATGCATTACATGGACTTAAAGATCTTGTTTTTATTTTATGTATGGTGATATTT
TTTCTGGGTTTTGCTTG
Done.