Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:7727 original size:22 final size:22
Alignment explanation
Indices: 7701--7748 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
7691 ATTATTATAA
*
7701 TTATACATTTAATCCTTATTGC
1 TTATACATTTAATCCTTATTAC
*
7723 TTATACATTTAGTCCTTATTAC
1 TTATACATTTAATCCTTATTAC
7745 TTAT
1 TTAT
7749 GTATTGTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (22 bp):
TTATACATTTAATCCTTATTAC
Found at i:9782 original size:29 final size:29
Alignment explanation
Indices: 9745--9802 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
9735 CATTCACAAA
9745 CTGAGATTATTTATCTCATTTTAATAGAT
1 CTGAGATTATTTATCTCATTTTAATAGAT
*
9774 CTGAGATTATTTATTTCATTTTAATAGAT
1 CTGAGATTATTTATCTCATTTTAATAGAT
9803 ATTTGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (29 bp):
CTGAGATTATTTATCTCATTTTAATAGAT
Found at i:12762 original size:23 final size:23
Alignment explanation
Indices: 12736--12792 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
12726 TCAGTGTTCG
12736 TTCGTGAACATGTTCATTTAATA
1 TTCGTGAACATGTTCATTTAATA
* * *
12759 TTCGCGGACATGTTCATTTAATG
1 TTCGTGAACATGTTCATTTAATA
12782 TTCGTGAACAT
1 TTCGTGAACAT
12793 ATTTGTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (23 bp):
TTCGTGAACATGTTCATTTAATA
Found at i:14324 original size:21 final size:20
Alignment explanation
Indices: 14296--14365 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
14286 CTCCATCCAT
14296 TTGACCTAGTGAGATCACCA
1 TTGACCTAGTGAGATCACCA
**
14316 TTGAGCCTA--GA-CCCATCCA
1 TTGA-CCTAGTGAGATCA-CCA
14335 TTTGACCTAGTGAGATCACCA
1 -TTGACCTAGTGAGATCACCA
14356 TTGAGCCTAG
1 TTGA-CCTAG
14366 ACCCATCACA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 2 0.05
19 9 0.23
20 12 0.31
21 14 0.36
22 2 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (20 bp):
TTGACCTAGTGAGATCACCA
Found at i:14332 original size:40 final size:40
Alignment explanation
Indices: 14288--14372 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
14278 TATAACACCT
14288 CCATCCATTTGACCTAGTGAGATCACCATTGAGCCTAGAC
1 CCATCCATTTGACCTAGTGAGATCACCATTGAGCCTAGAC
14328 CCATCCATTTGACCTAGTGAGATCACCATTGAGCCTAGAC
1 CCATCCATTTGACCTAGTGAGATCACCATTGAGCCTAGAC
14368 CCATC
1 CCATC
14373 ACAATGCTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (40 bp):
CCATCCATTTGACCTAGTGAGATCACCATTGAGCCTAGAC
Found at i:14373 original size:21 final size:21
Alignment explanation
Indices: 14309--14374 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
14299 ACCTAGTGAG
14309 ATCACCATTGAGCCTAGACCC
1 ATCACCATTGAGCCTAGACCC
****
14330 AT--CCATTTGA-CCTAGTGAG
1 ATCACCA-TTGAGCCTAGACCC
14349 ATCACCATTGAGCCTAGACCC
1 ATCACCATTGAGCCTAGACCC
14370 ATCAC
1 ATCAC
14375 AATGCTAGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 10 0.30
20 8 0.24
21 15 0.45
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCACCATTGAGCCTAGACCC
Found at i:21804 original size:18 final size:18
Alignment explanation
Indices: 21770--21805 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21760 AAAGTTGGGG
*
21770 GCCAAATTATAGCTCAAA
1 GCCAAATTAGAGCTCAAA
*
21788 GCCAAATTAGAGGTCAAA
1 GCCAAATTAGAGCTCAAA
21806 TTACAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (18 bp):
GCCAAATTAGAGCTCAAA
Found at i:38238 original size:17 final size:18
Alignment explanation
Indices: 38202--38245 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
38192 TTCGTATAGC
**
38202 TTTAATTTCAATTATCCA
1 TTTAATTTCAATTAAACA
38220 TTTAATTTC-ATTAAACA
1 TTTAATTTCAATTAAACA
38237 TTTATATTT
1 TTTA-ATTT
38246 GCATGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAATTTCAATTAAACA
Found at i:39694 original size:15 final size:15
Alignment explanation
Indices: 39653--39698 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
39643 TTAAATTTTG
*
39653 CAAAGTATTATTCTA
1 CAAAGTATTATTATA
*
39668 C-AA-TATTTTTATA
1 CAAAGTATTATTATA
39681 CAAAGTATTATTATA
1 CAAAGTATTATTATA
39696 CAA
1 CAA
39699 TTAAATAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (15 bp):
CAAAGTATTATTATA
Found at i:50446 original size:36 final size:36
Alignment explanation
Indices: 50281--50445 Score: 222
Period size: 36 Copynumber: 4.6 Consensus size: 36
50271 GATTGGAGAA
*
50281 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
*
50317 AAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
50353 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * * *
50389 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAACC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* *
50425 AAAGCATCTTAAGTCTTCACC
1 AAACCATCTTAAGCCTTCACC
50446 AAAAAGTAGT
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 115 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (36 bp):
AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:50454 original size:36 final size:36
Alignment explanation
Indices: 50380--50458 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
50370 CACCGGAGAA
* * *
50380 TAGTGAAGCAAACCATCATAAGTCTTCACCAGAGAG
1 TAGTGAACCAAACCATCATAAGTCTTCACCAAAAAG
* *
50416 TAGTGAACCAAAGCATCTTAAGTCTTCACCAAAAAG
1 TAGTGAACCAAACCATCATAAGTCTTCACCAAAAAG
50452 TAGTGAA
1 TAGTGAA
50459 GCATATCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (36 bp):
TAGTGAACCAAACCATCATAAGTCTTCACCAAAAAG
Found at i:51001 original size:54 final size:53
Alignment explanation
Indices: 50861--51332 Score: 483
Period size: 54 Copynumber: 8.7 Consensus size: 53
50851 AAGATTATTT
* * *
50861 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTATGAAG-A-TATCC
1 GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGTTTCC
* * *
50912 GAGTTCTATACT-CCTTAATGAAAGAAGGAGTGAACCCGTTTGAAGAAAGTTTCC
1 GAGTTCTATACTCCCTGAA-GAAAGAGGGAGCGAACCCGTTTGAAG-AAGTTTCC
* * * * *
50966 AAGTTCTATACTCCCTGAAAAAAGAGGGAGCGAACCTGTTTGCAGAAGATTATTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-TT-TCC
* * ** * *
51021 GAGTTCTATACTTCCTGAAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATTCTT
1 GAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAGTTTC-C
* *
51076 GAGTTCTATACTTCCTGAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTAT-C
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-TT-TCC
* *
51130 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCAGAAGAA-TTGTTC
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TTT--GAAGAAGTT-TCC
* *
51186 GAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTTGAAGAAGATGTT-T
1 GAGTTCTATACTCCCTGAAGAAAGAG-GGAGCGAACCCGTTTGAAGAAG-T-TTCC
* *
51241 GAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATTTCC
1 GAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAG-AAGTTTCC
* *
51295 AAGTTCTATACTCCCTGAAGAAAGAGGGAGCGGACCCG
1 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG
51333 ATTATTGAAG
Statistics
Matches: 357, Mismatches: 40, Indels: 45
0.81 0.09 0.10
Matches are distributed among these distances:
50 4 0.01
51 35 0.10
53 6 0.02
54 155 0.43
55 90 0.25
56 49 0.14
57 18 0.05
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (53 bp):
GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGTTTCC
Found at i:51265 original size:165 final size:160
Alignment explanation
Indices: 50850--51372 Score: 607
Period size: 165 Copynumber: 3.2 Consensus size: 160
50840 TGAAGCAAAT
* * * * * *
50850 GAAGATTATTTGAGTTCCATACTCCCT-AGAGAAAGAG-GGAGCGAACCCG-T-ATGAAGATATC
1 GAAGATTGTTCGAGTTCTATACTCCCTGA-AGAAAGAGCGAAGCGAACCCGTTGAAGAAGAT-TT
* * *
50911 CGAGTTCTATACTCCTTA-ATGAAAGAAGGAGTGAACCCGTTTGAAGAAAGTTTCCAAGTTCTAT
64 TGAGTTCTATACTCCCTAGA-GAAAG-AGGAGCGAACCCGTTTGAAGAAA-TTTCCAAGTTCTAT
* * *
50975 ACTCCCTGAAAAAAGAGGGAGCGAACCTGTTTGCA
126 ACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTTCA
* * *
51010 GAAGATTATTCGAGTTCTATACTTCCTGAAGAAAGAGCGAAGCGAACCCGTAAGAAGAAGATTCT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGT-TGAAGAAGATT-T
* *
51075 TGAGTTCTATACTTCCT-GAAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATTAT-CGAGTTCTA
64 TGAGTTCTATACTCCCTAG-AGAAAGAGG-AGCGAACCCGTTTGAAGAA-ATT-TCCAAGTTCTA
*
51138 TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTTCA
125 TACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTTCA
51174 GAAGAATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTTGAAGAAGATGT
1 GAAG-ATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCG-TTGAAGAAGAT-T
*
51239 TTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAAATTTCCAAGTTCTAT
63 TTGAGTTCTATACTCCCTAGAGAAAGA-GGAGCGAACCCGTTTGAAG-AAATTTCCAAGTTCTAT
*
51304 ACTCCCTGAAGAAAGAGGGAGCGGACCCGATTATT--
126 ACTCCCTGAAGAAAGAGGGAGCGAACCCG-TT-TTCA
**
51339 GAAGATTGTTCGAG-TCTTATACTCTTTGAAGAAA
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAA
51373 TAAGGAATAA
Statistics
Matches: 316, Mismatches: 26, Indels: 38
0.83 0.07 0.10
Matches are distributed among these distances:
160 32 0.10
161 12 0.04
163 6 0.02
164 116 0.37
165 139 0.44
166 9 0.03
167 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (160 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGCGAAGCGAACCCGTTGAAGAAGATTTTG
AGTTCTATACTCCCTAGAGAAAGAGGAGCGAACCCGTTTGAAGAAATTTCCAAGTTCTATACTCC
CTGAAGAAAGAGGGAGCGAACCCGTTTTCA
Found at i:51369 original size:55 final size:55
Alignment explanation
Indices: 51301--51423 Score: 149
Period size: 55 Copynumber: 2.3 Consensus size: 55
51291 TTCCAAGTTC
* * * ** *
51301 TATACTCCCTGAAGAAAGAGGGAGCGGACCCGATTATTGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGAAAGAAGGAACAAACACGATTATTGAAGATTGTTCGAGTCT
* * * *
51356 TATACTCTTTGAAGAAATAAGGAATAAACACGATTGTTGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGAAAGAAGGAACAAACACGATTATTGAAGATTGTTCGAGTCT
51411 TATAC-CTCTGAAG
1 TATACTCTCTGAAG
51424 CATAGAGAAC
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 7 0.12
55 50 0.88
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (55 bp):
TATACTCTCTGAAGAAAGAAGGAACAAACACGATTATTGAAGATTGTTCGAGTCT
Found at i:57377 original size:15 final size:15
Alignment explanation
Indices: 57356--57395 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
57346 AGCCTACACA
57356 TTTGTTTTTTTTGTTG
1 TTTGTTTTTTTT-TTG
*
57372 -TTGTTTTCTTTTTG
1 TTTGTTTTTTTTTTG
57386 TTTGTTTTTT
1 TTTGTTTTTT
57396 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (15 bp):
TTTGTTTTTTTTTTG
Found at i:58786 original size:37 final size:36
Alignment explanation
Indices: 58711--58786 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
58701 TTTTTTATAT
*
58711 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
58747 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
58784 TTT
1 TTT
58787 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:58953 original size:20 final size:19
Alignment explanation
Indices: 58924--58963 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
58914 AGTAATCCTA
*
58924 TTCCCTGGTAATCTTTTAT
1 TTCCCTGGTAATCTTATAT
58943 TTCCACTGGTAATCTTATAT
1 TTCC-CTGGTAATCTTATAT
58963 T
1 T
58964 CCGTGAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (19 bp):
TTCCCTGGTAATCTTATAT
Found at i:63913 original size:42 final size:43
Alignment explanation
Indices: 63842--63924 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
63832 GTTTAAACTC
63842 TAAAATAAAAATCCATAAATACACCAAACTAACATATTAAAGT
1 TAAAATAAAAATCCATAAATACACCAAACTAACATATTAAAGT
* * **
63885 TAAAGTAAAAATCCA-CAATACATTAAACTAACATATTAAA
1 TAAAATAAAAATCCATAAATACACCAAACTAACATATTAAA
63925 AACATTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (43 bp):
TAAAATAAAAATCCATAAATACACCAAACTAACATATTAAAGT
Found at i:69945 original size:26 final size:26
Alignment explanation
Indices: 69915--69966 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
69905 ATTTAAAGTT
69915 CCGTAAGTTAAATATCACTATATAAC
1 CCGTAAGTTAAATATCACTATATAAC
* *
69941 CCGTAAGTTTAATGTCACTATATAAC
1 CCGTAAGTTAAATATCACTATATAAC
69967 TTGATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (26 bp):
CCGTAAGTTAAATATCACTATATAAC
Found at i:80514 original size:81 final size:81
Alignment explanation
Indices: 80427--80585 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
80417 AAATGTAATA
* *
80427 TTTTTAAAAATTTATAATTGAGATGGATAGTTTGTAGTTGGATACTATTTATTATACTTAATTAC
1 TTTTTAAAAATTTATAATTAAGATGGATAGTTTGTAGTTAGATACTATTTATTATACTTAATTAC
*
80492 TATGAGATGGGCAATT
66 TATGACATGGGCAATT
* * *
80508 TTTTTAAAAGTTTATAATTAAGATGGATGGTTTGTAGTTAGATACTCTTTATTATACTTAATTAC
1 TTTTTAAAAATTTATAATTAAGATGGATAGTTTGTAGTTAGATACTATTTATTATACTTAATTAC
80573 TATGACATGGGCA
66 TATGACATGGGCA
80586 GATAGTACTC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (81 bp):
TTTTTAAAAATTTATAATTAAGATGGATAGTTTGTAGTTAGATACTATTTATTATACTTAATTAC
TATGACATGGGCAATT
Found at i:86002 original size:21 final size:22
Alignment explanation
Indices: 85978--86026 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
85968 TTTATATTTT
* *
85978 TTATCAGATA-TTTTTCTTAAG
1 TTATCAAATATTTTTTCTTAAA
85999 TTATTTCAAATATTTTTTCTTAAA
1 TTA--TCAAATATTTTTTCTTAAA
86023 TTAT
1 TTAT
86027 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
21 3 0.13
22 1 0.04
23 6 0.26
24 13 0.57
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (22 bp):
TTATCAAATATTTTTTCTTAAA
Found at i:90182 original size:34 final size:34
Alignment explanation
Indices: 90143--90212 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
90133 CAAATCAAAC
*
90143 ATAAACATCTTAATTAACTTATTCATCAAAGTTT
1 ATAAACATCTTAATTAACTTATCCATCAAAGTTT
90177 ATAAACATCTTAATTAACTTATCCATCAAAGTTT
1 ATAAACATCTTAATTAACTTATCCATCAAAGTTT
90211 AT
1 AT
90213 CAAGTAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (34 bp):
ATAAACATCTTAATTAACTTATCCATCAAAGTTT
Found at i:90223 original size:30 final size:32
Alignment explanation
Indices: 90153--90223 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
90143 ATAAACATCT
* **
90153 TAATTAACTTATTCATCAAAGTTTATAAACATCT
1 TAATTAACTTATCCATCAAAGTTTAT--ACATAG
90187 TAATTAACTTATCCATCAAAGTTTAT-CA-AG
1 TAATTAACTTATCCATCAAAGTTTATACATAG
90217 TAATTAA
1 TAATTAA
90224 TCATGCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.21
31 2 0.06
34 25 0.74
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (32 bp):
TAATTAACTTATCCATCAAAGTTTATACATAG
Found at i:98628 original size:19 final size:19
Alignment explanation
Indices: 98603--98649 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
98593 TCGTTATTCT
98603 ATTTTAAAAAATC-AACTC
1 ATTTTAAAAAATCAAACTC
* *
98621 TTTTTTAAAAAGTCAAACTC
1 -ATTTTAAAAAATCAAACTC
98641 ATTTTAAAA
1 ATTTTAAAA
98650 TTTACAAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAATCAAACTC
Found at i:100421 original size:22 final size:22
Alignment explanation
Indices: 100370--100421 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
100360 TAAAAATCAC
* *
100370 TTATTTAAAATTCAAGTACAAA
1 TTATTTATAATTCAAGCACAAA
* *
100392 TT-TATTATAATTTAAGCAGAAA
1 TTAT-TTATAATTCAAGCACAAA
100414 TTATTTAT
1 TTATTTAT
100422 CACTCAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (22 bp):
TTATTTATAATTCAAGCACAAA
Found at i:109919 original size:21 final size:21
Alignment explanation
Indices: 109869--109920 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
109859 ATTAAGTTAT
* *
109869 TATTTTAAATACATATAAAAT
1 TATTTAAAATACATATAAAAA
**
109890 TATCAAAAAT-CATATAAAAGA
1 TATTTAAAATACATATAAAA-A
109911 TATTTAAAAT
1 TATTTAAAAT
109921 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
TATTTAAAATACATATAAAAA
Found at i:110763 original size:16 final size:16
Alignment explanation
Indices: 110742--110775 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
110732 TTACTATTCA
*
110742 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
110758 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
110774 CG
1 CG
110776 ATCGACGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:135210 original size:21 final size:21
Alignment explanation
Indices: 135156--135210 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
135146 TAACCTGTTA
135156 TTTATATGATTTTATTTTATCT
1 TTTATATGA-TTTATTTTATCT
* * ** *
135178 TATCTAACATTTATTTTTTCT
1 TTTATATGATTTATTTTATCT
135199 TTTATATGATTT
1 TTTATATGATTT
135211 CGAAGAAAAT
Statistics
Matches: 24, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTATATGATTTATTTTATCT
Found at i:150676 original size:5 final size:5
Alignment explanation
Indices: 150666--150690 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
150656 TGAAATTACA
150666 AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC
150691 GATTAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:155334 original size:102 final size:104
Alignment explanation
Indices: 155158--155360 Score: 311
Period size: 102 Copynumber: 2.0 Consensus size: 104
155148 ACACGGACTC
* *
155158 GGGTGTTTGTGTCGGATACGGTTATGAATCCAACATGGTATTTACTAAGCTTTTTCACATATTTG
1 GGGTGTTTGTGTCGGATACGGTTATGAATCCAACATGGTATTTACTAAGATTTTTCACATATTCG
*
155223 GTGAG-T-CATATCCCATATCCATAGTCGGATATATGTT
66 GAGAGATACATATCCCATATCCATAGTCGGATATATGTT
* * *
155260 GGGTGTTTGTGTCGGATACGGTTATGAATCCGACATGGTATTTTCTGAGATTTTTCACATATTCG
1 GGGTGTTTGTGTCGGATACGGTTATGAATCCAACATGGTATTTACTAAGATTTTTCACATATTCG
*
155325 GAGGGTCATACATATCCCATATCCATAGTCGGATAT
66 GAGAG--ATACATATCCCATATCCATAGTCGGATAT
155361 GAGTTGAACA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 63 0.70
105 1 0.01
106 26 0.29
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (104 bp):
GGGTGTTTGTGTCGGATACGGTTATGAATCCAACATGGTATTTACTAAGATTTTTCACATATTCG
GAGAGATACATATCCCATATCCATAGTCGGATATATGTT
Found at i:156841 original size:22 final size:22
Alignment explanation
Indices: 156811--156855 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
156801 TTATTTAGAG
156811 TTCGCGAACATGCTCGTTAATA
1 TTCGCGAACATGCTCGTTAATA
* * *
156833 TTCGTGAACATGTTCGTTTATA
1 TTCGCGAACATGCTCGTTAATA
156855 T
1 T
156856 GCTCAACAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (22 bp):
TTCGCGAACATGCTCGTTAATA
Found at i:157881 original size:59 final size:60
Alignment explanation
Indices: 157767--157888 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 60
157757 TATAATTTTT
* *
157767 ATTCTAAATTAATCTCTAAACCTTTAAATATTTTAAATCTATCTCCAAATTATGACTCTC
1 ATTCTAAATTAATCTCTAAACCTTTAAATATTTTAAATCTATCCCCAAACTATGACTCTC
** * *
157827 ATTCTAAATTAATCTC-AAATTTTTTAGTATTTTAAAT-TCA-CCCCTAAACTATGACTCTC
1 ATTCTAAATTAATCTCTAAACCTTTAAATATTTTAAATCT-ATCCCC-AAACTATGACTCTC
157886 ATT
1 ATT
157889 TTAATTGGTC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
58 4 0.07
59 34 0.63
60 16 0.30
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (60 bp):
ATTCTAAATTAATCTCTAAACCTTTAAATATTTTAAATCTATCCCCAAACTATGACTCTC
Found at i:161673 original size:20 final size:20
Alignment explanation
Indices: 161653--161689 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
161643 ATTTTTTAAT
*
161653 TTATTTATT-AATTAATAAA
1 TTATATATTAAATTAATAAA
161672 TTATATATTAAATTAATA
1 TTATATATTAAATTAATA
161690 GTTCAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATATATTAAATTAATAAA
Found at i:169435 original size:20 final size:20
Alignment explanation
Indices: 169410--169459 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
169400 AACCAAGCCT
169410 GGATGTGATCGGATCACACG
1 GGATGTGATCGGATCACACG
169430 GGATGTGATCGGATCACACG
1 GGATGTGATCGGATCACACG
*
169450 GGATATGATC
1 GGATGTGATC
169460 ATTATCCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (20 bp):
GGATGTGATCGGATCACACG
Found at i:172625 original size:41 final size:41
Alignment explanation
Indices: 172579--172775 Score: 313
Period size: 41 Copynumber: 4.8 Consensus size: 41
172569 TAGTTGAAAA
* *
172579 TCGCGTTGCGATAGTCTACAGTATCGTTGCTATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
172620 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* * * *
172661 TCGCGTTGCAATAGTGTACAGTGTCGTTGCGATTTTTCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
172702 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTTCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
172743 TCGCGTTGCGGTAGTCTACAGTGTCATTGCGAT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
172776 AGTCTACAGT
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:172669 original size:20 final size:20
Alignment explanation
Indices: 172603--172669 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
172593 TCTACAGTAT
*
172603 CGTTGCTATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
172623 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
172643 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
172664 CGTTGC
1 CGTTGC
172670 AATAGTGTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 4 0.11
20 16 0.46
21 11 0.31
22 4 0.11
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:172710 original size:20 final size:20
Alignment explanation
Indices: 172685--172752 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
172675 TGTACAGTGT
172685 CGTTGCGATTTTTCATCTCG
1 CGTTGCGATTTTTCATCTCG
* * *
172705 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTTCATCTCG
*
172725 TCGTTGCGATTTTTCATTTCG
1 -CGTTGCGATTTTTCATCTCG
172746 CGTTGCG
1 CGTTGCG
172753 GTAGTCTACA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 4 0.11
20 18 0.49
21 11 0.30
22 4 0.11
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTTCATCTCG
Found at i:172876 original size:6 final size:6
Alignment explanation
Indices: 172865--172889 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
172855 GACACGTATT
172865 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
172890 GACGGCGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:173348 original size:21 final size:21
Alignment explanation
Indices: 173324--173392 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
173314 GAAAATCGCA
173324 TTGCGATAGTCTACAGTGTCG
1 TTGCGATAGTCTACAGTGTCG
* * * *
173345 TTGC--TATTTTCCA-TTTCGCG
1 TTGCGATAGTCTACAGTGT--CG
*
173365 TTGCGATAGTCTAGAGTGTCG
1 TTGCGATAGTCTACAGTGTCG
173386 TTGCGAT
1 TTGCGAT
173393 TTTCCATTTC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 6 0.18
21 13 0.38
22 5 0.15
23 2 0.06
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (21 bp):
TTGCGATAGTCTACAGTGTCG
Found at i:173370 original size:41 final size:41
Alignment explanation
Indices: 173319--173555 Score: 327
Period size: 41 Copynumber: 5.8 Consensus size: 41
173309 TAGTTGAAAA
* *
173319 TCGCATTGCGATAGTCTACAGTGTCGTTGCTATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
173360 TCGCGTTGCGATAGTCTAGAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
* *
173401 TCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTCCATT
* * * * *
173442 TCGTGTCGCGATAGTGTACAGTGTCGTTGCGATTTTTCATC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
173483 TCGCGTTGCGGTAGTCTACAGTGTCGTTGCGA-TTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
173523 TCGCGTTGCGATAGTCTACAGAGTCGTTGCGAT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGAT
173556 AGTCTACAGT
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
40 38 0.22
41 132 0.77
42 2 0.01
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:173512 original size:21 final size:21
Alignment explanation
Indices: 173486--173565 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
173476 TTTCATCTCG
*
173486 CGTTGCGGTAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* *
173507 CGTTGCGAT--T-TCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
*
173524 CGCGTTGCGATAGTCTACAGAGT
1 --CGTTGCGATAGTCTACAGTGT
173547 CGTTGCGATAGTCTACAGT
1 CGTTGCGATAGTCTACAGT
173566 AAATTAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 2 0.04
18 3 0.07
19 10 0.22
21 27 0.59
22 3 0.07
23 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:173656 original size:6 final size:6
Alignment explanation
Indices: 173645--173671 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
173635 GACACGTATT
173645 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
173672 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:174301 original size:21 final size:21
Alignment explanation
Indices: 174275--174351 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
174265 TTTACTGTAG
174275 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
174296 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
*
174317 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
174337 ACTATCGCAATGCGA
1 ACTATCGCAACGCGA
174352 AATGCAACGC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:174372 original size:41 final size:41
Alignment explanation
Indices: 174278--174355 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
174268 ACTGTAGACT
174278 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
174319 ATCGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
174356 CAACGCGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:174746 original size:6 final size:6
Alignment explanation
Indices: 174725--174761 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
174715 TCTCCTCTCG
174725 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
174762 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:174874 original size:21 final size:21
Alignment explanation
Indices: 174848--174965 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 21
174838 TTTACTGTAG
174848 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
** **
174869 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
* *** *
174890 A-AATCGCGTTGCGATTCTCA
1 ACTATCGCAACGCGATTTTCA
** **
174910 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGATTTTCA
*
174931 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
174951 ACTATCGCAATGCGA
1 ACTATCGCAACGCGA
174966 AATGCAACGC
Statistics
Matches: 66, Mismatches: 29, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 26 0.39
21 40 0.61
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:174911 original size:41 final size:41
Alignment explanation
Indices: 174851--174969 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
174841 ACTGTAGACT
174851 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*** *
174892 ATCGCGTTGCGATTCTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
174933 ATCGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
174970 CAACGCGAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:182566 original size:17 final size:17
Alignment explanation
Indices: 182544--182586 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
182534 ATTATATTGT
*
182544 TTAAACCTTCTATTAGC
1 TTAAACCTCCTATTAGC
182561 TTAAACCTCCTATTAGC
1 TTAAACCTCCTATTAGC
182578 TTAAACCTC
1 TTAAACCTC
182587 ATGTTTTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (17 bp):
TTAAACCTCCTATTAGC
Found at i:186377 original size:35 final size:36
Alignment explanation
Indices: 186326--186398 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
186316 TAAACTGGAC
* * *
186326 TCGCGATGGTAAACTTTTT-GTTCTGTTTTATCTAG
1 TCGCAATGGTAAACTTTTTACTTCTGTCTTATCTAG
*
186361 TCGCAATGGTATACTTTTTACTTCTGTCTTATCTAG
1 TCGCAATGGTAAACTTTTTACTTCTGTCTTATCTAG
186397 TC
1 TC
186399 ATTTTTTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (36 bp):
TCGCAATGGTAAACTTTTTACTTCTGTCTTATCTAG
Found at i:188753 original size:25 final size:25
Alignment explanation
Indices: 188725--188776 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
188715 ATGTTGTGTG
188725 TTTAAGACACGAACACATGTATGCA
1 TTTAAGACACGAACACATGTATGCA
188750 TTTAAGACACGAACACATGTATGCA
1 TTTAAGACACGAACACATGTATGCA
188775 TT
1 TT
188777 ATATTGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (25 bp):
TTTAAGACACGAACACATGTATGCA
Found at i:192654 original size:24 final size:22
Alignment explanation
Indices: 192599--192663 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 22
192589 AGCCATAATG
192599 AGAAATAGCTTAGCAAAG-AGA
1 AGAAATAGCTTAGCAAAGCAGA
*
192620 ATGAAAAAGCTTAGCAAAGCAAGGA
1 A-GAAATAGCTTAGCAAAGC-A-GA
192645 AGAAATAGCTTAGCAAAGC
1 AGAAATAGCTTAGCAAAGC
192664 TATGAGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.42
24 18 0.47
25 3 0.08
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (22 bp):
AGAAATAGCTTAGCAAAGCAGA
Found at i:193958 original size:22 final size:22
Alignment explanation
Indices: 193933--193974 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
193923 ACCATCTACC
*
193933 TGCAAATAAATGTTATCATCGT
1 TGCAAACAAATGTTATCATCGT
193955 TGCAAACAAATGTTATCATC
1 TGCAAACAAATGTTATCATC
193975 ATAATTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TGCAAACAAATGTTATCATCGT
Found at i:195627 original size:12 final size:11
Alignment explanation
Indices: 195607--195672 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
195597 TTTAGTTGTC
195607 AATTTTAATTTT
1 AATTTTAA-TTT
*
195619 AATTCTAATTCT
1 AATTTTAATT-T
*
195631 AATTCTAATTCT
1 AATTTTAATT-T
* *
195643 AATCTAAATTT
1 AATTTTAATTT
195654 -ATTTTATATTT
1 AATTTTA-ATTT
195665 AATTTTAA
1 AATTTTAA
195673 AGTAAAGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.09
11 8 0.18
12 33 0.73
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:195633 original size:18 final size:18
Alignment explanation
Indices: 195607--195672 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
195597 TTTAGTTGTC
*
195607 AATTTTAATTTTAATTCT
1 AATTCTAATTTTAATTCT
*
195625 AATTCTAATTCTAATTCT
1 AATTCTAATTTTAATTCT
* *
195643 AA-TCTAAATTT-ATTTT
1 AATTCTAATTTTAATTCT
195659 ATATT-TAATTTTAA
1 A-ATTCTAATTTTAA
195673 AGTAAAGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.13
17 14 0.36
18 20 0.51
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTCTAATTTTAATTCT
Found at i:196197 original size:12 final size:12
Alignment explanation
Indices: 196180--196204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
196170 CGAATGACTC
196180 AACAAAACAAAA
1 AACAAAACAAAA
196192 AACAAAACAAAA
1 AACAAAACAAAA
196204 A
1 A
196205 GGAATTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAAACAAAA
Found at i:198165 original size:59 final size:60
Alignment explanation
Indices: 198072--198208 Score: 199
Period size: 59 Copynumber: 2.3 Consensus size: 60
198062 CTCTCTCAAT
* * *
198072 GGATCATTTTGTAACTTTTAATAATCGAATGACTCAACAAAGTAGCGTCCTATAGTTAGA
1 GGATCATTTTGTAACTTTTAATAATCGAAAGACTCAACAAAGTAGCGTCCTATAATTAAA
*
198132 -GATCATTTTGTAACTTTTAATAATC-ATAAGACTCAACAAAGTAGTGTCCTATAATTAAA
1 GGATCATTTTGTAACTTTTAATAATCGA-AAGACTCAACAAAGTAGCGTCCTATAATTAAA
198191 GGATCATTTGTGT-ACTTT
1 GGATCATTT-TGTAACTTT
198209 ATCCTTAGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 1 0.01
59 53 0.76
60 13 0.19
61 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (60 bp):
GGATCATTTTGTAACTTTTAATAATCGAAAGACTCAACAAAGTAGCGTCCTATAATTAAA
Found at i:200333 original size:40 final size:39
Alignment explanation
Indices: 200274--200395 Score: 154
Period size: 40 Copynumber: 3.1 Consensus size: 39
200264 TCGTCTACAT
* *
200274 CATTTAAATAAATTAAAAACTCATATCCTACTATTATAAA
1 CATTTAAATAAATT-AAAACCCAAATCCTACTATTATAAA
* * *
200314 CATTTGAATAAATGTAAAACCCAGATCCTCCTATTATAAA
1 CATTTAAATAAAT-TAAAACCCAAATCCTACTATTATAAA
* *
200354 CATTTTAATAAATTTAAAACCCAAATCCTACTATTAAAAA
1 CATTTAAATAAA-TTAAAACCCAAATCCTACTATTATAAA
200394 CA
1 CA
200396 AAGATTATTC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
40 70 0.97
41 2 0.03
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (39 bp):
CATTTAAATAAATTAAAACCCAAATCCTACTATTATAAA
Found at i:207123 original size:35 final size:35
Alignment explanation
Indices: 207076--207161 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
207066 AAAACAGTCA
* * *
207076 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
207111 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
207146 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
207162 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:207155 original size:21 final size:21
Alignment explanation
Indices: 207130--207172 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
207120 TTCTAAACCC
207130 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
207151 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
207172 T
1 T
207173 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:207322 original size:16 final size:18
Alignment explanation
Indices: 207290--207323 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
207280 TATTAATGTA
207290 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
207308 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
207324 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:207984 original size:125 final size:128
Alignment explanation
Indices: 207793--208034 Score: 373
Period size: 125 Copynumber: 1.9 Consensus size: 128
207783 AATTTTCTTC
* * * *
207793 TAATTAGGAGGTGACATGTGTCACTAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
207858 CCTGATT-AATGATTAATTTATTAAA-TT-TTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTATTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
207918 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
207983 CCTAATTAAATGATTAATTTATTAAATTTTATTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAA-TTTATTAATTTAGGACCAAATTGAT
208035 TATATAAAAT
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 63 0.61
126 18 0.17
128 2 0.02
129 21 0.20
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (128 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTATTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:209813 original size:2 final size:2
Alignment explanation
Indices: 209806--209830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
209796 TGTATGAACA
209806 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
209831 CAAAAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:212539 original size:24 final size:22
Alignment explanation
Indices: 212499--212575 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
212489 ATGCAATTAA
212499 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
212518 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
212541 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
212562 TGCATCGATGCACT
1 TGCATCGATGCACT
212576 TCAAGGGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:214142 original size:23 final size:23
Alignment explanation
Indices: 214112--214164 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
214102 CATTTTATAT
214112 GGCACTTC-GATGCAATTCTACGC
1 GGCACTTCAG-TGCAATTCTACGC
*
214135 GGCACTTCAGTGCAATTCTACGT
1 GGCACTTCAGTGCAATTCTACGC
214158 GGCACTT
1 GGCACTT
214165 AGGTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTCTACGC
Found at i:216529 original size:23 final size:23
Alignment explanation
Indices: 216503--216562 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
216493 TATGACTTTT
216503 TGGTCAAAGTCAACTGTCAAATA
1 TGGTCAAAGTCAACTGTCAAATA
216526 TGGTCAAAGTCAACTGTCAAATA
1 TGGTCAAAGTCAACTGTCAAATA
*
216549 TGGCCAAAGTCAAC
1 TGGTCAAAGTCAAC
216563 GGGTCAGGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (23 bp):
TGGTCAAAGTCAACTGTCAAATA
Found at i:216619 original size:20 final size:20
Alignment explanation
Indices: 216566--216607 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
216556 AGTCAACGGG
*
216566 TCAGGTCCGATTGACTAAGT
1 TCAGGTCGGATTGACTAAGT
*
216586 TCAGGTCGGATTGACTTAGT
1 TCAGGTCGGATTGACTAAGT
216606 TC
1 TC
216608 GAGTCGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TCAGGTCGGATTGACTAAGT
Found at i:221279 original size:2 final size:2
Alignment explanation
Indices: 221272--221323 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
221262 TTGTGTAATA
221272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
221314 AT AC AT AT AT
1 AT AT AT AT AT
221324 GTGTGTGTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222692 original size:19 final size:19
Alignment explanation
Indices: 222670--222710 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
222660 TTTGGTGAAC
222670 AATTTAA-AATGAATGTTAT
1 AATTTAAGAATGAATG-TAT
*
222689 AATTTAAGTATGAATGTAT
1 AATTTAAGAATGAATGTAT
222708 AAT
1 AAT
222711 ATTTTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (19 bp):
AATTTAAGAATGAATGTAT
Found at i:222765 original size:186 final size:186
Alignment explanation
Indices: 222451--222820 Score: 607
Period size: 186 Copynumber: 2.0 Consensus size: 186
222441 ATAATTTAAA
*
222451 GATTAATATTGAATGTTTTAAAATTTGGAGAACAATTTAAAATTAAGGTCATAATTTAAGAATGA
1 GATTAATATTGAATGTTTTAAAATTTGGAGAACAATTTAAAATGAAGGTCATAATTTAAGAATGA
*
222516 ATATATAATATTTTAAAGTTTTAAAACTGATTTAGAATGAGAATTATAATTCAGGGACTCTTTGT
66 ATATATAATATTTTAAAGTTTTAAAACTGATTTAAAATGAGAATTATAATTCAGGGACTCTTTGT
* *
222581 ATGGGGTGAATACAGGGTGTAATATATCTTCGAAAGGCTATCAACCATTTGATAAT
131 ATGGGGTGAACACAGGGTGTAATATATATTCGAAAGGCTATCAACCATTTGATAAT
* * * *
222637 GATTAATATTGAATGTTTTAAAATTTGGTGAACAATTTAAAATGAATGTTATAATTTAAGTATGA
1 GATTAATATTGAATGTTTTAAAATTTGGAGAACAATTTAAAATGAAGGTCATAATTTAAGAATGA
* * *
222702 ATGTATAATATTTTAAAG-TTTAAAGATTGATTTAAAATGAGAATTATAATTTAGGGACTCTTTG
66 ATATATAATATTTTAAAGTTTTAAA-ACTGATTTAAAATGAGAATTATAATTCAGGGACTCTTTG
* *
222766 TATGGGGTGAACACAGGGTGTAATATATATTCGAAAGGCTCTCAATCATTTGATA
130 TATGGGGTGAACACAGGGTGTAATATATATTCGAAAGGCTATCAACCATTTGATA
222821 GTAATAGCTT
Statistics
Matches: 170, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
185 6 0.04
186 164 0.96
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.38
Consensus pattern (186 bp):
GATTAATATTGAATGTTTTAAAATTTGGAGAACAATTTAAAATGAAGGTCATAATTTAAGAATGA
ATATATAATATTTTAAAGTTTTAAAACTGATTTAAAATGAGAATTATAATTCAGGGACTCTTTGT
ATGGGGTGAACACAGGGTGTAATATATATTCGAAAGGCTATCAACCATTTGATAAT
Found at i:223143 original size:13 final size:13
Alignment explanation
Indices: 223125--223150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223115 ATACTATAGA
223125 ATTATAGTTTAGT
1 ATTATAGTTTAGT
223138 ATTATAGTTTAGT
1 ATTATAGTTTAGT
223151 TGACAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTATAGTTTAGT
Found at i:228726 original size:200 final size:200
Alignment explanation
Indices: 228383--228753 Score: 514
Period size: 200 Copynumber: 1.9 Consensus size: 200
228373 TCCTCCTTTT
* * * * *
228383 AACAATGCACATTATCAAAACAAAAAGACATTCATAGCCAATTCGAATCCCCGGAAACTCGTATT
1 AACAATGCACATTATCAAAACAAAAAAAAATTCATAACCAATTCGAATCCCCGAAAACTCGTATC
* * * *
228448 TGACACTCACATCCAAATTTAAATAGCATAGCTTTGATGATCAAATTCGTGTGTATCATATGAAA
66 TGACACTCACACCCAAATCTAAATAACATAGCTTTGATGATCAAAATCGTGTGTATCATATGAAA
228513 ACTAAAATTTACCTTGAAAACAAGTGCA-GGATCTACCAAGAGAACAGTAGCAGAAACAAGGGCA
131 ACTAAAATTTACCTTGAAAACAAGTGCATGG-TCTACCAAGAGAACAGTAGCAGAAACAAGGGCA
228577 AACATA
195 AACATA
* * * **
228583 AACAATGCACATTGTCAAAACAAAACAAAAATT-ATAACCAATTTGATTCGTCGAAAACTCGTAT
1 AACAATGCACATTATCAAAACAAAA-AAAAATTCATAACCAATTCGAATCCCCGAAAACTCGTAT
* * * *
228647 CTGAGACTCACACCCGAGTCTAAATAACATAG-TTTCGATTATCAAAATCGTGTGTATCATATGA
65 CTGACACTCACACCCAAATCTAAATAACATAGCTTT-GATGATCAAAATCGTGTGTATCATATGA
* *
228711 AAACTCAAATTTACCTTGAAAGCAAGTGCATGGTCTACCAAGA
129 AAACTAAAATTTACCTTGAAAACAAGTGCATGGTCTACCAAGA
228754 CAATAGTCAT
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
199 3 0.02
200 138 0.93
201 7 0.05
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (200 bp):
AACAATGCACATTATCAAAACAAAAAAAAATTCATAACCAATTCGAATCCCCGAAAACTCGTATC
TGACACTCACACCCAAATCTAAATAACATAGCTTTGATGATCAAAATCGTGTGTATCATATGAAA
ACTAAAATTTACCTTGAAAACAAGTGCATGGTCTACCAAGAGAACAGTAGCAGAAACAAGGGCAA
ACATA
Found at i:230533 original size:22 final size:25
Alignment explanation
Indices: 230499--230545 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
230489 ACTCATAATT
230499 AAAATAATATTTTAA-T-ATATAAA
1 AAAATAATATTTTAATTAATATAAA
230522 AAAATAAT-TTTTAATTAATATAAA
1 AAAATAATATTTTAATTAATATAAA
230546 CCTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATAATATTTTAATTAATATAAA
Found at i:234355 original size:183 final size:183
Alignment explanation
Indices: 234047--234414 Score: 556
Period size: 183 Copynumber: 2.0 Consensus size: 183
234037 CCTTTTTAAT
* * * * * *
234047 AATGCACATTGTCAGAACAAAAGACATTCATAACCGATTTAAATCGTCAGAAACTCGTATCTGGC
1 AATGCACATTGTCAAAACAAAAGACATTCAGAACCAATTTAAATCATCAAAAACTCGTATCTGAC
*
234112 ACTCACACCCGAGTCTAAATAACATAGCTTAAATGATCAAATTCGTGTGTATCATATGAAAACTC
66 ACTCACACCCGAGTCTAAATAACATAGCTCAAATGATCAAATTCGTGTGTATCATATGAAAACTC
* *
234177 AAATTTATCTTGAAAGCAAGTGTAGGATCTACCAAGAAAACAGAAGCAGAAAC
131 AAATTTACCTTGAAAGCAAGTGCAGGATCTACCAAGAAAACAGAAGCAGAAAC
* * * * *
234230 AATGCACATTGTCAAAACAAAAGACATTCCGAATCAATTTGATTCATCAAAAACTTGTATCTGAC
1 AATGCACATTGTCAAAACAAAAGACATTCAGAACCAATTTAAATCATCAAAAACTCGTATCTGAC
* ** * *
234295 GCTCACACTTGAGTCTAAATAACATAGCTCAGATGATCGAATTCGTGTGTATCATATGAAAACTC
66 ACTCACACCCGAGTCTAAATAACATAGCTCAAATGATCAAATTCGTGTGTATCATATGAAAACTC
*
234360 AAATTTACCTTGAAAGCAAGTGCAGGGTCTACCAAGAAAACAGAAGCAGAAAC
131 AAATTTACCTTGAAAGCAAGTGCAGGATCTACCAAGAAAACAGAAGCAGAAAC
234413 AA
1 AA
234415 GGGCAAGCAA
Statistics
Matches: 165, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (183 bp):
AATGCACATTGTCAAAACAAAAGACATTCAGAACCAATTTAAATCATCAAAAACTCGTATCTGAC
ACTCACACCCGAGTCTAAATAACATAGCTCAAATGATCAAATTCGTGTGTATCATATGAAAACTC
AAATTTACCTTGAAAGCAAGTGCAGGATCTACCAAGAAAACAGAAGCAGAAAC
Found at i:236601 original size:15 final size:16
Alignment explanation
Indices: 236572--236612 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
236562 TTATAAAATA
236572 ATATTTTAATTATTTAT
1 ATATTTTAA-TATTTAT
236589 ATATTTTAA-ATTTAT
1 ATATTTTAATATTTAT
236604 -T-TTTTAATA
1 ATATTTTAATA
236613 AATAGTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 2 0.09
15 6 0.26
17 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTTAATATTTAT
Found at i:237723 original size:2 final size:2
Alignment explanation
Indices: 237716--237799 Score: 56
Period size: 2 Copynumber: 44.5 Consensus size: 2
237706 CCGTCCCGAT
* * *
237716 TA TA TA TA TA TA TA TA TA TA TA CTA T- TT TA TA TT TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
237757 TA -A T- TA TA TA TA TA CTA T- TT TA TA TA T- TT TA TA TA TA -A
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
237795 TA TA T
1 TA TA T
237800 TTTTGGATTC
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
1 7 0.10
2 57 0.84
3 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:237766 original size:33 final size:34
Alignment explanation
Indices: 237718--237799 Score: 132
Period size: 33 Copynumber: 2.4 Consensus size: 34
237708 GTCCCGATTA
237718 TATATATATATATATATATACTATTTTATAT-TTT
1 TATATATA-ATATATATATACTATTTTATATATTT
237752 TATAT-TAATTATATATATACTATTTTATATATTT
1 TATATATAA-TATATATATACTATTTTATATATTT
237786 TATATATAATATAT
1 TATATATAATATAT
237800 TTTTGGATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
32 1 0.02
33 23 0.51
34 18 0.40
35 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATATAATATATATATACTATTTTATATATTT
Found at i:237788 original size:25 final size:25
Alignment explanation
Indices: 237744--237803 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
237734 TATACTATTT
237744 TATATTTTTATATTAATTATATAT-A
1 TATATTTTTATATT-ATTATATATAA
237769 TACTATTTTATATATT-TTATATATAA
1 TA-TATTTT-TATATTATTATATATAA
237795 TATATTTTT
1 TATATTTTT
237804 GGATTCGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.03
25 16 0.50
26 9 0.28
27 6 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTTTTATATTATTATATATAA
Found at i:237799 original size:43 final size:43
Alignment explanation
Indices: 237718--237800 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
237708 GTCCCGATTA
**
237718 TATATATATATATATATATACTATTTTATATTTTTATATTAAT
1 TATATATATATATATATATACTATTTTATATTAATATATTAAT
*
237761 TATATATATACTAT-TTTATA-TATTTTATATATAATATATT
1 TATATATATA-TATATATATACTATTTTATAT-TAATATATT
237801 TTTGGATTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 10 0.29
43 22 0.63
44 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (43 bp):
TATATATATATATATATATACTATTTTATATTAATATATTAAT
Found at i:238240 original size:14 final size:14
Alignment explanation
Indices: 238221--238247 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
238211 ATCTGTACAA
238221 TTTCCCCAACATTT
1 TTTCCCCAACATTT
238235 TTTCCCCAACATT
1 TTTCCCCAACATT
238248 GATGTAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTCCCCAACATTT
Found at i:241139 original size:77 final size:77
Alignment explanation
Indices: 241046--241196 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 77
241036 GTAGAGTTTA
* *
241046 GATTGATTAACATTTGATGAAAATTGTGAATTCAAATGTGTTCAAGTGCAAGCGTCTCTAATTTA
1 GATTGATTAACATTTGATAAAAATTGTGAATTCAAATGTATTCAAGTGCAAGCGTCTCTAATTTA
241111 CGAGTTTTGGAG
66 CGAGTTTTGGAG
* * * * *
241123 GATTGATTGACATTTGATAAAAATTGTGAATTCGAATGTATTTAAGTGCAAGTGTCTCTAATTTT
1 GATTGATTAACATTTGATAAAAATTGTGAATTCAAATGTATTCAAGTGCAAGCGTCTCTAATTTA
241188 CGAGTTTTG
66 CGAGTTTTG
241197 AAAGAATGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (77 bp):
GATTGATTAACATTTGATAAAAATTGTGAATTCAAATGTATTCAAGTGCAAGCGTCTCTAATTTA
CGAGTTTTGGAG
Found at i:241351 original size:26 final size:25
Alignment explanation
Indices: 241318--241375 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
241308 AATAATGATG
241318 TTTAAATATTC-CTATAGATGTTATT
1 TTTAAATA-TCACTATAGATGTTATT
241343 TATTAAATATCACTATAGATGTTATT
1 T-TTAAATATCACTATAGATGTTATT
241369 TTTAAAT
1 TTTAAAT
241376 TCGAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (25 bp):
TTTAAATATCACTATAGATGTTATT
Found at i:248804 original size:116 final size:118
Alignment explanation
Indices: 248576--248808 Score: 380
Period size: 116 Copynumber: 2.0 Consensus size: 118
248566 CCAATTTTGT
* *
248576 CACTTACGAATGTGGTACCTATGTTCTTTTAACCAATTTGGTGCATATATTTATAAAATGTTACA
1 CACTTACAAATGTGGTACCTATGTTCTTTTAACCAATTTGGTACATATATTTATAAAATGTTACA
* *
248641 CATTTGGTACATGTATTTATAAAGTCAAATGCTTAAAAATATTATATGGATTC
66 CATTTGGTACATATATTTATAAAGTCAAATGCTTAAAAATATGATATGGATTC
248694 CACTTACAAATGTGGTACCTATGTTCTTTTAACCAATTTGGTACATATA-TTAT-AAATGTTACA
1 CACTTACAAATGTGGTACCTATGTTCTTTTAACCAATTTGGTACATATATTTATAAAATGTTACA
* * * *
248757 CATTTGGTACCTATATTTATAATGTCAAATGTTTGAAAATATGATATGGATT
66 CATTTGGTACATATATTTATAAAGTCAAATGCTTAAAAATATGATATGGATT
248809 TCATGTCATA
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 56 0.52
117 4 0.04
118 47 0.44
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (118 bp):
CACTTACAAATGTGGTACCTATGTTCTTTTAACCAATTTGGTACATATATTTATAAAATGTTACA
CATTTGGTACATATATTTATAAAGTCAAATGCTTAAAAATATGATATGGATTC
Found at i:253559 original size:22 final size:22
Alignment explanation
Indices: 253534--253588 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
253524 ATTGATGCTT
* *
253534 CAAAATGACATATTAAACTAGA
1 CAAAGTGACATATTAAACCAGA
253556 CAAAGTGACATATTAAACCAGA
1 CAAAGTGACATATTAAACCAGA
253578 CAAAGTGACAT
1 CAAAGTGACAT
253589 TTTGAGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (22 bp):
CAAAGTGACATATTAAACCAGA
Found at i:253937 original size:23 final size:23
Alignment explanation
Indices: 253911--253961 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
253901 TCAACCAAAA
253911 CTCGATTTTGAGCTCGA-TTCAAG
1 CTCGATTTTGAGCTC-ATTTCAAG
* *
253934 CTCGGTTTTGAGCTCATTTGAAG
1 CTCGATTTTGAGCTCATTTCAAG
253957 CTCGA
1 CTCGA
253962 AACGGGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (23 bp):
CTCGATTTTGAGCTCATTTCAAG
Found at i:255613 original size:21 final size:21
Alignment explanation
Indices: 255583--255655 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
255573 CATAATCAGA
255583 TTTA-GGTTTAGGGTATATAG
1 TTTAGGGTTTAGGGTATATAG
* *
255603 TTTAGGGTTTATGATATATAG
1 TTTAGGGTTTAGGGTATATAG
* *
255624 TTTAAGGTTTAGGGTTTATAG
1 TTTAGGGTTTAGGGTATATAG
255645 TTTAGGGTTTA
1 TTTAGGGTTTA
255656 TTGCAAAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 4 0.09
21 41 0.91
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTATATAG
Found at i:255640 original size:14 final size:15
Alignment explanation
Indices: 255585--255656 Score: 71
Period size: 14 Copynumber: 5.1 Consensus size: 15
255575 TAATCAGATT
*
255585 TAGGTTTAGGGTATA
1 TAGGTTTAGGGTTTA
255600 TA-GTTTAGGGTTTA
1 TAGGTTTAGGGTTTA
* * **
255614 T-GATATATAGTTTA
1 TAGGTTTAGGGTTTA
255628 -AGGTTTAGGGTTTA
1 TAGGTTTAGGGTTTA
255642 TA-GTTTAGGGTTTA
1 TAGGTTTAGGGTTTA
255656 T
1 T
255657 TGCAAAGATA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 42 0.93
15 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (15 bp):
TAGGTTTAGGGTTTA
Found at i:262487 original size:27 final size:30
Alignment explanation
Indices: 262424--262495 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
262414 CGATTTAACG
262424 GTTCAATGGTATAATTGAAACGAAAATCAAA
1 GTTCAATGGTATAATT-AAACGAAAATCAAA
* *
262455 GTTCAATGTTATAATT-AAC-AAAATTAAA
1 GTTCAATGGTATAATTAAACGAAAATCAAA
262483 -TTCAATGGTATAA
1 GTTCAATGGTATAA
262496 ACAATACAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 12 0.32
28 8 0.21
29 3 0.08
31 15 0.39
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (30 bp):
GTTCAATGGTATAATTAAACGAAAATCAAA
Found at i:263605 original size:27 final size:27
Alignment explanation
Indices: 263571--263637 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
263561 GATAATGGTT
263571 CTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
*
263598 TTGAATCATTCAGAATGTACTTCTATG
1 CTGAATCATTCAGAATGTACTTCTATG
263625 CTGAATCATTCAG
1 CTGAATCATTCAG
263638 CACTGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTATG
Found at i:265418 original size:13 final size:13
Alignment explanation
Indices: 265402--265448 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
265392 TATAATTTAA
265402 TTATTTTTATATT
1 TTATTTTTATATT
* *
265415 TTATTTTAATAAT
1 TTATTTTTATATT
* *
265428 TTAATTTTATATA
1 TTATTTTTATATT
265441 TT-TTTTTA
1 TTATTTTTA
265449 AAATTTATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTTATATT
Found at i:265429 original size:30 final size:26
Alignment explanation
Indices: 265386--265455 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 26
265376 AAAATTCAGA
*
265386 TTTTTATATAATTTAATTATTTTTATATTT
1 TTTTTA-ATAATTTAA-T-TTTATATA-TT
265416 TATTTTAATAATTTAATTTTATATATT
1 T-TTTTAATAATTTAATTTTATATATT
265443 TTTTTAA-AATTTA
1 TTTTTAATAATTTA
265456 TAATTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 6 0.16
26 6 0.16
27 3 0.08
28 7 0.18
29 1 0.03
30 10 0.26
31 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTTAATAATTTAATTTTATATATT
Found at i:265461 original size:27 final size:26
Alignment explanation
Indices: 265406--265455 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
265396 ATTTAATTAT
265406 TTTTATATTTTATTTTAATAATTTAA
1 TTTTATATTTTATTTTAATAATTTAA
265432 TTTTATATATTT-TTTTAA-AATTTA
1 TTTTATAT-TTTATTTTAATAATTTA
265456 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 14 0.61
27 3 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTATATTTTATTTTAATAATTTAA
Found at i:275007 original size:42 final size:39
Alignment explanation
Indices: 274959--275037 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 39
274949 TACATCGTGT
* *
274959 TATTTTC-AAATGGTATTTTTTTTTAATTTTAAATAAATTTTA
1 TATTTTCTAAATCGT-TTTTATTTT-ATTTT--ATAAATTTTA
275001 TATTTTCTAAATCGTTTTTATTTTATTTTATAAATTT
1 TATTTTCTAAATCGTTTTTATTTTATTTTATAAATTT
275038 AACGTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 8 0.24
41 5 0.15
42 15 0.44
43 6 0.18
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (39 bp):
TATTTTCTAAATCGTTTTTATTTTATTTTATAAATTTTA
Found at i:275154 original size:15 final size:15
Alignment explanation
Indices: 275130--275172 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
275120 ATATTATTAA
*
275130 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
275145 GTTAAATTATAAAAT
1 ATTAAATTATAAAAT
275160 ATTAAATATATAA
1 ATTAAAT-TATAA
275173 TTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:275187 original size:23 final size:22
Alignment explanation
Indices: 275149--275212 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
275139 TAAAATGTTA
* *
275149 AATTATAAAATATTAAATATAT
1 AATTATAAATTATTAAAAATAT
*
275171 AATTATAAATTAGTTAAAAATTT
1 AATTATAAATTA-TTAAAAATAT
* *
275194 AAATATAATTTAATTAAAA
1 AATTATAAATT-ATTAAAA
275213 TACAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 11 0.31
23 23 0.66
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTATAAATTATTAAAAATAT
Found at i:275799 original size:2 final size:2
Alignment explanation
Indices: 275792--275826 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
275782 AATGAAAATA
275792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
275827 AACAAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:276775 original size:22 final size:23
Alignment explanation
Indices: 276740--276787 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
276730 CATTTAGAGT
276740 TTTAACTAATTTATAA-TTATATG
1 TTTAACTAATTTATAATTTA-ATG
*
276763 TTTAA-TACTTTATAATTTAATG
1 TTTAACTAATTTATAATTTAATG
276785 TTT
1 TTT
276788 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAATG
Found at i:278031 original size:26 final size:23
Alignment explanation
Indices: 277983--278032 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
277973 CAGATCCAAT
*
277983 ACGATCCAAAAAATAATCGAAAA
1 ACGATCCAAAAAATAACCGAAAA
278006 ACGATCCAAAAACCGATAACCGAAAA
1 ACGATCCAAAAA---ATAACCGAAAA
278032 A
1 A
278033 AACTAAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
26 11 0.48
ACGTcount: A:0.58, C:0.22, G:0.10, T:0.10
Consensus pattern (23 bp):
ACGATCCAAAAAATAACCGAAAA
Found at i:280707 original size:22 final size:22
Alignment explanation
Indices: 280664--280707 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
280654 TGTCTCTTAA
*
280664 TTGAACCATTCAACACTGAATG
1 TTGAACCATTCAACACTCAATG
* * *
280686 TTGAACCGTTCATCATTCAATG
1 TTGAACCATTCAACACTCAATG
280708 CGTTTATTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
TTGAACCATTCAACACTCAATG
Found at i:280934 original size:17 final size:18
Alignment explanation
Indices: 280906--280941 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
280896 TGCAATTATT
280906 CAAAAAAGTAAGCAAAAA
1 CAAAAAAGTAAGCAAAAA
*
280924 CAAAAAA-TAAGTAAAAA
1 CAAAAAAGTAAGCAAAAA
280941 C
1 C
280942 GGTGTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.72, C:0.11, G:0.08, T:0.08
Consensus pattern (18 bp):
CAAAAAAGTAAGCAAAAA
Found at i:284966 original size:20 final size:20
Alignment explanation
Indices: 284941--284979 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
284931 ATAGTCCAAG
284941 TTCGCGTTGCGAATTTCCAT
1 TTCGCGTTGCGAATTTCCAT
*
284961 TTCGCGTTGCGATTTTCCA
1 TTCGCGTTGCGAATTTCCA
284980 AATTCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTCCAT
Found at i:288546 original size:50 final size:50
Alignment explanation
Indices: 288368--288625 Score: 284
Period size: 51 Copynumber: 5.1 Consensus size: 50
288358 ATCTTCAGCA
* *
288368 AACGAGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC
1 AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
** * * * *
288418 GATTGAG-TCGCTCCCTTTTTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTTC
1 -AACGGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAAAA---TCTTC
* * * *
288472 TACGGGTTCGCTCATTCTCTCTTTAAAGAGTATAGAACTCGAAAATCTTC
1 AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
** * *
288522 AACGGGTTCGCTCCTTCTCACTTTAAAGAGTATAGAACTCGAACATCTTC
1 AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
* * *
288572 AAACGGGTTCGCTCCTTCTTTCATTAAGGAGAATAGAACTCGAATATCTTC
1 -AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
288623 AAC
1 AAC
288626 AATCGTGTCT
Statistics
Matches: 175, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
50 59 0.34
51 77 0.44
53 29 0.17
54 10 0.06
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (50 bp):
AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTC
Found at i:288668 original size:54 final size:53
Alignment explanation
Indices: 288604--288777 Score: 251
Period size: 54 Copynumber: 3.2 Consensus size: 53
288594 ATTAAGGAGA
288604 ATAGAACTCGAATATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGT
1 ATAG-ACTCGAATATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGT
* *
288658 ATGAGACTCG-ATCAATTTTCAACAATCGTGTCTGCTCCCTATTTTTTCAGAGAGT
1 AT-AGACTCGAAT--ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGT
* *
288713 ATAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGT
1 ATAGACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGT
288767 ATAAGACTCGA
1 AT-AGACTCGA
288778 TCAATCTTCG
Statistics
Matches: 108, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
53 2 0.02
54 54 0.50
55 52 0.48
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (53 bp):
ATAGACTCGAATATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGT
Found at i:288685 original size:55 final size:54
Alignment explanation
Indices: 288617--288786 Score: 286
Period size: 55 Copynumber: 3.1 Consensus size: 54
288607 GAACTCGAAT
288617 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGATCA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTAT-AGACTCGATCA
* * *
288672 ATTTTCAACAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGACTCGATCA
*
288726 ATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTAT-AGACTCGATCA
288781 ATCTTC
1 ATCTTC
288787 GATTATCGTT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 50 0.47
55 57 0.53
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (54 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGACTCGATCA
Found at i:289791 original size:8 final size:8
Alignment explanation
Indices: 289780--289820 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
289770 CTTTTTCCCA
289780 TTTTTCAT
1 TTTTTCAT
289788 TTTTT-AT
1 TTTTTCAT
289795 TATTTT-AT
1 T-TTTTCAT
289803 TTTTTC-T
1 TTTTTCAT
289810 TTTTTCAT
1 TTTTTCAT
289818 TTT
1 TTT
289821 CACTCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCAT
Found at i:289804 original size:15 final size:15
Alignment explanation
Indices: 289780--289820 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
289770 CTTTTTCCCA
289780 TTTTTCATTTTTTAT
1 TTTTTCATTTTTTAT
*
289795 TATTTT-ATTTTTTCT
1 T-TTTTCATTTTTTAT
289810 TTTTTCATTTT
1 TTTTTCATTTT
289821 CACTCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCATTTTTTAT
Found at i:305157 original size:2 final size:2
Alignment explanation
Indices: 305150--305178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
305140 ATGTGAATCT
305150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
305179 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:312442 original size:19 final size:18
Alignment explanation
Indices: 312412--312447 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
312402 GGGGTTTTGT
312412 AATTTTGGATTTTTTAGG
1 AATTTTGGATTTTTTAGG
312430 AATTTTAGGATTTTTTAG
1 AATTTT-GGATTTTTTAG
312448 AAAATTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
AATTTTGGATTTTTTAGG
Found at i:313174 original size:12 final size:13
Alignment explanation
Indices: 313157--313190 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
313147 CTAGTTTTAA
313157 TTAATTTAAT-AT
1 TTAATTTAATGAT
*
313169 TTAATTTAATGTT
1 TTAATTTAATGAT
313182 TTAATTTAA
1 TTAATTTAA
313191 AATGACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTAATTTAATGAT
Found at i:315179 original size:19 final size:20
Alignment explanation
Indices: 315147--315186 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
315137 TTAAAATTAA
* *
315147 ATTTTAAATTTAAAGTTTTT
1 ATTTTAAATATAAAATTTTT
315167 ATTTTAAA-ATAAAATTTTT
1 ATTTTAAATATAAAATTTTT
315186 A
1 A
315187 AAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTAAATATAAAATTTTT
Found at i:315185 original size:20 final size:20
Alignment explanation
Indices: 315147--315186 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
315137 TTAAAATTAA
* *
315147 ATTTTAAATTTAAAGTTTTT
1 ATTTTAAAATAAAAGTTTTT
315167 ATTTTAAAATAAAA-TTTTT
1 ATTTTAAAATAAAAGTTTTT
315186 A
1 A
315187 AAATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTTAAAATAAAAGTTTTT
Found at i:319830 original size:20 final size:19
Alignment explanation
Indices: 319796--319842 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
319786 TTTGAGTTAA
319796 TTAAAATATTTTAAAG-TGT
1 TTAAAATATTTTAAAGCT-T
*
319815 TTAAAATGTGTTTAAAGCTT
1 TTAAAATAT-TTTAAAGCTT
319835 TTAAAATA
1 TTAAAATA
319843 ATAAGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
TTAAAATATTTTAAAGCTT
Found at i:324840 original size:54 final size:54
Alignment explanation
Indices: 324554--325147 Score: 654
Period size: 54 Copynumber: 11.1 Consensus size: 54
324544 CTTGAAAAAC
* * * * *
324554 CTTCTGTC-AACGGGTTCGTTCCCTCTTTCT-TCATGGAGTATATAACTTGAGCAAT
1 CTTCT-TCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-AT
* * * *
324609 CATT-TGCAAACGAGTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACAT
1 C-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * *
324663 CTTCTTCTTACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACAT
* * * *
324717 --TCTTCAAACGGGTTCGCCCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAA-CAT
* * *
324771 CTTCTGCAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * * * *
324825 CTTCTTCAAACAGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAA-CAT
* *
324880 CTTCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * * *
324934 CTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
*
324987 --TCTTCAAACGGGTTCGCTCCCTCTTTCTGTAGGGAGTATAGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
*** * * *
325039 CTTCTTCTTGCGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * *
325093 CTTC-T--AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
325144 CTTC
1 CTTC
325148 AAACGTGTCT
Statistics
Matches: 459, Mismatches: 67, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
51 87 0.19
52 47 0.10
53 4 0.01
54 172 0.37
55 120 0.26
56 29 0.06
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (54 bp):
CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
Found at i:324884 original size:109 final size:107
Alignment explanation
Indices: 324562--325147 Score: 679
Period size: 105 Copynumber: 5.5 Consensus size: 107
324552 ACCTTCTGTC
* * * * * * *
324562 AACGGGTTCGTTCCCTCTTTCT-TCATGGAGTATATAACTTGAGCAATCATT-TGCAAACGAGTT
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-ATC-TTCTTCAAACGGGTT
* * * * *
324625 TGCTCCCTCTTTCTCTAGGGAGTATAGAACTC-AAACATCTTCTTCT
63 CGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAAA-ATCTTC-TCA
* * *
324671 TACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAACA---TCTTCAAACGGGTTCG
1 AACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCG
** * * * *
324733 CCCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCA
65 TTCCCTCTTTATCT-AGGGAGTATGGAACTCGAA-AATCTTCT-CA
* * *
324779 AACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAATATCTTCTTCAAACAGGTTCGT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
324844 TCCCTCTTTATCTAGGGAGTATGGAACTCGAATAATCTTCTGCA
66 TCCCTCTTTATCTAGGGAGTATGGAACTCGAA-AATCTTCT-CA
* **
324888 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
*
324953 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATC-T-TCA
66 TCCCTCTTTATCTAGGGAGTATGGAACTCGAAAATCTTCTCA
* ***
324993 AACGGGTTCGCTCCCTCTTTCTGTAGGGAGTATAGAACTCGAACATCTTCTTCTTGCGGGTTCGT
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
*
325058 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT--
66 TCCCTCTTTATCTAGGGAGTATGGAACTCGAAAATCTTCTCA
* * *
325098 AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAATCTTC
1 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTC
325148 AAACGTGTCT
Statistics
Matches: 427, Mismatches: 39, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
105 148 0.35
106 25 0.06
107 37 0.09
108 33 0.08
109 142 0.33
110 42 0.10
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (107 bp):
AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGT
TCCCTCTTTATCTAGGGAGTATGGAACTCGAAAATCTTCTCA
Found at i:325224 original size:53 final size:53
Alignment explanation
Indices: 325154--325313 Score: 241
Period size: 53 Copynumber: 3.0 Consensus size: 53
325144 CTTCAAACGT
* *
325154 GTCTGCTCCCTATTTCTTTAGAGAGTATAAGACCCACAATCTTCAACGATCGC
1 GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGC
*
325207 GTCTGC-CTCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGT
1 GTCTGCTC-CCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGC
* *
325260 GTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCG
1 GTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCG
325314 TTGGGAAACC
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
52 1 0.01
53 78 0.80
54 2 0.02
55 17 0.17
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (53 bp):
GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGC
Found at i:326323 original size:8 final size:8
Alignment explanation
Indices: 326310--326373 Score: 73
Period size: 8 Copynumber: 8.4 Consensus size: 8
326300 TCTTGAAACC
326310 TCATTTTT
1 TCATTTTT
326318 TCATTTTT
1 TCATTTTT
*
326326 T--TTTCAT
1 TCATTT-TT
326333 TCATTTTT
1 TCATTTTT
326341 T-ATTTTT
1 TCATTTTT
*
326348 TTATTTTT
1 TCATTTTT
326356 T-ATTTTT
1 TCATTTTT
326363 TCATTTTT
1 TCATTTTT
326371 TCA
1 TCA
326374 CTCATTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
6 3 0.06
7 16 0.33
8 27 0.55
9 3 0.06
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (8 bp):
TCATTTTT
Found at i:326337 original size:15 final size:14
Alignment explanation
Indices: 326313--326404 Score: 75
Period size: 15 Copynumber: 6.6 Consensus size: 14
326303 TGAAACCTCA
326313 TTTT-TTCATTTTT
1 TTTTCTTCATTTTT
326326 TTTTCATTCATTTTT
1 TTTTC-TTCATTTTT
* *
326341 TATTTTTTTATTTTT
1 T-TTTCTTCATTTTT
*
326356 TATTTTTTCA-TTTT
1 T-TTTCTTCATTTTT
**
326370 TTCAC-TCATTTTT
1 TTTTCTTCATTTTT
*
326383 TTTTCTTC-TTCTT
1 TTTTCTTCATTTTT
326396 TTTTCTTCA
1 TTTTCTTCA
326405 AGCAAAATAC
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.05
13 24 0.38
14 7 0.11
15 27 0.42
16 3 0.05
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTCATTTTT
Found at i:326348 original size:30 final size:30
Alignment explanation
Indices: 326312--326371 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
326302 TTGAAACCTC
326312 ATTTTTTCATTTTTT-TTTCATTCATTTTTT
1 ATTTTTTCATTTTTTATTT-ATTCATTTTTT
* *
326342 ATTTTTTTATTTTTTATTTTTTCATTTTTT
1 ATTTTTTCATTTTTTATTTATTCATTTTTT
326372 CACTCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (30 bp):
ATTTTTTCATTTTTTATTTATTCATTTTTT
Found at i:341058 original size:18 final size:19
Alignment explanation
Indices: 341018--341061 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
341008 TTTGGTTCAC
* *
341018 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAG-G
341038 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
341056 GGAATA
1 GGAATA
341062 GGATTGCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:341283 original size:35 final size:36
Alignment explanation
Indices: 341213--341284 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
341203 GTTGAAAAAT
* * *
341213 ATTTATATATTTTCTTTAAAAAATTTAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAATTAAAATCATAAA
*
341249 ATTTATATAATTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAATT-AAAATCATAAA
341284 A
1 A
341285 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATAATTTCTTTAAAAAATTAAAATCATAAA
Found at i:341977 original size:16 final size:16
Alignment explanation
Indices: 341956--341993 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
341946 CCTGGTAAGA
341956 TTTCTTCTCCTCTCCC
1 TTTCTTCTCCTCTCCC
*
341972 TTTCTTCTCCTCTCGC
1 TTTCTTCTCCTCTCCC
341988 TTTCTT
1 TTTCTT
341994 TACAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTCTTCTCCTCTCCC
Done.