Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015223.1 Kokia drynarioides strain JFW-HI SEQ_130267, 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: 583935
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 856 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:307533 original size:21 final size:24
Alignment explanation
Indices: 307507--307561 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 24
307497 GACTTGCGTT
*
307507 GTATCGGTAGTTC-A-ATAT-GAA
1 GTATCGGTAGTTCTAGACATAGAA
*
307528 GTATCGGTGGTTCTAGACATAGAA
1 GTATCGGTAGTTCTAGACATAGAA
307552 GTATCGGTAG
1 GTATCGGTAG
307562 ATGATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.43
22 1 0.04
23 3 0.11
24 12 0.43
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (24 bp):
GTATCGGTAGTTCTAGACATAGAA
Found at i:311227 original size:131 final size:131
Alignment explanation
Indices: 311050--311312 Score: 526
Period size: 131 Copynumber: 2.0 Consensus size: 131
311040 CTGAAGTATC
311050 TGATGACTCAAAAAGAACTGAATCTGAGGCAACACCGATGTTAGAACTATTGAAAGATTATGATC
1 TGATGACTCAAAAAGAACTGAATCTGAGGCAACACCGATGTTAGAACTATTGAAAGATTATGATC
311115 TGGTAATTGATTATCATCCAGGGAAGGCTAATGTTGTTAATGATGCTTTGAGCCAAAAATCGTTG
66 TGGTAATTGATTATCATCCAGGGAAGGCTAATGTTGTTAATGATGCTTTGAGCCAAAAATCGTTG
311180 T
131 T
311181 TGATGACTCAAAAAGAACTGAATCTGAGGCAACACCGATGTTAGAACTATTGAAAGATTATGATC
1 TGATGACTCAAAAAGAACTGAATCTGAGGCAACACCGATGTTAGAACTATTGAAAGATTATGATC
311246 TGGTAATTGATTATCATCCAGGGAAGGCTAATGTTGTTAATGATGCTTTGAGCCAAAAATCGTTG
66 TGGTAATTGATTATCATCCAGGGAAGGCTAATGTTGTTAATGATGCTTTGAGCCAAAAATCGTTG
311311 T
131 T
311312 T
1 T
311313 TGCATTGAGG
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (131 bp):
TGATGACTCAAAAAGAACTGAATCTGAGGCAACACCGATGTTAGAACTATTGAAAGATTATGATC
TGGTAATTGATTATCATCCAGGGAAGGCTAATGTTGTTAATGATGCTTTGAGCCAAAAATCGTTG
T
Found at i:313771 original size:25 final size:25
Alignment explanation
Indices: 313720--313772 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
313710 ATGGATTTTG
* ** *
313720 GCTCGTAAGAGCGTTATTCTGTTTA
1 GCTCGAAAGAGCGAAATTCTGTCTA
*
313745 GCTCGAAAGAGCGAAATTTTGTCTA
1 GCTCGAAAGAGCGAAATTCTGTCTA
313770 GCT
1 GCT
313773 TAGAAGAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (25 bp):
GCTCGAAAGAGCGAAATTCTGTCTA
Found at i:313920 original size:78 final size:78
Alignment explanation
Indices: 313716--313921 Score: 220
Period size: 78 Copynumber: 2.6 Consensus size: 78
313706 TATTATGGAT
* * * *
313716 TTTGGCTCGTAAGAGCGTTATTCTGTTTAGCTCGAAAGAGCGAAATTTTGTCTAGCTTAGAAGAG
1 TTTGGCTCGTAAGAGCGTTATTCTGTTTGGCTCGATAGAGCAAAATTTTGTCTAGCTGAGAAGAG
*
313781 CAATATTCTAAAT
66 CAATATTCTAAAG
* * ** * *
313794 TTTGGCTCGCAAGTGCGAAACTT-TGTTTGGCTC-ATATGAGCAATATTTTGTCTGGCTCGA-AA
1 TTTGGCTCGTAAGAGCGTTA-TTCTGTTTGGCTCGATA-GAGCAAAATTTTGTCTAGCT-GAGAA
313856 GAGCAATATTCTAAAG
63 GAGCAATATTCTAAAG
** * * *
313872 TTTGGCTCGTAAGAGCGTTATTCTGTCGGGCTCGTTAGAGCTACATTTTG
1 TTTGGCTCGTAAGAGCGTTATTCTGTTTGGCTCGATAGAGCAAAATTTTG
313922 GAAGACTCGA
Statistics
Matches: 103, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
77 4 0.04
78 94 0.91
79 5 0.05
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (78 bp):
TTTGGCTCGTAAGAGCGTTATTCTGTTTGGCTCGATAGAGCAAAATTTTGTCTAGCTGAGAAGAG
CAATATTCTAAAG
Found at i:320703 original size:18 final size:18
Alignment explanation
Indices: 320666--320705 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
320656 TTGTTTTTAC
*
320666 TTTTAATTCAATTTATTT
1 TTTTAATTCAATTTAGTT
* *
320684 TTTTAATTCTATTTGGTT
1 TTTTAATTCAATTTAGTT
320702 TTTT
1 TTTT
320706 GCACATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTAATTCAATTTAGTT
Found at i:321540 original size:15 final size:15
Alignment explanation
Indices: 321520--321576 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
321510 ATTCAATATT
321520 AATATTTTAATAATA
1 AATATTTTAATAATA
*
321535 AATATTTATTACGATGATA
1 AATA-TT-TTA--ATAATA
*
321554 AATATATTAATAATA
1 AATATTTTAATAATA
*
321569 AATGTTTT
1 AATATTTT
321577 GCAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 15 0.45
16 2 0.06
17 6 0.18
18 1 0.03
19 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:327189 original size:20 final size:21
Alignment explanation
Indices: 327150--327191 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
327140 ATTGACTTAT
*
327150 AAATAGGATTAATTAGAGTTA
1 AAATAGGATTAAGTAGAGTTA
*
327171 AAATATGATTAAGTA-AGTTA
1 AAATAGGATTAAGTAGAGTTA
327191 A
1 A
327192 TCATTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATAGGATTAAGTAGAGTTA
Found at i:334237 original size:15 final size:15
Alignment explanation
Indices: 334217--334258 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
334207 ATCGCGACAA
334217 TGTCTTCCTCTTTCT
1 TGTCTTCCTCTTTCT
334232 TGTCTT-C-CTTTCT
1 TGTCTTCCTCTTTCT
*
334245 T-TCTTCTTCTTTCT
1 TGTCTTCCTCTTTCT
334259 CTTCTGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 7 0.29
15 6 0.25
ACGTcount: A:0.00, C:0.31, G:0.05, T:0.64
Consensus pattern (15 bp):
TGTCTTCCTCTTTCT
Found at i:335231 original size:38 final size:38
Alignment explanation
Indices: 335172--335246 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
335162 GTTTGGATTA
* *
335172 TTTTCGGTCCAGACAAGACCATTGATGCACAAATCATG
1 TTTTCGGTCCAAACAACACCATTGATGCACAAATCATG
335210 TTTTCGGTCCAAACAACACCATTGATGCACAAATCAT
1 TTTTCGGTCCAAACAACACCATTGATGCACAAATCAT
335247 TCAGTAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (38 bp):
TTTTCGGTCCAAACAACACCATTGATGCACAAATCATG
Found at i:345937 original size:24 final size:24
Alignment explanation
Indices: 345910--345958 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
345900 AGTTAAAAAA
345910 TGACTAAGTAAGTTAATCATAAAG
1 TGACTAAGTAAGTTAATCATAAAG
345934 TGACTAAGTAAGTTAATCATAAAG
1 TGACTAAGTAAGTTAATCATAAAG
345958 T
1 T
345959 TGTTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (24 bp):
TGACTAAGTAAGTTAATCATAAAG
Found at i:346297 original size:71 final size:71
Alignment explanation
Indices: 346181--346327 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
346171 CTAGGGACCA
*
346181 ATTTGTGAATATTTCAAATGTCATAAAACTTGTCATTATTGGAAATGCTTACTCTTGAAAGCTTT
1 ATTTGTGAATATTTCAAATGTCATAAAACTTGCCATTATTGGAAATGCTTACTCTTGAAAGCTTT
346246 TGATAG
66 TGATAG
* * *
346252 ATTTGTGAATATTTCAAATGTTATAAAACTTGCCATTGTTGGAAATGCTTACTCTTGGAAGCTTT
1 ATTTGTGAATATTTCAAATGTCATAAAACTTGCCATTATTGGAAATGCTTACTCTTGAAAGCTTT
346317 TGATAG
66 TGATAG
346323 ATTTG
1 ATTTG
346328 ACTGCTTGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (71 bp):
ATTTGTGAATATTTCAAATGTCATAAAACTTGCCATTATTGGAAATGCTTACTCTTGAAAGCTTT
TGATAG
Found at i:347317 original size:21 final size:21
Alignment explanation
Indices: 347293--347349 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
347283 CCTATGACAA
*
347293 TTCTACCAATACTAATGAAGC
1 TTCTACCAATACTAATCAAGC
* * *
347314 TTCTACCAAAACAAATCATGC
1 TTCTACCAATACTAATCAAGC
* *
347335 TTTTACCAGTACTAA
1 TTCTACCAATACTAA
347350 AAACTCCAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (21 bp):
TTCTACCAATACTAATCAAGC
Found at i:348143 original size:52 final size:52
Alignment explanation
Indices: 348081--348372 Score: 444
Period size: 52 Copynumber: 5.6 Consensus size: 52
348071 TTCACATTTA
* *
348081 ATACTCACGATGACACATTGTCATCGGACCTCATAATCCG-AATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAA-AGGATTCAT
** * *
348133 ATACTCACGATGACACATAGTCATCGGACCTCGTAATTCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
348185 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
*
348237 ATACTCACGAT-ATCACATAGTCATCGAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGA-CACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
* ** *
348289 ATACTCACGATGACACATAGTTATCGGACCTTATAATTTGTAAAGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
*
348341 ATACTCACGATGACACATAGTCATCAGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
348373 TTGCATTTAT
Statistics
Matches: 221, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.00
52 217 0.98
53 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
Found at i:359676 original size:18 final size:18
Alignment explanation
Indices: 359650--359688 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
359640 TTTTTTAAAA
*
359650 ATTATAATAATATAAAT-T
1 ATTAAAATAATA-AAATGT
359668 ATTAAAATAATAAAATGT
1 ATTAAAATAATAAAATGT
359686 ATT
1 ATT
359689 TTTATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAAATAATAAAATGT
Found at i:360135 original size:26 final size:25
Alignment explanation
Indices: 360098--360148 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
360088 TAAAAATAGG
360098 AAAAAAAAA-TTTAAATCCC-TTAAT
1 AAAAAAAAATTTTAAA-CCCATTAAT
360122 AAAAAATAATATTTTAAACCCATTAAT
1 AAAAAA-AA-ATTTTAAACCCATTAAT
360149 CTTAAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 4 0.17
27 11 0.48
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAAAAATTTTAAACCCATTAAT
Found at i:361538 original size:27 final size:28
Alignment explanation
Indices: 361508--361560 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
361498 GCCAAACCCT
361508 CAAAAC-CTTTTTCCTTTAATTTCTCCC
1 CAAAACACTTTTTCCTTTAATTTCTCCC
* *
361535 CAAAACATTTTTTCTTTTAATTTCTC
1 CAAAACACTTTTTCCTTTAATTTCTC
361561 ATCAAAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.25, C:0.26, G:0.00, T:0.49
Consensus pattern (28 bp):
CAAAACACTTTTTCCTTTAATTTCTCCC
Found at i:361566 original size:28 final size:27
Alignment explanation
Indices: 361507--361568 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
361497 TGCCAAACCC
*
361507 TCAAAACCTTTTTCCTTTAATTTCTCC
1 TCAAAACCTTTTTCCTTTAATTTCTCA
* * *
361534 CCAAAACATTTTTTCTTTTAATTTCTCA
1 TCAAAAC-CTTTTTCCTTTAATTTCTCA
361562 TCAAAAC
1 TCAAAAC
361569 GTTTACTTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (27 bp):
TCAAAACCTTTTTCCTTTAATTTCTCA
Found at i:362544 original size:23 final size:24
Alignment explanation
Indices: 362517--362590 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
362507 AGAAATAATC
*
362517 TTTCAGTTAAACTAT-TTAAATTG
1 TTTCAATTAAACTATGTTAAATTG
* * *
362540 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTATGTTAAATTG
* * *
362564 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTATGTTAAATTG
362588 TTT
1 TTT
362591 AAGTCAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 13 0.28
24 33 0.72
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTAAATTG
Found at i:362567 original size:24 final size:24
Alignment explanation
Indices: 362537--362590 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
362527 ACTATTTAAA
362537 TTGTTTCAATTAAACTCTGTTTAT
1 TTGTTTCAATTAAACTCTGTTTAT
362561 TTGTTTCAATTAAACTCTGTTTAT
1 TTGTTTCAATTAAACTCTGTTTAT
362585 TTGTTT
1 TTGTTT
362591 AAGTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.57
Consensus pattern (24 bp):
TTGTTTCAATTAAACTCTGTTTAT
Found at i:369392 original size:52 final size:52
Alignment explanation
Indices: 369170--369568 Score: 505
Period size: 52 Copynumber: 7.6 Consensus size: 52
369160 GTAAATGCAA
* * *
369170 AAGGTCCGATGGCTCTGTGTCATCGTGAGTTATATGAATCTTTTACGGATTTT
1 AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCTTTTACGGATTAT
* * * *
369223 GAGGTCCAATGACTATGTGTCATCATGAGTTATATGAATCTTTTACGTATT-T
1 AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCTTTTACGGATTAT
* * * **
369275 CAAGGTTCGATAACTATGTGTCATCATGAGTTATATGAATCTTTTACAAATT-T
1 -AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCTTTTACGGATTAT
* * *
369328 CAGGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTAT
1 -AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* *
369381 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* **
369433 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACAAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* * *
369485 GAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
* * *
369537 GAGGTCCGATGACTATGTATCATCATGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
369569 TAAATAAGAA
Statistics
Matches: 309, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
52 191 0.62
53 118 0.38
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAT
Found at i:373779 original size:52 final size:52
Alignment explanation
Indices: 373621--373819 Score: 240
Period size: 52 Copynumber: 3.8 Consensus size: 52
373611 GCTATAAACG
* * *
373621 AAAGGGTCCAATGACTAAGTGTCATCGTGAGTAAACGAATCTTTTACGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
373673 AAAGGGTTC-ACTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGGGTCCGA-TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
373725 AAAGGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATAATGGGTT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
373777 AAA-GGTCCGATAACTCAGTGTCATCATGAGTATATGAAATCCT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATG-AATCCT
373820 ATATGGAACA
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
51 29 0.23
52 97 0.76
53 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (52 bp):
AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:373837 original size:104 final size:103
Alignment explanation
Indices: 373621--373861 Score: 238
Period size: 104 Copynumber: 2.3 Consensus size: 103
373611 GCTATAAACG
** ** * * *
373621 AAAGGGTCCAATGACTAAGTGTCATCGTGAGTAAACGAATCTTTTACGGATTAAAGGGTTCACTG
1 AAAGGGTCTGATGACTAAGTGTCATCGTGAGTAAACGAATCCATAACGGATTAAAGGGTCCACTA
* *
373686 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
66 ACTAAGTGTCATCATGAGTAAATGAATCCTATACAGA-T
* * *
373725 AAAGGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATAATGGGTTAAA-GGTCCGA-T
1 AAAGGGTCTGATGACTAAGTGTCATCGTGAGTAAACGAATCCATAACGGATTAAAGGGTCC-ACT
* * **
373788 AACTCAGTGTCATCATGAGTATATGAAATCCTATATGGA-
65 AACTAAGTGTCATCATGAGTAAATG-AATCCTATACAGAT
* *
373827 ACAAGAGGTCTGATAACTATA-TGTCATTGTGAGTA
1 A-AAG-GGTCTGATGACTA-AGTGTCATCGTGAGTA
373862 TTAAATAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
102 1 0.01
103 29 0.25
104 83 0.73
105 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (103 bp):
AAAGGGTCTGATGACTAAGTGTCATCGTGAGTAAACGAATCCATAACGGATTAAAGGGTCCACTA
ACTAAGTGTCATCATGAGTAAATGAATCCTATACAGAT
Found at i:380260 original size:17 final size:16
Alignment explanation
Indices: 380240--380296 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
380230 GCTGTCATCA
380240 CATTTCGTTTGTCATTG
1 CATTTC-TTTGTCATTG
*
380257 CATTTTTCTTGTCATTG
1 CATTTCT-TTGTCATTG
*
380274 CATCTTCATTGTCATTG
1 CAT-TTCTTTGTCATTG
380291 CATTTC
1 CATTTC
380297 CATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 4 0.11
17 29 0.83
18 2 0.06
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (16 bp):
CATTTCTTTGTCATTG
Found at i:383746 original size:52 final size:52
Alignment explanation
Indices: 383680--383945 Score: 397
Period size: 52 Copynumber: 5.1 Consensus size: 52
383670 ACATATTGTA
* * * * * *
383680 ATCGAACCTCATAATCTGAAAAGGATTCATATACTTACAATGACACATAGTC
1 ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
** *
383732 ATCGGACCTTATAATCTATAAAGGATTCATATACTCATGATGACACATAGTC
1 ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
* *
383784 ATCGAACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTC
1 ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
*
383836 ATCAGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
1 ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
* * *
383888 ATCGGACATTATAATCCGTAAAGGATTCATATACTCATGATGACACATAGCC
1 ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
383940 ATCGGA
1 ATCGGA
383946 TCTTTTGCAT
Statistics
Matches: 195, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 195 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (52 bp):
ATCGGACCTTATAATCCGTAAAGGATTCATATACTCACGATGACACATAGTC
Found at i:390831 original size:52 final size:52
Alignment explanation
Indices: 390750--390989 Score: 202
Period size: 52 Copynumber: 4.6 Consensus size: 52
390740 AAAAGGGCTT
* * *
390750 GATGACTAAGTGTCATAGTGAGTAAATGAATCATTTACGGATTATGAGGCCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAGGCCC
* * *
390802 GATGACTAAGTGTCATTGTGAGTATATGAAATTC-TTTATGGA-TATAAAGGCCT
1 GATGACTAAGTGTCATCGTGAGTATATG-AA-TCATTTACGGATTAT-AAGGCCC
* * * *
390855 GATGACTAAGTGTGATCGTGAGTATATGGATCATTTACAGATTA-AGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCATTTACGGATTATA-AGGCCC
* * * ** * * *
390907 GATGACTATGTGTTATCGTGGGTATACAAATCCCATGT--GGATTATAAAGTCC
1 GATGACTAAGTGTCATCGTGAGTATATGAAT--CATTTACGGATTATAAGGCCC
* * *
390959 GATGGCTATGTGTCATTGTGAGTATATGAAT
1 GATGACTAAGTGTCATCGTGAGTATATGAAT
390990 GAAGTGGAAT
Statistics
Matches: 152, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
51 3 0.02
52 100 0.66
53 43 0.28
54 6 0.04
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (52 bp):
GATGACTAAGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAGGCCC
Found at i:390953 original size:105 final size:105
Alignment explanation
Indices: 390749--390989 Score: 279
Period size: 105 Copynumber: 2.3 Consensus size: 105
390739 AAAAAGGGCT
* * *
390749 TGATGACTAAGTGTCATAGTGAGTAAATGAATCATTTACGGATTATGAGGCCCGATGACTAAGTG
1 TGATGACTAAGTGTCATAGTGAGTATATGAATCATTTACAGATTAAGAGGCCCGATGACTAAGTG
* * * **
390814 TCATTGTGAGTATATGAAATTCTTTATGGATATAAAGGCC
66 TCATCGTGAGTATATCAAATCCCATATGGATATAAAGGCC
* * * * *
390854 TGATGACTAAGTGTGATCGTGAGTATATGGATCATTTACAGATTAAGAGGTCCGATGACTATGTG
1 TGATGACTAAGTGTCATAGTGAGTATATGAATCATTTACAGATTAAGAGGCCCGATGACTAAGTG
* * * *
390919 TTATCGTGGGTATA-CAAATCCCATGTGGATTATAAAGTCC
66 TCATCGTGAGTATATCAAATCCCATATGGA-TATAAAGGCC
* * *
390959 -GATGGCTATGTGTCATTGTGAGTATATGAAT
1 TGATGACTAAGTGTCATAGTGAGTATATGAAT
390990 GAAGTGGAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
104 36 0.32
105 77 0.68
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (105 bp):
TGATGACTAAGTGTCATAGTGAGTATATGAATCATTTACAGATTAAGAGGCCCGATGACTAAGTG
TCATCGTGAGTATATCAAATCCCATATGGATATAAAGGCC
Found at i:398118 original size:53 final size:51
Alignment explanation
Indices: 397998--398245 Score: 228
Period size: 52 Copynumber: 4.8 Consensus size: 51
397988 AAATGAAAAA
* *
397998 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTATATGAATCCTTTATGGATT
* * ** *
398049 ATGAGGTCCGAAGACTAAGCATCATCATGAGTATATGAAATCCCTTATGGATTT
1 A-AAGGTCCGATGACTAAGTGTCATCATGAGTATATG-AATCCTTTATGGA-TT
* * *
398103 AAAGGTCTGATGACTAAGTGTCATCATGAGTATATGGATCCTTTATAGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTATATGAATCCTTTATGGATT
* * * * ** ****
398154 AAGAGGTCTGATGACTCTA-TGTCATCGTGAGCATACAAATCCCACGTGGATT
1 AA-AGGTCCGATGACT-AAGTGTCATCATGAGTATATGAATCCTTTATGGATT
* * *
398206 ATAAGGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
1 A-AAGGTCCGATGACTAAGTGTCATCATGAGTATATGAAT
398246 GAAGTGAAAT
Statistics
Matches: 157, Mismatches: 33, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
51 5 0.03
52 106 0.68
53 43 0.27
54 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAGTATATGAATCCTTTATGGATT
Found at i:402561 original size:17 final size:17
Alignment explanation
Indices: 402541--402597 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
402531 GTTGTCATCA
402541 CATTTCATTTGTCATTG
1 CATTTCATTTGTCATTG
* *
402558 CATTT-TTCTTGTCACTG
1 CATTTCAT-TTGTCATTG
*
402575 CATCTTCA-TTATCATTG
1 CAT-TTCATTTGTCATTG
402592 CATTTC
1 CATTTC
402598 CATATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.12
17 26 0.81
18 2 0.06
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.51
Consensus pattern (17 bp):
CATTTCATTTGTCATTG
Found at i:407174 original size:50 final size:51
Alignment explanation
Indices: 407059--407295 Score: 298
Period size: 51 Copynumber: 4.6 Consensus size: 51
407049 CTATAAACGA
*
407059 AAAGGTCCGATGACGAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
* *
407110 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAAT-CTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
* * * *
407160 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
* * * * * **
407211 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGAAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTAAGGATT
*
407263 AAGAGGTCCGATGATTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
407296 TTAAATGAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 47 0.29
51 80 0.49
52 8 0.05
53 26 0.16
54 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATT
Found at i:407234 original size:101 final size:101
Alignment explanation
Indices: 407059--407249 Score: 310
Period size: 101 Copynumber: 1.9 Consensus size: 101
407049 CTATAAACGA
* *
407059 AAAGGTCCGATGACGAAGTGTCATCGTGAGTAAATGAATCCTTTAAGGATTAAAGGTCCGATGAC
1 AAAGGTCCGATGACGAAGTGTCATCGTGAGTAAATGAATCCATGAAGGATTAAAGGTCCGATGAC
407124 TAAGTGTCATCATGAGTAAATGAATCTTTACGGATT
66 TAAGTGTCATCATGAGTAAATGAATCTTTACGGATT
* * *
407160 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCGATGAC
1 AAAGGTCCGATGACGAAGTGTCATCGTGAGTAAATGAATCCATGAAGGATTAAAGGTCCGATGAC
* * *
407225 TCAGTGTCATCGTGAGTATATGAAT
66 TAAGTGTCATCATGAGTAAATGAAT
407250 TCCTATACGA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (101 bp):
AAAGGTCCGATGACGAAGTGTCATCGTGAGTAAATGAATCCATGAAGGATTAAAGGTCCGATGAC
TAAGTGTCATCATGAGTAAATGAATCTTTACGGATT
Found at i:410283 original size:16 final size:16
Alignment explanation
Indices: 410262--410296 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
410252 TAGTAATTTT
410262 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
410278 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
410294 AAT
1 AAT
410297 TACAAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:416123 original size:16 final size:16
Alignment explanation
Indices: 416101--416155 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
416091 GTTTGGTTCA
416101 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
416117 GTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
416133 CTGTAATGGAATAG-G
1 CTGTAATGGAATAGAG
416148 ACTGTAAT
1 -CTGTAAT
416156 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 1 0.03
16 35 0.97
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:416408 original size:57 final size:58
Alignment explanation
Indices: 416327--416453 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 58
416317 TTTTAATAAG
* * * *
416327 ATTATTATTAAATATAATTTAATAAAAATAATA-ATTAATTTAATTAT-ATTTTAACATA
1 ATTATTATTAAATACAATTCAAT-AAAATAATATA-CAATTTAATAATGATTTTAACATA
* *
416385 ATTA-TATTAAATACAATTCAATAAAATAATATACAATTTAATAATGTTTTTAATATA
1 ATTATTATTAAATACAATTCAATAAAATAATATACAATTTAATAATGATTTTAACATA
416442 ATTATTATTAAA
1 ATTATTATTAAA
416454 ATATGAATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 19 0.32
57 30 0.50
58 11 0.18
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTATTATTAAATACAATTCAATAAAATAATATACAATTTAATAATGATTTTAACATA
Found at i:416473 original size:25 final size:24
Alignment explanation
Indices: 416445--416495 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
416435 TAATATAATT
*
416445 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
416470 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
416494 AT
1 AT
416496 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:421459 original size:6 final size:6
Alignment explanation
Indices: 421445--421508 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
421435 TTTAATTTAT
* * *
421445 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA TTT-AA TGTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
421491 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
421509 AGTCCAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
5 12 0.26
6 31 0.66
7 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:421461 original size:17 final size:17
Alignment explanation
Indices: 421438--421508 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
421428 CCTTTTTTTT
421438 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
421455 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
421472 AATTTAATGTAAATTTA
1 AATTTATTTTAAATTTA
* *
421489 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
421507 AA
1 AA
421509 AGTCCAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 35 0.78
18 10 0.22
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:421498 original size:11 final size:11
Alignment explanation
Indices: 421438--421495 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
421428 CCTTTTTTTT
*
421438 AATTTATTTTA
1 AATTTAATTTA
421449 AATTTAGATTT-
1 AATTTA-ATTTA
*
421460 ATTTTAAATTTA
1 AATTT-AATTTA
*
421472 AATTTAATGTA
1 AATTTAATTTA
421483 AATTTAAATTTA
1 AATTT-AATTTA
421495 A
1 A
421496 TTTCAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 24 0.63
12 14 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:441702 original size:18 final size:18
Alignment explanation
Indices: 441677--441716 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
441667 TTAAAAAATC
441677 TTTTAAAAATAAAT-TAA
1 TTTTAAAAATAAATATAA
*
441694 TTTTAAAAAATATATATAA
1 TTTT-AAAAATAAATATAA
441713 TTTT
1 TTTT
441717 TTGGACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTAAAAATAAATATAA
Found at i:446577 original size:20 final size:21
Alignment explanation
Indices: 446552--446593 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
446542 AACTTTCAGA
446552 GATTTATA-TACTAACTGTTT
1 GATTTATAGTACTAACTGTTT
*
446572 GATTTATAGTTCTAACTGTTT
1 GATTTATAGTACTAACTGTTT
446593 G
1 G
446594 TTGGGACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (21 bp):
GATTTATAGTACTAACTGTTT
Found at i:450890 original size:186 final size:185
Alignment explanation
Indices: 450523--451044 Score: 927
Period size: 186 Copynumber: 2.8 Consensus size: 185
450513 ATTATCAACG
450523 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCA
1 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCA
* *
450588 ACGGCGCCGTATTTTTTTATTTTTTAATTTTCCTTTCCATTTTATGAACCTTCCTCTACTTTAGA
66 ACGGCGCCGTGTTTTTTTATTTTTTAATTTTCCTCTCCATTTTATGAACCTTCCTCTACTTTAGA
*
450653 TCAGATTTAGATTTAATCAATCATGTTTTATCTAATCCTTGCGCCTACGTCAAAA
131 TCAGATTTAGATTTAATCAATCATGTTCTATCTAATCCTTGCGCCTACGTCAAAA
*
450708 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGAACCGGGTTCGATCCCCGGCA
1 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCA
*
450773 ACGGCGCCGTGTTTTTTTATTTTTTTAATTTTCCTCTCCATTTTATGAAGCTTCCTCTACTTTAG
66 ACGGCGCCGTGTTTTTTTA-TTTTTTAATTTTCCTCTCCATTTTATGAACCTTCCTCTACTTTAG
* *
450838 ATCAGATTTAGATTTAATCAATCATGTTCTATCTAATCCTTGCGCTTACGTCAAAG
130 ATCAGATTTAGATTTAATCAATCATGTTCTATCTAATCCTTGCGCCTACGTCAAAA
*
450894 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACCCGGGTGACCCGGGTTCGATCCCCGGCA
1 TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCA
* * *
450959 ACGGCGCCGTGTTTATTTATTTTTTAATTTTCCTCTCCATTTTATGCACCTTCCTCTACTTTATA
66 ACGGCGCCGTGTTTTTTTATTTTTTAATTTTCCTCTCCATTTTATGAACCTTCCTCTACTTTAGA
*
451024 TCAGATTTAGATTGAATCAAT
131 TCAGATTTAGATTTAATCAAT
451045 AATATTTTAT
Statistics
Matches: 322, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
185 145 0.45
186 177 0.55
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (185 bp):
TCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCA
ACGGCGCCGTGTTTTTTTATTTTTTAATTTTCCTCTCCATTTTATGAACCTTCCTCTACTTTAGA
TCAGATTTAGATTTAATCAATCATGTTCTATCTAATCCTTGCGCCTACGTCAAAA
Found at i:451184 original size:15 final size:14
Alignment explanation
Indices: 451168--451202 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
451158 TTAAAGTTAT
451168 TTTAGTTTTTTTTA
1 TTTAGTTTTTTTTA
*
451182 TTTAATTTTTTTTA
1 TTTAGTTTTTTTTA
451196 TTTAGTT
1 TTTAGTT
451203 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTAGTTTTTTTTA
Found at i:451194 original size:18 final size:18
Alignment explanation
Indices: 451173--451207 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
451163 GTTATTTTAG
*
451173 TTTTT-TTTATTTAATTT
1 TTTTTATTTAGTTAATTT
451190 TTTTTATTTAGTTAATTT
1 TTTTTATTTAGTTAATTT
451208 AAAATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTATTTAGTTAATTT
Found at i:454116 original size:22 final size:23
Alignment explanation
Indices: 454076--454126 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
454066 AATTTTATGT
454076 AATTATATAAATAAAATAT-TAA
1 AATTATATAAATAAAATATATAA
*
454098 AATTATATAAA-AATGATATATAA
1 AATTATATAAATAA-AATATATAA
*
454121 ATTTAT
1 AATTAT
454127 TTGAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 8 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTATATAAATAAAATATATAA
Found at i:461136 original size:6 final size:6
Alignment explanation
Indices: 461111--461149 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
461101 ACAATTCATA
* * *
461111 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
461150 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:481009 original size:13 final size:13
Alignment explanation
Indices: 480991--481015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
480981 AATGTGACTC
480991 GAATTTAGCAAAT
1 GAATTTAGCAAAT
481004 GAATTTAGCAAA
1 GAATTTAGCAAA
481016 AGTAAGAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
GAATTTAGCAAAT
Found at i:495515 original size:18 final size:18
Alignment explanation
Indices: 495478--495512 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
495468 ATATTATGTG
495478 AAAAATATAAAAAAAATT
1 AAAAATATAAAAAAAATT
*
495496 AAAAATA-AAAATAAATT
1 AAAAATATAAAAAAAATT
495513 TAACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATAAAAAAAATT
Found at i:501280 original size:12 final size:11
Alignment explanation
Indices: 501250--501305 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
501240 ATCACTAATT
501250 ACCAAAAAAAA
1 ACCAAAAAAAA
*
501261 TACAAAAACAAAA
1 -ACCAAAA-AAAA
501274 ACCAAAAAAAA
1 ACCAAAAAAAA
* *
501285 A--GAGAAAAA
1 ACCAAAAAAAA
501294 ACCAAAAAAAA
1 ACCAAAAAAAA
501305 A
1 A
501306 AATAAGAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.20
11 12 0.34
12 12 0.34
13 4 0.11
ACGTcount: A:0.80, C:0.14, G:0.04, T:0.02
Consensus pattern (11 bp):
ACCAAAAAAAA
Found at i:501292 original size:25 final size:24
Alignment explanation
Indices: 501253--501316 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
501243 ACTAATTACC
* * * *
501253 AAAAAAAATACAAAAACAAAAACCA
1 AAAAAAAAGAGAAAAACCAAAA-AA
501278 AAAAAAAAGAGAAAAAACCAAAAAA
1 AAAAAAAAGAG-AAAAACCAAAAAA
*
501303 AAAAATAAGAGAAA
1 AAAAAAAAGAGAAA
501317 CCTAAGTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 3 0.09
25 20 0.61
26 10 0.30
ACGTcount: A:0.81, C:0.09, G:0.06, T:0.03
Consensus pattern (24 bp):
AAAAAAAAGAGAAAAACCAAAAAA
Found at i:501294 original size:27 final size:25
Alignment explanation
Indices: 501264--501316 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
501254 AAAAAAATAC
501264 AAAAACAAAAACCAAAAAAAAAGAGAA
1 AAAAACAAAAA--AAAAAAAAAGAGAA
* *
501291 AAAACCAAAAAAAAAAATAAGAGAA
1 AAAAACAAAAAAAAAAAAAAGAGAA
501316 A
1 A
501317 CCTAAGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.58
27 10 0.42
ACGTcount: A:0.81, C:0.09, G:0.08, T:0.02
Consensus pattern (25 bp):
AAAAACAAAAAAAAAAAAAAGAGAA
Found at i:504292 original size:21 final size:21
Alignment explanation
Indices: 504246--504293 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
504236 TCAATCCTAA
* *
504246 AATATATTATTATTTTATTTT
1 AATATATTATTACTTTATTAT
*
504267 GATATATTATATACTTTA-TAT
1 AATATATTAT-TACTTTATTAT
504288 AATATA
1 AATATA
504294 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
AATATATTATTACTTTATTAT
Found at i:505469 original size:33 final size:34
Alignment explanation
Indices: 505414--505477 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
505404 CAATTCAGTA
505414 TATTTAATTTGTTTTTATCAAATTCAGTACACTT
1 TATTTAATTTGTTTTTATCAAATTCAGTACACTT
505448 TATTTAATTT-TTTTTGA-CAAATTCAGTACA
1 TATTTAATTTGTTTTT-ATCAAATTCAGTACA
505478 ATTAATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (34 bp):
TATTTAATTTGTTTTTATCAAATTCAGTACACTT
Found at i:511497 original size:17 final size:17
Alignment explanation
Indices: 511461--511503 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
511451 TGAATCTATT
* *
511461 TTTAAA-TTATTTTAAG
1 TTTAAATTTATTCTAAA
511477 TTTAAATTTATTCTAAA
1 TTTAAATTTATTCTAAA
511494 TTTAAATTTA
1 TTTAAATTTA
511504 AATATCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTCTAAA
Found at i:512272 original size:16 final size:17
Alignment explanation
Indices: 512240--512273 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
512230 ATCAAGAAAT
512240 ATTAATAATAAATAAAA
1 ATTAATAATAAATAAAA
*
512257 ATTAAT-ATATATAAAA
1 ATTAATAATAAATAAAA
512273 A
1 A
512274 CATATAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTAATAATAAATAAAA
Found at i:513298 original size:29 final size:30
Alignment explanation
Indices: 513256--513664 Score: 270
Period size: 29 Copynumber: 14.2 Consensus size: 30
513246 CAGAAATAAT
* * *
513256 ATTTTGACCC-TAAATTTCTTAAAAATTAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
* *
513285 ATTTTT-CCCTTAAACTTC-CAAAAATAAT
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
* * *
513313 ATTTTTACCCCTAAACTTATTAAAAATTAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
**
513343 A--TTTAGCCCCAAAACTTC-C-AAAATTCAC
1 ATTTTTA-CCCTTAAACTTCTCAAAAATT-AC
*
513371 ATTTTTACCC-TAGAACTTCTCAAAAATTAT
1 ATTTTTACCCTTA-AACTTCTCAAAAATTAC
*
513401 ATTTTTA-CCTCTAAACTTC-CAAAAATCAC
1 ATTTTTACCCT-TAAACTTCTCAAAAATTAC
* * *
513430 ATTTTTACCCTCAAAGTTCTCAAAAGTTAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
* ** * *
513460 ATTTTTGCCCCCCCAAAGTTC-CAAAAATCAC
1 ATTTTT--ACCCTTAAACTTCTCAAAAATTAC
** *
513491 -TTTTTACCCTCGAACTTC-CAAAAATCAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
*
513519 A-TTTTACCCTCAAACTTC-CAAAAATTAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
** *
513547 A--TTTACCCCCAAACTT-TCAAAAATCAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
* * * *
513574 ATTTTT-GCCTCAAACTTCTAAAAAATCAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
* ** *
513603 ATTTTTACCC-TGAAC-TCTCCTAAATGAC
1 ATTTTTACCCTTAAACTTCTCAAAAATTAC
*
513631 A-TTTTACCCTTAAAACTT-TCTAAAATTAC
1 ATTTTTACCCTT-AAACTTCTCAAAAATTAC
513660 ATTTT
1 ATTTT
513665 AACCTCGAAC
Statistics
Matches: 307, Mismatches: 47, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
27 38 0.12
28 89 0.29
29 98 0.32
30 55 0.18
31 16 0.05
32 11 0.04
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTTACCCTTAAACTTCTCAAAAATTAC
Found at i:513338 original size:58 final size:57
Alignment explanation
Indices: 513256--513664 Score: 355
Period size: 58 Copynumber: 7.1 Consensus size: 57
513246 CAGAAATAAT
* * * * * *
513256 ATTTTGACCCTAAATTTCTTAAAAATTACATTTTTCCCTTAAACTTCCAAAAATAAT
1 ATTTTTACCCTAAACTTCTCAAAAATTACATTTTTCCCTCAAACTTCCAAAAATCAC
* * ** *
513313 ATTTTTACCCCTAAACTTATTAAAAATTACATTTAGCCC-CAAAACTTCCAAAATTCAC
1 ATTTTTA-CCCTAAACTTCTCAAAAATTACATTTTTCCCTC-AAACTTCCAAAAATCAC
* *
513371 ATTTTTACCCTAGAACTTCTCAAAAATTATATTTTTACCTCTAAACTTCCAAAAATCAC
1 ATTTTTACCCTA-AACTTCTCAAAAATTACATTTTTCCCTC-AAACTTCCAAAAATCAC
* * * *
513430 ATTTTTACCCTCAAAGTTCTCAAAAGTTACATTTTTGCCCCCCCAAAGTTCCAAAAATCAC
1 ATTTTTACCCT-AAACTTCTCAAAAATTACATTTTT---CCCTCAAACTTCCAAAAATCAC
* * * *
513491 -TTTTTACCCTCGAACTTC-CAAAAATCACATTTTACCCTCAAACTTCCAAAAATTAC
1 ATTTTTACCCT-AAACTTCTCAAAAATTACATTTTTCCCTCAAACTTCCAAAAATCAC
* * * *
513547 A--TTTACCCCCAAACTT-TCAAAAATCACATTTTTGCCTCAAACTTCTAAAAAATCAC
1 ATTTTTA-CCCTAAACTTCTCAAAAATTACATTTTTCCCTCAAACTTC-CAAAAATCAC
* ** * * * * * *
513603 ATTTTTACCCTGAAC-TCTCCTAAATGACATTTTACCCTTAAAACTTTCTAAAATTAC
1 ATTTTTACCCTAAACTTCTCAAAAATTACATTTTTCCC-TCAAACTTCCAAAAATCAC
513660 ATTTT
1 ATTTT
513665 AACCTCGAAC
Statistics
Matches: 287, Mismatches: 49, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
55 35 0.12
56 32 0.11
57 44 0.15
58 79 0.28
59 61 0.21
60 17 0.06
61 16 0.06
62 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (57 bp):
ATTTTTACCCTAAACTTCTCAAAAATTACATTTTTCCCTCAAACTTCCAAAAATCAC
Found at i:513665 original size:29 final size:28
Alignment explanation
Indices: 513256--513675 Score: 157
Period size: 28 Copynumber: 14.6 Consensus size: 28
513246 CAGAAATAAT
*
513256 ATTTTGACCCT-AAA-TTTCTTAAAAATTAC
1 ATTTT-ACCCTCAAACTTTC-T-AAAATCAC
* * * * * *
513285 ATTTTTCCCTTAAACTTCCAAAAATAAT
1 ATTTTACCCTCAAACTTTCTAAAATCAC
*
513313 ATTTTTACCC-CTAAACTTAT-TAAAAATTAC
1 A-TTTTACCCTC-AAACTT-TCT-AAAATCAC
*
513343 A-TTTAGCCC-CAAAAC-TTCCAAAATTCAC
1 ATTTTA-CCCTC-AAACTTTCTAAAA-TCAC
* * *
513371 ATTTTTACCCT-AGAACTTCTCAAAAATTAT
1 A-TTTTACCCTCA-AACTT-TCTAAAATCAC
* *
513401 ATTTTTA-CCTCTAAACTTCCAAAAATCAC
1 A-TTTTACCCTC-AAACTTTCTAAAATCAC
* *
513430 ATTTTTACCCTCAAA-GTTCTCAAAAGTTAC
1 A-TTTTACCCTCAAACTTTCT-AAAA-TCAC
* * * * *
513460 ATTTTTGCCCCCCCAAAGTTCCAAAAATCAC
1 A-TTTT--ACCCTCAAACTTTCTAAAATCAC
* * * *
513491 TTTTTACCCTCGAACTTCCAAAAATCAC
1 ATTTTACCCTCAAACTTTCTAAAATCAC
* * *
513519 ATTTTACCCTCAAACTTCCAAAAATTAC
1 ATTTTACCCTCAAACTTTCTAAAATCAC
* *
513547 A-TTTACCCCCAAACTTTCAAAAATCAC
1 ATTTTACCCTCAAACTTTCTAAAATCAC
**
513574 ATTTTTGCCTCAAAC-TTCTAAAAAATCAC
1 ATTTTACCCTCAAACTTTCT--AAAATCAC
* * *
513603 ATTTTTACCCT-GAACTCTCCT-AAATGAC
1 A-TTTTACCCTCAAACT-TTCTAAAATCAC
* *
513631 ATTTTACCCTTAAAACTTTCTAAAATTAC
1 ATTTTACCC-TCAAACTTTCTAAAATCAC
* *
513660 ATTTTAACCTCGAACT
1 ATTTTACCCTCAAACT
513676 CTCCAAAACT
Statistics
Matches: 303, Mismatches: 56, Indels: 65
0.71 0.13 0.15
Matches are distributed among these distances:
27 40 0.13
28 94 0.31
29 90 0.30
30 53 0.17
31 13 0.04
32 11 0.04
33 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
ATTTTACCCTCAAACTTTCTAAAATCAC
Found at i:513821 original size:15 final size:15
Alignment explanation
Indices: 513797--513835 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
513787 TTCATAATTT
513797 GTAT-TTTATTTTTC
1 GTATATTTATTTTTC
*
513811 TTATATTTA-TTTTC
1 GTATATTTATTTTTC
513825 GTATATTTATT
1 GTATATTTATT
513836 CATTCGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (15 bp):
GTATATTTATTTTTC
Found at i:514102 original size:97 final size:97
Alignment explanation
Indices: 513967--514160 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
513957 TAAATATTTG
* * *
513967 AAATCGAGACAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCATTAACTTACTAGGCGCGAT
1 AAATCGAGACAATATTCCTTTATCTCGGGTTTTAAAAATTTGTGCATTAACTTACTAGGCGCAAA
514032 TTTTCTTCAAATCAGGATAATCAAATACTCTT
66 TTTTCTTCAAATCAGGATAATCAAATACTCTT
* * *
514064 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTAAAAATTTGTGCCTTAATTTACTAGGCGCAAA
1 AAATCGAGACAATATTCCTTTATCTCGGGTTTTAAAAATTTGTGCATTAACTTACTAGGCGCAAA
* *
514129 TTTTCTTCAAATCGGGATAATCGAATACTCTT
66 TTTTCTTCAAATCAGGATAATCAAATACTCTT
514161 TTTCAAGGTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (97 bp):
AAATCGAGACAATATTCCTTTATCTCGGGTTTTAAAAATTTGTGCATTAACTTACTAGGCGCAAA
TTTTCTTCAAATCAGGATAATCAAATACTCTT
Found at i:518054 original size:31 final size:29
Alignment explanation
Indices: 518011--518068 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
518001 AGTATTATGA
518011 TTTTTTTTTAATTTGGTACTTAAATTTTT
1 TTTTTTTTTAATTTGGTACTTAAATTTTT
*
518040 TTTTTTTGTCTAATTTGGTACTTATATTT
1 TTTTTTT-T-TAATTTGGTACTTAAATTT
518069 AATTCTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 1 0.04
31 18 0.69
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (29 bp):
TTTTTTTTTAATTTGGTACTTAAATTTTT
Found at i:518306 original size:14 final size:13
Alignment explanation
Indices: 518277--518310 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
518267 TCAATTACTT
*
518277 TTAATTTTATTTA
1 TTAATTTCATTTA
518290 TTAATTTCATGTTA
1 TTAATTTCAT-TTA
518304 TTAATTT
1 TTAATTT
518311 AAAATAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (13 bp):
TTAATTTCATTTA
Found at i:518945 original size:21 final size:19
Alignment explanation
Indices: 518904--518952 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
518894 TTTCATTTTA
* *
518904 AAAAAAATTAAATTCAGAT
1 AAAAATATTAAATTCAAAT
518923 AAAAATATTAAAATTCAAAAT
1 AAAAATATT-AAATTC-AAAT
*
518944 AAAATTATT
1 AAAAATATT
518953 GATGTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAATATTAAATTCAAAT
Found at i:527886 original size:28 final size:28
Alignment explanation
Indices: 527822--527890 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
527812 AGGTTTAAGG
527822 TTCATGGTTTTGATGTTTAGGGTCTATA
1 TTCATGGTTTTGATGTTTAGGGTCTATA
* *
527850 TT-TTGGGTTTTG-TGTTTAGGATTCT-TGA
1 TTCAT-GGTTTTGATGTTTAGG-GTCTAT-A
527878 TTCATGGTTTTGA
1 TTCATGGTTTTGA
527891 ATTTTGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
27 10 0.30
28 22 0.67
29 1 0.03
ACGTcount: A:0.14, C:0.06, G:0.26, T:0.54
Consensus pattern (28 bp):
TTCATGGTTTTGATGTTTAGGGTCTATA
Found at i:528116 original size:17 final size:18
Alignment explanation
Indices: 528083--528185 Score: 75
Period size: 17 Copynumber: 5.5 Consensus size: 18
528073 GGTTTAAATT
*
528083 AATTCAAATTTATTTTTA
1 AATTTAAATTTATTTTTA
*
528101 AATTTAAGTTTATTTTAAATTTA
1 AATTTAAATTTA--TT---TTTA
*
528124 AATTTAAAATTATCTTTTA
1 AATTTAAATTTAT-TTTTA
**
528143 AATTTAAATTT-GCTTTA
1 AATTTAAATTTATTTTTA
* *
528160 AATTTAAATTTA-ATTAA
1 AATTTAAATTTATTTTTA
528177 AATTTAAAT
1 AATTTAAAT
528186 GAATTTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
17 27 0.39
18 10 0.14
19 14 0.20
20 2 0.03
21 1 0.01
22 1 0.01
23 14 0.20
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTTAAATTTATTTTTA
Found at i:528133 original size:7 final size:6
Alignment explanation
Indices: 528075--528185 Score: 79
Period size: 6 Copynumber: 19.2 Consensus size: 6
528065 CTTTATTGGG
* ** * *
528075 TTTAAA -TT-AA TTCAAA TTTATT TTTAAA TTTAAG TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** **
528120 TTTAAA TTTAAA ATTATCT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
528168 TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
528186 GAATTTAAAA
Statistics
Matches: 78, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
4 2 0.03
5 14 0.18
6 59 0.76
7 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:528141 original size:25 final size:23
Alignment explanation
Indices: 528097--528172 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
528087 CAAATTTATT
*
528097 TTTAAATTTAAGTTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
* *
528120 TTTAAATTTAAAATTA-TCT---
1 TTTAAATTTAAATTTATTTTAAA
**
528139 TTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
528162 TTTAAATTTAA
1 TTTAAATTTAA
528173 TTAAAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 14 0.33
20 2 0.05
22 2 0.05
23 25 0.58
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:528142 original size:42 final size:41
Alignment explanation
Indices: 528075--528172 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
528065 CTTTATTGGG
* * * *
528075 TTTAAA-TT-AATTCAAATTTATTTTTAAATTTAAGTTTAT
1 TTTAAATTTAAATTTAAAATTATTTTTAAATTTAAATTTAC
*
528114 TTTAAATTTAAATTTAAAATTATCTTTTAAATTTAAATTTGC
1 TTTAAATTTAAATTTAAAATTAT-TTTTAAATTTAAATTTAC
528156 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
528173 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
39 6 0.12
40 2 0.04
41 11 0.22
42 32 0.63
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (41 bp):
TTTAAATTTAAATTTAAAATTATTTTTAAATTTAAATTTAC
Found at i:528193 original size:17 final size:17
Alignment explanation
Indices: 528159--528200 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
528149 AATTTGCTTT
*
528159 AAATTTAAATTTAATTA
1 AAATTTAAATTGAATTA
528176 AAATTTAAA-TGAATTTA
1 AAATTTAAATTGAA-TTA
*
528193 AAACTTAA
1 AAATTTAA
528201 TTAAAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTGAATTA
Found at i:528911 original size:3 final size:3
Alignment explanation
Indices: 528905--528976 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
528895 ATAAATGCTT
* * * *
528905 TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TAA TAC TAA TGA CAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
528950 TAA TTAA TTAA TAA TAA TAA TAA TAA T
1 TAA -TAA -TAA TAA TAA TAA TAA TAA T
528977 GAGTACAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 49 0.84
4 8 0.14
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:530187 original size:30 final size:29
Alignment explanation
Indices: 530042--530343 Score: 231
Period size: 29 Copynumber: 10.2 Consensus size: 29
530032 TAAGCTATCC
*
530042 AAAAATTCCATTTTTACCCCCG-AACTTCC
1 AAAAATTCCATTTTTA-CCCCGAAACTTCT
* * *
530071 AAAAA-TCTCATTTTTACCTCGAAGCTTCA
1 AAAAATTC-CATTTTTACCCCGAAACTTCT
* * *
530100 AAAAATTCCATTTTGACCCCAAAACATCT
1 AAAAATTCCATTTTTACCCCGAAACTTCT
* *
530129 AAAAATTCTATTTTTACCCTTG-AACTTCT
1 AAAAATTCCATTTTTACCC-CGAAACTTCT
*
530158 AAAAATCCCATTTTTGACCCCGAAACTTCT
1 AAAAATTCCATTTTT-ACCCCGAAACTTCT
* *
530188 AAAAAAAATTCTATTTTTACCCCTAAACTTCT
1 ---AAAAATTCCATTTTTACCCCGAAACTTCT
* * *
530220 AAAAATCCCATTTTTAACCTCGAAA-TGTCC
1 AAAAATTCCATTTTT-ACCCCGAAACT-TCT
***
530250 AAAAATTTTGTTTTTACCCTCG-AACTTCT
1 AAAAATTCCATTTTTACCC-CGAAACTTCT
** *
530279 AAAAA-TCTCATTTTTAACCCTAAAACTTCC
1 AAAAATTC-CATTTTT-ACCCCGAAACTTCT
* *
530309 AAAAATTTCATTTTTACCCCCG-AACTTCC
1 AAAAATTCCATTTTTA-CCCCGAAACTTCT
530338 AAAAAT
1 AAAAAT
530344 GCCAAAAATG
Statistics
Matches: 215, Mismatches: 40, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
28 7 0.03
29 120 0.56
30 61 0.28
31 1 0.00
32 13 0.06
33 13 0.06
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCGAAACTTCT
Found at i:530191 original size:59 final size:59
Alignment explanation
Indices: 530042--530459 Score: 382
Period size: 59 Copynumber: 6.9 Consensus size: 59
530032 TAAGCTATCC
* ** * *
530042 AAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAA-TCTCATTTTTA-CCTCGAAGCTTCA
1 AAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCT-ATTTTTACCCTCGAA-CTTCT
* * *
530100 AAAAATTCCA-TTTTGACCCCAAAACATCTAAAAATTCTATTTTTACCCTTGAACTTCT
1 AAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACCCTCGAACTTCT
* *
530158 AAAAATCCCATTTTTGACCCCGAAACTTCTAAAAAAAATTCTATTTTTACCC-CTAAACTTCT
1 AAAAATCCCATTTTTGACCCCAAAACTTCT---AAAAATTCTATTTTTACCCTC-GAACTTCT
* * * * * *
530220 AAAAATCCCATTTTTAACCTCGAAA-TGTCCAAAAATTTTGTTTTTACCCTCGAACTTCT
1 AAAAATCCCATTTTTGACCCCAAAACT-TCTAAAAATTCTATTTTTACCCTCGAACTTCT
* * * * * *
530279 AAAAATCTCATTTTTAACCCTAAAACTTCCAAAAATT-TCATTTTTACCCCCGAACTTCC
1 AAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCT-ATTTTTACCCTCGAACTTCT
*
530338 AAAAATGCCAAAAATGCTATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACACTCGAACT
1 AAAAAT-CC-------C-ATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACCCTCGAACT
530403 TCT
57 TCT
* * * * *
530406 AAAAATCCCATTTTTTATCCCAAAACTTCTAAAAATTCCATTTTTGCCCCCGAA
1 AAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACCCTCGAA
530460 TGTCTTAAAA
Statistics
Matches: 301, Mismatches: 37, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
57 4 0.01
58 46 0.15
59 143 0.48
60 4 0.01
61 1 0.00
62 51 0.17
67 3 0.01
68 48 0.16
69 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACCCTCGAACTTCT
Found at i:530381 original size:30 final size:30
Alignment explanation
Indices: 530347--530456 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 30
530337 CAAAAATGCC
* *
530347 AAAAATGCTATTTTTGACCCCAAAACTTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCT
* * *
530377 AAAAATTCTATTTTT-ACACTC-GAACTTCT
1 AAAAATTCCATTTTTGAC-CCCAAAACTTCT
* * *
530406 AAAAATCCCATTTTTTATCCCAAAACTTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCT
*
530436 AAAAATTCCATTTTTGCCCCC
1 AAAAATTCCATTTTTGACCCC
530457 GAATGTCTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
29 24 0.37
30 41 0.63
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAAATTCCATTTTTGACCCCAAAACTTCT
Found at i:530390 original size:68 final size:68
Alignment explanation
Indices: 530279--530411 Score: 180
Period size: 68 Copynumber: 2.0 Consensus size: 68
530269 TCGAACTTCT
* *
530279 AAAAATCTCATTTTTAACCCTAAAACTTCCAAAAATTTCATTTTTACCCCCGAACTTCCAAAAAT
1 AAAAATCTCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACACCCGAACTTCCAAAAAT
530344 GCC
66 GCC
* * * *
530347 AAAAATGCT-ATTTTTGACCCCAAAACTTCTAAAAA-TTCTATTTTTACACTCGAACTTCTAAAA
1 AAAAAT-CTCATTTTTAACCCCAAAACTTCCAAAAATTTC-ATTTTTACACCCGAACTTCCAAAA
530410 AT
64 AT
530412 CCCATTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 3 0.05
68 52 0.91
69 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (68 bp):
AAAAATCTCATTTTTAACCCCAAAACTTCCAAAAATTTCATTTTTACACCCGAACTTCCAAAAAT
GCC
Found at i:530478 original size:59 final size:59
Alignment explanation
Indices: 530347--530479 Score: 160
Period size: 59 Copynumber: 2.3 Consensus size: 59
530337 CAAAAATGCC
* * *
530347 AAAAATGCTATTTTTGACCCCAAAACTTCTAAAAATTCTATTTTTACACTCGAACTTCT
1 AAAAATCCTATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACTTCT
* * * * *
530406 AAAAATCCCATTTTTTATCCCAAAACTTCTAAAAATTCCATTTTTGCCCCCGAA-TGTCT
1 AAAAATCCTATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACT-TCT
* *
530465 TAAAATTCTATTTTT
1 AAAAATCCTATTTTT
530480 AAACCTTAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (59 bp):
AAAAATCCTATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACTTCT
Found at i:541771 original size:27 final size:27
Alignment explanation
Indices: 541732--541791 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
541722 AATTTTCAAC
*
541732 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAAT-ATTGTTTCCTTTGATCCTCTTCT
541760 TAATATTGTTTCCTTTGATCCTCTTCT
1 TAATATTGTTTCCTTTGATCCTCTTCT
541787 TAATA
1 TAATA
541792 GAATTTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (27 bp):
TAATATTGTTTCCTTTGATCCTCTTCT
Found at i:542627 original size:206 final size:206
Alignment explanation
Indices: 542266--542864 Score: 875
Period size: 206 Copynumber: 2.9 Consensus size: 206
542256 ATATCCACAG
*
542266 ACGATGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAATCAAACCCACGCTCAAAGCG
1 ACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCG
*
542331 AGCAAAATCTTCGAACCCCA-ACTTCCTGATGAGACATCGAGAAGCAGGTCGAAGTAATAAACGG
66 AGCAAAATCTTCAAACCCCAGA-TTCCTGATGAGACATCGAGAAGCAGGTCGAAGTAATAAACGG
*
542395 TTAGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGC
130 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGC
542460 GGATTGAAACAA
195 GGATTGAAACAA
* *
542472 GCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCAAAGCG
1 ACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCG
* * * * *
542537 AGCAAAATCTTCAAACCCCAGGTCCCTGATGAGACACCGAGAAGCAGGTCAAAGCAATAAACGGT
66 AGCAAAATCTTCAAACCCCAGATTCCTGATGAGACATCGAGAAGCAGGTCGAAGTAATAAACGGT
* *
542602 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAAATACAGAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCG
542667 GATTGAAACAA
196 GATTGAAACAA
** * * * * *
542678 ACGACACGATCATCTTCCTGATAAGATACTTAGAAGAAGACCAAATCAAACCCACGCTC-GA-TG
1 ACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCG
* * * *
542741 AAC-AAATCTTCTAACCCCAGATTCCTGATGAGATATTGAGAAGCAGGTCGAAGTAATAAAACGG
66 AGCAAAATCTTCAAACCCCAGATTCCTGATGAGACATCGAGAAGCAGGTCGAAGTAAT-AAACGG
* * * * * *
542805 ATAGCTTCCTGATGAAATAC-GAGAAAGTAAACCAAAATCATCTTCCTAATGAGATACAAA
130 TTAGCTTCCTGATGAGATACTGAG-AAGTGAACCAAATTCGTCTTCCTGATGAGATACAAA
542865 ATTTTACAAA
Statistics
Matches: 352, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
203 49 0.14
204 57 0.16
205 1 0.00
206 245 0.70
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (206 bp):
ACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAAAGCG
AGCAAAATCTTCAAACCCCAGATTCCTGATGAGACATCGAGAAGCAGGTCGAAGTAATAAACGGT
TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCG
GATTGAAACAA
Found at i:548648 original size:29 final size:31
Alignment explanation
Indices: 548609--548679 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
548599 AAACGATAAT
**
548609 ATAAGTGACTAAAACGTAA-C-ATTTCAAAC
1 ATAAGTGACTAAAACGTAATCTAAGTCAAAC
*
548638 ATAAGTGACTAAAATGTAATCTAAGTCAAAC
1 ATAAGTGACTAAAACGTAATCTAAGTCAAAC
*
548669 AAAAGTGACTA
1 ATAAGTGACTA
548680 TTTTTGCGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 18 0.50
30 1 0.03
31 17 0.47
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (31 bp):
ATAAGTGACTAAAACGTAATCTAAGTCAAAC
Found at i:548675 original size:31 final size:29
Alignment explanation
Indices: 548611--548679 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
548601 ACGATAATAT
** *
548611 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACAAGTCAAACAA
*
548640 AAGTGACTAAAATGTAATCTAAGTCAAACAA
1 AAGTGACTAAAACGTAA-C-AAGTCAAACAA
548671 AAGTGACTA
1 AAGTGACTA
548680 TTTTTGCGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.47
30 1 0.03
31 17 0.50
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACAAGTCAAACAA
Found at i:548889 original size:37 final size:37
Alignment explanation
Indices: 548817--548889 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
548807 CTTTTTAATT
* *
548817 TTAAATATAGTTTTAATTTTACCTTTACTTTTATATG
1 TTAAATATAGTTTTAATTTTACCTTTAATTATATATG
* * *
548854 TTAAATGTAGTTTATACTTTTA-TTTTAATTATATAT
1 TTAAATATAGTTT-TAATTTTACCTTTAATTATATAT
548890 CTTTTTAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 23 0.77
38 7 0.23
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
TTAAATATAGTTTTAATTTTACCTTTAATTATATATG
Found at i:548933 original size:20 final size:20
Alignment explanation
Indices: 548866--548934 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
548856 AAATGTAGTT
*
548866 TATACTTTTAT-TTTAATTA
1 TATATTTTTATATTTAATTA
548885 TATATCTTTT-TAATTTTAATGCT-
1 TATAT-TTTTAT-A-TTTAAT--TA
548908 TA-ATTTTTATATTTAATTA
1 TATATTTTTATATTTAATTA
548927 TATATTTT
1 TATATTTT
548935 AAAATGCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 17
0.69 0.02 0.29
Matches are distributed among these distances:
18 1 0.03
19 7 0.17
20 15 0.38
21 5 0.12
22 9 0.22
23 2 0.05
24 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (20 bp):
TATATTTTTATATTTAATTA
Found at i:557832 original size:17 final size:18
Alignment explanation
Indices: 557807--557843 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
557797 TCTTTTAAAA
557807 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
557825 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
557842 AT
1 AT
557844 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:575982 original size:29 final size:28
Alignment explanation
Indices: 575916--575982 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
575906 TCTTCACAAA
575916 TTTAAAATTTAATCCCTATACTTTTAAC
1 TTTAAAATTTAATCCCTATACTTTTAAC
* * * * *
575944 TTCAAGAATTTATTCCCTCTATTTTTAAAT
1 TTTAA-AATTTAATCCCTATACTTTT-AAC
575974 TTTAAAATT
1 TTTAAAATT
575983 CAAGTTCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.13
29 21 0.68
30 6 0.19
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTAAAATTTAATCCCTATACTTTTAAC
Found at i:578329 original size:2 final size:2
Alignment explanation
Indices: 578322--578359 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
578312 TTTCGAGCTA
578322 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
578360 GGTGTGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:578726 original size:14 final size:15
Alignment explanation
Indices: 578709--578737 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
578699 TTTTAATTAG
578709 TTTCTTTT-TTTTTT
1 TTTCTTTTCTTTTTT
578723 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
578738 CTCGTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:578861 original size:21 final size:22
Alignment explanation
Indices: 578835--578885 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
578825 TTTAATTCGA
*
578835 TTAATTT-ATCGGTAGTT-AATT
1 TTAATTTGATCAG-AGTTAAATT
578856 TTAATTTGATCAGAGTTAAATT
1 TTAATTTGATCAGAGTTAAATT
578878 TATAATTT
1 T-TAATTT
578886 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (22 bp):
TTAATTTGATCAGAGTTAAATT
Found at i:580728 original size:25 final size:25
Alignment explanation
Indices: 580700--580754 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
580690 ATATATATTT
* *
580700 AAATTATAAAATACAAAAAATCACA
1 AAATTACAAAAAACAAAAAATCACA
* * *
580725 AAATTACAAAAAAGAAAATATTACA
1 AAATTACAAAAAACAAAAAATCACA
580750 AAATT
1 AAATT
580755 GACCCTAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (25 bp):
AAATTACAAAAAACAAAAAATCACA
Found at i:581459 original size:2 final size:2
Alignment explanation
Indices: 581452--581485 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
581442 AAACAAATCA
581452 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
581486 AGCCATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:581671 original size:22 final size:22
Alignment explanation
Indices: 581646--581698 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
581636 AAATGACAGT
* *
581646 AAAACAATTAGAAAATAGTAAC
1 AAAACAATTAGAAAACAATAAC
* *
581668 AAAACAGTGAGAAAACAATAAC
1 AAAACAATTAGAAAACAATAAC
*
581690 AAATCAATT
1 AAAACAATT
581699 TTTTTTTGTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAACAATTAGAAAACAATAAC
Done.