Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000280.1 Hibiscus syriacus cultivar Beakdansim tig00000519_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 132255
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2900 original size:55 final size:55
Alignment explanation
Indices: 2833--2964 Score: 176
Period size: 56 Copynumber: 2.4 Consensus size: 55
2823 ATTACCAAAT
* *
2833 GGCACTATGTGTGCAAAACTATGAAATTCATAATAAGGTTATGAATTTCCGTATA
1 GGCACTATGTGTGCAAAACTATGAAATTCATAACAAGGTTATGAATTACCGTATA
* * * * *
2888 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAACAAGTTTATGAATTACTGTATT
1 GGCACTATGTGTGCAAAA-CTATGAAATTCATAACAAGGTTATGAATTACCGTATA
*
2944 GGCACTACGTGTGC-AAACTAT
1 GGCACTATGTGTGCAAAACTAT
2965 AGAGATTATA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
54 3 0.05
55 20 0.30
56 43 0.65
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTATGAAATTCATAACAAGGTTATGAATTACCGTATA
Found at i:3233 original size:47 final size:47
Alignment explanation
Indices: 3180--3271 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
3170 TTAGATGAAG
*
3180 AACAATGCATAATTGACATGAAAGGATGCCATAAATGAAA-ATGTATA
1 AACAATGCATAATTGACATGAAAGG-TGCCACAAATGAAATATGTATA
*
3227 AACAATGCATAATTGGCATGAAAGGTGCCACAAATGAAATATGTA
1 AACAATGCATAATTGACATGAAAGGTGCCACAAATGAAATATGTA
3272 GAAGTATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 13 0.31
47 29 0.69
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (47 bp):
AACAATGCATAATTGACATGAAAGGTGCCACAAATGAAATATGTATA
Found at i:7261 original size:54 final size:56
Alignment explanation
Indices: 7196--7428 Score: 320
Period size: 54 Copynumber: 4.3 Consensus size: 56
7186 TTACCAAATT
* *
7196 GCACTATGTGTGCAAAA-CTAA-AAATTCATAATAAGTTTATGAATTTCTGTATGA
1 GCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
7250 GCACTTTGTGTGC-AAA-CTAAGAAATTCATAATAAGTTTATGAA-TTCTGTATGG
1 GCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
* **
7303 GCA-TTTGTGTGCAAAAGCTAATAAATTCATAATAAG-TTATGAATTTCCATATGG
1 GCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
* *
7357 GCACTTTGTGTGCAAAAGCTAAGAAATACATAATAAGTTTATGAATTATC-GTATTG
1 GCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATT-TCTGTATGG
**
7413 GCACTACGTGTGCAAA
1 GCACTTTGTGTGCAAA
7429 CTAGAAGTTA
Statistics
Matches: 161, Mismatches: 11, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
52 9 0.06
53 29 0.18
54 63 0.39
55 31 0.19
56 27 0.17
57 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (56 bp):
GCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGG
Found at i:7442 original size:107 final size:107
Alignment explanation
Indices: 7196--7428 Score: 335
Period size: 107 Copynumber: 2.1 Consensus size: 107
7186 TTACCAAATT
**
7196 GCACTATGTGTGCAAAACTAAAAATTCATAATAAGTTTATGAATTTCTGTATGAGCACTTTGTGT
1 GCACTATGTGTGCAAAACTAAAAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGTGT
* *
7261 GCAAACTAAGAAATTCATAATAAGTTTATGAATTCTGTATGG
66 GCAAACTAAGAAATACATAATAAGTTTATGAATTATGTATGG
* *
7303 GCA-TTTGTGTGCAAAAGCTAATAAATTCATAATAAG-TTATGAATTTCCATATGGGCACTTTGT
1 GCACTATGTGTGCAAAA-CTAA-AAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGT
*
7366 GTGCAAAAGCTAAGAAATACATAATAAGTTTATGAATTATCGTATTG
64 GTGC-AAA-CTAAGAAATACATAATAAGTTTATGAATTAT-GTATGG
*
7413 GCACTACGTGTGCAAA
1 GCACTATGTGTGCAAA
7429 CTAGAAGTTA
Statistics
Matches: 111, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
106 12 0.11
107 35 0.32
108 17 0.15
109 29 0.26
110 8 0.07
111 10 0.09
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (107 bp):
GCACTATGTGTGCAAAACTAAAAATTCATAATAAGTTTATGAATTTCCATATGAGCACTTTGTGT
GCAAACTAAGAAATACATAATAAGTTTATGAATTATGTATGG
Found at i:9609 original size:19 final size:19
Alignment explanation
Indices: 9585--9623 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9575 TTTAGGTTAA
9585 TTTAGGATCTTTGTATTAT
1 TTTAGGATCTTTGTATTAT
* *
9604 TTTAGGATTTTTTTATTAT
1 TTTAGGATCTTTGTATTAT
9623 T
1 T
9624 GTATCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.64
Consensus pattern (19 bp):
TTTAGGATCTTTGTATTAT
Found at i:10041 original size:2 final size:2
Alignment explanation
Indices: 10036--10076 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10026 ACATTGTGTG
10036 TA 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 TA T
10077 CAGTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10190 original size:23 final size:23
Alignment explanation
Indices: 10164--10207 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10154 ACATCAAACT
*
10164 AAACCCTAA-ACTAGGCCCAAATA
1 AAACCCAAACACT-GGCCCAAATA
10187 AAACCCAAACACTGGCCCAAA
1 AAACCCAAACACTGGCCCAAA
10208 CGTATCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.48, C:0.34, G:0.09, T:0.09
Consensus pattern (23 bp):
AAACCCAAACACTGGCCCAAATA
Found at i:11454 original size:21 final size:20
Alignment explanation
Indices: 11413--11456 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
11403 TATGTTTCTA
*
11413 TTTTTATGTTTTATATTATT
1 TTTTTATGTTTGATATTATT
11433 TTTTTATTGTTTGA-ATTCATT
1 TTTTTA-TGTTTGATATT-ATT
11454 TTT
1 TTT
11457 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTTATGTTTGATATTATT
Found at i:13209 original size:10 final size:10
Alignment explanation
Indices: 13194--13258 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
13184 AGAATATACA
*
13194 TATTTTTACT
1 TATTTTTATT
13204 TA-TTTTATT
1 TATTTTTATT
* *
13213 TATCTCTATT
1 TATTTTTATT
13223 TACTTTTTATT
1 TA-TTTTTATT
*
13234 TATTCTTATT
1 TATTTTTATT
13244 TA-TTTT-TT
1 TATTTTTATT
13252 TATTTTT
1 TATTTTT
13259 TCTCTTTACT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 4 0.09
9 15 0.33
10 18 0.40
11 8 0.18
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTTATT
Found at i:13232 original size:21 final size:20
Alignment explanation
Indices: 13206--13280 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
13196 TTTTTACTTA
13206 TTTTATTTATCTCTATTTACT
1 TTTTATTTAT-TCTATTTACT
*
13227 TTTTATTTATTCTTATTTATTT
1 TTTTATTTATTC-TATTTA-CT
* *
13249 TTTTATTTTTTCTCTTTACT
1 TTTTATTTATTCTATTTACT
*
13269 TTCTA-TTATTCT
1 TTTTATTTATTCT
13281 TGTCATATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.13
20 7 0.15
21 21 0.46
22 12 0.26
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTATTCTATTTACT
Found at i:18523 original size:35 final size:35
Alignment explanation
Indices: 18479--18550 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
18469 TTGTTATCCC
*
18479 TTAGAATTTTATAAATT-TATCTTTATAATATAAAA
1 TTAGAATTTTATAAATTCGA-CTTTATAATATAAAA
18514 TTAGAATTTTATAAATTCGACTTTATAATATAAAA
1 TTAGAATTTTATAAATTCGACTTTATAATATAAAA
18549 TT
1 TT
18551 TTACGTCCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (35 bp):
TTAGAATTTTATAAATTCGACTTTATAATATAAAA
Found at i:20491 original size:20 final size:19
Alignment explanation
Indices: 20466--20507 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
20456 TTTATTTCTT
20466 AATATTTATTTACTAAAATA
1 AATATTTATTTA-TAAAATA
*
20486 AATATTTATTTATTAAATA
1 AATATTTATTTATAAAATA
20505 AAT
1 AAT
20508 TTAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTTATTTATAAAATA
Found at i:20506 original size:24 final size:25
Alignment explanation
Indices: 20468--20516 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
20458 TATTTCTTAA
* *
20468 TATTTATTTACTAAA-ATAAATATT
1 TATTTATTAAATAAATATAAATATT
*
20492 TATTTATTAAATAAATTTAAATATT
1 TATTTATTAAATAAATATAAATATT
20517 AAATAGTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTTATTAAATAAATATAAATATT
Found at i:22050 original size:46 final size:46
Alignment explanation
Indices: 21979--22070 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
21969 TTTATGAGCA
* * *
21979 TAAAGTTATTATGACCACTAGTAGATTGATATGATAAATAGATATG
1 TAAAGTTATTATGACCACTAATAGATTGACATGAAAAATAGATATG
*
22025 TAAAGTTATTATGACTACTAATAGATTGACATGAAAAATAGATATG
1 TAAAGTTATTATGACCACTAATAGATTGACATGAAAAATAGATATG
22071 ATCACATGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (46 bp):
TAAAGTTATTATGACCACTAATAGATTGACATGAAAAATAGATATG
Found at i:28276 original size:110 final size:103
Alignment explanation
Indices: 28153--28363 Score: 305
Period size: 110 Copynumber: 2.0 Consensus size: 103
28143 TATTGTATAT
* *
28153 TACTAAAAGAAAAAGAAAAACTCATTTAATTAAGCACATGTTAGATTACACCCTAAACTTTAAAT
1 TACTAAAAGAAAAAGAAAAACTCATTTAATTAAGCACATATTAAATTACACCCTAAAC------T
*
28218 CATAAGTCCTAAACCCTAAACCCTTAATCCGATTATGTGATAGGA
60 C-TAAATCCTAAACCCTAAACCCTTAATCCGATTATGTGATAGGA
* * *
28263 TACTAAAAGAAAAATAAAATCTCATTTAATTAAGCACATATTAAATTACACCCTAAGCTCTAAAT
1 TACTAAAAGAAAAAGAAAAACTCATTTAATTAAGCACATATTAAATTACACCCTAAACTCTAAAT
28328 CCTAAACCCTAAACCCTTAATCCGATTATGTGATAG
66 CCTAAACCCTAAACCCTTAATCCGATTATGTGATAG
28364 TGGTTAAGTT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
103 40 0.42
104 2 0.02
110 53 0.56
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (103 bp):
TACTAAAAGAAAAAGAAAAACTCATTTAATTAAGCACATATTAAATTACACCCTAAACTCTAAAT
CCTAAACCCTAAACCCTTAATCCGATTATGTGATAGGA
Found at i:29611 original size:16 final size:18
Alignment explanation
Indices: 29566--29635 Score: 113
Period size: 18 Copynumber: 3.8 Consensus size: 18
29556 CCACACCGGA
*
29566 CGCTGAAAAGAGTTAGAG
1 CGCTGAAGAGAGTTAGAG
29584 CGCTGAAGAGAGTTAGAG
1 CGCTGAAGAGAGTTAGAG
29602 CGCTGAAGAGAGTTAGAG
1 CGCTGAAGAGAGTTAGAG
*
29620 CGCTGGAGAGCAGTTA
1 CGCTGAAGAG-AGTTA
29636 TAAAAGAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
18 44 0.90
19 5 0.10
ACGTcount: A:0.33, C:0.13, G:0.37, T:0.17
Consensus pattern (18 bp):
CGCTGAAGAGAGTTAGAG
Found at i:34536 original size:30 final size:30
Alignment explanation
Indices: 34500--34556 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
34490 ACAGTCAGAA
34500 GAACATTAATAAATGAAATTTGCTCTAAGG
1 GAACATTAATAAATGAAATTTGCTCTAAGG
*
34530 GAACATTAATAAATGAAGTTTGCTCTA
1 GAACATTAATAAATGAAATTTGCTCTA
34557 TGGGCACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (30 bp):
GAACATTAATAAATGAAATTTGCTCTAAGG
Found at i:42028 original size:60 final size:59
Alignment explanation
Indices: 41926--42050 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 59
41916 AAATCCATGA
* * * *
41926 ATAAAAACTATGTGAATGATAAGGAGTTAATGCTCAACTATGTTACTAGGTAAGCCAAG
1 ATAAAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
* *
41985 ATAAGAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTTGGTACGCCAAG
1 ATAA-AAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
42045 ATAAAA
1 ATAAAA
42051 TTCGTATGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (59 bp):
ATAAAAACCATGTGAATGATAAAGAGCTAAGGCTCAACTATGTTACTAGGTAAGCCAAG
Found at i:43398 original size:40 final size:40
Alignment explanation
Indices: 43348--43695 Score: 347
Period size: 40 Copynumber: 8.8 Consensus size: 40
43338 TAAGAAACAT
* *
43348 ATTTTTAGGTTGCAACCTTATTTATCATATAGAAACCTGA
1 ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
*
43388 ATTTCTAGGTTACAACCTGATTTATCATATA-AAACCTGAA
1 ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTG-A
*
43428 ATTT-TAGGTTGCAACCTGATTTATCATATAGAAACTTGA
1 ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * *
43467 ATTTCTAGGTCGCAACCTGATTTATCATATACAAACTTGA
1 ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* *
43507 ATTTCTAGGTTGCAACCTGATTTATCATATGGAAACCCGA
1 ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
** * *
43547 ACTTT-TAGGTTGCAGTCTGATTGATCATGTAGAAACCTG-
1 A-TTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
* * * * *
43586 ATTTTTA-GTTGCAACCTAATTTATC-TCATTGTAACTTG-
1 ATTTCTAGGTTGCAACCTGATTTATCAT-ATAGAAACCTGA
* * * *
43624 ATTTCTTTTTA-GTTGCAACCTTATTTTTGATTATAGAAACC-AA
1 ATTTC----TAGGTTGCAACCTGATTTATCA-TATAGAAACCTGA
*
43667 ATTT-TAGGTTGCAACCTGATTTTTCATAT
1 ATTTCTAGGTTGCAACCTGATTTATCATAT
43696 GGAATTATGT
Statistics
Matches: 258, Mismatches: 36, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
37 1 0.00
38 33 0.13
39 57 0.22
40 136 0.53
41 3 0.01
42 17 0.07
43 10 0.04
44 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (40 bp):
ATTTCTAGGTTGCAACCTGATTTATCATATAGAAACCTGA
Found at i:43423 original size:19 final size:19
Alignment explanation
Indices: 43361--43426 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
43351 TTTAGGTTGC
*
43361 AACCTTATTTATCATATAGA
1 AACCTGATTTATCATATA-A
* *
43381 AACCTGAATT-TC-TAGGTTAC
1 AACCTGATTTATCATA---TAA
43401 AACCTGATTTATCATATAA
1 AACCTGATTTATCATATAA
43420 AACCTGA
1 AACCTGA
43427 AATTTTAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 17 0.47
21 4 0.11
22 2 0.06
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (19 bp):
AACCTGATTTATCATATAA
Found at i:43639 original size:120 final size:119
Alignment explanation
Indices: 43348--43687 Score: 352
Period size: 119 Copynumber: 2.8 Consensus size: 119
43338 TAAGAAACAT
* * * * * *
43348 ATTTTTAGGTTGCAACCTTATTTATCATATAGAAACCTGAATTTCTAGGTTACAACCTGATTTAT
1 ATTTCTAGGTCGCAACCTAATTTATCATATACAAACTTGAATTTCTAGGTTGCAACCTGATTTAT
* * * *
43413 CATATAAAACCTGAAATTTTAGGTTGCAACCTGATTTATCATATAGAAACTTGA
66 CATATGAAACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGA
*
43467 ATTTCTAGGTCGCAACCTGATTTATCATATACAAACTTGAATTTCTAGGTTGCAACCTGATTTAT
1 ATTTCTAGGTCGCAACCTAATTTATCATATACAAACTTGAATTTCTAGGTTGCAACCTGATTTAT
* ** *
43532 CATATGGAAACCCGAACTTTTAGGTTGCAGTCTGATTGATCATGTAGAAACCTG-
66 CATAT-GAAACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGA
* * *** *
43586 ATTTTTA-GTTGCAACCTAATTTATC-TCATTGTAACTTG-ATTTCTTTTTA-GTTGCAACCTTA
1 ATTTCTAGGTCGCAACCTAATTTATCAT-ATACAAACTTGAATTTC----TAGGTTGCAACCTGA
* *
43647 TTTTTGATTATAGAAA-CC-AAATTTTAGGTTGCAACCTGATT
61 TTTATCA-TAT-GAAACCCGAAATTTTAGGTTGCAACCTGATT
43688 TTTCATATGG
Statistics
Matches: 187, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
117 6 0.03
118 24 0.13
119 90 0.48
120 58 0.31
121 9 0.05
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (119 bp):
ATTTCTAGGTCGCAACCTAATTTATCATATACAAACTTGAATTTCTAGGTTGCAACCTGATTTAT
CATATGAAACCCGAAATTTTAGGTTGCAACCTGATTGATCATATAGAAACCTGA
Found at i:47360 original size:12 final size:12
Alignment explanation
Indices: 47343--47408 Score: 75
Period size: 12 Copynumber: 5.7 Consensus size: 12
47333 GTATATTTTA
47343 TCTGATTTCTGT
1 TCTGATTTCTGT
47355 TCTGATTTC--T
1 TCTGATTTCTGT
*
47365 TCTGATTTCTAT
1 TCTGATTTCTGT
* *
47377 TCTAATTTCTGC
1 TCTGATTTCTGT
47389 TCTGATTTCTGCT
1 TCTGATTTCTG-T
47402 T-TGATTT
1 TCTGATTT
47409 ATGATATCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 10 0.22
12 35 0.76
13 1 0.02
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:47368 original size:22 final size:23
Alignment explanation
Indices: 47343--47408 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
47333 GTATATTTTA
47343 TCTGATTTCTGTTCTGATTTCT-
1 TCTGATTTCTGTTCTGATTTCTC
* *
47365 TCTGATTTCTATTCTAATTTCTGC
1 TCTGATTTCTGTTCTGATTTCT-C
47389 TCTGATTTCTGCTT-TGATTT
1 TCTGATTTCTG-TTCTGATTT
47409 ATGATATCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 20 0.54
24 15 0.41
25 2 0.05
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (23 bp):
TCTGATTTCTGTTCTGATTTCTC
Found at i:47603 original size:32 final size:31
Alignment explanation
Indices: 47551--47638 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 31
47541 TAAGGCGACC
* * *
47551 CTTGGGTAGGCTCTGGGGCCCTAAGATTTTT
1 CTTGGGTAGGCTCTGAGGCCCTAAGAATTAT
* * *
47582 CTTGGGTAAGCCTCTGTGGCCCCAAGAATTAT
1 CTTGGGT-AGGCTCTGAGGCCCTAAGAATTAT
*
47614 CTTGGGTAGGCTCTCAGGCCCTAAG
1 CTTGGGTAGGCTCTGAGGCCCTAAG
47639 GTAATCTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 21 0.45
32 26 0.55
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCTAAGAATTAT
Found at i:51105 original size:12 final size:12
Alignment explanation
Indices: 51084--51142 Score: 82
Period size: 12 Copynumber: 4.9 Consensus size: 12
51074 GGATATTTTC
51084 TCTGATTTCTGT
1 TCTGATTTCTGT
* * *
51096 TTTTATTTCTGC
1 TCTGATTTCTGT
51108 TCTGATTTCTGT
1 TCTGATTTCTGT
*
51120 TCTGATTTCTGC
1 TCTGATTTCTGT
51132 TCTGATTTCTG
1 TCTGATTTCTG
51143 ATATCCCCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.08, C:0.19, G:0.15, T:0.58
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:51111 original size:24 final size:24
Alignment explanation
Indices: 51083--51142 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
51073 TGGATATTTT
* *
51083 CTCTGATTTCTGTTTTTATTTCTG
1 CTCTGATTTCTGTTCTGATTTCTG
51107 CTCTGATTTCTGTTCTGATTTCTG
1 CTCTGATTTCTGTTCTGATTTCTG
51131 CTCTGATTTCTG
1 CTCTGATTTCTG
51143 ATATCCCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.08, C:0.20, G:0.15, T:0.57
Consensus pattern (24 bp):
CTCTGATTTCTGTTCTGATTTCTG
Found at i:53850 original size:23 final size:24
Alignment explanation
Indices: 53806--53867 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
53796 TTGAAAATAA
53806 TTTTGAGAAAAATATAATATATAG
1 TTTTGAGAAAAATATAATATATAG
* *
53830 TTTTTAGAAAACATATAATATATAC
1 TTTTGAGAAAA-ATATAATATATAG
* *
53855 TTTTAAAAAAAAT
1 TTTTGAGAAAAAT
53868 CGGTTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (24 bp):
TTTTGAGAAAAATATAATATATAG
Found at i:53997 original size:2 final size:2
Alignment explanation
Indices: 53990--54014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53980 AACATTTTGA
53990 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 A
54015 GTTTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54069 original size:81 final size:80
Alignment explanation
Indices: 53919--54087 Score: 216
Period size: 81 Copynumber: 2.1 Consensus size: 80
53909 TTTTAAAAAC
*
53919 ATATATAATAAATAGTTTTTGAAAACATTTTAAAAAACGTATATAATATATAGTTTTTGAAAACA
1 ATATATAATAAATAGTTTTTGAAAACATTTTAAAAAAC-TATATAATATATAGTTTTAGAAAACA
53984 TTTTGAATATATATAT
65 TTTTGAATATATATAT
* ** * **
54000 ATATATATATATATAG-TTTTGAAAACAATTTTTGAAAA-TATATATTATATAGTTTTAGAAATG
1 ATATATA-ATAAATAGTTTTTGAAAAC-ATTTTAAAAAACTATATAATATATAGTTTTAGAAAAC
54063 ATTTTTGAATATATATAT
64 A-TTTTGAATATATATAT
54081 ACTATAT
1 A-TATAT
54088 GATTTTGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
80 22 0.29
81 34 0.44
82 21 0.27
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (80 bp):
ATATATAATAAATAGTTTTTGAAAACATTTTAAAAAACTATATAATATATAGTTTTAGAAAACAT
TTTGAATATATATAT
Found at i:54143 original size:38 final size:38
Alignment explanation
Indices: 53871--54174 Score: 207
Period size: 38 Copynumber: 7.9 Consensus size: 38
53861 AAAAAATCGG
*
53871 TTTTGAAATATATATATATAATATAGTTTTTG--AA-AAT
1 TTTTGAAA-ATATATATATTATATAG-TTTTGAAAACAAT
* * * *
53908 GTTTTAAAAACATATATAATAAATAGTTTTTGAAAAC-AT
1 -TTTTGAAAATATATATATTATATAG-TTTTGAAAACAAT
** ** *
53947 TTTAAAAAACGTATATAATATATAGTTTTTGAAAAC-A-
1 TTTTGAAAATATATATATTATATAG-TTTTGAAAACAAT
53984 TTTTGAATATATATATATATATATATATATAGTTTTGAAAACAAT
1 TTTTG---A-A-A-ATATATATAT-TATATAGTTTTGAAAACAAT
**
54029 TTTTG-AAA-ATATATATTATATAGTTTT-AGAAATGAT
1 TTTTGAAAATATATATATTATATAGTTTTGA-AAACAAT
* * **
54065 TTTTGAATATATATATACTATAT-GATTTTGAAAATGAT
1 TTTTGAAAATATATATATTATATAG-TTTTGAAAACAAT
*
54103 TTTTGAAAATATATATATTATATGGTTTTGAAAACAA-
1 TTTTGAAAATATATATATTATATAGTTTTGAAAACAAT
* * * *
54140 TTTTCAAAAGCATATATAATATATAGTTTTAAAAA
1 TTTTGAAAA-TATATATATTATATAGTTTTGAAAA
54175 TGATATTTTT
Statistics
Matches: 221, Mismatches: 26, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
35 1 0.00
36 21 0.10
37 41 0.19
38 117 0.53
39 7 0.03
40 2 0.01
41 1 0.00
42 1 0.00
43 17 0.08
44 8 0.04
45 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (38 bp):
TTTTGAAAATATATATATTATATAGTTTTGAAAACAAT
Found at i:54209 original size:13 final size:11
Alignment explanation
Indices: 54178--54272 Score: 85
Period size: 10 Copynumber: 8.7 Consensus size: 11
54168 TTAAAAATGA
*
54178 TATT-TTTATA
1 TATTATTTATT
*
54188 TATTATATTA-A
1 TATTAT-TTATT
54199 TATTATTTATT
1 TATTATTTATT
54210 T-TTATTTATT
1 TATTATTTATT
54220 TATT-TTTATT
1 TATTATTTATT
54230 TATTTATTTTATT
1 TA-TTA-TTTATT
54243 TATTTATTTA-T
1 TA-TTATTTATT
54254 TATT-TTTATT
1 TATTATTTATT
54264 TATTTATTT
1 TA-TTATTT
54273 TCGTTTCAGG
Statistics
Matches: 74, Mismatches: 1, Indels: 18
0.80 0.01 0.19
Matches are distributed among these distances:
9 4 0.05
10 30 0.41
11 18 0.24
12 10 0.14
13 12 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTATTTATT
Found at i:54210 original size:4 final size:4
Alignment explanation
Indices: 54182--54272 Score: 91
Period size: 4 Copynumber: 22.8 Consensus size: 4
54172 AAATGATATT
* *
54182 TTTA TATA TTATA TTAA TATTA TTTA -TT- TTTA TTTA TTTA -TT- TTTA
1 TTTA TTTA TT-TA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
54228 TTTA TTTA TTTTA TTTA TTTA TTTA TTATT TTTA TTTA TTTA TTT
1 TTTA TTTA -TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTT
54273 TCGTTTCAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
3 8 0.11
4 51 0.70
5 14 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:55550 original size:4 final size:4
Alignment explanation
Indices: 55541--55586 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
55531 TATTCTTATT
*
55541 TTTA TTTA TTTA TCTTTA TTTA TTTA TCTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA --TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
55587 TTATTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 29 0.78
5 4 0.11
6 4 0.11
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:55553 original size:14 final size:14
Alignment explanation
Indices: 55536--55592 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
55526 TTTAATATTC
55536 TTATTTTTATTTAT
1 TTATTTTTATTTAT
*
55550 TTATCTTTATTTAT
1 TTATTTTTATTTAT
55564 TTATCTATTTATTTATT
1 TTAT-T-TTTATTTA-T
55581 TTATTTTTATTT
1 TTATTTTTATTT
55593 TTTCCTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
14 17 0.45
15 7 0.18
16 9 0.24
17 5 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTTTTATTTAT
Found at i:59468 original size:99 final size:99
Alignment explanation
Indices: 59292--59471 Score: 288
Period size: 99 Copynumber: 1.8 Consensus size: 99
59282 TTATAATATT
* * * *
59292 ATATGTATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTGGTTAAACGCCTCATCTTTATGG
1 ATATCTATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTGGTTAAACGCCCCAACTTTATAG
59357 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* * * *
59391 ATATCTATACAATAAAGCTTGAGCTGTCCTTCTAGAGCAATTGGTTAAACGCCCCAACTTTATAG
1 ATATCTATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTGGTTAAACGCCCCAACTTTATAG
59456 ATAAGATTCAGCTAGC
66 ATAAGATTCAGCTAGC
59472 AAGACAATGC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTTGAACTGTCCCTATAGAGAAATTGGTTAAACGCCCCAACTTTATAG
ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
Found at i:61040 original size:85 final size:85
Alignment explanation
Indices: 60776--61328 Score: 811
Period size: 85 Copynumber: 6.5 Consensus size: 85
60766 ATAACTCAAC
* *
60776 TATCTGTCAACAAAAACCTTCAAGTTCGATTATATTCAGCTCAAGGGCATATCAAATTTACAGCA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
*
60841 TAGCTCAAGGCGAGAAGGGC
66 TAGCTCAAGGCGAGAAGGGT
* *
60861 TATCTGTCAACAAAAATCTTCGAGTTCGATTACATTCAGCT-AAGGGCATATCAAATATACAGCA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
60925 TAGCTCAAGGCGAGAAGGGT
66 TAGCTCAAGGCGAGAAGGGT
* * *
60945 TATCTGTCAACAAAAACCTTCGAGTTCGATTATATTCAGCTCAATGGCATATCAAATTTATAGCA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
* *
61010 TATCTTAAGGCGAGAAGGGT
66 TAGCTCAAGGCGAGAAGGGT
* * * * *
61030 TATTTATCAACAAAAACCTTCAAGTTTGATTACATTCAGCTCAAGGGCATATCAAATTTACAACA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
* *
61095 TAGCGCAAGGCGAGAAGGGA
66 TAGCTCAAGGCGAGAAGGGT
* * *
61115 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAACTCATGGGCATATCACATTTACAGCA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
* * *
61180 TAACTCAAGGCGATAAGGGC
66 TAGCTCAAGGCGAGAAGGGT
* * * *
61200 TATCTGTCAACAAAAACCTTCGAATTCGATTCCATTCAGCTCAAGGGAATACCAAATTTACAGCA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
* *
61265 TAGCTCAAGGCGATAATGGT
66 TAGCTCAAGGCGAGAAGGGT
* * *
61285 TATATGGCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
1 TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
61329 TGACAACGAT
Statistics
Matches: 418, Mismatches: 49, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
84 80 0.19
85 338 0.81
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
TATCTGTCAACAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCA
TAGCTCAAGGCGAGAAGGGT
Found at i:62002 original size:39 final size:38
Alignment explanation
Indices: 61918--62021 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 38
61908 TTTTGAAAAT
* * * *
61918 AATTTTGAAAAAAATATAATATATAGTTTTTAGAAAACG
1 AATTTTG-AAAAAATATAATATATACTTTTAAAAAAACA
** *
61957 GTTTTTGAAAACATATAATATATACTTTTAAAAAAATCA
1 AATTTTGAAAAAATATAATATATACTTTTAAAAAAA-CA
*
61996 AATTTTGAAATATATATATATATATA
1 AATTTTGAAA-AAATATA-ATATATA
62022 TATATATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 25 0.48
39 14 0.27
40 6 0.12
41 7 0.13
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (38 bp):
AATTTTGAAAAAATATAATATATACTTTTAAAAAAACA
Found at i:62010 original size:2 final size:2
Alignment explanation
Indices: 62005--62041 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61995 AAATTTTGAA
62005 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
62042 GTTTTTGAAA
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:62078 original size:35 final size:35
Alignment explanation
Indices: 62029--62357 Score: 201
Period size: 36 Copynumber: 9.5 Consensus size: 35
62019 ATATATATAT
*
62029 ATATATATATATAGTTTTTGAAAGCATTTT-AAAA
1 ATATATATATATAGTTTTTGAAAACATTTTGAAAA
*
62063 ACATATATAATATAGTTTTTGAAAACATTTTGAAAA
1 ATATATAT-ATATAGTTTTTGAAAACATTTTGAAAA
*
62099 ATACATATATATAG-TTTTGAAAACATTTTG---A
1 ATATATATATATAGTTTTTGAAAACATTTTGAAAA
* * * * * * *
62130 ATATATATATATA-TATAT--ATATA-TAT-ATAT
1 ATATATATATATAGTTTTTGAAAACATTTTGAAAA
*
62160 ATATATAT-TATAG-TTTTGAAAATATTTTGAAAACA
1 ATATATATATATAGTTTTTGAAAACATTTTG-AAA-A
*
62195 TATATATAATATATAGTTTTTGAAAATAGTTTT-AAAA
1 -ATATAT-ATATATAGTTTTTGAAAACA-TTTTGAAAA
***
62232 ATATAT-TATATAG-TTTT-AAATTTTTTTG-AAA
1 ATATATATATATAGTTTTTGAAAACATTTTGAAAA
* * *
62263 ATATATATTATATAG-TTTTAAAAATGATTTTTG-AAT
1 ATATATA-TATATAGTTTTTGAAAA-CA-TTTTGAAAA
* * *
62299 ATATATATATTATATGGTTTTGAAAATAATTTTTAAAA
1 ATATATATA-TATA-GTTTTTGAAAA-CATTTTGAAAA
62337 GCATATATGATATATAGTTTT
1 --ATATAT-ATATATAGTTTT
62358 AAAAATGATT
Statistics
Matches: 236, Mismatches: 28, Indels: 57
0.74 0.09 0.18
Matches are distributed among these distances:
28 2 0.01
29 9 0.04
30 8 0.03
31 32 0.14
32 6 0.03
33 15 0.06
34 35 0.15
35 29 0.12
36 40 0.17
37 8 0.03
38 20 0.08
39 15 0.06
40 14 0.06
41 3 0.01
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (35 bp):
ATATATATATATAGTTTTTGAAAACATTTTGAAAA
Found at i:62096 original size:131 final size:129
Alignment explanation
Indices: 61896--62251 Score: 404
Period size: 127 Copynumber: 2.7 Consensus size: 129
61886 ATATATGGTA
*
61896 ATATAGTATA-ATTTTTGAAAATAATTTTGAAAAAAATATA-ATATATAGTTTTTAGAAAACGGT
1 ATATA-TATATATTTTTGAAAA-AATTTTGAAAAAAATATATATATATAGTTTTT-GAAAAC--A
*
61959 TTTTGAAAACATATAATATATACTTTTAAAAAAATCAAATTTTGAA-ATATATATATATATATAT
61 TTTTGAAAA-ATATAATATATAGTTTTAAAAAAA-C--ATTTTGAATATATATATATATATATAT
62023 ATATATAT
122 ATATATAT
** *
62031 ATATATATATAGTTTTTGAAAGCATTTT-AAAAACATATATA-ATATAGTTTTTGAAAACATTTT
1 ATATATATATA-TTTTTGAAAAAATTTTGAAAAAAATATATATATATAGTTTTTGAAAACATTTT
* *
62094 GAAAAATACATATATATAGTTTT--GAAAACATTTTGAATATATATATATATATATATATATATA
65 GAAAAATATA-ATATATAGTTTTAAAAAAACATTTTGAATATATATATATATATATATATATATA
62157 T
129 T
* * *
62158 ATATATATATTATAGTTTTGAAAATATTTTGAAAACATATATATAATATATAGTTTTTGAAAATA
1 ATATATATA-TAT--TTTTGAAAAAATTTTGAAAA-AAATATAT-ATATATAGTTTTTGAAAACA
*
62223 GTTTT-AAAAATATATTATATAGTTTTAAA
61 -TTTTGAAAAATATAATATATAGTTTTAAA
62252 TTTTTTTGAA
Statistics
Matches: 192, Mismatches: 14, Indels: 31
0.81 0.06 0.13
Matches are distributed among these distances:
126 8 0.04
127 36 0.19
128 3 0.02
129 17 0.09
130 8 0.04
131 27 0.14
132 12 0.06
133 31 0.16
134 29 0.15
135 12 0.06
136 9 0.05
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (129 bp):
ATATATATATATTTTTGAAAAAATTTTGAAAAAAATATATATATATAGTTTTTGAAAACATTTTG
AAAAATATAATATATAGTTTTAAAAAAACATTTTGAATATATATATATATATATATATATATAT
Found at i:62137 original size:2 final size:2
Alignment explanation
Indices: 62130--62171 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
62120 AACATTTTGA
62130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
62171 A
1 A
62172 GTTTTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62267 original size:105 final size:107
Alignment explanation
Indices: 62156--62360 Score: 267
Period size: 105 Copynumber: 1.9 Consensus size: 107
62146 ATATATATAT
* *
62156 ATATATATATATTATAGTTTTGAAAAT-A-TTTTGAAAACATATATATAATATATAGTTTTTGAA
1 ATATATAT-TA-TATAGTTTTAAAAATGATTTTTG--AACATATATATAATATAT-GGTTTTGAA
62219 AAT-AGTTTTAAAA-ATATAT-TATATAGTTTTAAATTTTTTTGAAA
61 AATAAGTTTTAAAACATATATATATATAGTTTTAAATTTTTTTGAAA
* *
62263 ATATATATTATATAGTTTTAAAAATGATTTTTGAATATATATATATTATATGGTTTTGAAAATAA
1 ATATATATTATATAGTTTTAAAAATGATTTTTGAACATATATATAATATATGGTTTTGAAAATAA
*
62328 TTTTTAAAAGCATATATGATATATAGTTTTAAA
66 GTTTTAAAA-CATATAT-ATATATAGTTTTAAA
62361 AATGATTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
104 11 0.13
105 39 0.45
106 3 0.03
107 19 0.22
109 14 0.16
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.47
Consensus pattern (107 bp):
ATATATATTATATAGTTTTAAAAATGATTTTTGAACATATATATAATATATGGTTTTGAAAATAA
GTTTTAAAACATATATATATATAGTTTTAAATTTTTTTGAAA
Found at i:62267 original size:131 final size:129
Alignment explanation
Indices: 61896--62276 Score: 377
Period size: 129 Copynumber: 2.9 Consensus size: 129
61886 ATATATGGTA
* * * *
61896 ATATAGTATAATTTTTGAAAATAATTTTGAAAAAAATATA-ATATATAGTTTTTAGAAAACGGTT
1 ATATA-TATAGTTTTTGAAAA-CATTTT-AAAAACATATATA-ATATAGTTTTT-GAAAAC--AT
* * *
61960 TTTGAAAACATATA-ATATATACTTTTAAAAAAATCAAATTTTG--AA-ATATATATATATATAT
59 TTTGAAAA-ATACATATATATAGTTTT--GAAAA-C--ATTTTGAAAATATATATATATATATAT
62021 ATATATATATAT
118 ATATATATATAT
*
62033 ATATATATAGTTTTTGAAAGCATTTTAAAAACATATATAATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAGTTTTTGAAAACATTTTAAAAACATATATAATATAGTTTTTGAAAACATTTTGAAA
*
62098 AATACATATATATAGTTTTGAAAACATTTTGAATATATATATATATATATATATATATATATAT
66 AATACATATATATAGTTTTGAAAACATTTTGAAAATATATATATATATATATATATATATATAT
* * *
62162 ATATATTATAG-TTTTGAAAATATTTTGAAAACATATATATAATATATAGTTTTTGAAAATAGTT
1 ATATA-TATAGTTTTTGAAAACATTTT-AAAA-ACATATAT-A-ATATAGTTTTTGAAAACA-TT
* ***
62226 TT-AAAAATATAT-TATATAGTTTT-AAATTTTTTTGAAAATATATAT-TATATA
60 TTGAAAAATACATATATATAGTTTTGAAAACATTTTGAAAATATATATATATATA
62277 GTTTTAAAAA
Statistics
Matches: 215, Mismatches: 18, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
126 6 0.03
128 2 0.01
129 50 0.23
130 19 0.09
131 45 0.21
132 12 0.06
133 32 0.15
134 25 0.12
135 6 0.03
136 13 0.06
137 5 0.02
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (129 bp):
ATATATATAGTTTTTGAAAACATTTTAAAAACATATATAATATAGTTTTTGAAAACATTTTGAAA
AATACATATATATAGTTTTGAAAACATTTTGAAAATATATATATATATATATATATATATATAT
Found at i:62370 original size:38 final size:34
Alignment explanation
Indices: 62029--62370 Score: 240
Period size: 38 Copynumber: 9.9 Consensus size: 34
62019 ATATATATAT
**
62029 ATATATATATATAGTTTTTGAAAGCA-TTTTAAAA
1 ATATATATATATAG-TTTTGAAAATATTTTTAAAA
* * *
62063 ACATATATAATATAGTTTTTGAAAACATTTTGAAAA
1 ATATATAT-ATATAG-TTTTGAAAATATTTTTAAAA
* * *
62099 ATACATATATATAGTTTTGAAAACA-TTTT--GA
1 ATATATATATATAGTTTTGAAAATATTTTTAAAA
* * * * * *
62130 ATATATATATATA--TAT--ATATATATATATAT
1 ATATATATATATAGTTTTGAAAATATTTTTAAAA
*
62160 ATATATAT-TATAGTTTTGAAAATATTTTGAAAACA
1 ATATATATATATAGTTTTGAAAATATTTT-TAAA-A
*
62195 TATATATAATATATAGTTTTTGAAAATAGTTTTAAAA
1 -ATATAT-ATATATAG-TTTTGAAAATATTTTTAAAA
* *
62232 ATATAT-TATATAGTTTT--AAATTTTTTTGAAA
1 ATATATATATATAGTTTTGAAAATATTTTTAAAA
* *
62263 ATATATATTATATAGTTTTAAAAATGATTTTTGAATAT
1 ATATATA-TATATAGTTTTGAAAAT-ATTTTT-AA-AA
*
62301 ATATATATTATATGGTTTTGAAAATAATTTTTAAAA
1 ATATATA-TATATAGTTTTGAAAAT-ATTTTTAAAA
*
62337 GCATATATGATATATAGTTTTAAAAATGATTTTT
1 --ATATAT-ATATATAGTTTTGAAAAT-ATTTTT
62371 TATATCTTAT
Statistics
Matches: 246, Mismatches: 37, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 2 0.01
29 6 0.02
30 8 0.03
31 32 0.13
33 24 0.10
34 27 0.11
35 27 0.11
36 31 0.13
37 6 0.02
38 65 0.26
39 15 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (34 bp):
ATATATATATATAGTTTTGAAAATATTTTTAAAA
Found at i:62408 original size:28 final size:30
Alignment explanation
Indices: 62365--62438 Score: 98
Period size: 28 Copynumber: 2.5 Consensus size: 30
62355 TTTAAAAATG
* *
62365 ATTTTTTATATCTTATATTAATA-TTATTT
1 ATTTTTTATTTATTATATTAATATTTATTT
62394 A-TTTTTATTTATTATATTAATATTTTATTT
1 ATTTTTTATTTATTATATTAATA-TTTATTT
62424 ATTTTTTTATTTATT
1 A-TTTTTTATTTATT
62439 TTCTTATCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 19 0.49
29 1 0.03
30 7 0.18
32 12 0.31
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTTTTTATTTATTATATTAATATTTATTT
Found at i:62433 original size:12 final size:12
Alignment explanation
Indices: 62388--62445 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 12
62378 TATATTAATA
62388 TTATTTATTTTTAT
1 TTATTTA-TTTT-T
62402 TTATTATATTAATATT
1 TTATT-TATT--T-TT
62418 TTATTTATTTTT
1 TTATTTATTTTT
*
62430 TTATTTATTTTC
1 TTATTTATTTTT
62442 TTAT
1 TTAT
62446 CAGGTCCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 17 0.44
13 1 0.03
14 7 0.18
15 6 0.15
16 7 0.18
17 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:63645 original size:15 final size:16
Alignment explanation
Indices: 63625--63656 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
63615 TTGATTTTTA
63625 TCTATTTA-TTTATTT
1 TCTATTTATTTTATTT
63640 TCTATTTATTTTATTT
1 TCTATTTATTTTATTT
63656 T
1 T
63657 ATTAACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTATTTATTTTATTT
Found at i:63666 original size:16 final size:16
Alignment explanation
Indices: 63647--63684 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
63637 TTTTCTATTT
63647 ATTTTATTTTATTAAC
1 ATTTTATTTTATTAAC
*
63663 A-TTTATTTTCTTAAC
1 ATTTTATTTTATTAAC
63678 ATTTTAT
1 ATTTTAT
63685 ATATTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATTTTATTAAC
Found at i:63749 original size:18 final size:16
Alignment explanation
Indices: 63718--63751 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
63708 AAAATTTAAC
63718 TTTTTTTCTTTTTATT
1 TTTTTTTCTTTTTATT
63734 TTTTATTTCATTTTTATT
1 TTTT-TTTC-TTTTTATT
63752 GTAATATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTTTATT
Found at i:64938 original size:19 final size:19
Alignment explanation
Indices: 64911--64950 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
64901 TATTTTTTAC
64911 TATTATAA-TTATAAATATT
1 TATTATAATTTA-AAATATT
*
64930 TATTGTAATTTAAAATATT
1 TATTATAATTTAAAATATT
64949 TA
1 TA
64951 ATATTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTATAATTTAAAATATT
Found at i:65357 original size:18 final size:19
Alignment explanation
Indices: 65336--65382 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
65326 TTAAAAGATA
*
65336 AAAATATATTATCAATA-T
1 AAAATATATTATAAATACT
*
65354 AAAATATAATATAAATATCT
1 AAAATATATTATAAATA-CT
65374 AAAATATAT
1 AAAATATAT
65383 AATGATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
20 9 0.38
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATATTATAAATACT
Found at i:67428 original size:34 final size:33
Alignment explanation
Indices: 67358--67433 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
67348 ATCTCTGTTC
67358 AAAATTTAACGATAAATTTTGAGAAAAAATTGA
1 AAAATTTAACGATAAATTTTGAGAAAAAATTGA
* *
67391 AAAATTTAGCGTTAAATTTTGAGAAAAAAAATT-A
1 AAAATTTAACGATAAATTTTGAG--AAAAAATTGA
67425 AAAATTTAA
1 AAAATTTAA
67434 AAGCTTAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 21 0.55
34 9 0.24
35 8 0.21
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (33 bp):
AAAATTTAACGATAAATTTTGAGAAAAAATTGA
Found at i:72489 original size:23 final size:24
Alignment explanation
Indices: 72454--72502 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
72444 TCACCTGAAA
72454 AATACATATATAAAATTATATATT
1 AATACATATATAAAATTATATATT
*
72478 AATACA-ATATAATATTATATATT
1 AATACATATATAAAATTATATATT
72501 AA
1 AA
72503 ATCAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AATACATATATAAAATTATATATT
Found at i:76229 original size:17 final size:16
Alignment explanation
Indices: 76209--76285 Score: 66
Period size: 17 Copynumber: 4.6 Consensus size: 16
76199 GTTAGATTGT
76209 AAAAAATATATATAAAA
1 AAAAAATA-ATATAAAA
*
76226 AAAATATTAATATAATAA
1 AAAA-AATAATATAA-AA
* *
76244 TAAAAATAAAATAAATGA
1 AAAAAATAATATAAA--A
*
76262 AAAAAATAATA-AAAT
1 AAAAAATAATATAAAA
76277 AAAAAATAA
1 AAAAAATAA
76286 AAGTAGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 9 0.18
16 1 0.02
17 21 0.43
18 18 0.37
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (16 bp):
AAAAAATAATATAAAA
Found at i:76239 original size:21 final size:20
Alignment explanation
Indices: 76213--76287 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
76203 GATTGTAAAA
76213 AATATATATAAAAAAAATATT
1 AATATA-ATAAAAAAAATATT
* *
76234 AATATAATAATAAAAATA-A
1 AATATAATAAAAAAAATATT
* *
76253 AATA-AATGAAAAAAATAAT
1 AATATAATAAAAAAAATATT
*
76272 AAAATAA-AAAATAAAA
1 AATATAATAAAA-AAAA
76288 GTAGAAAGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.25
19 10 0.23
20 17 0.39
21 6 0.14
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (20 bp):
AATATAATAAAAAAAATATT
Found at i:76280 original size:15 final size:16
Alignment explanation
Indices: 76208--76285 Score: 63
Period size: 18 Copynumber: 4.6 Consensus size: 16
76198 TGTTAGATTG
76208 TAAAAAATATATATAAA
1 TAAAAAATA-ATATAAA
76225 -AAAAATATTAATAT-AA
1 TAAAAA-A-TAATATAAA
*
76241 TAATAAAAATAAAATAAA
1 T-A-AAAAATAATATAAA
76259 TGAAAAAAATAATA-AAA
1 T--AAAAAATAATATAAA
76276 TAAAAAATAA
1 TAAAAAATAA
76286 AAGTAGAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
15 9 0.17
16 7 0.13
17 14 0.27
18 16 0.31
19 6 0.12
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (16 bp):
TAAAAAATAATATAAA
Found at i:76335 original size:18 final size:16
Alignment explanation
Indices: 76245--76378 Score: 74
Period size: 17 Copynumber: 7.8 Consensus size: 16
76235 ATATAATAAT
76245 AAAAATAAAATAAATGAA
1 AAAAATAAAA-AAATG-A
*
76263 AAAAATAATAAAAT-A
1 AAAAATAAAAAAATGA
**
76278 AAAAATAAAAGTA-GA
1 AAAAATAAAAAAATGA
76293 AAGGTAAAGTAAAAGAAATGA
1 AA---AAA-TAAAA-AAATGA
*
76314 AAAACTAAAAAAATGAA
1 AAAAATAAAAAAATG-A
* *
76331 TAAAAAGAAAAAAATAGT
1 -AAAAATAAAAAAAT-GA
* *
76349 TAAAGTAAAAAACATGA
1 AAAAATAAAAAA-ATGA
*
76366 AATAATAAAAAAA
1 AAAAATAAAAAAA
76379 CCTAAAAAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
15 14 0.16
16 6 0.07
17 29 0.33
18 28 0.32
19 6 0.07
20 1 0.01
21 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAAATGA
Found at i:76459 original size:9 final size:9
Alignment explanation
Indices: 76445--76488 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
76435 AAAACAATTT
76445 AAAAAAGAA
1 AAAAAAGAA
76454 AAAAAAGAA
1 AAAAAAGAA
76463 TAAAAAATGAA
1 -AAAAAA-GAA
*
76474 ATAAAAGAA
1 AAAAAAGAA
76483 AAAAAA
1 AAAAAA
76489 TGACACGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 17 0.55
10 11 0.35
11 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:76468 original size:20 final size:19
Alignment explanation
Indices: 76445--76488 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
76435 AAAACAATTT
76445 AAAAAAGAAAAAAAAGAATA
1 AAAAAAGAAAAAAAAGAA-A
* *
76465 AAAAATGAAATAAAAGAAA
1 AAAAAAGAAAAAAAAGAAA
76484 AAAAA
1 AAAAA
76489 TGACACGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAGAAA
Found at i:76489 original size:19 final size:20
Alignment explanation
Indices: 76444--76491 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
76434 TAAAACAATT
76444 TAAAAAA-GAAAAAAAAGAA
1 TAAAAAATGAAAAAAAAGAA
*
76463 TAAAAAATGAAATAAAAGAA
1 TAAAAAATGAAAAAAAAGAA
76483 -AAAAAATGA
1 TAAAAAATGA
76492 CACGAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (20 bp):
TAAAAAATGAAAAAAAAGAA
Found at i:76612 original size:26 final size:26
Alignment explanation
Indices: 76582--76682 Score: 134
Period size: 26 Copynumber: 4.0 Consensus size: 26
76572 AACACACCTT
76582 AAACCACTACACCTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
* *
76608 AAACCACTACACTTATTAAAGTAATC
1 AAACCACTACACCTATTAAAATAATC
* *
76634 AAATCTCTACACCTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
* *
76660 AAACCA--ATATCTATTAAAATAAT
1 AAACCACTACACCTATTAAAATAAT
76683 TAAATCAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
24 15 0.23
26 50 0.77
ACGTcount: A:0.50, C:0.22, G:0.01, T:0.28
Consensus pattern (26 bp):
AAACCACTACACCTATTAAAATAATC
Found at i:76883 original size:2 final size:2
Alignment explanation
Indices: 76878--76968 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
76868 AAACGTTATG
76878 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
76920 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
76962 AT AT AT A
1 AT AT AT A
76969 AGAATGTTTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77093 original size:18 final size:18
Alignment explanation
Indices: 77072--77110 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
77062 AAAAAAATAG
77072 TAAAAAATAAAATAAAAA
1 TAAAAAATAAAATAAAAA
* * *
77090 TAAAATATATAATAATAA
1 TAAAAAATAAAATAAAAA
77108 TAA
1 TAA
77111 CCAAAAGGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATAAAATAAAAA
Found at i:77587 original size:14 final size:14
Alignment explanation
Indices: 77507--77590 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
77497 TTAGATTGCA
*
77507 AAAAAAT-ATAAAA
1 AAAAAATAATAAAT
77520 AAAAGAATAATAAA-
1 AAAA-AATAATAAAT
* *
77534 AAATATTAATATAAT
1 AAAAAATAATA-AAT
*
77549 AATAACAGTAACATAAAT
1 AA-AA-AAT-A-ATAAAT
77567 GAAAAAATAATAAAT
1 -AAAAAATAATAAAT
77582 AAAAAATAA
1 AAAAAATAA
77591 AAGGTAAAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
13 10 0.18
14 17 0.30
15 13 0.23
16 2 0.04
17 4 0.07
18 6 0.11
19 5 0.09
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:77636 original size:17 final size:18
Alignment explanation
Indices: 77602--77639 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
77592 AGGTAAAAGT
*
77602 AAAAGTAAAAGAAATAAA
1 AAAACTAAAAGAAATAAA
*
77620 AAAACTAAAA-AACTAAA
1 AAAACTAAAAGAAATAAA
77637 AAA
1 AAA
77640 TGAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (18 bp):
AAAACTAAAAGAAATAAA
Found at i:77637 original size:16 final size:15
Alignment explanation
Indices: 77613--77714 Score: 53
Period size: 17 Copynumber: 6.1 Consensus size: 15
77603 AAAGTAAAAG
77613 AAATAAAAAAACTAAA
1 AAAT-AAAAAACTAAA
77629 AAACTAAAAAA-TGAATAA
1 AAA-TAAAAAACT--A-AA
* *
77647 AAAGAAAAAAATAATTA
1 AAATAAAAAACTAA--A
*
77664 AATTAAAAAACATGAAA
1 AAATAAAAAAC-T-AAA
*
77681 TAATAAAAAACCTAAA
1 AAATAAAAAA-CTAAA
*
77697 ATAATAAAAACCTAAA
1 A-AATAAAAAACTAAA
77713 AA
1 AA
77715 TGATTATCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 23
0.68 0.08 0.23
Matches are distributed among these distances:
15 3 0.04
16 19 0.28
17 35 0.52
18 8 0.12
19 2 0.03
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.17
Consensus pattern (15 bp):
AAATAAAAAACTAAA
Found at i:77715 original size:17 final size:17
Alignment explanation
Indices: 77667--77713 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
77657 ATAATTAAAT
* *
77667 TAAAAAACATGAAATAA
1 TAAAAAACCTAAAATAA
77684 TAAAAAACCTAAAATAA
1 TAAAAAACCTAAAATAA
77701 T-AAAAACCTAAAA
1 TAAAAAACCTAAAA
77714 ATGATTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.17
Consensus pattern (17 bp):
TAAAAAACCTAAAATAA
Found at i:77757 original size:3 final size:3
Alignment explanation
Indices: 77749--77773 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
77739 CTAAAAACAA
77749 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
77774 TTTAAAACAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77958 original size:26 final size:26
Alignment explanation
Indices: 77922--77996 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 26
77912 AACCCACCCT
77922 AAACCACTACACCTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
*
77948 AAACCACTACACTTATTAAAATAATC
1 AAACCACTACACCTATTAAAATAATC
77974 AAACCACT--ACCTATTAAAATAAT
1 AAACCACTACACCTATTAAAATAAT
77997 TAAATCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.30
26 33 0.70
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (26 bp):
AAACCACTACACCTATTAAAATAATC
Found at i:79936 original size:42 final size:42
Alignment explanation
Indices: 79851--79940 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
79841 TAGTTGTTTG
** *
79851 ATTATTTTAATAGGTGTAGTGGTTTAGGGTGTGTTTGATTTA
1 ATTATTTTAATAGGTGTAGTGGTTTAGGGTGAATTTGAGTTA
* *
79893 ATTATTTTAATAGGTGTAGTGGTTTAGGTTGAATTTGGGTTA
1 ATTATTTTAATAGGTGTAGTGGTTTAGGGTGAATTTGAGTTA
79935 ATTATT
1 ATTATT
79941 ATCTTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (42 bp):
ATTATTTTAATAGGTGTAGTGGTTTAGGGTGAATTTGAGTTA
Found at i:80130 original size:27 final size:26
Alignment explanation
Indices: 80100--80154 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
80090 GTTTTTAAAA
80100 TTTAACTATTTTTTCTT-TTTATTCATT
1 TTTAACT-TTTTTT-TTATTTATTCATT
* *
80127 TTTAAGTTTTTTTTTATTTATTTATT
1 TTTAACTTTTTTTTTATTTATTCATT
80153 TT
1 TT
80155 ACTTTTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 17 0.68
27 6 0.24
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTAACTTTTTTTTTATTTATTCATT
Found at i:84241 original size:99 final size:99
Alignment explanation
Indices: 84134--84331 Score: 229
Period size: 99 Copynumber: 2.0 Consensus size: 99
84124 TTGTAATATT
* * *
84134 ATATATATACAACAAAGCTTGAACT-ATC-CCTATAGAGCAATTGGTTAAATGCCTCAGCTTTAT
1 ATATATATACAACAAAACTTGAACTGATCGCCTA-AGA-CAATTGGTTAAACGCCACAGCTTTAT
* *
84197 GGATAATATTCACCTAGCCTGATAAAGGTGATTATA
64 GGATAAGATTCACCTAACCTGATAAAGGTGATTATA
* * ** * * *
84233 ATATATATACAATAAAATTTGAGTTGTTCGTCTAAGACAATTGGTTAAACGCCACGGCTTTATGG
1 ATATATATACAACAAAACTTGAACTGATCGCCTAAGACAATTGGTTAAACGCCACAGCTTTATGG
* * *
84298 ATAAGATTCAGCTAACTTGATAAAGGTGTTTATA
66 ATAAGATTCACCTAACCTGATAAAGGTGATTATA
84332 TATTGAGTTG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
99 74 0.90
100 5 0.06
101 3 0.04
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAACAAAACTTGAACTGATCGCCTAAGACAATTGGTTAAACGCCACAGCTTTATGG
ATAAGATTCACCTAACCTGATAAAGGTGATTATA
Found at i:85016 original size:18 final size:18
Alignment explanation
Indices: 84990--85037 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
84980 GAAGAAAATG
* *
84990 GGACAAGATCGATTTCCA
1 GGACCAGATCGATTCCCA
85008 GGACCAGATCGATTCCCA
1 GGACCAGATCGATTCCCA
*
85026 AGACCAGATCGA
1 GGACCAGATCGA
85038 CATACAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (18 bp):
GGACCAGATCGATTCCCA
Found at i:85829 original size:85 final size:85
Alignment explanation
Indices: 85592--86506 Score: 1210
Period size: 85 Copynumber: 10.8 Consensus size: 85
85582 GAACTGTTGG
* * *
85592 CAGCATAACTCATGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* *
85657 TCAAAGGAATATTAAATTTA
66 TCAAAGGCATATCAAATTTA
* *
85677 CAACATAGCTC-AGGCGAGAA-GGTCTATCTATCAACAAAGACCTTCGAGTTCGATTACATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGT-TATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAG
*
85740 CTCAAAGGCACATCAAATTTA
65 CTCAAAGGCATATCAAATTTA
* * * * *
85761 CAGCATAACTCAAGGTGAGAAGGGTTATCTGTCAACGAAGTCCTTCAAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* *
85826 TCAAAGGCACATCAAATTTG
66 TCAAAGGCATATCAAATTTA
* * *
85846 CAGCATAGCTCAAGGCGAGAAGGGTTATCTTTCAATAAAGACCTTTGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
85911 TCAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * *** * *
85931 CACCATAGCTCAAGGCAAGAAGTACTATATGTCAACAAAGACATTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
85996 TCAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * *
86016 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAATAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
86081 TCAAAGACATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * *
86101 CAACATAACTCAAGGTGAGAAGGGTTATCTATC-A-ATAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
86164 TCAAAGACATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * *
86184 CAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAACAAAGACTTTCGAGTTCGATTACATTCAAC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
86249 TCAAAGGCATATTAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * * * * *
86269 CAACATAACTCATGGAGAGAAGGGTTATATGTCAATAAAGACCTTCGAGTTCAATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
*
86334 TTAAAGGCATATCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * * *
86354 CATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAATACCTTCGAGTTCGATTCCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
* *
86419 TCAATGGCATGTCAAATTTA
66 TCAAAGGCATATCAAATTTA
* * ** ** * *
86439 CAGCTTAGCTTAAGTTGAGAAAAGTTATCTGTCAAC-AAGAAACTGTCGAGTTCGATTCCATTCA
1 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAG-ACCT-TCGAGTTCGATTACATTCA
86503 GCTC
64 GCTC
86507 GATGACACAT
Statistics
Matches: 728, Mismatches: 95, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
83 78 0.11
84 76 0.10
85 548 0.75
86 26 0.04
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
TCAAAGGCATATCAAATTTA
Found at i:86389 original size:423 final size:423
Alignment explanation
Indices: 85592--86506 Score: 1298
Period size: 423 Copynumber: 2.2 Consensus size: 423
85582 GAACTGTTGG
*
85592 CAGCATAACTCATGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAGACCTTCGAGTTCGATTACATTCAGC
* *
85657 TCAAAGGAATATTAAATTTACAACATAGCTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTC
65 TCAAAGGAATATCAAATTTACAACATAACTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTC
* * *
85722 GAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAACTCAAGGTGAGAAGGGTT
130 GAGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCT
* * * * * *
85787 ATCTGTCAACGAAGTCCTTCAAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTGCAGCAT
195 ATATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAACAT
* * * * * *
85852 AGCTCAAGGCGAGAAGGGTTATCTTTCAATAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAG
260 AACTCAAGGAGAGAAGGGTTATATGTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTCAAAG
*
85917 GCATATCAAATTTACACCATAGCTCAAGGCAAGAAGTACTATATGTCAACAAAGACATTCGAGTT
325 GCATATCAAATTTACACCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCGAGTT
85982 CGATTACATTCAGCTCAAAGGCATATCAAATTTA
390 CGATTACATTCAGCTCAAAGGCATATCAAATTTA
* *
86016 CAGCATAACTCAAGGCGAGAAGGGTTATCTATCAATAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAGACCTTCGAGTTCGATTACATTCAGC
* *
86081 TCAAA-GACATATCAAATTTACAACATAACTCAAGGTGAGAAGGGT-TATCTATC-A-ATAGACC
65 TCAAAGGA-ATATCAAATTTACAACATAACTC-AGGCGAGAA-GGTCTATCTATCAACAAAGACC
* *
86142 TTCGAGTTCGATTACATTCAGCTCAAAGACATATCAAATTTACAGCATAGCTCAAGGCGAGAAGG
127 TTCGAGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGG
* * * *
86207 GCTATATGTCAACAAAGACTTTCGAGTTCGATTACATTCAACTCAAAGGCATATTAAATTTACAA
192 GCTATATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAA
* *
86272 CATAACTCATGGAGAGAAGGGTTATATGTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTTA
257 CATAACTCAAGGAGAGAAGGGTTATATGTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTCA
* * * * * *
86337 AAGGCATATCAAATTTACATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAATACCTTCGA
322 AAGGCATATCAAATTTACACCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCGA
* * *
86402 GTTCGATTCCATTCAGCTCAATGGCATGTCAAATTTA
387 GTTCGATTACATTCAGCTCAAAGGCATATCAAATTTA
* * * ** ** * *
86439 CAGCTTAGCTTAAGTTGAGAAAAGTTATCTGTCAACAAGAAACTGTCGAGTTCGATTCCATTCAG
1 CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAG-ACCT-TCGAGTTCGATTACATTCAG
86504 CTC
64 CTC
86507 GATGACACAT
Statistics
Matches: 434, Mismatches: 52, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
422 3 0.01
423 302 0.70
424 110 0.25
425 16 0.04
426 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (423 bp):
CAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAGACCTTCGAGTTCGATTACATTCAGCT
CAAAGGAATATCAAATTTACAACATAACTCAGGCGAGAAGGTCTATCTATCAACAAAGACCTTCG
AGTTCGATTACATTCAGCTCAAAGACACATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCTA
TATGTCAACAAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGCACATCAAATTTACAACATA
ACTCAAGGAGAGAAGGGTTATATGTCAATAAAGACCTTCGAGTTCAATTACATTCAGCTCAAAGG
CATATCAAATTTACACCATAGCTCAAGGCAAGAAGGACTATATGTCAACAAAGACATTCGAGTTC
GATTACATTCAGCTCAAAGGCATATCAAATTTA
Found at i:88267 original size:23 final size:23
Alignment explanation
Indices: 88238--88286 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
88228 ATTATTATTA
88238 TATATTTCAT-TTCATTTCATTTT
1 TATATTT-ATATTCATTTCATTTT
* *
88261 TATATTTATATTTATTTTATTTT
1 TATATTTATATTCATTTCATTTT
88284 TAT
1 TAT
88287 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (23 bp):
TATATTTATATTCATTTCATTTT
Found at i:88307 original size:29 final size:29
Alignment explanation
Indices: 88275--88330 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
88265 TTTATATTTA
* *
88275 TTTTATTTTTATTTTTTACTATTTTTTCG
1 TTTTAGTTTCATTTTTTACTATTTTTTCG
* * *
88304 TTTTGGTTTCCTTTTTTATTATTTTTT
1 TTTTAGTTTCATTTTTTACTATTTTTT
88331 TCTTTTCTCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (29 bp):
TTTTAGTTTCATTTTTTACTATTTTTTCG
Found at i:88741 original size:11 final size:10
Alignment explanation
Indices: 88725--88807 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 10
88715 TATTAGATTG
88725 TAAAAAATATA
1 TAAAAAATA-A
88736 TAAAAAATAA
1 TAAAAAATAA
88746 TAAAAATATTAA
1 TAAAAA-A-TAA
*
88758 TATAATAATAA
1 TA-AAAAATAA
*
88769 GAATAAAATAAA
1 TAA-AAAAT-AA
88781 TGAAAAAATAA
1 T-AAAAAATAA
* *
88792 AAAATAAAAAA
1 TAAA-AAATAA
88803 TAAAA
1 TAAAA
88808 GGTAAAAGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
10 12 0.21
11 28 0.48
12 13 0.22
13 5 0.09
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:88752 original size:20 final size:20
Alignment explanation
Indices: 88727--88773 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
88717 TTAGATTGTA
88727 AAAAATATATAA-AAAATAAT
1 AAAAATAT-TAATAAAATAAT
*
88747 AAAAATATTAATATAATAAT
1 AAAAATATTAATAAAATAAT
*
88767 AAGAATA
1 AAAAATA
88774 AAATAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATATTAATAAAATAAT
Found at i:88795 original size:7 final size:7
Alignment explanation
Indices: 88778--88807 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
88768 AGAATAAAAT
88778 AAATGAAA
1 AAAT-AAA
88786 AAATAAA
1 AAATAAA
88793 AAATAAA
1 AAATAAA
88800 AAATAAA
1 AAATAAA
88807 A
1 A
88808 GGTAAAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:88988 original size:10 final size:9
Alignment explanation
Indices: 88968--89005 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
88958 AAACAATTTA
88968 AAAAAGAA-
1 AAAAAGAAT
*
88976 AAAAGGAAT
1 AAAAAGAAT
88985 AAAAAGAA-
1 AAAAAGAAT
88993 AAAAAGAAT
1 AAAAAGAAT
89002 AAAA
1 AAAA
89006 GGTTACGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 15 0.58
9 11 0.42
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (9 bp):
AAAAAGAAT
Found at i:88988 original size:17 final size:17
Alignment explanation
Indices: 88968--89005 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
88958 AAACAATTTA
*
88968 AAAAAGAAAAAAGGAAT
1 AAAAAGAAAAAAAGAAT
88985 AAAAAGAAAAAAAGAAT
1 AAAAAGAAAAAAAGAAT
89002 AAAA
1 AAAA
89006 GGTTACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAT
Found at i:89083 original size:26 final size:25
Alignment explanation
Indices: 89054--89127 Score: 107
Period size: 26 Copynumber: 3.0 Consensus size: 25
89044 AATTCAACCT
89054 AAACCACTACACCTATTAAAATAATC
1 AAACCACTA-ACCTATTAAAATAATC
*
89080 AAACCACTAAACCTGTTAAAATAATC
1 AAACCACT-AACCTATTAAAATAATC
89106 AAACCACT-ACCTATT-AAATAAT
1 AAACCACTAACCTATTAAAATAAT
89128 TAAATCAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
23 7 0.16
24 6 0.13
26 31 0.69
27 1 0.02
ACGTcount: A:0.50, C:0.24, G:0.01, T:0.24
Consensus pattern (25 bp):
AAACCACTAACCTATTAAAATAATC
Found at i:90937 original size:85 final size:85
Alignment explanation
Indices: 90840--91608 Score: 1065
Period size: 85 Copynumber: 9.0 Consensus size: 85
90830 CTCAAGTTAA
* * * *
90840 GCTGTAAATTTGACATGCCCTTGAGCTGAATGAAATCGAACTCGAAGGTATTTGTTGACAGATAG
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
* * *
90905 CCCTTATCGCCTTAAGCAAT
66 CCCTTCTCGCCTTGAGCTAT
* * *
90925 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTATTGACAGATAA
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
90990 CCCTTCTCGCCTTGAG-TAAT
66 CCCTTCTCGCCTTGAGCT-AT
* *
91010 -CTTGTAAATTTGATATGTCTTTGAGTTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA
1 GC-TGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA
* *
91074 GTCCTTCTCGCCTTAAGCTAT
65 GCCCTTCTCGCCTTGAGCTAT
* * * * *
91095 GCTGTAAATTTGATATGTCTTTGAGCTGAATGTAATCGAACTCGAAGATCATTATTGACAGATAA
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
* *
91160 CCCTTCTCACCTTGAGTTAT
66 CCCTTCTCGCCTTGAGCTAT
*
91180 GTTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
* *
91245 CCCTTCTTGCCTTGAGTTAT
66 CCCTTCTCGCCTTGAGCTAT
* * * *
91265 GCTGTAAATTTAATATGACTTTGAGTTGAATGTAATCGAACTCGAAGGTCTTTATTGACAGATAG
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
*
91330 CCCTTCTCTCCTTGAGCTAT
66 CCCTTCTCGCCTTGAGCTAT
* * * * * * *
91350 GCTGCAAATTTGATGTGTCTTTAAGCTGAATATAATTGAACTCGAAGGTCTTTTTTGACAGATAG
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
*
91415 CCCTTCTCGCCTTGAGTTAT
66 CCCTTCTCGCCTTGAGCTAT
* * * * *
91435 GCTATAAATTTGATGTGCATTTGAGCTGAATGTAATCGAACTCGAAGGACTTTGTTGACAGATAA
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
91500 CCCTTCTCGCCTTGAGCTAT
66 CCCTTCTCGCCTTGAGCTAT
* * * * *
91520 GCTGTAAATTTGATATACCTTTGAGCTGACTGTAATCGAACTCGAAGGTCTTGGTTGATAGATAA
1 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
* *
91585 ACCTTCTCGCCTTGAGTTAT
66 CCCTTCTCGCCTTGAGCTAT
91605 GCTG
1 GCTG
91609 CCAATAGTTC
Statistics
Matches: 606, Mismatches: 74, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
84 1 0.00
85 603 1.00
86 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (85 bp):
GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
CCCTTCTCGCCTTGAGCTAT
Found at i:96154 original size:18 final size:17
Alignment explanation
Indices: 96133--96184 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
96123 TAAAAAAAGA
*
96133 ATAATAAAAAATATTAAT
1 ATAATAAAAAATA-AAAT
96151 ATAATAATAACAATAAAAT
1 ATAATAA-AA-AATAAAAT
96170 A-AATAAAAAATAAAA
1 ATAATAAAAAATAAAA
96185 GTAAAAAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 7 0.23
17 2 0.06
18 12 0.39
19 6 0.19
20 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAATAAAAAATAAAAT
Found at i:96175 original size:21 final size:20
Alignment explanation
Indices: 96122--96190 Score: 52
Period size: 22 Copynumber: 3.3 Consensus size: 20
96112 TAAAAAATAT
*
96122 ATAAAA-AAAGAATAATAAA
1 ATAAAATAAATAATAATAAA
*
96141 A-AATATTAATATAATAATAACA
1 ATAA-AATAA-ATAATAATAA-A
*
96163 ATAAAATAAATAAAAAATAAA
1 ATAAAATAAAT-AATAATAAA
96184 AGTAAAA
1 A-TAAAA
96191 AGGTAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 2 0.05
21 13 0.33
22 18 0.46
23 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (20 bp):
ATAAAATAAATAATAATAAA
Found at i:96468 original size:26 final size:24
Alignment explanation
Indices: 96439--96487 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
96429 AATTCAACCT
96439 AAACCACTACACTTATTAAAATAATA
1 AAACCACTAC-C-TATTAAAATAATA
*
96465 AAACCATTACCTATTAAAATAAT
1 AAACCACTACCTATTAAAATAAT
96488 TAAATCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 1 0.05
26 9 0.41
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (24 bp):
AAACCACTACCTATTAAAATAATA
Found at i:96831 original size:28 final size:27
Alignment explanation
Indices: 96785--96867 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
96775 TAACGTTAGG
*
96785 AGAAAGAAAAAATAATAAAAAATGAAA
1 AGAAAGAAAAAATAATAAAAAATAAAA
* *
96812 AGAAACGAAAAAGTAGTAAAAAATAAAA
1 AGAAA-GAAAAAATAATAAAAAATAAAA
* *
96840 ATAAAAAACAAAATAA-AATAAAATAAAA
1 AGAAAGAA-AAAATAATAA-AAAATAAAA
96868 TATATAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 9 0.20
28 37 0.80
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.12
Consensus pattern (27 bp):
AGAAAGAAAAAATAATAAAAAATAAAA
Found at i:96876 original size:17 final size:16
Alignment explanation
Indices: 96831--96883 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
96821 AAAGTAGTAA
96831 AAAAT-AAA-AATAA-
1 AAAATAAAATAATAAT
*
96844 AAAACAAAATAA-AAT
1 AAAATAAAATAATAAT
96859 AAAATAAAATATATAAT
1 AAAATAAAATA-ATAAT
96876 AATAATAA
1 AA-AATAA
96884 TAACCAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 4 0.12
14 5 0.16
15 12 0.38
16 1 0.03
17 5 0.16
18 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAATAAT
Found at i:108241 original size:14 final size:13
Alignment explanation
Indices: 108218--108247 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
108208 AACATACTAA
108218 AAATATAAAAATCT
1 AAATA-AAAAATCT
108232 AAATAAAAAATCT
1 AAATAAAAAATCT
108245 AAA
1 AAA
108248 ATATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAAAAATCT
Found at i:108249 original size:14 final size:15
Alignment explanation
Indices: 108217--108252 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
108207 AAACATACTA
108217 AAAATATAAAAATCT
1 AAAATATAAAAATCT
108232 -AAATA-AAAAATCT
1 AAAATATAAAAATCT
108245 AAAATATA
1 AAAATATA
108253 TGATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.42
14 10 0.53
15 1 0.05
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATATAAAAATCT
Found at i:112082 original size:22 final size:22
Alignment explanation
Indices: 112057--112099 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
112047 TGTAACAGAG
112057 TTGCA-CATATTGTAGTTCTTAA
1 TTGCACCATATTG-AGTTCTTAA
112079 TTGCATCCATATTGAGTTCTT
1 TTGCA-CCATATTGAGTTCTT
112100 TTGTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (22 bp):
TTGCACCATATTGAGTTCTTAA
Found at i:117338 original size:15 final size:17
Alignment explanation
Indices: 117307--117338 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
117297 ATGTATTTTT
117307 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
117324 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
117339 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:117440 original size:29 final size:31
Alignment explanation
Indices: 117398--117471 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
117388 CATAAAAGAT
**
117398 AGAATAAGAGAAAATAATGTAAC-AAAGAAA-A
1 AGAA-AAGA-AAAATAAAATAACAAAAGAAATA
117429 AGAAAAGAAAAATAAAATAACAAAAGAAATA
1 AGAAAAGAAAAATAAAATAACAAAAGAAATA
* *
117460 AAAAAATAAAAA
1 AGAAAAGAAAAA
117472 ATCATGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.30
30 11 0.30
31 15 0.41
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (31 bp):
AGAAAAGAAAAATAAAATAACAAAAGAAATA
Found at i:117455 original size:19 final size:19
Alignment explanation
Indices: 117431--117472 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
117421 AAAGAAAAAG
*
117431 AAAAGAAA-AATAAAATAA
1 AAAAGAAATAAAAAAATAA
117449 CAAAAGAAATAAAAAAATAA
1 -AAAAGAAATAAAAAAATAA
117469 AAAA
1 AAAA
117473 TCATGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (19 bp):
AAAAGAAATAAAAAAATAA
Found at i:120762 original size:14 final size:14
Alignment explanation
Indices: 120743--120769 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
120733 TAATTAAGCT
120743 ATTAAGTTTGTAAC
1 ATTAAGTTTGTAAC
120757 ATTAAGTTTGTAA
1 ATTAAGTTTGTAA
120770 ATATCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
ATTAAGTTTGTAAC
Found at i:121283 original size:3 final size:3
Alignment explanation
Indices: 121275--121345 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
121265 ATTTATAACA
121275 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
121322 TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
121346 TGTGGAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:128687 original size:57 final size:56
Alignment explanation
Indices: 128594--128882 Score: 434
Period size: 57 Copynumber: 5.1 Consensus size: 56
128584 AACTTCTCAG
* * * * *
128594 TTTTTGAACATAAAGTGCTCATACGAAAATTCATAAACTAATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCATACG-AAATTCATAAACTTATTATGAATTTCTTAGC
* *
128651 TTTTTGCACACAAAGTGCCCATACAGAAATTTATAAACTTGTTATGAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATAC-GAAATTCATAAACTTATTATGAATTTCTTAGC
128708 TTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATACG-AAATTCATAAACTTATTATGAATTTCTTAGC
* *
128765 TTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTTATTATAAATTTCTTAGC
1 TTTTTGCACACAAAGTGCCCATA-CGAAATTCATAAACTTATTATGAATTTCTTAGC
* *
128822 TTTTTGTACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
1 TTTTTGCACACAAAGTGCCCATAC-GAAATTCATAAACTTATTATGAATTTCTTAGC
128879 TTTT
1 TTTT
128883 ATACACTCGG
Statistics
Matches: 213, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
56 1 0.00
57 210 0.99
58 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (56 bp):
TTTTTGCACACAAAGTGCCCATACGAAATTCATAAACTTATTATGAATTTCTTAGC
Done.