Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009575.1 Kokia drynarioides strain JFW-HI SEQ_124289, 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: 339441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:48 original size:19 final size:20
Alignment explanation
Indices: 6--48 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1 ATTTT
***
6 AATTTATTTTTATTTATTGG
1 AATTTATTTTTATTTATAAA
26 AATTTA-TTTTATTTATAAA
1 AATTTATTTTTATTTATAAA
45 AATT
1 AATT
49 AGGTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
AATTTATTTTTATTTATAAA
Found at i:3870 original size:32 final size:32
Alignment explanation
Indices: 3834--3897 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3824 TGGATTAATC
*
3834 AGGTGATTATACATCAGATAAACAAATCTCCT
1 AGGTGATTAAACATCAGATAAACAAATCTCCT
*
3866 AGGTGATTAAACATCAGATAAACGAATCTCCT
1 AGGTGATTAAACATCAGATAAACAAATCTCCT
3898 TACTCCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (32 bp):
AGGTGATTAAACATCAGATAAACAAATCTCCT
Found at i:9284 original size:21 final size:23
Alignment explanation
Indices: 9259--9312 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
9249 CATACTTATT
9259 TTATTTTATTTTATT-T-ATTAG
1 TTATTTTATTTTATTCTAATTAG
*
9280 TTATTTT-TATTTATTCTAATTAT
1 TTATTTTAT-TTTATTCTAATTAG
9303 TTA-TTTATTT
1 TTATTTTATTT
9313 CTATCATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 13 0.46
22 6 0.21
23 8 0.29
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTTTATTTTATTCTAATTAG
Found at i:9310 original size:27 final size:27
Alignment explanation
Indices: 9257--9312 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
9247 TGCATACTTA
* *
9257 TTTTATTTTATTTTATTTATTAGTTAT
1 TTTTATTTTATTCTAATTATTAGTTAT
*
9284 TTTTA-TTTATTCTAATTATTTATTTAT
1 TTTTATTTTATTCTAATTA-TTAGTTAT
9311 TT
1 TT
9313 CTATCATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTATTTTATTCTAATTATTAGTTAT
Found at i:13503 original size:14 final size:15
Alignment explanation
Indices: 13475--13503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13465 TTATGAATGT
13475 TAATAAATCTTCTTC
1 TAATAAATCTTCTTC
13490 TAATAAAT-TTCTTC
1 TAATAAATCTTCTTC
13504 ACTTGAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATAAATCTTCTTC
Found at i:16843 original size:15 final size:18
Alignment explanation
Indices: 16798--16844 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
16788 CGGGGCATCT
16798 TCCTTCTCTTCTTCCGGG
1 TCCTTCTCTTCTTCCGGG
16816 TCCTTCTCTTCTTCCGGG
1 TCCTTCTCTTCTTCCGGG
16834 TCCTTCTCTTC
1 TCCTTCTCTTC
16845 AAGTCCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.00, C:0.40, G:0.13, T:0.47
Consensus pattern (18 bp):
TCCTTCTCTTCTTCCGGG
Found at i:24937 original size:100 final size:99
Alignment explanation
Indices: 24833--25318 Score: 450
Period size: 100 Copynumber: 4.9 Consensus size: 99
24823 TTAAAACTAT
* ** *
24833 AGTAGCAAATCTTTATCTCCCTGAAGTTATAGTGGATCAAGATGAAGCTACCACACCAAATCTTA
1 AGTAGAAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCTTA
24898 TAT-CCTGAAGTTGCAGTGGATCAGATTAAAATGGA
65 TATCCCTGAAGTTGCAGTGGATCAGATTAAAAT-GA
* * * * *
24933 AGTAGAAAATCTTTGTCTCCCTAAAGTTCCAATGGAGCAA-ATGAAGCTACCACACCAAATTTTA
1 AGTAGAAAATC-TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCTTA
* * *
24997 TATCCCTAAAGTTACAATGGATCAGATTAAAATGAA
65 TATCCCTGAAGTTGCAGTGGATCAGATTAAAATG-A
* ** * *
25033 AATAGAAAATCTT-TCTCTTTGAAGTTGCAGTAGAGCAAGATGAAGCTA-CATCACCAAATCATA
1 AGTAGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCA-CACCAAATCTTA
* ** *
25096 TATCACTGAAGTTGCAGTGGATTGGATTGAAACT-A
65 TATCCCTGAAGTTGCAGTGGATCAGATT-AAAATGA
* * ** *
25131 CAGTGGCAAATCTTATCTCCCT-AGAGTTGCAGTGGAGCAAGATGAAGCTATAACACCAAATCCT
1 -AGTAGAAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCTT
25195 ATATCCCTGAAGTTGCAGTGGATCATG-TTGAAGCAAT--
64 ATATCCCTGAAGTTGCAGTGGATCA-GATT-AA--AATGA
* * * * * * * * ** *
25232 AGAAGCAAATTTTATCTCACTGAGGATGCAGTGGAGCAAGATGAAGTTACAACATAAAATCCTAT
1 AGTAGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCTTAT
* *
25297 ATCCCTAAAGTAGCAGTGGATC
66 ATCCCTGAAGTTGCAGTGGATC
25319 GAATTGAAAC
Statistics
Matches: 322, Mismatches: 51, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
98 22 0.07
99 81 0.25
100 214 0.66
101 3 0.01
102 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (99 bp):
AGTAGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACCACACCAAATCTTAT
ATCCCTGAAGTTGCAGTGGATCAGATTAAAATGA
Found at i:25113 original size:50 final size:50
Alignment explanation
Indices: 25052--25316 Score: 176
Period size: 50 Copynumber: 5.3 Consensus size: 50
25042 TCTTTCTCTT
* *
25052 TGAAGTTGCAGTAGAGCAAGATGAAGCTACATCACCAAATCATATATCAC
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACATCACCAAATCATATATCCC
*** * ** * *
25102 TGAAGTTGCAGTGGA-TTGGATTGAAACTACAGT-GGCAAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAAGA-TGAAGCTACA-TCACCAAATCATATATCCC
* * *
25152 T-AGAGTTGCAGTGGAGCAAGATGAAGCTATAACACCAAATCCTATATCCC
1 TGA-AGTTGCAGTGGAGCAAGATGAAGCTACATCACCAAATCATATATCCC
* * * * * ** * ** * *
25202 TGAAGTTGCAGTGGATCATGTTGAAGCAATAGAAGCAAATTTTATCTCAC
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACATCACCAAATCATATATCCC
* * * * ** *
25252 TGAGGATGCAGTGGAGCAAGATGAAGTTACAACATAAAATCCTATATCCC
1 TGAAGTTGCAGTGGAGCAAGATGAAGCTACATCACCAAATCATATATCCC
* *
25302 TAAAGTAGCAGTGGA
1 TGAAGTTGCAGTGGA
25317 TCGAATTGAA
Statistics
Matches: 158, Mismatches: 51, Indels: 12
0.71 0.23 0.05
Matches are distributed among these distances:
49 3 0.02
50 151 0.96
51 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (50 bp):
TGAAGTTGCAGTGGAGCAAGATGAAGCTACATCACCAAATCATATATCCC
Found at i:25396 original size:100 final size:99
Alignment explanation
Indices: 24783--25383 Score: 448
Period size: 100 Copynumber: 6.0 Consensus size: 99
24773 GAATCAGTGA
* ** * * * * * *
24783 AACATCAAATCCTATATCTTTGATGATGCAATGGATTGAATTAAAACTATAGTAGCAAATCTTTA
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGAATTGAAACTACAGTAGCAAATC-TTA
* ** *
24848 TCTCCCTGAAGTTATAGTGGATCAAGATGAAGCTAC
65 TCT-CCTGAAGATGCAGTGGAGCAAGATGAAGCTAC
* * * *
24884 CACACCAAATCTTATAT-CCTGAAGTTGCAGTGGATC-AGATT-AAAATGGA-AGTAGAAAATCT
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGA-ATTGAAACT--ACAGTAGCAAATC-
* * * * *
24945 TTGTCTCCCTAAAGTTCCAATGGAGCAA-ATGAAGCTAC
62 TTATCT-CCTGAAGATGCAGTGGAGCAAGATGAAGCTAC
* ** * * * * * * *
24983 CACACCAAATTTTATATCCCTAAAGTTACAATGGATC-AGATT-AAAATGAAAATAGAAAATCTT
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGA-ATTGAAACT-ACAGTAGCAAATCTT
* * *
25046 -TCTCTTTGAAGTTGCAGTAGAGCAAGATGAAGCTAC
64 ATCTC-CTGAAGATGCAGTGGAGCAAGATGAAGCTAC
* * * * * *
25082 ATCACCAAATCATATATCACTGAAGTTGCAGTGGATTGGATTGAAACTACAGTGGCAAATCTTAT
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGAATTGAAACTACAGTAGCAAATCTTAT
* *
25147 CTCCCT-AGAGTTGCAGTGGAGCAAGATGAAGCTAT
66 CT-CCTGA-AGATGCAGTGGAGCAAGATGAAGCTAC
* * * * * *
25182 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATC-ATGTTGAAGCAATAGAAGCAAATTTTA
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGA-ATTGAAACTACAGTAGCAAATCTTA
* *
25246 TCTCACTGAGGATGCAGTGGAGCAAGATGAAGTTAC
65 TCTC-CTGAAGATGCAGTGGAGCAAGATGAAGCTAC
** * * * * *
25282 AACATAAAATCCTATATCCCTAAAGTAGCAGTGGATCGAATTGAAACTACATTAGCAAGTCCTAT
1 AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGAATTGAAACTACAGTAGCAAATCTTAT
* * *
25347 CTCCTTGAAGATGTAATGGAGCAAGATAAAGCTAC
66 CTCC-TGAAGATGCAGTGGAGCAAGATGAAGCTAC
25382 AA
1 AA
25384 TGTCAAATCC
Statistics
Matches: 404, Mismatches: 79, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
97 1 0.00
98 18 0.04
99 90 0.22
100 277 0.69
101 18 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (99 bp):
AACACCAAATCCTATATCCCTGAAGTTGCAGTGGATCGAATTGAAACTACAGTAGCAAATCTTAT
CTCCTGAAGATGCAGTGGAGCAAGATGAAGCTAC
Found at i:25826 original size:13 final size:12
Alignment explanation
Indices: 25803--25844 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
25793 TACCTATTAC
25803 CCAATACCCAAAT
1 CCAA-ACCCAAAT
25816 ACCAAACCCAAAT
1 -CCAAACCCAAAT
*
25829 CCTAACCCAAA-
1 CCAAACCCAAAT
25840 CCAAA
1 CCAAA
25845 ACTCAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 4 0.15
12 10 0.38
13 8 0.31
14 4 0.15
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (12 bp):
CCAAACCCAAAT
Found at i:27193 original size:16 final size:14
Alignment explanation
Indices: 27128--27193 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 14
27118 TATTTATTTA
27128 TTATATTTTATATT
1 TTATATTTTATATT
27142 TTAT-TTTTAT-TT
1 TTATATTTTATATT
27154 TTATTTATTTCTAGTATT
1 TTA--TATTT-TA-TATT
27172 TT-TATTTTATAATAT
1 TTATATTTTAT-AT-T
27187 TTATATT
1 TTATATT
27194 CTTAACCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
12 5 0.12
13 7 0.16
14 9 0.21
15 11 0.26
16 6 0.14
17 1 0.02
18 4 0.09
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TTATATTTTATATT
Found at i:33878 original size:18 final size:18
Alignment explanation
Indices: 33857--33926 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
33847 ATTTCCACAA
*
33857 GATCTTCTTCTTCTTTAG
1 GATCTTCTTCTTCTTCAG
33875 GATCTTCTTCTT-TCTCAG
1 GATCTTCTTCTTCT-TCAG
* *
33893 GATCTTTTTCTTCCTCAG
1 GATCTTCTTCTTCTTCAG
33911 GATCTTCTTCTTCTTC
1 GATCTTCTTCTTCTTC
33927 TTCAGCTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
17 1 0.02
18 44 0.98
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.53
Consensus pattern (18 bp):
GATCTTCTTCTTCTTCAG
Found at i:35538 original size:19 final size:20
Alignment explanation
Indices: 35516--35563 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
35506 TAAACTTTTG
35516 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
35535 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
35555 -TAAT-ATTAA
1 ATAATAATTAA
35564 AAATTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:42753 original size:18 final size:18
Alignment explanation
Indices: 42730--42772 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42720 ACCAAGACAA
* *
42730 ACCGTTGACTGACCGTTG
1 ACCGTTGACCGACAGTTG
*
42748 ACCGTTGACCGGCAGTTG
1 ACCGTTGACCGACAGTTG
42766 ACCGTTG
1 ACCGTTG
42773 CCTTTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (18 bp):
ACCGTTGACCGACAGTTG
Found at i:43653 original size:18 final size:18
Alignment explanation
Indices: 43626--43662 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43616 TTAGTTACAA
43626 TTTATATTATTTT-ATTT
1 TTTATATTATTTTGATTT
43643 TTTATTATTATTTTGATTT
1 TTTA-TATTATTTTGATTT
43662 T
1 T
43663 GGATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTATATTATTTTGATTT
Found at i:43668 original size:19 final size:18
Alignment explanation
Indices: 43630--43671 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
43620 TTACAATTTA
**
43630 TATTATTTTATTTTTTAT
1 TATTATTTTATTTTGGAT
43648 TATTATTTTGATTTTGGAT
1 TATTATTTT-ATTTTGGAT
43667 TATTA
1 TATTA
43672 ATATTCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (18 bp):
TATTATTTTATTTTGGAT
Found at i:52609 original size:26 final size:26
Alignment explanation
Indices: 52565--52617 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
52555 ATATATGTAA
52565 ATGAAATGGTAAAATGAAACGGTTAT
1 ATGAAATGGTAAAATGAAACGGTTAT
* *
52591 ATGAAATGGTTATAA-GAAATGGTTAT
1 ATGAAATGG-TAAAATGAAACGGTTAT
52617 A
1 A
52618 GGGAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (26 bp):
ATGAAATGGTAAAATGAAACGGTTAT
Found at i:52624 original size:13 final size:13
Alignment explanation
Indices: 52567--52617 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
52557 ATATGTAAAT
*
52567 GAAATGG-TAAAA
1 GAAATGGTTATAA
* *
52579 TGAAACGGTTATAT
1 -GAAATGGTTATAA
52593 GAAATGGTTATAA
1 GAAATGGTTATAA
52606 GAAATGGTTATA
1 GAAATGGTTATA
52618 GGGAATGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 29 0.91
14 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (13 bp):
GAAATGGTTATAA
Found at i:52624 original size:26 final size:26
Alignment explanation
Indices: 52580--52642 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
52570 ATGGTAAAAT
* * * *
52580 GAAACGGTTATATGAAATGGTTATAA
1 GAAATGGTTATAGGAAATGATTACAA
* *
52606 GAAATGGTTATAGGGAATGATTACAT
1 GAAATGGTTATAGGAAATGATTACAA
*
52632 GAAATGATTAT
1 GAAATGGTTAT
52643 GAGAAAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (26 bp):
GAAATGGTTATAGGAAATGATTACAA
Found at i:55713 original size:514 final size:515
Alignment explanation
Indices: 54737--55779 Score: 1621
Period size: 514 Copynumber: 2.0 Consensus size: 515
54727 CAAAATGAAA
*
54737 AATAA-TCATTCGATCATAATAAACAAGTTGAATTGTGAAATATTAAATATATATTTTTTTCAAA
1 AATAATTCAATCGATCATAATAAACAAGTTGAATTGTGAAATATTAAATATATATTTTTTTCAAA
* * * *
54801 AATTTTACCATGGATAAAATTGTTATTATTTTACTAGAGGTAAAATTGAGATGAGAAATTTATTT
66 AATTTTACCATGGATAAAATCGTTATAATTTTACTAGAGGTAAAATTGAGATGAAAAAATTATTT
* * * * *
54866 AATTGAATATAAATATTGAATTTTACTTTGGGAAATAGAAAAGCGGAATCAGGTTGGGTCAAATT
131 AATTGAATATAAATATTAAATCTTACTTTGGGAAATAGAAAAGCAGAATCAAGTTGAGTCAAATT
*
54931 ACAAAGTATTGGGTTGAAAATCCGGAAAATACTCATAATTAGATCTTATGTCAGAGAGGCCCAAA
196 ACAAAGTATTGGGTTGAAAATCCGGAAAATACTCATAATTAGATCTGATGTCAGAGAGGCCCAAA
* * * ** * *
54996 AACCCTTCATAGATATGAGGGGAGTAGCAACCCTAGTAGGAATACTAGGGGATGTTGTCCACCCT
261 AACCCCTCATAGATATGAGGGGAGGAGCAACCCTAATAAAAATACTAAGAGATGTTGTCCACCCT
* * *
55061 ACTCATACTCTAAGTAAAATGTTGTTTTTCTAGTTGAAATAAATTTTCTATAATTTAACAAGGGT
326 ACTCATACTCTAAGTAAAAAGTTATTTTTCTAGTTGAAATAAATTTTCTACAATTTAACAAGGGT
* * * *
55126 TCTACTTTCTTTCCTTATAAATAGATGGCACCGATAGAGTTATTAACACAACTTTAAGATATTGT
391 TCTACTTTCTCTCCCTATAAATAGATGGCACCGATAAAGCTATTAACACAACTTTAAGATATTGT
*
55191 TATTCTGCCAAAAAATAGAGAGAATTTATTTTCAACTATTAAATATA-TTTTTTCAGAAT
456 TATTCTGCCAAAAAATAGAGAGAATTTATTTTCAACTATTAAATATATTTTTTTCAAAAT
* *
55250 AGTAATTCAGTCGATCATAATAAACAAGTTGAATTGTGAAATATT-AA-ATATATTTTTTTCAAA
1 AATAATTCAATCGATCATAATAAACAAGTTGAATTGTGAAATATTAAATATATATTTTTTTCAAA
* * * * *
55313 ACTTTTACCGTTGATAAAATCGTTATAATTTTACTAGGGGTAAAATTGGGATGAAAAAATTATTT
66 AATTTTACCATGGATAAAATCGTTATAATTTTACTAGAGGTAAAATTGAGATGAAAAAATTATTT
*
55378 AATTGAATATAAATATTAAATCTTATTTTGGGAAATAGAAAAAGCAGAATCAAGTTGAGTCAAAT
131 AATTGAATATAAATATTAAATCTTACTTTGGGAAATAG-AAAAGCAGAATCAAGTTGAGTCAAAT
* * * * * *
55443 TACAAAGTATTGGGTTGAAAAGTTCGGGAAGTACTCGTAATTAGATCTGATGTGAGAGAGGTCCA
195 TACAAAGTATTGGGTTGAAAA-TCCGGAAAATACTCATAATTAGATCTGATGTCAGAGAGGCCCA
*
55508 AAAACCCCTCATGGATATGAGGGGAGCGA-CAACCCTAATAAAAATACTAAGAGATGTTGTCCAC
259 AAAACCCCTCATAGATATGAGGGGAG-GAGCAACCCTAATAAAAATACTAAGAGATGTTGTCCAC
*
55572 CCTACTCCTACTCTAAGTAAAAAGTTATTTTTCTAGTTGAAATAAATTTTCTACAATTTAACAAG
323 CCTACTCATACTCTAAGTAAAAAGTTATTTTTCTAGTTGAAATAAATTTTCTACAATTTAACAAG
55637 GGTTCTACTTTCTCTCCCTATAAATAGATGGCACCGATAAAGCTATTAACAC-ACTTTTAAGATA
388 GGTTCTACTTTCTCTCCCTATAAATAGATGGCACCGATAAAGCTATTAACACAAC-TTTAAGATA
*
55701 TTGTTATTCTGCCAAAAAATAGAGAGAATTTATTTTCAATTATTAAATATATTTTTTTCAAAAT
452 TTGTTATTCTGCCAAAAAATAGAGAGAATTTATTTTCAACTATTAAATATATTTTTTTCAAAAT
55765 AATAATTCAATCGAT
1 AATAATTCAATCGAT
55780 TTTTATTTGA
Statistics
Matches: 480, Mismatches: 44, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
512 107 0.22
513 52 0.11
514 296 0.62
515 25 0.05
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (515 bp):
AATAATTCAATCGATCATAATAAACAAGTTGAATTGTGAAATATTAAATATATATTTTTTTCAAA
AATTTTACCATGGATAAAATCGTTATAATTTTACTAGAGGTAAAATTGAGATGAAAAAATTATTT
AATTGAATATAAATATTAAATCTTACTTTGGGAAATAGAAAAGCAGAATCAAGTTGAGTCAAATT
ACAAAGTATTGGGTTGAAAATCCGGAAAATACTCATAATTAGATCTGATGTCAGAGAGGCCCAAA
AACCCCTCATAGATATGAGGGGAGGAGCAACCCTAATAAAAATACTAAGAGATGTTGTCCACCCT
ACTCATACTCTAAGTAAAAAGTTATTTTTCTAGTTGAAATAAATTTTCTACAATTTAACAAGGGT
TCTACTTTCTCTCCCTATAAATAGATGGCACCGATAAAGCTATTAACACAACTTTAAGATATTGT
TATTCTGCCAAAAAATAGAGAGAATTTATTTTCAACTATTAAATATATTTTTTTCAAAAT
Found at i:57111 original size:7 final size:7
Alignment explanation
Indices: 57099--57126 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
57089 TTCTGGCACC
57099 TTTCTTT
1 TTTCTTT
57106 TTTCTTT
1 TTTCTTT
57113 TTTCTTT
1 TTTCTTT
57120 TTTCTTT
1 TTTCTTT
57127 ACTCATGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTCTTT
Found at i:58508 original size:16 final size:15
Alignment explanation
Indices: 58487--58516 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
58477 CAAAGAGCAA
58487 AAAATTTGTGTGAAAG
1 AAAATTTGT-TGAAAG
58503 AAAATTTGTTGAAA
1 AAAATTTGTTGAAA
58517 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAATTTGTTGAAAG
Found at i:60580 original size:91 final size:95
Alignment explanation
Indices: 60450--60639 Score: 246
Period size: 91 Copynumber: 2.0 Consensus size: 95
60440 AAACTTTCTC
* * *
60450 AAAAAAAGCAATTAAGCCCTCTTTTTTTTTTTGGCACTCATTTGAGTACTTCAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCCCTCTATTTTTTTTTGGCACTCAATTGAGTACTTAAACTTTCAAAATG
60515 -ATAAAAAAAAACCCTCAAAC-CTTTCAAAA
66 CAT-AAAAAAAACCCTCAAACTCTTTCAAAA
* * *
60544 AAAAAAAGCAATTAA-TCC-CTATTTTTTTTT-GCACTCAATTGAGTATTTAAACTTTTAAAATG
1 AAAAAAAGCAATTAAGCCCTCTATTTTTTTTTGGCACTCAATTGAGTACTTAAACTTTCAAAATG
* * *
60606 CATCAAAAAAACTCTCAAACTTTTTTCAAAA
66 CATAAAAAAAACCCTCAAAC-TCTTTCAAAA
60637 AAA
1 AAA
60640 GCAATTAAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
91 43 0.51
92 13 0.15
93 13 0.15
94 15 0.18
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (95 bp):
AAAAAAAGCAATTAAGCCCTCTATTTTTTTTTGGCACTCAATTGAGTACTTAAACTTTCAAAATG
CATAAAAAAAACCCTCAAACTCTTTCAAAA
Found at i:60690 original size:18 final size:19
Alignment explanation
Indices: 60659--60702 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
60649 CCCCTGCTTT
60659 TATTAAAAAATATAAA-AA
1 TATTAAAAAATATAAATAA
** *
60677 TATTAAAAGCTATAAATAT
1 TATTAAAAAATATAAATAA
60696 TATTAAA
1 TATTAAA
60703 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TATTAAAAAATATAAATAA
Found at i:60784 original size:19 final size:19
Alignment explanation
Indices: 60738--60803 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
60728 AGAAAAGAAA
*
60738 TATAGAAATCGTAAAAAATAT
1 TATAAAAATCGT--AAAATAT
* * * *
60759 AAAAAAAATTGTAAAATTT
1 TATAAAAATCGTAAAATAT
60778 TATAAAAATCGTAAAATAT
1 TATAAAAATCGTAAAATAT
60797 TATAAAA
1 TATAAAA
60804 TATATAAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 28 0.78
21 8 0.22
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (19 bp):
TATAAAAATCGTAAAATAT
Found at i:60793 original size:29 final size:28
Alignment explanation
Indices: 60761--60868 Score: 89
Period size: 29 Copynumber: 3.9 Consensus size: 28
60751 AAAAATATAA
*
60761 AAAAAATTGTAAAATTTTATAAAAATCGT
1 AAAAAATTATAAAA-TTTATAAAAATCGT
* * *
60790 AAAATATTATAAAATATATAAAAAT-AT
1 AAAAAATTATAAAATTTATAAAAATCGT
* *
60817 AAAAAA-TATACAACTTTAT-AAAGTCGT
1 AAAAAATTATA-AAATTTATAAAAATCGT
*
60844 AAAAAAATTATACAAA-ATATAAAAA
1 -AAAAAATTATA-AAATTTATAAAAA
60869 ATATAAAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
26 8 0.13
27 13 0.21
28 19 0.31
29 22 0.35
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAAAATTATAAAATTTATAAAAATCGT
Found at i:60811 original size:19 final size:19
Alignment explanation
Indices: 60770--60877 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 19
60760 AAAAAAATTG
* *
60770 TAAAATTTTATAAAA-ATCG
1 TAAAATATTATAAAATAT-A
60789 TAAAATATTATAAAATATA
1 TAAAATATTATAAAATATA
*
60808 TAAAA-A-TATAAAAAATA
1 TAAAATATTATAAAATATA
* * *
60825 TACAACT-TTATAAAGTCGTA
1 TA-AAATATTATAAAAT-ATA
*
60845 -AAAAAATTATACAAA-ATA
1 TAAAATATTATA-AAATATA
*
60863 TAAAA-AATATAAAAT
1 TAAAATATTATAAAAT
60878 TTGTAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
17 15 0.22
18 12 0.18
19 35 0.51
20 6 0.09
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAATATTATAAAATATA
Found at i:60903 original size:9 final size:9
Alignment explanation
Indices: 60762--60886 Score: 51
Period size: 9 Copynumber: 13.6 Consensus size: 9
60752 AAAATATAAA
*
60762 AAAAATTGT
1 AAAAATTAT
*
60771 AAAATTTTAT
1 AAAA-ATTAT
**
60781 AAAAATCGT
1 AAAAATTAT
60790 AAAATATTAT
1 AAAA-ATTAT
60800 -AAAATATAT
1 AAAAAT-TAT
60809 AAAAA-TAT
1 AAAAATTAT
*
60817 AAAAAATAT
1 AAAAATTAT
* *
60826 ACAACTT-T
1 AAAAATTAT
* *
60834 ATAAAGTCGTAA
1 A-AAAAT--TAT
60846 AAAAATTAT
1 AAAAATTAT
60855 ACAAAA-TAT
1 A-AAAATTAT
*
60864 AAAAAATAT
1 AAAAATTAT
* *
60873 AAAATTTGT
1 AAAAATTAT
60882 AAAAA
1 AAAAA
60887 AAATTTATAA
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
8 16 0.19
9 46 0.53
10 18 0.21
11 5 0.06
12 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:70187 original size:16 final size:16
Alignment explanation
Indices: 70166--70205 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
70156 ATATACCATT
70166 TTTTTTAAATTATGAA
1 TTTTTTAAATTATGAA
* *
70182 TTTTTT-AATTTTTAA
1 TTTTTTAAATTATGAA
70197 TTTTTTAAA
1 TTTTTTAAA
70206 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTTAAATTATGAA
Found at i:73663 original size:52 final size:52
Alignment explanation
Indices: 73587--73768 Score: 253
Period size: 52 Copynumber: 3.5 Consensus size: 52
73577 TTGAAAAAGA
*
73587 TCCGATGAC-AT-TGTCATCATGAGTATATGAATCCTTTACGGATTATAGGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAGGG
* *
73637 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAGGG
* ** *
73689 TCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTTTGGATTAT-GACG
1 TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAG-GG
* *
73741 TTCGATGACAATGTGTCATCGTGAGTAT
1 TCCGATGACTATGTGTCATCGTGAGTAT
73769 TAAATGAGAA
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
50 9 0.08
51 2 0.02
52 106 0.91
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAGGG
Found at i:74548 original size:21 final size:22
Alignment explanation
Indices: 74524--74573 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
74514 GATTTGTTTT
**
74524 GGTAGAATCT-TCATTGGTATC
1 GGTAGAATCTGTCATAAGTATC
*
74545 GGTAGAA-CTGTCATAAGTATT
1 GGTAGAATCTGTCATAAGTATC
74566 GGTAGAAT
1 GGTAGAAT
74574 TCTACACTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (22 bp):
GGTAGAATCTGTCATAAGTATC
Found at i:78108 original size:23 final size:23
Alignment explanation
Indices: 78056--78208 Score: 89
Period size: 23 Copynumber: 6.6 Consensus size: 23
78046 TATACGGAAC
* *
78056 AAACAGAGAGCATATA-AGTGGT
1 AAACAGAGAGCACATACAGTGCT
78078 AGACAACAGAGAGCACATACAGTGCT
1 --A-AACAGAGAGCACATACAGTGCT
* * * **
78104 AAACAGAGAGTACACAAAGCACT
1 AAACAGAGAGCACATACAGTGCT
* *
78127 AATCAGAGAG--CATAAAGTGCT
1 AAACAGAGAGCACATACAGTGCT
* * * *
78148 AATCAGAAAGCACACACAATGCT
1 AAACAGAGAGCACATACAGTGCT
*
78171 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ATACAGTGCT
*
78196 AAACAGGGAGCAC
1 AAACAGAGAGCAC
78209 GCTAGTGTTC
Statistics
Matches: 102, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
21 17 0.17
23 45 0.44
24 4 0.04
25 28 0.27
26 8 0.08
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACATACAGTGCT
Found at i:78143 original size:21 final size:21
Alignment explanation
Indices: 78119--78159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
78109 GAGAGTACAC
*
78119 AAAGCACTAATCAGAGAGCAT
1 AAAGCACTAATCAGAAAGCAT
**
78140 AAAGTGCTAATCAGAAAGCA
1 AAAGCACTAATCAGAAAGCA
78160 CACACAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.15
Consensus pattern (21 bp):
AAAGCACTAATCAGAAAGCAT
Found at i:84508 original size:24 final size:24
Alignment explanation
Indices: 84481--84553 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
84471 AACATGTTGT
84481 ATGTCCATATAGGCATGATTTTGA
1 ATGTCCATATAGGCATGATTTTGA
* *
84505 ATGTTCA-AT--GTATGATTTTGA
1 ATGTCCATATAGGCATGATTTTGA
84526 ATGTCCATATAGGCATGATTTTGA
1 ATGTCCATATAGGCATGATTTTGA
84550 ATGT
1 ATGT
84554 TCAATGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 17 0.40
22 2 0.05
23 2 0.05
24 21 0.50
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (24 bp):
ATGTCCATATAGGCATGATTTTGA
Found at i:84519 original size:21 final size:21
Alignment explanation
Indices: 84495--84565 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 21
84485 CCATATAGGC
84495 ATGATTTTGAATGTTCAATGT
1 ATGATTTTGAATGTTCAATGT
* *
84516 ATGATTTTGAATGTCCATATAGGC
1 ATGATTTTGAATGTTCA-AT--GT
84540 ATGATTTTGAATGTTCAATGT
1 ATGATTTTGAATGTTCAATGT
*
84561 TTGAT
1 ATGAT
84566 ATGGTTGGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 21 0.50
22 2 0.05
23 2 0.05
24 17 0.40
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (21 bp):
ATGATTTTGAATGTTCAATGT
Found at i:85430 original size:239 final size:240
Alignment explanation
Indices: 84971--85449 Score: 739
Period size: 239 Copynumber: 2.0 Consensus size: 240
84961 TAAAAAATAT
*
84971 CTCCAATTTACTTATAACTTGACTAAGACATGTTCACCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTTACTTATAACTTGACTAAGACATGTCCACCAAACTTATCTAATTTAAAACTTAAATT
* * * * *
85036 AGAGATTTTTTACTCCTAATAAGAACTCTAAAGGATACCTAAATAATTCTAGTAAAATACTTTCA
66 AAAGATTTTTTACTCCTAACAAGAACTCTAAAAGATACCTAAATAATTCTAATAAAATACCTTCA
*
85101 ATTATTAAAATTAATTCTATTTTAAAATCCTAAAAAAACCTAAAAAAATTACTAATGAATTAAGA
131 ATTATTAAAATTAATTCTATTTTAAAATCCTAAAAAAAACTAAAAAAATTACTAATGAATTAAGA
*
85166 GAAATATTAAAATTCATCTACAACTTATTCAATCTTTTATCATTA
196 GAAATATTAAAATTCATCCACAACTTATTCAATCTTTTATCATTA
* * ** *
85211 CTCCGATTTACTTGTAACTTGACTAAGATGTGTCCATCAAACTTATCTAATTTAAAACTTAAATT
1 CTCCAATTTACTTATAACTTGACTAAGACATGTCCACCAAACTTATCTAATTTAAAACTTAAATT
* * *
85276 AAAGA-TTTTTACTTCTAACGAGAA-TCCTAAAAGATACTTAAATAATTCTAATAAAATACCTTC
66 AAAGATTTTTTACTCCTAACAAGAACT-CTAAAAGATACCTAAATAATTCTAATAAAATACCTTC
* * *
85339 AATTCTTAAAATTAATTCTATTTTAGAATCCTAAAAAAAAC-ATAAAAATTACTAATGAATTAAG
130 AATTATTAAAATTAATTCTATTTTAAAATCCTAAAAAAAACTAAAAAAATTACTAATGAATTAAG
*
85403 AGAAATATTAAAATTTCATCCACAACTTATTCGATCTTTTATCATTA
195 AGAAATATTAAAA-TTCATCCACAACTTATTCAATCTTTTATCATTA
85450 TTATGATTTT
Statistics
Matches: 217, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
238 36 0.17
239 118 0.54
240 63 0.29
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (240 bp):
CTCCAATTTACTTATAACTTGACTAAGACATGTCCACCAAACTTATCTAATTTAAAACTTAAATT
AAAGATTTTTTACTCCTAACAAGAACTCTAAAAGATACCTAAATAATTCTAATAAAATACCTTCA
ATTATTAAAATTAATTCTATTTTAAAATCCTAAAAAAAACTAAAAAAATTACTAATGAATTAAGA
GAAATATTAAAATTCATCCACAACTTATTCAATCTTTTATCATTA
Found at i:86963 original size:148 final size:147
Alignment explanation
Indices: 86491--87142 Score: 693
Period size: 149 Copynumber: 4.4 Consensus size: 147
86481 TAATTAAAAC
* * * * *
86491 AAAATTACTAGTTTACTTCAAAATCAAAATTTTTATTTCGAAATAGTTTAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTT
* * * *
86556 TGTTTAAAAATTTAAACTTTTTTCTTTAAAATCACTAAAAAACATATTTTTATTTTTTTAAAATC
65 TATTTAAAAATTTAAAC-TTTTTCTTTAAAATAACT-AAAAACAGATTTTTA-TTTTTTAAAATA
* * *
86621 TAAGCTTTTTTTTTTTTTAATG
127 TAAAC-TTTCTCTTTTTTAATG
* *
86643 AAAATCACTACTTTGCATAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
* * * * *
86708 TATTAAAAAATTTAAACTTTTTCTTTAAATTAACTAAAAAAAGTTTTTTATTTTTCAAAATATAA
65 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACAGATTTTTATTTTTTAAAATATAA
* *
86773 ATTTTCTTTCTTTTTAATG
130 ACTTTCTCT-TTTTTAATG
* *
86792 AAAATCACTACTTTACTTAAAAAT-TCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAATTT
1 AAAATCACTACTTTACTTAAAAATCT-AAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTT
* *
86856 TATTTAAAAATTTAAACTTTTTCTTTAAAATAATTGAAAAACAGATTTTTATTTTTAAAAATATA
65 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAACAGATTTTTATTTTTTAAAATATA
*
86921 AACTTTCTCCTTTTTTCATG
129 AACTTTCT-CTTTTTTAATG
* * * ** *
86941 AAAATCACTAATTT-CTTAAAAATCTAAACATTTATTTTG-TTTA--AAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * * *
87002 GTTTAAAAATTTAAA-TTTTTC----GAA-AA--AAAAACAGATTTTTATTTTTTGAAATCTAGA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACAGATTTTTATTTTTTAAAATATAAA
*
87059 CTTTCTCTTTTTTAAAG
131 CTTTCTCTTTTTTAATG
* * * * * *
87076 AAAATCACTATTTTTACTTTAAAAT-AAAAGATTTTATTTCGAAATTGTTTAAAAAAACCAAAAC
1 AAAATCACTA-CTTTACTTAAAAATCTAAA-CTTTTATTTCGAAATAG-TTAAAAAAATCAAAAC
87140 TTT
63 TTT
87143 TCTCAAAATC
Statistics
Matches: 428, Mismatches: 59, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
135 19 0.04
136 39 0.09
137 16 0.04
138 1 0.00
139 2 0.00
140 2 0.00
141 16 0.04
144 6 0.01
145 30 0.07
147 2 0.00
148 74 0.17
149 120 0.28
150 13 0.03
151 18 0.04
152 70 0.16
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (147 bp):
AAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACAGATTTTTATTTTTTAAAATATAAA
CTTTCTCTTTTTTAATG
Found at i:88102 original size:42 final size:42
Alignment explanation
Indices: 88033--88743 Score: 947
Period size: 42 Copynumber: 16.9 Consensus size: 42
88023 AAAAAATAAA
* * * * * *
88033 TAAATGGACCTCTACGCCTAGGACTCTAAATGTAATAAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
*
88075 TAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* *
88117 TAAATGAACCTCCATACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * * * * *
88159 TAAATGGGCCTCTACACTTGGACCTCTAAATGTAATGAAAGG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * * * *
88201 TAAATGGGCCACCACACTTGAGCCTCTAAATGTAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* *
88243 TAAATGGATCTCCACACCTGGGCCTTTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* *
88285 TAAATGGGCCTTCACACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * *
88327 TAAATGGACCTCCATACCTGAGCCTTTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
*
88369 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * *
88411 TAAATGGGCCTCCACACCTAGGCCTATAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
*
88453 TAAATGGACCTCCACACCTGAGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * * * * *
88495 TAAATGGGCCTCTACACCTGGGCCTTTGAATGCGATGAAATG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * ** *
88537 TAAATGGACATCCACACCTAGGTTTATAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
** *
88579 TAAATGGACCTCCACATGTGGGCCTCTAAATACAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
88621 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
* * * *
88663 TAAAT-GAGCCTCCACACTTGGGCCTCTGAATGCGATGAAAAA
1 TAAATGGA-CCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
*
88705 TAAATGGACCTCCACATCTGGGCCTCTAAATGCAATGAA
1 TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
88744 TGCTTTCCTT
Statistics
Matches: 580, Mismatches: 87, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
41 2 0.00
42 576 0.99
43 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
TAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAAAAG
Found at i:89161 original size:12 final size:12
Alignment explanation
Indices: 89144--89169 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
89134 TTGCTCTCTC
89144 TTTCTATTTTTT
1 TTTCTATTTTTT
89156 TTTCTATTTTTT
1 TTTCTATTTTTT
89168 TT
1 TT
89170 GTATGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTATTTTTT
Found at i:89178 original size:12 final size:11
Alignment explanation
Indices: 89144--89182 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
89134 TTGCTCTCTC
89144 TTTCTATTTTTT
1 TTTCTA-TTTTT
89156 TTTCTATTTTT
1 TTTCTATTTTT
* *
89167 TTTGTATGTTT
1 TTTCTATTTTT
89178 TTTCT
1 TTTCT
89183 TGATTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTCTATTTTT
Found at i:100514 original size:25 final size:25
Alignment explanation
Indices: 100480--100529 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
100470 GCCACCTATT
100480 GTCTAAAAGTCTAGAATTAATACTA
1 GTCTAAAAGTCTAGAATTAATACTA
100505 GTCTAAAAGTCTAGAATTAATACTA
1 GTCTAAAAGTCTAGAATTAATACTA
100530 AGAAAAATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (25 bp):
GTCTAAAAGTCTAGAATTAATACTA
Found at i:102133 original size:150 final size:150
Alignment explanation
Indices: 101993--102493 Score: 709
Period size: 150 Copynumber: 3.4 Consensus size: 150
101983 TGATTAAAAT
*
101993 AAAATCACAACTTTACTTCAAAAA-CAAAACTTTTATTTTGAAATAGTTAAAAATATCAAAACTT
1 AAAATCACAACTTTACTT-AAAAATCAAAACTTTTATTTCGAAATAGTTAAAAATATCAAAACTT
* *
102057 TATTTAAAAATTTAAACTTTTTTCTTTAAAATCACT-AAAAACAGATTTTTATTTTTTAAAAATC
65 TATTTAAAAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA-TTTTTAAAAATA
102121 TAAACTTTCTTTTTTTTTTAATG
129 TAAACTTTC-TTTTTTTTTAATG
* * *
102144 AAAATCACTACTTTACTTAAAAA-CTTAAACTTTTATTTCG-AATAGTTAAAAAAATCAAAACTT
1 AAAATCACAACTTTACTTAAAAATC-AAAACTTTTATTTCGAAATAGTTAAAAATATCAAAACTT
*
102207 TATTTAAAAATTTAAAC-TTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATAT
65 TATTTAAAAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
*
102271 AAAATTTCTTTCTTTTTTAATG
130 AAACTTTCTTT-TTTTTTAATG
* *
102293 AAAATCACTACTTTACTTAAAAATCCAAAA-TTTTATTTCGAAATAGTTTAAAATATCAAAACTT
1 AAAATCACAACTTTACTTAAAAAT-CAAAACTTTTATTTCGAAATAGTTAAAAATATCAAAACTT
* * * *
102357 TATTTAAAAATTTAAA-TTTTTTCTTTAAAATAATTGAAAAACAGATTTTTATGTTT-AGAATAT
65 TATTTAAAAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATAT
102420 AAACTTTCTCCTTTTTTTTAAT-
130 AAACTTTCT--TTTTTTTTAATG
*
102442 AAAATCACTAA-TTT-CTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAA
1 AAAATCAC-AACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAA
102494 AAAGGCATAA
Statistics
Matches: 319, Mismatches: 20, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
147 4 0.01
148 34 0.11
149 104 0.33
150 144 0.45
151 33 0.10
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (150 bp):
AAAATCACAACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAATATCAAAACTTT
ATTTAAAAATTTAAACTTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
AACTTTCTTTTTTTTTAATG
Found at i:103060 original size:28 final size:28
Alignment explanation
Indices: 103029--103098 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 28
103019 AATATCATTA
103029 TTTAATAATTATTAT-TTCAAAAAATAAT
1 TTTAATAATT-TTATATTCAAAAAATAAT
*
103057 TTTAATAATTTTATACTTTAAAAAATAAT
1 TTTAATAATTTTATA-TTCAAAAAATAAT
103086 TTTAATAATTTTA
1 TTTAATAATTTTA
103099 AAATCATTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 4 0.10
28 10 0.26
29 25 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTAATAATTTTATATTCAAAAAATAAT
Found at i:103101 original size:20 final size:20
Alignment explanation
Indices: 103051--103107 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
103041 TATTTCAAAA
103051 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
* *
103069 -ATACTTTAAAAAATAATTTT
1 AATAATTT-TAAAATAATTTT
*
103089 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
103108 GCTGACATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 6 0.20
20 18 0.60
21 6 0.20
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:110053 original size:25 final size:25
Alignment explanation
Indices: 110001--110056 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
109991 CTTTGGATTT
* * **
110001 TGGCTCGTAAGAGCGATATTTTGTC
1 TGGCTCGCAAGAGCGATATTCTAAC
*
110026 TGGCTCGCAAGAGCGTTATTCTAAC
1 TGGCTCGCAAGAGCGATATTCTAAC
110051 TGGCTC
1 TGGCTC
110057 ATATGAGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (25 bp):
TGGCTCGCAAGAGCGATATTCTAAC
Found at i:110214 original size:20 final size:20
Alignment explanation
Indices: 110178--110215 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
110168 GAATTTGTTT
*
110178 AAATTACTCTTCTTGTAACC
1 AAATTACTATTCTTGTAACC
110198 AAATATACTATTC-TGTAA
1 AAAT-TACTATTCTTGTAA
110216 GTTACCTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (20 bp):
AAATTACTATTCTTGTAACC
Found at i:114062 original size:11 final size:11
Alignment explanation
Indices: 114027--114056 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
114017 TTGTGACATA
114027 AATGATGTCAT
1 AATGATGTCAT
*
114038 GATGATGTCAT
1 AATGATGTCAT
114049 AATGATGT
1 AATGATGT
114057 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (11 bp):
AATGATGTCAT
Found at i:117280 original size:21 final size:19
Alignment explanation
Indices: 117256--117309 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
117246 AATGTCGTAC
*
117256 AAATATTTTAATTATGATTA
1 AAATATTTTAATTAT-AGTA
117276 GAAATTATTTT-ATTATAGTA
1 -AAA-TATTTTAATTATAGTA
*
117296 ATATATTTTAATTA
1 AAATATTTTAATTA
117310 AATAATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 3 0.10
21 8 0.28
22 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (19 bp):
AAATATTTTAATTATAGTA
Found at i:122696 original size:16 final size:17
Alignment explanation
Indices: 122675--122714 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
122665 CATTTGGTTT
122675 GCTGTAATGGAATA-GA
1 GCTGTAATGGAATATGA
122691 GCTGTAATGGAATATGA
1 GCTGTAATGGAATATGA
122708 -CTGTAAT
1 GCTGTAAT
122715 CAGTAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (17 bp):
GCTGTAATGGAATATGA
Found at i:122907 original size:58 final size:57
Alignment explanation
Indices: 122826--122977 Score: 214
Period size: 58 Copynumber: 2.6 Consensus size: 57
122816 GATTATTGTT
* *
122826 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAATAAGAATAATAAATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAA-AATAATAAATAATTTA
* * * *
122884 ATTATATTTTAACATAATAATTATTAAATACAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
*
122941 ATAATATTTTAATATAATTATTATTAAAATATGAATT
1 ATTATATTTTAATATAATTATTATT-AAATAT-AATT
122978 AGTAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
57 37 0.45
58 41 0.50
59 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
Found at i:122910 original size:26 final size:26
Alignment explanation
Indices: 122881--122967 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
122871 AATAAATAAT
*
122881 TTAATTATATTTTAACATAATAATTA
1 TTAATTATATTTTAAAATAATAATTA
* * *
122907 TTAAATACAATTTAATAAAATAATATATAA
1 TTAATTA-TATTT--TAAAATAATA-ATTA
* * *
122937 TTTAATAATATTTTAATATAATTATTA
1 -TTAATTATATTTTAAAATAATAATTA
122964 TTAA
1 TTAA
122968 AATATGAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
26 10 0.22
27 7 0.15
28 8 0.17
29 9 0.20
30 7 0.15
31 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATTATATTTTAAAATAATAATTA
Found at i:122958 original size:57 final size:58
Alignment explanation
Indices: 122831--122968 Score: 215
Period size: 57 Copynumber: 2.4 Consensus size: 58
122821 TTGTTATTAA
* * *
122831 ATTTTAATAAAATTATTATTAAATATAATTTAATAAGAATAATAAATAATTTAATTAT
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAGAATAATAAATAATTTAATAAT
* * *
122889 ATTTTAACATAATAATTATTAAATACAATTTAATAA-AATAATATATAATTTAATAAT
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAGAATAATAAATAATTTAATAAT
122946 ATTTTAATATAATTATTATTAAA
1 ATTTTAATATAATTATTATTAAA
122969 ATATGAATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
57 40 0.56
58 32 0.44
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAAGAATAATAAATAATTTAATAAT
Found at i:123000 original size:57 final size:55
Alignment explanation
Indices: 122831--123000 Score: 173
Period size: 58 Copynumber: 3.0 Consensus size: 55
122821 TTGTTATTAA
* * * *
122831 ATTTTAATAAAATTATTATTAAATATAATTTAATAAGAATAATAAATAATTTAATTAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATTAT-AAT-A-TTAATAAT
* * *
122889 ATTTTAACATAATAATTATTAAATACAATTTAATAAAATAATATATAAT-TTAATAAT
1 ATTTTAATATAATTATTATTAAATATAATTTAAT-AAA-AAT-TATAATATTAATAAT
*
122946 ATTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATATAATA
1 ATTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATTATAATAT-TAATA
123001 TTAAAAAAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 15
0.78 0.09 0.12
Matches are distributed among these distances:
55 6 0.06
56 4 0.04
57 33 0.35
58 39 0.41
59 4 0.04
60 6 0.06
61 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (55 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATTATAATATTAATAAT
Found at i:125695 original size:3 final size:3
Alignment explanation
Indices: 125687--125713 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
125677 AAATATAATA
125687 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
125714 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:136164 original size:16 final size:16
Alignment explanation
Indices: 136143--136176 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
136133 AAAGATATTT
136143 AAAAT-AAAGAAAATAA
1 AAAATAAAAG-AAATAA
136159 AAAATAAAAGAAATAA
1 AAAATAAAAGAAATAA
136175 AA
1 AA
136177 GAAAATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAATAAAAGAAATAA
Found at i:136166 original size:21 final size:21
Alignment explanation
Indices: 136142--136181 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
136132 TAAAGATATT
* *
136142 TAAAATAAAGAAAATAAAAAA
1 TAAAAGAAAGAAAAGAAAAAA
*
136163 TAAAAGAAATAAAAGAAAA
1 TAAAAGAAAGAAAAGAAAA
136182 TAACGAAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (21 bp):
TAAAAGAAAGAAAAGAAAAAA
Found at i:139140 original size:29 final size:29
Alignment explanation
Indices: 139098--139155 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
139088 AAAAACAAAA
139098 ATTTTCATCTTTCTTTTATGCTCTGTTTC
1 ATTTTCATCTTTCTTTTATGCTCTGTTTC
* * *
139127 ATTTTCTTCTTTCTTTTGTTCTCTGTTTC
1 ATTTTCATCTTTCTTTTATGCTCTGTTTC
139156 TCACGAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (29 bp):
ATTTTCATCTTTCTTTTATGCTCTGTTTC
Found at i:159716 original size:27 final size:27
Alignment explanation
Indices: 159674--159728 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
159664 AAAGGCCTTA
* *
159674 TTAGAGTACGCCACAAGGGTAGTCCAT
1 TTAGAGTACGCCACAAAGGCAGTCCAT
*
159701 TTAGAGTACGCTACAAAGGCAGTCCAT
1 TTAGAGTACGCCACAAAGGCAGTCCAT
159728 T
1 T
159729 CAGAAGGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (27 bp):
TTAGAGTACGCCACAAAGGCAGTCCAT
Found at i:161347 original size:44 final size:44
Alignment explanation
Indices: 161144--161353 Score: 330
Period size: 44 Copynumber: 4.8 Consensus size: 44
161134 GAATTAACCG
* * * *
161144 TATGCTCTATCCAAGTCATAAGTTCTTCCATTTACAAATAATCT
1 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
* * * *
161188 TATGCTCTAGCCGGGACATAATTTCTTCCATTTACAAATAATCT
1 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
161232 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
1 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
161276 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
1 TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
* *
161320 TATACTCTAACCGAGACATAAGTTCTTTAATTTA
1 TATGCTCTAACCGAGACATAAGTTCTTTCATTTA
161354 GTAATCACCA
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 155 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (44 bp):
TATGCTCTAACCGAGACATAAGTTCTTTCATTTACAAATAATCT
Found at i:167693 original size:26 final size:26
Alignment explanation
Indices: 167657--167716 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
167647 AACATGGGAC
*
167657 ATAAAAAATTAACATCAGAATATAAA
1 ATAAAAAATTAACATCAAAATATAAA
* *
167683 ATAAGAAATTAACATCAAAATTTAAA
1 ATAAAAAATTAACATCAAAATATAAA
*
167709 ACAAAAAA
1 ATAAAAAA
167717 CCATTTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (26 bp):
ATAAAAAATTAACATCAAAATATAAA
Found at i:168000 original size:50 final size:50
Alignment explanation
Indices: 167946--168047 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
167936 ATACAAAAAA
* * *
167946 AAAATTATATACAAGTATAATTCATTGATAAAAGAATACGTGGTACTATG
1 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGTGCTACTATG
*
167996 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGTGCTAGTATG
1 AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGTGCTACTATG
168046 AA
1 AA
168048 CTAAACCTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (50 bp):
AAAATTATATACAAATATAATTCATTGATAAAAGAATAAGTGCTACTATG
Found at i:183108 original size:27 final size:27
Alignment explanation
Indices: 183073--183141 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
183063 GTTTTTTTAA
*
183073 GGTTAAGGTTTTGTTTTTTTAAAAGTAG
1 GGTTAAGGTTTTGTTTATTT-AAAGTAG
*
183101 GGTT-AGGTTTTTGTTTATTTAAATTAG
1 GGTTAAGG-TTTTGTTTATTTAAAGTAG
*
183128 TGTTAAGGTTTTGT
1 GGTTAAGGTTTTGT
183142 GGATTTTAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.54
Consensus pattern (27 bp):
GGTTAAGGTTTTGTTTATTTAAAGTAG
Found at i:184663 original size:24 final size:24
Alignment explanation
Indices: 184636--184684 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
184626 TTTTCACCAA
184636 CAAGACAAACTTTTGGCCTCGTGG
1 CAAGACAAACTTTTGGCCTCGTGG
* *
184660 CAAGACAAAGTTTTGGTCTCGTGG
1 CAAGACAAACTTTTGGCCTCGTGG
184684 C
1 C
184685 TGTTATCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (24 bp):
CAAGACAAACTTTTGGCCTCGTGG
Found at i:187868 original size:28 final size:28
Alignment explanation
Indices: 187825--187882 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
187815 TTATTGAGTT
*
187825 GATTTTTCATCTATTGTGCAAAACTGTC
1 GATTTTTCATCCATTGTGCAAAACTGTC
187853 GATTTTTCATCCATTGTGCAAAACTGTC
1 GATTTTTCATCCATTGTGCAAAACTGTC
187881 GA
1 GA
187883 AAATAGATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (28 bp):
GATTTTTCATCCATTGTGCAAAACTGTC
Found at i:194067 original size:82 final size:82
Alignment explanation
Indices: 193923--194086 Score: 258
Period size: 82 Copynumber: 2.0 Consensus size: 82
193913 GCGGTCATTA
* *
193923 GTTAAATCCGAAAGGATAACCTGACACGATCATTTTGATTCTGATTAGCTGGCGAGCATAAACGT
1 GTTAAATCCAAAAGGATAACCTGACACGATCATTTTGATTCTGATTAGCTGACGAGCATAAACGT
193988 TCTAGACTTACGTATTG
66 TCTAGACTTACGTATTG
* **
194005 GTTAAATCCAAAAGGATAACCTGACAC-AGTCATTTTGATTCTGATTAGCTGATGAGTGTAAACG
1 GTTAAATCCAAAAGGATAACCTGACACGA-TCATTTTGATTCTGATTAGCTGACGAGCATAAACG
*
194069 TTCTTGACTTACGTATTG
65 TTCTAGACTTACGTATTG
194087 AATACTTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 1 0.01
82 74 0.99
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (82 bp):
GTTAAATCCAAAAGGATAACCTGACACGATCATTTTGATTCTGATTAGCTGACGAGCATAAACGT
TCTAGACTTACGTATTG
Found at i:212466 original size:37 final size:36
Alignment explanation
Indices: 212425--212535 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 36
212415 GACACACAGT
*
212425 CCGAATACACTAGCATGAAGCCTGCTAGGTACATAGC
1 CCGAATACACT-GCACGAAGCCTGCTAGGTACATAGC
* * *
212462 CCGAATACACTGACACAAAGCCTACTAGGCACATAGC
1 CCGAATACACTG-CACGAAGCCTGCTAGGTACATAGC
* * *
212499 CTGGATACACTGGCACGAAGCCTGTTAGGTACATAGC
1 CCGAATACACT-GCACGAAGCCTGCTAGGTACATAGC
212536 TTGAATTTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 1 0.02
37 60 0.97
38 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (36 bp):
CCGAATACACTGCACGAAGCCTGCTAGGTACATAGC
Found at i:218858 original size:25 final size:25
Alignment explanation
Indices: 218821--218868 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
218811 TCTATTGTTC
*
218821 TCCATTCTTCCCCTTTATGTCTCAT
1 TCCATTCTTCCCCCTTATGTCTCAT
*
218846 TCCA-TCTTACCCCCTTATTTCTC
1 TCCATTCTT-CCCCCTTATGTCTC
218869 CCTCTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.12, C:0.40, G:0.02, T:0.46
Consensus pattern (25 bp):
TCCATTCTTCCCCCTTATGTCTCAT
Found at i:224540 original size:21 final size:21
Alignment explanation
Indices: 224493--224545 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
224483 CCCTTGACAG
* *
224493 TTCTACCGATACAAGTGAGGC
1 TTCTACCGATACAAGTCAAGC
**
224514 AACTACCGATACAAGTCAAGC
1 TTCTACCGATACAAGTCAAGC
224535 TTCTACCGATA
1 TTCTACCGATA
224546 TTAAAAACTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
TTCTACCGATACAAGTCAAGC
Found at i:227454 original size:13 final size:13
Alignment explanation
Indices: 227438--227467 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
227428 AATATTTTAC
227438 TTTTTTATTTAAT
1 TTTTTTATTTAAT
*
227451 TTTTTTTTTTAAT
1 TTTTTTATTTAAT
227464 TTTT
1 TTTT
227468 ATATGGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTATTTAAT
Found at i:233403 original size:34 final size:35
Alignment explanation
Indices: 233365--233430 Score: 125
Period size: 34 Copynumber: 1.9 Consensus size: 35
233355 AACTAAAGAA
233365 TTGTAACATACACATTACAC-AAACCATCTATAGC
1 TTGTAACATACACATTACACAAAACCATCTATAGC
233399 TTGTAACATACACATTACACAAAACCATCTAT
1 TTGTAACATACACATTACACAAAACCATCTAT
233431 GAAGGTGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 20 0.65
35 11 0.35
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.27
Consensus pattern (35 bp):
TTGTAACATACACATTACACAAAACCATCTATAGC
Found at i:241312 original size:24 final size:24
Alignment explanation
Indices: 241296--241370 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
241286 AGTTTGACTC
241296 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
241320 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
241344 AAACAATTAAACAGAGTTTAAGTG
1 AAACAAATAAACAGAGTTTAATTG
241368 AAA
1 AAA
241371 GATTATTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:243328 original size:24 final size:24
Alignment explanation
Indices: 243310--243384 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
243300 AGTTTGACTC
*
243310 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
243334 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
243358 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
243382 AAA
1 AAA
243385 AATTATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:243797 original size:28 final size:28
Alignment explanation
Indices: 243766--243857 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
243756 AGTTGCGATT
* *
243766 TGACCGTTACAATATGACCATTGAAATC
1 TGACCGTTACAATATGATCATTGGAATC
**
243794 TGACATTTACAATAT-AGTCATTGGAATC
1 TGACCGTTACAATATGA-TCATTGGAATC
* * *
243822 TGATCGTTACAATATGATCGTTGGAATT
1 TGACCGTTACAATATGATCATTGGAATC
243850 TGACCGTT
1 TGACCGTT
243858 GAATTTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 50 0.96
29 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (28 bp):
TGACCGTTACAATATGATCATTGGAATC
Found at i:259774 original size:3 final size:3
Alignment explanation
Indices: 259761--259820 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
259751 TATGGGTATT
* *
259761 GAA GCA GAA GAA GAA GAAA GAA -AA GAA GAA GAA AAA GAA G-A GAA
1 GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
259805 GGAA GAA AAA GAA GAA
1 -GAA GAA GAA GAA GAA
259821 TACGTTGCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:259818 original size:18 final size:17
Alignment explanation
Indices: 259761--259819 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 17
259751 TATGGGTATT
259761 GAAGCAGAAGAAGAAGAAA
1 GAAG-AGAAGAAGAA-AAA
*
259780 GAAAAGAAGAAGAAAAA
1 GAAGAGAAGAAGAAAAA
259797 GAAGAGAAGGAAGAAAAA
1 GAAGAGAA-GAAGAAAAA
259815 GAAGA
1 GAAGA
259820 ATACGTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 10 0.27
18 24 0.65
19 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (17 bp):
GAAGAGAAGAAGAAAAA
Found at i:262799 original size:52 final size:51
Alignment explanation
Indices: 262718--262907 Score: 240
Period size: 52 Copynumber: 3.6 Consensus size: 51
262708 AAAAAAGTCC
*
262718 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTT-TCGAATTATGAGGTCT
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTAT-GAATTA-GAGGTCT
* * *
262770 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATTGATTTAAAGATCT
1 GATGACTAAGTGTCATCGTGAGTATATG-AATCCTTTA-TGAATTAGAGGTCT
*
262823 GATGACTAAGTGTCATCGTGAGTATAT-AGATCCTTTATGGATTAAGAGGTCT
1 GATGACTAAGTGTCATCGTGAGTATATGA-ATCCTTTATGAATT-AGAGGTCT
** *
262875 GATGACTCTGTGTCATCGTGAGTATACGAATCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCC
262908 CTCGTGGATT
Statistics
Matches: 121, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
51 5 0.04
52 69 0.57
53 41 0.34
54 5 0.04
55 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (51 bp):
GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGAATTAGAGGTCT
Found at i:262827 original size:53 final size:52
Alignment explanation
Indices: 262718--262951 Score: 237
Period size: 52 Copynumber: 4.5 Consensus size: 52
262708 AAAAAAGTCC
* *
262718 GATGACTAAGTGTCATCGTGAGTAAATG-AATCCTTT-TCGAATTATGAGGTCT
1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATCG-ATTA-AAGGTCT
* *
262770 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATTGATTTAAAGATCT
1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATCGA-TTAAAGGTCT
* *
262823 GATGACTAAGTGTCATCGTGAGTATAT-AGATCCTTTATGGATTAAGAGGTCT
1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATCGATTAA-AGGTCT
** * * ** *
262875 GATGACTCTGTGTCATCGTGAGTATACG-AATCCCTCGTGGATTATAAGGT-T
1 GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATCGATTA-AAGGTCT
*
262926 AGATGACTATA-TGTCATTGTGAGTAT
1 -GATGACTA-AGTGTCATCGTGAGTAT
262952 TAAATGAAAT
Statistics
Matches: 157, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
51 5 0.03
52 105 0.67
53 42 0.27
54 5 0.03
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (52 bp):
GATGACTAAGTGTCATCGTGAGTATATGAAATCCTTTATCGATTAAAGGTCT
Found at i:267195 original size:30 final size:30
Alignment explanation
Indices: 267159--267217 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
267149 TTTATTTTAT
267159 TTTAAAATATATT-TTTATTAGGATTTAATA
1 TTTAAAA-ATATTATTTATTAGGATTTAATA
* *
267189 TTTAAAAATATTATTTATTTGTATTTAAT
1 TTTAAAAATATTATTTATTAGGATTTAAT
267218 TTATGCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTAAAAATATTATTTATTAGGATTTAATA
Found at i:268026 original size:15 final size:16
Alignment explanation
Indices: 268006--268035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
267996 CTTCCCTATT
268006 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
268021 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
268036 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:268027 original size:22 final size:22
Alignment explanation
Indices: 268001--268061 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
267991 TTCGACTTCC
268001 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
268023 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
*
268045 CT-GTTTCTTTTACTTTT
1 CTATTTTCTTTTACTTTT
268062 CCTCAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:268051 original size:21 final size:22
Alignment explanation
Indices: 268005--268061 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
267995 ACTTCCCTAT
*
268005 TTTCTATTT-CTTTTAATTCTAT
1 TTTCT-TTTACTTTTAATTCTAG
*
268027 TTTCTTTTATTTTTAATTCT-G
1 TTTCTTTTACTTTTAATTCTAG
268048 TTTCTTTTACTTTT
1 TTTCTTTTACTTTT
268062 CCTCAGATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTCTTTTACTTTTAATTCTAG
Found at i:269392 original size:21 final size:21
Alignment explanation
Indices: 269368--269428 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
269358 GCTATCTATA
*
269368 GATTTTCAAAAGCAAATTGTG
1 GATTTTCAAAAGCAAACTGTG
269389 GATTTTCAAAAGCAAACTGTG
1 GATTTTCAAAAGCAAACTGTG
*
269410 GATTTTCAAAAGAAAACTG
1 GATTTTCAAAAGCAAACTG
269429 AGACATCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
GATTTTCAAAAGCAAACTGTG
Found at i:273065 original size:23 final size:23
Alignment explanation
Indices: 273033--273164 Score: 176
Period size: 23 Copynumber: 5.7 Consensus size: 23
273023 AAGGGGTGTT
273033 ACATTAATATTTGAA-CACAAATC
1 ACATTAATATTT-AAGCACAAATC
* * *
273056 ATATTAATATTTAAGCATAAATT
1 ACATTAATATTTAAGCACAAATC
* *
273079 AGATTAATACTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
*
273102 ACATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
* *
273125 ATATTAAAATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
273148 ACATTAATATTTAAGCA
1 ACATTAATATTTAAGCA
273165 TGGATATAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
22 2 0.02
23 91 0.98
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.33
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:273102 original size:46 final size:46
Alignment explanation
Indices: 273035--273165 Score: 201
Period size: 46 Copynumber: 2.8 Consensus size: 46
273025 GGGGTGTTAC
* *
273035 ATTAATATTTGAA-CACAAATCATATTAATATTTAAGCATAAATTAG
1 ATTAATATTT-AAGCACAAATCACATTAATATTTAAGCATAAATCAG
* *
273081 ATTAATACTTAAGCACAAATCACATTAATATTTAAGCATAAATCAT
1 ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCAG
*
273127 ATTAAAATTTAAGCACAAATCACATTAATATTTAAGCAT
1 ATTAATATTTAAGCACAAATCACATTAATATTTAAGCAT
273166 GGATATAAGA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.03
46 76 0.97
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (46 bp):
ATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAATCAG
Found at i:273154 original size:69 final size:69
Alignment explanation
Indices: 273033--273164 Score: 194
Period size: 69 Copynumber: 1.9 Consensus size: 69
273023 AAGGGGTGTT
* * * *
273033 ACATTAATATTTGAACACAAATCATATTAATATTTAAGCATAAATTAGATTAATACTTAAGCACA
1 ACATTAATATTTGAACACAAATCATATTAAAATTTAAGCACAAATCACATTAATACTTAAGCACA
273098 AATC
66 AATC
* *
273102 ACATTAATATTT-AAGCATAAATCATATTAAAATTTAAGCACAAATCACATTAATATTTAAGCA
1 ACATTAATATTTGAA-CACAAATCATATTAAAATTTAAGCACAAATCACATTAATACTTAAGCA
273165 TGGATATAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 2 0.04
69 54 0.96
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.33
Consensus pattern (69 bp):
ACATTAATATTTGAACACAAATCATATTAAAATTTAAGCACAAATCACATTAATACTTAAGCACA
AATC
Found at i:274644 original size:25 final size:25
Alignment explanation
Indices: 274616--274666 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
274606 AATGTTTGAA
274616 TAAGAAAGGTTCATCCCAATAATAG
1 TAAGAAAGGTTCATCCCAATAATAG
*
274641 TAAGAAGGGTTCATCCCAATAATAG
1 TAAGAAAGGTTCATCCCAATAATAG
274666 T
1 T
274667 GCCTGACATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (25 bp):
TAAGAAAGGTTCATCCCAATAATAG
Found at i:279541 original size:193 final size:194
Alignment explanation
Indices: 279187--279631 Score: 528
Period size: 193 Copynumber: 2.3 Consensus size: 194
279177 GAAACCGACG
* *
279187 CGATGACTGA-GTACCACATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTCC
1 CGATGATTGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCC
* *
279251 GAAAATAAGTAAAGAATCCAAGAATTGATTACAAGCCCTACGATGACTAAGATTTATGCATAAGT
66 GAAAATAAGTAAAGAATCC-AGAATGGATTACAAGCCCTACGATGACTAAGACTTATGCATAAGT
*** * * *
279316 GCATATTTTCGACAACTCGTGTGAGCAGCATCGTTAGG-GAACAATTATAT-GCACATATACAGT
130 GCATACACTAGACAACTCGTGTGAGCAGCATCGTTAGGAG-ACAATTATATAG-ACAGACACAGT
*
279379 AT
193 AC
* * *
279381 CGATGATTGAGGTACCACATATGTTGTGAGTCCTCGACAACTCATGTGAGCAGCATCGTGAGT-C
1 CGATGATTGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCC
* **
279445 GAAAA-AAG-AGATATGAATCC-GAATGGATTAC-AGTCCCTACGATGGCTGGGACTTATGCATA
66 GAAAATAAGTA-A-A-GAATCCAGAATGGATTACAAG-CCCTACGATGACTAAGACTTATGCATA
* * * * * *
279506 AGTGCATACACTAGATAGCTCGTGTGAGTAGCATCGTTAGGAGACAGTTATATAGACAGACGCTG
127 AGTGCATACACTAGACAACTCGTGTGAGCAGCATCGTTAGGAGACAATTATATAGACAGACACAG
279571 TAC
192 TAC
* ** *
279574 CGATGATTGGGGTACTGCATATGTTGCGAGTCCTCAACAGCTCGTGTGAGCAGCATCG
1 CGATGATTGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
279632 GGTATTGGTA
Statistics
Matches: 214, Mismatches: 30, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
192 3 0.01
193 139 0.65
194 18 0.08
195 54 0.25
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (194 bp):
CGATGATTGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCC
GAAAATAAGTAAAGAATCCAGAATGGATTACAAGCCCTACGATGACTAAGACTTATGCATAAGTG
CATACACTAGACAACTCGTGTGAGCAGCATCGTTAGGAGACAATTATATAGACAGACACAGTAC
Found at i:283820 original size:21 final size:21
Alignment explanation
Indices: 283796--283835 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
283786 TGTGAATGTA
*
283796 TCTGC-GTGTGTTTATTGTAGT
1 TCTGCTGT-TGTTGATTGTAGT
283817 TCTGCTGTTGTTGATTGTA
1 TCTGCTGTTGTTGATTGTA
283836 ATTCCCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.10, C:0.10, G:0.28, T:0.53
Consensus pattern (21 bp):
TCTGCTGTTGTTGATTGTAGT
Found at i:318940 original size:14 final size:14
Alignment explanation
Indices: 318875--319004 Score: 63
Period size: 14 Copynumber: 9.4 Consensus size: 14
318865 CAACCCAACT
*
318875 CGTTTACTA-TGAC
1 CGTTGACTATTGAC
* *
318888 CGTTGACTGTT-AA
1 CGTTGACTATTGAC
* *
318901 CTTTGACCATTGAC
1 CGTTGACTATTGAC
* * *
318915 CATTTACAATTGAC
1 CGTTGACTATTGAC
318929 CGTTGACTATTGAC
1 CGTTGACTATTGAC
* *
318943 TGTTGACTGTTGAC
1 CGTTGACTATTGAC
* *
318957 AGTTAAC-AGTTGAC
1 CGTTGACTA-TTGAC
* *
318971 AGTTGA-TCGTTGAC
1 CGTTGACT-ATTGAC
318985 CGTTGA-TAATTGAC
1 CGTTGACT-ATTGAC
*
318999 CATTGA
1 CGTTGA
319005 ATTTTTTGAG
Statistics
Matches: 88, Mismatches: 24, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
13 16 0.18
14 72 0.82
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (14 bp):
CGTTGACTATTGAC
Found at i:318948 original size:21 final size:20
Alignment explanation
Indices: 318884--318956 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
318874 TCGTTTACTA
*
318884 TGACCGTTGACTGTTAACTT
1 TGACCGTTGACTATTAACTT
* * * *
318904 TGACCATTGACCATTTACAAT
1 TGACCGTTGACTATTAAC-TT
*
318925 TGACCGTTGACTATTGACTGT
1 TGACCGTTGACTATTAACT-T
*
318946 TGACTGTTGAC
1 TGACCGTTGAC
318957 AGTTAACAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TGACCGTTGACTATTAACTT
Found at i:318975 original size:7 final size:7
Alignment explanation
Indices: 318924--318990 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
318914 CCATTTACAA
*
318924 TTGACCG
1 TTGACAG
318931 TTGACTA-
1 TTGAC-AG
*
318938 TTGACTG
1 TTGACAG
*
318945 TTGACTG
1 TTGACAG
318952 TTGACAG
1 TTGACAG
*
318959 TTAACAG
1 TTGACAG
318966 TTGACAG
1 TTGACAG
318973 TTGATC-G
1 TTGA-CAG
*
318980 TTGACCG
1 TTGACAG
318987 TTGA
1 TTGA
318991 TAATTGACCA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 1 0.02
7 49 0.96
8 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (7 bp):
TTGACAG
Found at i:320235 original size:6 final size:6
Alignment explanation
Indices: 320210--320252 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
320200 GTTAAAGACC
*
320210 TTATAT TATATATT TATATAT TTATAG TTATAT TTATAT TTAT
1 TTATAT T-TATA-T T-TATAT TTATAT TTATAT TTATAT TTAT
320253 GAATGATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 20 0.61
7 6 0.18
8 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:328026 original size:36 final size:36
Alignment explanation
Indices: 327950--328026 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
327940 TAATAATCAG
* **
327950 TCACATGACATGAAGAATATACCCACATATTTTCTA
1 TCACATGACATGAAGAACATACCCACATATTCACTA
*
327986 TCACATGACATGAAGAACATACCCACATATTCACTT
1 TCACATGACATGAAGAACATACCCACATATTCACTA
328022 TCACA
1 TCACA
328027 ACAGTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.27
Consensus pattern (36 bp):
TCACATGACATGAAGAACATACCCACATATTCACTA
Found at i:328133 original size:23 final size:23
Alignment explanation
Indices: 328098--328382 Score: 401
Period size: 23 Copynumber: 12.4 Consensus size: 23
328088 ATCTTAATTC
* *
328098 TTTAAACACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
328121 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
328144 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
328167 TTTAAACATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
328190 TTTGAGCACAAATCATATT-ATA
1 TTTAAGCATAAATCACATTAATA
328212 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
328235 TTTAAGTATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
328258 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
328281 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
328304 CTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
328327 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
328350 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
328373 TTTAAGCATA
1 TTTAAGCATA
328383 GACATAAGAA
Statistics
Matches: 228, Mismatches: 33, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
22 19 0.08
23 209 0.92
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:333497 original size:21 final size:21
Alignment explanation
Indices: 333472--333517 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
333462 TAGTGTTTTA
*
333472 AACCGTTTCCATGTTTCATGG
1 AACCGTTTCCATGTTTCACGG
333493 AACCGTTTCCATGTTTCACGG
1 AACCGTTTCCATGTTTCACGG
333514 AACC
1 AACC
333518 CTTCACCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (21 bp):
AACCGTTTCCATGTTTCACGG
Done.