Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 97 of 126
Found at i:29698716 original size:11 final size:11
Alignment explanation
Indices: 29698700--29698750 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
29698690 CCAATCTTTA
29698700 ATTTTAAATTT
1 ATTTTAAATTT
29698711 ATTTTAAATTT
1 ATTTTAAATTT
29698722 A----AAATTT
1 ATTTTAAATTT
*
29698729 ATTCTAAATTT
1 ATTTTAAATTT
29698740 AATTTTAAATT
1 -ATTTTAAATT
29698751 GAGTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
7 7 0.21
11 18 0.53
12 9 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:29698722 original size:17 final size:17
Alignment explanation
Indices: 29698696--29698746 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
29698686 AAACCCAATC
*
29698696 TTTAATTTTAAATTTAT
1 TTTAAATTTAAATTTAT
29698713 TTTAAATTTAAAATTTAT
1 TTTAAATTT-AAATTTAT
* *
29698731 TCTAAATTTAATTTTA
1 TTTAAATTTAAATTTA
29698747 AATTGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:29698726 original size:18 final size:18
Alignment explanation
Indices: 29698699--29698741 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
29698689 CCCAATCTTT
* *
29698699 AATTTTAAATTTATTTTA
1 AATTTAAAATTTATTCTA
29698717 AATTTAAAATTTATTCTA
1 AATTTAAAATTTATTCTA
29698735 AATTTAA
1 AATTTAA
29698742 TTTTAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTAAAATTTATTCTA
Found at i:29699384 original size:9 final size:9
Alignment explanation
Indices: 29699372--29699405 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29699362 AAATACAATA
*
29699372 AATAATTTT
1 AATAATATT
29699381 AATAATATT
1 AATAATATT
*
29699390 AATAATAAT
1 AATAATATT
29699399 AATAATA
1 AATAATA
29699406 AAAGAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATAATATT
Found at i:29700468 original size:29 final size:30
Alignment explanation
Indices: 29700408--29700713 Score: 153
Period size: 29 Copynumber: 10.6 Consensus size: 30
29700398 CCCAAAAGGT
* *
29700408 CCCT-AAACTATCCAAAAATTACATTTTGA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
29700437 CCCTCAAACTTTCCAAAAATTACA-TTTAA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* * *
29700466 CCCTCAAACTTT-TAAAAACATACATTTTTA
1 CCCTCAAACTTTCCAAAAA-TTACATTTTAA
* * *
29700496 TCC-CATAAC-TTCTCAAAATTTATATTTT--
1 CCCTCA-AACTTTC-CAAAAATTACATTTTAA
* ** * *
29700524 TCCTCGTAC-TTCCAAAAATCACATTTTTA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
** * *
29700553 CCCTCGTA-TTTCCAAAAATAACATTTTTA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* * *
29700582 CCCT-ATACTTT-CAAAAATCACATTTTTA
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* ** * *
29700610 CCCCCGTAC-TACCAAAAATCACATTTT-A
1 CCCTCAAACTTTCCAAAAATTACATTTTAA
* *
29700638 CCCTCGAA-TTTCTCAAAAATTACATTTTTA
1 CCCTCAAACTTTC-CAAAAATTACATTTTAA
* * *
29700668 CCC-CTGAAC-TTCCAAAAATCACCATTTT-G
1 CCCTC-AAACTTTCCAAAAATTA-CATTTTAA
*
29700697 CCCTC-AATTTTCCAAAA
1 CCCTCAAACTTTCCAAAA
29700714 GTTCGACTTC
Statistics
Matches: 227, Mismatches: 29, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
27 12 0.05
28 46 0.20
29 114 0.50
30 51 0.22
31 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTACATTTTAA
Found at i:29700548 original size:86 final size:83
Alignment explanation
Indices: 29700420--29700695 Score: 252
Period size: 86 Copynumber: 3.2 Consensus size: 83
29700410 CTAAACTATC
* * ** * * *
29700420 CAAAAATTACATTTTGACCCTCAAACTTTCCAAAAATTACATTTAACCCTCAAACTTTTAAAAAC
1 CAAAAATCACATTTTTACCC-CGTAC-TTCCAAAAATCACATTTTACCCTCGAA-TTTTAAAAA-
29700485 ATACATTTTTATCCCATAACTTCT
62 ATACATTTTTA-CCC-TAACTTCT
* * * * * **
29700509 CAAAATTTATATTTTT-CCTCGTACTTCCAAAAATCACATTTTTACCCTCGTATTTCCAAAAATA
1 CAAAAATCACATTTTTACCCCGTACTTCCAAAAATCACA-TTTTACCCTCGAATTTTAAAAAAT-
29700573 ACATTTTTACCCTATACTT-T
64 ACATTTTTACCCTA-ACTTCT
* *
29700593 CAAAAATCACATTTTTACCCCCGTACTACCAAAAATCACATTTTACCCTCGAATTTCTCAAAAAT
1 CAAAAATCACATTTTTA-CCCCGTACTTCCAAAAATCACATTTTACCCTCGAATTT-T-AAAAAA
29700658 TACATTTTTACCCCTGAACTTC-
63 TACATTTTTA-CCCT-AACTTCT
29700680 CAAAAATCACCATTTT
1 CAAAAATCA-CATTTT
29700696 GCCCTCAATT
Statistics
Matches: 155, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
84 16 0.10
85 24 0.15
86 58 0.37
87 35 0.23
88 9 0.06
89 13 0.08
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (83 bp):
CAAAAATCACATTTTTACCCCGTACTTCCAAAAATCACATTTTACCCTCGAATTTTAAAAAATAC
ATTTTTACCCTAACTTCT
Found at i:29700669 original size:58 final size:56
Alignment explanation
Indices: 29700536--29700713 Score: 214
Period size: 57 Copynumber: 3.1 Consensus size: 56
29700526 CTCGTACTTC
* * * *
29700536 CAAAAATCACATTTTTACCCTCGTATTTCCAAAAATAACATTTTTACCCT-ATACTTT
1 CAAAAATCACATTTTTACCCCCGTACTTCCAAAAATCACA-TTTTACCCTCA-ATTTT
*
29700593 CAAAAATCACATTTTTACCCCCGTACTACCAAAAATCACATTTTACCCTCGAATTTCT
1 CAAAAATCACATTTTTACCCCCGTACTTCCAAAAATCACATTTTACCCTC-AATTT-T
* * * *
29700651 CAAAAATTACATTTTTACCCCTGAACTTCCAAAAATCACCATTTTGCCCTCAATTTT
1 CAAAAATCACATTTTTACCCCCGTACTTCCAAAAATCA-CATTTTACCCTCAATTTT
*
29700708 CCAAAA
1 CAAAAA
29700714 GTTCGACTTC
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
56 9 0.08
57 45 0.42
58 41 0.39
59 11 0.10
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (56 bp):
CAAAAATCACATTTTTACCCCCGTACTTCCAAAAATCACATTTTACCCTCAATTTT
Found at i:29713091 original size:39 final size:39
Alignment explanation
Indices: 29713028--29713855 Score: 601
Period size: 39 Copynumber: 21.4 Consensus size: 39
29713018 GAAGATTCTG
* * * *
29713028 ATCTCTTACCCCGAGTCTGAGGCAGATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* *
29713067 ATCTCTTACCCCGAGCCTGGGGCAGAT--TGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-CCAGTCA
* * * *
29713106 ATCTCTTACCCCGAGCTTGGGGCATATTATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * **
29713145 ATCTCTTACCCCAAGCCT-GGG--GATTA-CAGCCCTTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGTCA
* * *
29713181 ATCTCTTACCCCAAGCTTGGGGCAGATCATCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTC-A
* * ** * * **
29713220 ATCTCTTACCCCGAGCTTGGGGTAGATTGTAACCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * *
29713259 ATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* *
29713298 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTC-A
* ** * * **
29713337 ATCTCTTACCCCGAGCCTGGGGTA-ATTGTAACCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * *
29713375 ATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
** * * * *
29713414 ATCTCTTACCCCGAGCCTAAGGCAGATTAT-AGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGTCA
* * * * *
29713453 ATCTTTTACCCCGAGTCAGGGGCAGATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* ** * * *
29713492 ATCTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * *
29713531 ATCTCTTACCTCGAGCTTGGGGCAGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * * * ** * *
29713570 ATCTTTTACCCCGTGCTTGGGGCAGAT-TTCAGTAATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGTCA
** * * *
29713609 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * * *
29713648 ATCTCTTACCCCGAGCCTAGGACGGATCATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* * *
29713687 ATCTCTTACCCCGAGCCT-GGGCAGATTA-CAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGTCA
* * **
29713725 ATCTCTCACCCCGAGCTTGGGGCAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
* *
29713764 ATCTCTTACCCCAAGCCTGGGGCAGAT--TGCAACC-GTTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-C-ACCAG-TCA
* * * * **
29713803 ATCTCTTACACTGAGCCTGAGGCAGATCA-CAATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ACCAGTCA
29713842 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
29713856 TCATGGGGTA
Statistics
Matches: 608, Mismatches: 154, Indels: 54
0.75 0.19 0.07
Matches are distributed among these distances:
35 2 0.00
36 25 0.04
37 7 0.01
38 66 0.11
39 498 0.82
40 9 0.01
41 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCA
Found at i:29713306 original size:153 final size:153
Alignment explanation
Indices: 29713028--29713316 Score: 436
Period size: 153 Copynumber: 1.9 Consensus size: 153
29713018 GAAGATTCTG
* *
29713028 ATCTCTTACCCCGAGTCTGAGGCAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCCAAGTCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* * * * * *
29713093 TTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCATATTATCACCAGCCAATCTCTTACCCCA
66 TTGCAACCATTCGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCA
29713158 AGCCTGGGGATTACAGCCCTTCA
131 AGCCTGGGGATTACAGCCCTTCA
* * *
29713181 ATCTCTTACCCCAAG-CTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGTAG
1 ATCTCTTACCCCAAGTC-TGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAG
* *
29713245 ATTGTAACCATTTGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCC
65 ATTGCAACCATTCGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCC
*
29713310 GAGCCTG
130 AAGCCTG
29713317 AGGCAGATCA
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
152 1 0.01
153 120 0.99
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (153 bp):
ATCTCTTACCCCAAGTCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
TTGCAACCATTCGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCA
AGCCTGGGGATTACAGCCCTTCA
Found at i:29713344 original size:117 final size:116
Alignment explanation
Indices: 29713022--29713790 Score: 662
Period size: 117 Copynumber: 6.6 Consensus size: 116
29713012 CATATTGAAG
* * * *
29713022 ATTCTGATCTCTTACCCCGAGTCTGAGGCAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGG
1 ATTC-GATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGG
* * *
29713087 GGCAGATTGCAGCCATTC-G--ATCTCTTACCCCGAGCTTGGGGCATATTATCACC
65 GGCAGA-T-CA-TCA-TCAGCAATCTCTTACCCCGAGCTTGGGGCAGATTATAACC
** * * * ** * *
29713140 AGCCAATCTCTTACCCCAAGCCT-GGG--GATTA-CAGCCCTTCAATCTCTTACCCCAAGCTTGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGTCAATCTCTTACCCCGAGCCTGG
* *
29713201 GGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTGTAACC
65 GGCAGATCATCATCAGC-AATCTCTTACCCCGAGCTTGGGGCAGATTATAACC
* * * * *
29713254 ATTTGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGAG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
* * *
29713319 GCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGTA-ATTGTAACC
66 GCAGATCATCATCAGC-AATCTCTTACCCCGAGCTTGGGGCAGATTATAACC
* * * * **
29713370 ATTTGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTAAG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
* * * * * * * *
29713435 GCAGATTAT-AGTCATTCGATCTTTTACCCCGAG-TCAGGGGCAGATCATCATC
66 GCAGATCATCA-TCA-GCAATCTCTTACCCCGAGCT-TGGGGCAGATTATAACC
* ** * ** * * * * *
29713487 AGTAAATCTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCTCGAGCTTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
* * * ***
29713552 GCAGATCATCACCAGCCAATCTTTTACCCCGTGCTTGGGGCAGATT-TCAGTA
66 GCAGATCATCATCAG-CAATCTCTTACCCCGAGCTTGGGGCAGATTAT-AACC
** * * * *
29713604 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
* * * * * *
29713669 ACGGATCATCACCAGCCAATCTCTTACCCCGAGCCT-GGGCAGATTACAGCC
66 GCAGATCATCATCAG-CAATCTCTTACCCCGAGCTTGGGGCAGATTATAACC
* * ** *
29713720 ATTCGATCTCTCACCCCGAGCTTGGGGCAGATCATCACCAACCAATCTCTTACCCCAAGCCTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
29713785 GCAGAT
66 GCAGAT
29713791 TGCAACCGTT
Statistics
Matches: 536, Mismatches: 97, Indels: 38
0.80 0.14 0.06
Matches are distributed among these distances:
110 2 0.00
111 3 0.01
112 2 0.00
113 3 0.01
114 78 0.15
115 4 0.01
116 176 0.33
117 262 0.49
118 6 0.01
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (116 bp):
ATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGTCAATCTCTTACCCCGAGCCTGGG
GCAGATCATCATCAGCAATCTCTTACCCCGAGCTTGGGGCAGATTATAACC
Found at i:29713524 original size:272 final size:270
Alignment explanation
Indices: 29713028--29713855 Score: 1092
Period size: 272 Copynumber: 3.1 Consensus size: 270
29713018 GAAGATTCTG
* *
29713028 ATCTCTTACCCCGAGTCTGAGGCAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* * * * * * *
29713093 TTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCATATTATCACCAGCCAATCTCTTACCCCA
66 TTGTAACCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCG
* * * *
29713158 AGCCTGG-GGATTACAGCCCTTCAATCTCTTACCCCAAGCTTGGGGCAGATCATCATCAGCAAAT
131 AGCCTGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAAT
* * *
29713222 CTCTTACCCCGAGCTTGGGGTAGATTGTAACCATTTGATCTCTTACCCCGAACCTAGGGCAGATC
196 CTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCCCGAGCCT-GGGCAGATC
29713287 ATCACCAGCCA
260 ATCACCAGCCA
*
29713298 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGTA-A
1 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
* *
29713362 TTGTAACCATTTGATCTCTTACCCCGAACCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCG
66 TTGTAACCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCG
* * * * *
29713427 AGCCTAAGGCAGATTATAGTCATTCGATCTTTTACCCCGAG-TCAGGGGCAGATCATCATCAGTA
131 AGCCT--GGCAGATTACAGCCATTCGATCTCTTACCCCGAGCT-TGGGGCAGATCATCATCAGCA
* *
29713491 AATCTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCTCGAGCTTGGGGCAG
193 AATCTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCCCGAGCCT-GGGCAG
29713556 ATCATCACCAGCCA
257 ATCATCACCAGCCA
* * * * * * * *
29713570 ATCTTTTACCCCGTGCTTGGGGCAGAT-TTCAGTAATTC-GATCTCTTACCCCGAGCCTGGGGCA
1 ATCTCTTACCCCGAGCCTGAGGCAGATCATCA-TCA-GCAAATCTCTTACCCCGAGCCTGGGGCA
* *
29713633 GATTGTAACCATTCGATCTCTTACCCCGAGCCTAGGACGGATCATCACCAGCCAATCTCTTACCC
64 GATTGTAACCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCATCACCAGCCAATCTCTTACCC
* * * *
29713698 CGAGCCTGGGCAGATTACAGCCATTCGATCTCTCACCCCGAGCTTGGGGCAGATCATCACCAACC
129 CGAGCCT-GGCAGATTACAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCA
* * * * * *
29713763 AATCTCTTACCCCAAGCCTGGGGCAGATTGCAACCGTTCGATCTCTTACACTGAGCCTGAGGCAG
193 AATCTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCCCGAGCCTG-GGCAG
* *
29713828 ATCA-CAATCAACCA
257 ATCATC-ACCAGCCA
29713842 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
29713856 TCATGGGGTA
Statistics
Matches: 486, Mismatches: 62, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
269 62 0.13
270 60 0.12
271 8 0.02
272 287 0.59
273 69 0.14
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (270 bp):
ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGA
TTGTAACCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCATCACCAGCCAATCTCTTACCCCG
AGCCTGGCAGATTACAGCCATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAAT
CTCTTACCCCGAGCCTGGGGTAGATTGTAACCATTCGATCTCTTACCCCGAGCCTGGGCAGATCA
TCACCAGCCA
Found at i:29713848 original size:194 final size:192
Alignment explanation
Indices: 29713027--29713855 Score: 644
Period size: 194 Copynumber: 4.3 Consensus size: 192
29713017 TGAAGATTCT
* * * * ** *
29713027 GATCTCTTACCCCGAGTCTGAGGCAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGGGGCAG
1 GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGAGCCTAGGGCAG
** * * * ** *
29713092 AT--TGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGCATATTATCACCAGCCAATCTCTTACC
66 ATCAT-CA-CCAGCCAATCTCTTACCCCGAGCCT-GGGCAGATTA-CACCATTCGATCTCTTACC
* * * *** * * *
29713155 CCAAGCCT-GGG--GATTA-CAGCCCTTCAATCTCTTACCCCAAGCTTGGGGCAGATCATCATCA
127 CCGAGCTTGGGGCAGATCATCA-CCAACCAATCTCTTACCCCAAGCCTGGGGCAGAT--TCAACC
29713216 G--C
189 GTTC
* * * * * * * *
29713218 AAATCTCTTACCCCGAGCTTGGGGTAGATTGTAACCATTTGATCTCTTACCCCGAACCTAGGGCA
1 -GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGAGCCTAGGGCA
* * * *
29713283 GATCATCACCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATCA-GCAAATCTCTTACC
65 GATCATCACCAGCCAATCTCTTACCCCGAGCCTG-GGCAGATTA-CACCATTC-GATCTCTTACC
* * ** * **** *
29713347 CCGAGCCTGGGGTA-ATTGTAACCATTTGATCTCTTACCCCGAA-CCTAGGGCAGA-TCATCACC
127 CCGAGCTTGGGGCAGATCATCACCAACCAATCTCTTACCCC-AAGCCTGGGGCAGATTCA--ACC
*
29713409 AG-CC
189 -GTTC
* * * * *
29713413 AATCTCTTACCCCGAGCCTAAGGCAGATTATAGTCATTCGATCTTTTACCCCGAGTC-AGGGGCA
1 GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGAGCCTA-GGGCA
* ** *
29713477 GATCATCATCAGTAAATCTCTTACCCCGAGCCTGGGGTAGATTGTA-ACCATTCGATCTCTTACC
65 GATCATCACCAGCCAATCTCTTACCCCGAGCCT-GGGCAGA-T-TACACCATTCGATCTCTTACC
* * * ** * ****
29713541 TCGAGCTTGGGGCAGATCATCACCAGCCAATCTTTTACCCCGTGCTTGGGGCAGATTTCAGTAAT
127 CCGAGCTTGGGGCAGATCATCACCAACCAATCTCTTACCCCAAGCCTGGGGCAGA-TTCAACCGT
29713606 TC
191 TC
* * * * *
29713608 GATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTCTTACCCCGAGCCTAGGACGG
1 GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGAGCCTAGGGCAG
*
29713673 ATCATCACCAGCCAATCTCTTACCCCGAGCCTGGGCAGATTACAGCCATTCGATCTCTCACCCCG
66 ATCATCACCAGCCAATCTCTTACCCCGAGCCTGGGCAGATTACA-CCATTCGATCTCTTACCCCG
29713738 AGCTTGGGGCAGATCATCACCAACCAATCTCTTACCCCAAGCCTGGGGCAGATTGCAACCGTTC
130 AGCTTGGGGCAGATCATCACCAACCAATCTCTTACCCCAAGCCTGGGGCAGATT-CAACCGTTC
* * * * ** *
29713802 GATCTCTTACACTGAGCCTGAGGCAGATCACAATCAACCAATCTCTTACCCCGA
1 GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGA
29713856 TCATGGGGTA
Statistics
Matches: 504, Mismatches: 106, Indels: 52
0.76 0.16 0.08
Matches are distributed among these distances:
191 5 0.01
192 106 0.21
193 11 0.02
194 260 0.52
195 117 0.23
196 2 0.00
197 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (192 bp):
GATCTCTTACCCCGAGCCTGAGGCAGATTATAATCATTCGATCTCTTACCCCGAGCCTAGGGCAG
ATCATCACCAGCCAATCTCTTACCCCGAGCCTGGGCAGATTACACCATTCGATCTCTTACCCCGA
GCTTGGGGCAGATCATCACCAACCAATCTCTTACCCCAAGCCTGGGGCAGATTCAACCGTTC
Found at i:29715927 original size:25 final size:24
Alignment explanation
Indices: 29715890--29716061 Score: 176
Period size: 23 Copynumber: 7.3 Consensus size: 24
29715880 ACACTAGCGC
*
29715890 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GT
29715913 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
* *
29715938 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
29715961 ACTCTCTATTATTAGCACTGTGTGT
1 GCTCTCT-GTATTAGCACTGTGTGT
* *
29715986 GCTCTCTG-ATTAGCACTTTGTAT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
29716009 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
* *
29716032 ACTCTTTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
29716055 GCTCTCT
1 GCTCTCT
29716062 ATTGCCCAGC
Statistics
Matches: 124, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
23 84 0.68
24 1 0.01
25 36 0.29
26 3 0.02
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:29715967 original size:48 final size:48
Alignment explanation
Indices: 29715914--29716110 Score: 197
Period size: 48 Copynumber: 4.2 Consensus size: 48
29715904 ACGTCTCGTG
*
29715914 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
* * *
29715962 CTCTCTATTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTATG
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
* * * * * * *
29716010 CTCTCTG--ATTAGTACTTTGTGTACTCTTTGTTTAGCACTGTGTGTG
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
* *** * *
29716056 CTCTCTATTGCCCAGCACT-TATGTGCTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTT-ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
29716102 CTCTCTGTT
1 CTCTCTGTT
29716111 TGTTCCGTAT
Statistics
Matches: 122, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
46 48 0.39
47 9 0.07
48 60 0.49
49 5 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (48 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTA
Found at i:29716012 original size:71 final size:69
Alignment explanation
Indices: 29715891--29716111 Score: 253
Period size: 71 Copynumber: 3.2 Consensus size: 69
29715881 CACTAGCGCG
* *
29715891 CTCTC-TGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGTAC
1 CTCTCTTGTTTAGCACTGTGT-GTGCTCTCTG--ATTAGCACTTTGT-TGCTCTCTGATTAGTAC
29715954 TTTGTGTA
62 TTTGTGTA
29715962 CTCTCTAT-TATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTATGCTCTCTGATTAGTACT
1 CTCTCT-TGT-TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT-TGCTCTCTGATTAGTACT
29716026 TTGTGTA
63 TTGTGTA
29716033 CTCT-TTGTTTAGCACTGTGTGTGCTCTCT-ATTGCCCAGCACTTATG-TGCTCTCTG-TTAGTA
1 CTCTCTTGTTTAGCACTGTGTGTGCTCTCTGATT----AGCACTT-TGTTGCTCTCTGATTAGTA
29716094 CTTTG-GTA
61 CTTTGTGTA
29716102 CTCTC-TGTTT
1 CTCTCTTGTTT
29716112 GTTCCGTATA
Statistics
Matches: 136, Mismatches: 3, Indels: 24
0.83 0.02 0.15
Matches are distributed among these distances:
68 3 0.02
69 34 0.25
70 13 0.10
71 55 0.40
72 8 0.06
73 20 0.15
74 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (69 bp):
CTCTCTTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:29716647 original size:6 final size:6
Alignment explanation
Indices: 29716624--29716694 Score: 81
Period size: 6 Copynumber: 11.5 Consensus size: 6
29716614 CAAACCCAAT
* * *
29716624 ATTTAA TTTTAA ATTTTAA ATTT-A TTTTAA GTTTAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
29716673 ATTTAAA ATTTAA ATTTAA ATT
1 ATTT-AA ATTTAA ATTTAA ATT
29716695 GAGTTTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
5 4 0.07
6 34 0.60
7 19 0.33
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:29716652 original size:24 final size:23
Alignment explanation
Indices: 29716625--29716694 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 23
29716615 AAACCCAATA
*
29716625 TTTAATTTTAAATTTTAAATTTAT
1 TTTAAGTTTAAA-TTTAAATTTAT
29716649 TTTAAGTTTAAATTTAAATTTAAAAT
1 TTTAAGTTTAAATTTAAATTT---AT
* *
29716675 TTAAAATTTAAATTTAAATT
1 TTTAAGTTTAAATTTAAATT
29716695 GAGTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.22
24 11 0.28
26 20 0.50
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTAAGTTTAAATTTAAATTTAT
Found at i:29717352 original size:15 final size:15
Alignment explanation
Indices: 29717332--29717397 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
29717322 TAAATAATTT
* *
29717332 TAATAACAAAAACAA
1 TAATAACAATAATAA
*
29717347 TAATAATAATAATAA
1 TAATAACAATAATAA
*
29717362 TAATAATAATAATAA
1 TAATAACAATAATAA
29717377 TAATAACAATAATAA
1 TAATAACAATAATAA
29717392 TAATAA
1 TAATAA
29717398 AGAAGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAACAATAATAA
Found at i:29717353 original size:3 final size:3
Alignment explanation
Indices: 29717345--29717397 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
29717335 TAACAAAAAC
*
29717345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29717393 AAT AA
1 AAT AA
29717398 AGAAGTCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29718516 original size:28 final size:28
Alignment explanation
Indices: 29718405--29718694 Score: 203
Period size: 28 Copynumber: 10.0 Consensus size: 28
29718395 GAGGTCTCTA
* * * *
29718405 AACTGTCCAAAAATTACATTTTAACCTTCA
1 AACT-TCCAAAAATCACATTTT-TCCCTCG
* *
29718435 AACTTCTTAAAAATTACATTTTTATCCCT-G
1 AACTTC-CAAAAATCACA-TTTT-TCCCTCG
* *
29718465 AACTTCTAAAAAATTACATTTTTTCCCTCG
1 AACTTC-CAAAAATCACA-TTTTTCCCTCG
29718495 AACTTCCAAAAATCACATTTTTACCC-CG
1 AACTTCCAAAAATCACATTTTT-CCCTCG
* * *
29718523 TACTTCCAAAAATCACATTTTACCCCCG
1 AACTTCCAAAAATCACATTTTTCCCTCG
*
29718551 TACTTCCAAAAATCACATTTTTACTCCT-G
1 AACTTCCAAAAATCACATTTTT-C-CCTCG
* *
29718580 TACTTTCAAAAATCACATTTTTACCCT-G
1 AACTTCCAAAAATCACATTTTT-CCCTCG
* ** *
29718608 TACTTCCAAAAGGCACATTTTTACCCTCA
1 AACTTCCAAAAATCACATTTTT-CCCTCG
* *
29718637 AACTTCTCAAAAATTACATTTCTACCC-CTG
1 AACTTC-CAAAAATCACATTT-TTCCCTC-G
* *
29718667 AACTTCCAAAAATTACCATTTTACCCTC
1 AACTTCCAAAAATCA-CATTTTTCCCTC
29718695 AATTTTTCAA
Statistics
Matches: 225, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
27 3 0.01
28 78 0.35
29 64 0.28
30 71 0.32
31 9 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
AACTTCCAAAAATCACATTTTTCCCTCG
Found at i:29718583 original size:57 final size:58
Alignment explanation
Indices: 29718443--29718693 Score: 269
Period size: 57 Copynumber: 4.3 Consensus size: 58
29718433 CAAACTTCTT
* * * * *
29718443 AAAAATTACATTTTTATCCCTGAACTTCTAAAAAATTACATTTTTTCCCTCGAACTTCC
1 AAAAATCACATTTTTA-CCCTGAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCC
* * *
29718502 AAAAATCACATTTTTACCCCGTACTTC-CAAAAATCACA-TTTTACCCCCGTACTTCC
1 AAAAATCACATTTTTACCCTGAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCC
* * *
29718558 AAAAATCACATTTTTACTCCTGTACTT-TCAAAAATCACATTTTTA-CCCTGTACTTCC
1 AAAAATCACATTTTTAC-CCTGAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCC
** * * * *
29718615 AAAAGGCACATTTTTACCCTCAAACTTCTCAAAAATTACATTTCTACCCCTGAACTTCC
1 AAAAATCACATTTTTACCCT-GAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCC
*
29718674 AAAAATTACCA-TTTTACCCT
1 AAAAATCA-CATTTTTACCCT
29718694 CAATTTTTCA
Statistics
Matches: 165, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
56 35 0.21
57 58 0.35
58 30 0.18
59 40 0.24
60 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAAATCACATTTTTACCCTGAACTTCTCAAAAATCACATTTTTACCCCCGAACTTCC
Found at i:29718705 original size:29 final size:27
Alignment explanation
Indices: 29718412--29718706 Score: 90
Period size: 29 Copynumber: 10.2 Consensus size: 27
29718402 CTAAACTGTC
*
29718412 CAAAAATTACATTTTAACCTTCAAACTTCTT
1 CAAAAATTACATTTT-ACCCTC-AA-TT-TT
* *
29718443 -AAAAATTACATTTTTATCCCTGAACTTCT
1 CAAAAATTACA-TTTTA-CCCTCAA-TTTT
* * * *
29718472 AAAAAATTACATTTTTTCCCTCGAACTTC
1 CAAAAATTACA-TTTTACCCTC-AATTTT
* * * *
29718501 CAAAAATCACATTTTTACCC-CGTACTTC
1 CAAAAATTACA-TTTTACCCTC-AATTTT
* * * * *
29718529 CAAAAATCACATTTTACCCCCGTACTTC
1 CAAAAATTACATTTTACCCTC-AATTTT
* ** *
29718557 CAAAAATCACATTTTTACTCCTGTACTTT
1 CAAAAATTACA-TTTTAC-CCTCAATTTT
* ** * *
29718586 CAAAAATCACATTTTTACCCTGTACTTC
1 CAAAAATTACA-TTTTACCCTCAATTTT
*** *
29718614 CAAAAGGCACATTTTTACCCTCAAACTTCT
1 CAAAAATTACA-TTTTACCCTC-AA-TTTT
* * *
29718644 CAAAAATTACATTTCTACCCCTGAACTTC
1 CAAAAATTACATTT-TA-CCCTCAATTTT
29718673 CAAAAATTACCATTTTACCCTCAATTTTT
1 CAAAAATTA-CATTTTACCCTCAA-TTTT
29718702 CAAAA
1 CAAAA
29718707 GTTCGACTTC
Statistics
Matches: 218, Mismatches: 33, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
27 8 0.04
28 71 0.33
29 75 0.34
30 53 0.24
31 11 0.05
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (27 bp):
CAAAAATTACATTTTACCCTCAATTTT
Found at i:29719060 original size:16 final size:16
Alignment explanation
Indices: 29719039--29719069 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29719029 TCGAGGCAAT
29719039 GTCCTTTTCGTGTGAG
1 GTCCTTTTCGTGTGAG
29719055 GTCCTTTTCGTGTGA
1 GTCCTTTTCGTGTGA
29719070 AAACCTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.29, T:0.45
Consensus pattern (16 bp):
GTCCTTTTCGTGTGAG
Found at i:29721553 original size:15 final size:16
Alignment explanation
Indices: 29721533--29721562 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29721523 CAATGTTAGC
29721533 AAAAGCAT-AATCCCA
1 AAAAGCATGAATCCCA
29721548 AAAAGCATGAATCCC
1 AAAAGCATGAATCCC
29721563 TGTTTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.27, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAGCATGAATCCCA
Found at i:29724870 original size:15 final size:15
Alignment explanation
Indices: 29724850--29724878 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29724840 AAGTGCTTTC
29724850 GAGAGGTGGAGCTAT
1 GAGAGGTGGAGCTAT
29724865 GAGAGGTGGAGCTA
1 GAGAGGTGGAGCTA
29724879 ATTATATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.48, T:0.17
Consensus pattern (15 bp):
GAGAGGTGGAGCTAT
Found at i:29726608 original size:29 final size:29
Alignment explanation
Indices: 29726552--29726608 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
29726542 GATAATACAA
* * *
29726552 ATACTTGAATATGTCTAAGTTAATTAAAT
1 ATACATGAATATGTCTAAATTAAATAAAT
29726581 ATACATGAATATGTC-AAATCTAAATAAA
1 ATACATGAATATGTCTAAAT-TAAATAAA
29726609 ATCAATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (29 bp):
ATACATGAATATGTCTAAATTAAATAAAT
Found at i:29731399 original size:3 final size:3
Alignment explanation
Indices: 29731391--29731435 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
29731381 CCTTGCACTT
*
29731391 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
29731436 GTTATGGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:29734703 original size:38 final size:39
Alignment explanation
Indices: 29734647--29734739 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 39
29734637 GGAAATTGGA
* *
29734647 AATTAAAATAA-TATAATAATTTTATATTTC-AAAAAA-
1 AATTATAATAATTTTAATAATTTTATATTTCAAAAAAAT
29734683 AATATATAATAATTTTAATAATTTTATATTTCAAAAAAAT
1 AAT-TATAATAATTTTAATAATTTTATATTTCAAAAAAAT
*
29734723 AATTTTAATAATTTTAA
1 AATTATAATAATTTTAA
29734740 AATCATTTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
36 3 0.06
37 7 0.14
38 18 0.36
39 19 0.38
40 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (39 bp):
AATTATAATAATTTTAATAATTTTATATTTCAAAAAAAT
Found at i:29734732 original size:39 final size:38
Alignment explanation
Indices: 29734660--29734739 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
29734650 TAAAATAATA
29734660 TAATAATTTTATATTTCAAAAAAAATATATAATAATTT
1 TAATAATTTTATATTTCAAAAAAAATATATAATAATTT
*
29734698 TAATAATTTTATATTTC-AAAAAAATAATTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAAAAT-A-TATAATAATTT
29734737 TAA
1 TAA
29734740 AATCATTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 8 0.21
38 18 0.46
39 13 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (38 bp):
TAATAATTTTATATTTCAAAAAAAATATATAATAATTT
Found at i:29736496 original size:29 final size:28
Alignment explanation
Indices: 29736463--29736724 Score: 136
Period size: 29 Copynumber: 9.0 Consensus size: 28
29736453 TTTGGTGAAA
*
29736463 TTGGGGTCAAAAATAGAATTTTAGAAAAT
1 TTGGGGTC-AAAATGGAATTTTAGAAAAT
* * *
29736492 TTGGGGCCAAAATGGAACTTTGGAAAATT
1 TTGGGGTCAAAATGGAATTTTAGAAAA-T
29736521 TTGGGGT-AAAATGGTAATTTT-GAATAAT
1 TTGGGGTCAAAATGG-AATTTTAGAA-AAT
** *
29736549 TCAAGGGT-AAAATGGTAAATTTTGGTAAAA-
1 T-TGGGGTCAAAATGG--AATTTTAG-AAAAT
* * * *
29736579 TCGAGGTTAAAAATGGAATTTTAGGAAACT
1 TTG-GGGTCAAAATGGAATTTTA-GAAAAT
* * *
29736609 TGGGGGTCAAAATGAAATTTTAGAAAGTT
1 TTGGGGTCAAAATGGAATTTTAGAAA-AT
* ** *
29736638 TTAGGGTCAAAATATAATTTTGGAAAAGT
1 TTGGGGTCAAAATGGAATTTTAGAAAA-T
* * *
29736667 TTAGGAGTCAAAATGTAATTTGTAGAAAGTT
1 TT-GGGGTCAAAATGGAATTT-TAGAAA-AT
* ** *
29736698 TTTGGGTCAAAATATAATTTTGGAAAA
1 TTGGGGTCAAAATGGAATTTTAGAAAA
29736725 GTTTAAGGGT
Statistics
Matches: 182, Mismatches: 35, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
28 32 0.18
29 87 0.48
30 43 0.24
31 18 0.10
32 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (28 bp):
TTGGGGTCAAAATGGAATTTTAGAAAAT
Found at i:29736503 original size:28 final size:30
Alignment explanation
Indices: 29736463--29736531 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 30
29736453 TTTGGTGAAA
*
29736463 TTGGGGTCAAAAATAGAATTTTAGAAAA-T
1 TTGGGGTCAAAAATAGAACTTTAGAAAATT
* * *
29736492 TTGGGG-CCAAAATGGAACTTTGGAAAATT
1 TTGGGGTCAAAAATAGAACTTTAGAAAATT
29736521 TTGGGGT-AAAA
1 TTGGGGTCAAAA
29736532 TGGTAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (30 bp):
TTGGGGTCAAAAATAGAACTTTAGAAAATT
Found at i:29736591 original size:116 final size:117
Alignment explanation
Indices: 29736436--29736659 Score: 281
Period size: 116 Copynumber: 1.9 Consensus size: 117
29736426 TGGATACCCG
* * * * *
29736436 AGGGCAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATAGAATTTTA-GAAAATTTGGGGCC
1 AGGGCAAAATGGTAAATTTTGGTAAAATCGAGGTCAAAAATAGAATTTTAGGAAAATTGGGGGCC
* * * *
29736500 AAAATGGAACTTTGGAAAATTTTGGGGT-AAAATGGTAATTTTGAATAATTCA
66 AAAATGAAACTTTAGAAAATTTTAGGGTCAAAAT-ATAATTTTGAATAATTCA
* * * * *
29736552 AGGGTAAAATGGTAAATTTTGGTAAAATCGAGGTTAAAAATGGAATTTTAGGAAACTTGGGGGTC
1 AGGGCAAAATGGTAAATTTTGGTAAAATCGAGGTCAAAAATAGAATTTTAGGAAAATTGGGGGCC
* *
29736617 AAAATGAAATTTTAGAAAGTTTTAGGGTCAAAATATAATTTTG
66 AAAATGAAACTTTAGAAAATTTTAGGGTCAAAATATAATTTTG
29736660 GAAAAGTTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
116 43 0.48
117 42 0.47
118 5 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (117 bp):
AGGGCAAAATGGTAAATTTTGGTAAAATCGAGGTCAAAAATAGAATTTTAGGAAAATTGGGGGCC
AAAATGAAACTTTAGAAAATTTTAGGGTCAAAATATAATTTTGAATAATTCA
Found at i:29736668 original size:30 final size:30
Alignment explanation
Indices: 29736612--29736848 Score: 221
Period size: 30 Copynumber: 7.9 Consensus size: 30
29736602 GGAAACTTGG
*
29736612 GGGTCAAAATGA-AATTTTAG-AAAGTTTTA
1 GGGTCAAAAT-ATAATTTTGGAAAAGTTTTA
29736641 GGGTCAAAATATAATTTTGGAAAAG-TTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTA
* * *
29736670 GGAGTCAAAATGTAA-TTTGTAGAAAGTTTTT
1 GG-GTCAAAATATAATTTTGGA-AAAGTTTTA
*
29736701 GGGTCAAAATATAATTTTGGAAAAGTTTAA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTA
* * * ** *
29736731 GGGTTAAAATGTATTTTTCAAAAAGTGTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTA
* * * *
29736761 GGGTTAAAATATAATTTTAGAGAAGTTTAA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTA
* * **
29736791 GGGTTAAAATGTAATTTTCAAAAAGTTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTTA
* * *
29736821 GGGTTAAAACATAATTTTGGAGAAGTTT
1 GGGTCAAAATATAATTTTGGAAAAGTTT
29736849 GAGGACTTTT
Statistics
Matches: 170, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.01
29 28 0.16
30 131 0.77
31 10 0.06
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTTA
Found at i:29736705 original size:60 final size:60
Alignment explanation
Indices: 29736612--29736848 Score: 309
Period size: 60 Copynumber: 4.0 Consensus size: 60
29736602 GGAAACTTGG
* *
29736612 GGGTCAAAATGAAATTTT-AGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTT-A
1 GGGTCAAAATGTAATTTTCAAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
* *
29736670 GGAGTCAAAATGTAATTTGT-AGAAAGTTTTTGGGTCAAAATATAATTTTGGAAAAGTTTAA
1 GG-GTCAAAATGTAATTT-TCAAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
* * * * * *
29736731 GGGTTAAAATGTATTTTTCAAAAAGTGTTAGGGTTAAAATATAATTTTAGAGAAGTTTAA
1 GGGTCAAAATGTAATTTTCAAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
* * * *
29736791 GGGTTAAAATGTAATTTTCAAAAAGTTTTAGGGTTAAAACATAATTTTGGAGAAGTTT
1 GGGTCAAAATGTAATTTTCAAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTT
29736849 GAGGACTTTT
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
58 2 0.01
59 15 0.09
60 141 0.88
61 3 0.02
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (60 bp):
GGGTCAAAATGTAATTTTCAAAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
Found at i:29736740 original size:90 final size:90
Alignment explanation
Indices: 29736612--29736853 Score: 269
Period size: 90 Copynumber: 2.7 Consensus size: 90
29736602 GGAAACTTGG
*
29736612 GGGTCAAAATGA-AATTTTAG-AAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGAGT
1 GGGTCAAAAT-ATAATTTTAGAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGTTTAGGAGT
* **
29736675 CAAAATGTAATTTGTAGA-AAGTTTTT
65 CAAAATATAATTT-TAGAGAAGTTTAA
* * * * **
29736701 GGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTATTTTTCAAAAAGTGTTAGG-GT
1 GGGTCAAAATATAATTTTAGAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGT-TTAGGAGT
*
29736765 TAAAATATAATTTTAGAGAAGTTTAA
65 CAAAATATAATTTTAGAGAAGTTTAA
* * * *
29736791 GGGTTAAAATGTAATTTTCA-AAAAGTTTTAGGGTTAAAACATAATTTTGGAGAAGTTTGAGGA
1 GGGTCAAAATATAATTTT-AGAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGTTT-AGGA
29736854 CTTTTAGGGC
Statistics
Matches: 125, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
88 1 0.01
89 23 0.18
90 96 0.77
91 5 0.04
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (90 bp):
GGGTCAAAATATAATTTTAGAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGTTTAGGAGTC
AAAATATAATTTTAGAGAAGTTTAA
Found at i:29738336 original size:17 final size:16
Alignment explanation
Indices: 29738314--29738403 Score: 99
Period size: 17 Copynumber: 5.3 Consensus size: 16
29738304 GGACATTTTG
*
29738314 TTAAATTTATAATAATT
1 TTAAATTTA-AATAAAT
29738331 TTAAATTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
**
29738348 CCAAATTTAAATTAAAT
1 TTAAATTTAAA-TAAAT
29738365 TTAAATTTAAGATAAAT
1 TTAAATTTAA-ATAAAT
*
29738382 TTAATTTTAAAATAAAT
1 TTAAATTT-AAATAAAT
29738399 TTAAA
1 TTAAA
29738404 ATGGTTTGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
16 2 0.03
17 58 0.92
18 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:29738341 original size:6 final size:6
Alignment explanation
Indices: 29738330--29738403 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
29738320 TTATAATAAT
**
29738330 TTTAAA TTTAAA -TTAAA TCCAAA TTTAAA -TTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
29738377 --TAAA TTTAAT TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29738404 ATGGTTTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 1 0.02
5 17 0.31
6 35 0.65
7 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:29738345 original size:11 final size:11
Alignment explanation
Indices: 29738330--29738403 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
29738320 TTATAATAAT
29738330 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
29738342 -TTAAATCCAAA
1 TTTAAAT-TAAA
29738353 TTTAAATTAAA
1 TTTAAATTAAA
*
29738364 TTTAAATTTAA
1 TTTAAATTAAA
** *
29738375 GATAAATTTAAT
1 TTTAAA-TTAAA
*
29738387 TTTAAAATAAA
1 TTTAAATTAAA
29738398 TTTAAA
1 TTTAAA
29738404 ATGGTTTGGT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
10 1 0.02
11 34 0.71
12 13 0.27
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:29738381 original size:28 final size:29
Alignment explanation
Indices: 29738326--29738403 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
29738316 AAATTTATAA
*
29738326 TAATTTTAAATTTAAA-TTAAATCCAAATT
1 TAATATTAAATTTAAATTTAAAT-CAAATT
29738355 TAA-ATTAAATTTAAATTTAAGAT-AAATT
1 TAATATTAAATTTAAATTTAA-ATCAAATT
* *
29738383 TAATTTTAAA-ATAAATTTAAA
1 TAATATTAAATTTAAATTTAAA
29738404 ATGGTTTGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 28 0.65
29 12 0.28
30 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TAATATTAAATTTAAATTTAAATCAAATT
Found at i:29738708 original size:39 final size:39
Alignment explanation
Indices: 29738665--29738758 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 39
29738655 GTTGATGGTG
29738665 ATCTGCCCCAGGCTCGGAAG-AAGAGATCAAATGGCT-TT
1 ATCTGCCCCAGGCTCGG-AGTAAGAGATCAAATGGCTATT
* * *
29738703 AATCTG-CCCAAGCTCGGGGTAAGAGATCGAATGGCTATT
1 -ATCTGCCCCAGGCTCGGAGTAAGAGATCAAATGGCTATT
*
29738742 ATCTGCCCCAGACTCGG
1 ATCTGCCCCAGGCTCGG
29738759 GTTATGAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.02
38 30 0.64
39 16 0.34
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.21
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGAGTAAGAGATCAAATGGCTATT
Found at i:29738727 original size:38 final size:39
Alignment explanation
Indices: 29738685--29738768 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 39
29738675 GGCTCGGAAG
29738685 AAGAGATCAAATGGCT-TTAATCTGCCCAAG-CTCGGGGT
1 AAGAGATCAAATGGCTATT-ATCTGCCCAAGACTCGGGGT
* * *
29738723 AAGAGATCGAATGGCTATTATCTGCCCCAGACTCGGGTT
1 AAGAGATCAAATGGCTATTATCTGCCCAAGACTCGGGGT
*
29738762 ATGAGAT
1 AAGAGAT
29738769 TGATTGACGG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 25 0.62
39 15 0.38
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (39 bp):
AAGAGATCAAATGGCTATTATCTGCCCAAGACTCGGGGT
Found at i:29739452 original size:100 final size:100
Alignment explanation
Indices: 29739120--29741382 Score: 3400
Period size: 100 Copynumber: 22.6 Consensus size: 100
29739110 CCGGGTTTGT
* * * * * * * *
29739120 CGTTGCGACTTAAACCTTTCCCTTCA-AATCTTCGTGGTATTAGATCCGCCGTTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29739184 TCCTTT-CCTTCCTGTTTCTGAGGTACACGGTCCGC
66 T-CTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * * * * **
29739219 CGTTACAACTTAGACCTTTCCCTTTTGTATCTTTACGGTACTGGATCCACCATTGAAGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
29739284 TCTTTCCCGTCGTGTCTTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGT-TTCTGAGGTACACGGTCCGC
* * * * *
29739320 CGTTACGACTTAGACCTTTCCCTTTAGTATCTTTACGGTACTAGATCCACAATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29739385 TCTTTTCCGTCGTGTTTCTAAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* ** *
29739420 CGTTGCGACTTAGACCTTTCCCTTTAGAATCTTTGCGGTACTGGATCCATCATTGCGGTCATAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29739485 TCTTTCCCGTCGTGTTTCTGAGGTACACGATCCAC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* *
29739520 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGATACTGGATCCGCCATTGCGGTCTTAAA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * * *
29739585 TCTTTCCCGTCGTGTTTCTGAGATACGCAGTCCGA
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
29739620 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * * **
29739685 TCTTTCCCGTCGTGTTTCTAAGGTACGCAGTTGGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29739720 CGTTGTGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTATTGGAACCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29739785 TCTTTCCCGTCGTGTTTCTGAGGTACACAGTCCAC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * * *
29739820 CGTTGTGACTTAGACCTTTCCCTTTAATATCTTTGCGGTACTGGATCCGTCATTGCGGTCTTAAA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * *
29739885 TATTTCTCGTCGTGTTTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29739920 CG-TACGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTCCGATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
** * * *
29739984 TCTTTCTAGTCGTGTTTCTGAGGTACACGATTCAC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
*
29740019 CGTTGCGACTTAGA-CTTTCCCCTTTAGTATCTTTACGGTACTGGATCCGCCATTGCGGTCTTAG
1 CGTTGCGACTTAGACCTTT-CCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAG
*
29740083 ATCTTTCCCGTCGTGTTCCTGAGGTACACGGTCCGC
65 ATCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* *
29740119 CGTTGCGACATAGACCTTTCCCTTTAGTATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * *
29740184 TCTTTCCCGTTGTGTTTCTGAGGTACGCAGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29740219 CGTTGCGACTTAGACATTTCCCTTTAGTATCTTTGCGGTATTAGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
29740284 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCTGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29740319 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGATACTGGATTCGCTATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
29740384 TCTTTCCCGTCGTGTTTCTGAGGTACACGATCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29740419 CGTTGCGACTTAAACCTTTCCCTTTAGTATCTTTGCGATACTGGATCCGTCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * *
29740484 TCTTTCCTGTCATGTTTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29740519 CGTTACGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTTCTGGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * * *
29740584 TCTTTCTCGTCTTGTTTTTGAGGTACACGGTTCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * *
29740619 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGATACTGGATCCGCCATTGCAGTTTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * *
29740684 TCTTTCCCGTCGTGTTTTTGAGGTACACGATCTGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
*
29740719 CGTTACGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29740784 TCTTTCCCGTCGTGTTTCTGAGGTACGCAGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* *
29740819 CGTTGTGACTTAAACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
29740884 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * * *
29740919 CGTTGCGAGTTAGACCTTTCCCTTTAGTATCTTTGCGATACTGGATCCACCATTACGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
29740984 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* *
29741019 CGTTGCGATTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGTCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
29741084 TCTTTCCCGTCGTGTTTCTGAGGTACATGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
*
29741119 CGTTGCGACTTAAACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
29741184 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* * * *
29741219 CGTTGTGACTTAAACCTTTCCCTTTAGTATCTGTGCGGTACTGGATCTGCCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
29741284 TCTTTCTCGTCGTGTTTTTGAGGTACACGGTCCGC
66 TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
* ** *
29741319 CGTTGCGACTTAGACGTTTCCCTTTAGTATCTTTGTAGTACTGGATCCGCCGTTGCGGTCTTAG
1 CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAG
29741383 GTTTTTCCTT
Statistics
Matches: 1964, Mismatches: 194, Indels: 11
0.91 0.09 0.01
Matches are distributed among these distances:
99 115 0.06
100 1753 0.89
101 96 0.05
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (100 bp):
CGTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
TCTTTCCCGTCGTGTTTCTGAGGTACACGGTCCGC
Found at i:29742694 original size:12 final size:14
Alignment explanation
Indices: 29742678--29742710 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29742668 TTTCTTCTTG
29742678 TTTTTTGCTTT-TC
1 TTTTTTGCTTTCTC
*
29742691 TTTTTTTCTTTCTC
1 TTTTTTGCTTTCTC
29742705 TTTTTT
1 TTTTTT
29742711 TATTGAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTGCTTTCTC
Found at i:29742706 original size:14 final size:14
Alignment explanation
Indices: 29742666--29742711 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
29742656 TTTTATTTTA
29742666 TTTTTC-TTCT-TGT
1 TTTTTCTTTCTCT-T
29742679 TTTTTGCTTT-TCTT
1 TTTTT-CTTTCTCTT
29742693 TTTTTCTTTCTCTT
1 TTTTTCTTTCTCTT
29742707 TTTTT
1 TTTTT
29742712 ATTGAATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.31
14 17 0.59
15 3 0.10
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTCTCTT
Found at i:29748125 original size:29 final size:28
Alignment explanation
Indices: 29748093--29748434 Score: 139
Period size: 29 Copynumber: 11.6 Consensus size: 28
29748083 GGATACTCGA
*
29748093 GGGTAAAATGGTAATTTTTGGTGAAA-TTG
1 GGGTAAAATGGTAA-TTTTGG-AAAATTTG
*
29748122 GGGTCAAAAATAG-AATTTTGGAAAATTTG
1 GGGT--AAAATGGTAATTTTGGAAAATTTG
* * * *
29748151 AGGTCAAAATGG-AACTCTGGGAAATTTTG
1 GGGT-AAAATGGTAA-TTTTGGAAAATTTG
*
29748180 GGGTAAAATGGTAATTTTGGAAAATTCAG
1 GGGTAAAATGGTAATTTTGGAAAATT-TG
* * *
29748209 GTGTAAAATGGTAAATTTTGGTAAGA-TCG
1 GGGTAAAATGGT-AATTTTGG-AAAATTTG
* * *
29748238 GGGTTAAAAATAG-AATTTTAGGAAACTTAG
1 GGG-T-AAAATGGTAATTTT-GGAAAATTTG
* * *
29748268 GGGTAAAAAT-GTAATTTTAGAAAGTTTTA
1 GGGT-AAAATGGTAATTTTGGAAA-ATTTG
* *
29748297 GGGTCAAAAT-ATAATTTT-GAAAAGTTTAA
1 GGGT-AAAATGGTAATTTTGGAAAA-TTT-G
* * *
29748326 GGGTCAAAATTGTAATTTGTAGAAAGTTTTG
1 GGGT-AAAATGGTAATTT-TGGAAA-ATTTG
*
29748357 GGGTCAAAAT-ATAATTTTGGAAAAGTTTAG
1 GGGT-AAAATGGTAATTTTGGAAAA-TTT-G
* *
29748387 GGGTTAAAAT-GTAATTTGTAGAAAGTTTTG
1 GGG-TAAAATGGTAATTT-TGGAAA-ATTTG
*
29748417 GGGTTAAAAT-ATAATTTT
1 GGG-TAAAATGGTAATTTT
29748435 AGAGAAGTTT
Statistics
Matches: 250, Mismatches: 38, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
28 39 0.16
29 106 0.42
30 63 0.25
31 35 0.14
32 7 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAAATTTG
Found at i:29748362 original size:60 final size:59
Alignment explanation
Indices: 29748119--29748503 Score: 326
Period size: 60 Copynumber: 6.5 Consensus size: 59
29748109 TTTGGTGAAA
* * * * * **
29748119 TTGGGGTCAAAAATAGAATTTTGGAAAA-TTTGA-GGTCAAAATGGAACTCTGGGAAA-TT
1 TTGGGGTC-AAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAA-TTTTAGAAAGTT
* * * * *
29748177 TTGGGGT-AAAATGGTAATTTTGGAAAA--TTCA-GGTGTAAAATGGTAAATTTTGGTAAG-A
1 TTGGGGTCAAAAT-ATAATTTTGGAAAAGTTTAAGGGT-TAAAAT-GT-AATTTTAGAAAGTT
* * * * * *
29748235 TCGGGGTTAAAAATAGAATTTTAGG-AAA-CTTAGGGGTAAAAATGTAATTTTAGAAAGTT
1 TTGGGG-TCAAAATATAATTTT-GGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAGTT
* *
29748294 TTAGGGTCAAAATATAATTTT-GAAAAGTTTAAGGGTCAAAATTGTAATTTGTAGAAAGTT
1 TTGGGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAA-TGTAATTT-TAGAAAGTT
*
29748354 TTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTGTAGAAAGTT
1 TTGGGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTT-TAGAAAGTT
* * *
29748414 TTGGGGTTAAAATATAATTTTAGAGAAGTTTAAGGGTTAAAATGTAATTTTCA-AAAGTT
1 TTGGGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTT-AGAAAGTT
* * * *
29748473 TTGAGGTTAAAACATAATTTTGGAGAAGTTT
1 TTGGGGTCAAAATATAATTTTGGAAAAGTTT
29748504 GGGGACTTTT
Statistics
Matches: 275, Mismatches: 35, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
56 12 0.04
57 20 0.07
58 53 0.19
59 61 0.22
60 108 0.39
61 21 0.08
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
TTGGGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAGTT
Found at i:29748443 original size:30 final size:29
Alignment explanation
Indices: 29748237--29748507 Score: 235
Period size: 30 Copynumber: 9.1 Consensus size: 29
29748227 TGGTAAGATC
* * *
29748237 GGGGTTAAAAATAGAATTTTAGGAAA-CTTA
1 GGGGTT-AAAATATAATTTTA-GAAAGTTTT
* *
29748267 GGGGTAAAAATGTAATTTTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTAGAAAGTTTT
* * *
29748296 AGGGTCAAAATATAATTTT-GAAAAGTTTA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
* * *
29748325 AGGGTCAAAATTGTAATTTGTAGAAAGTTTT
1 GGGGTTAAAA-TATAATTT-TAGAAAGTTTT
* * *
29748356 GGGGTCAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAG-AAAGTTTT
*
29748386 GGGGTTAAAATGTAATTTGTAGAAAGTTTT
1 GGGGTTAAAATATAATTT-TAGAAAGTTTT
*
29748416 GGGGTTAAAATATAATTTTAGAGAAGTTTA
1 GGGGTTAAAATATAATTTTAGA-AAGTTTT
* *
29748446 AGGGTTAAAATGTAATTTTCA-AAAGTTTT
1 GGGGTTAAAATATAATTTT-AGAAAGTTTT
* * *
29748475 GAGGTTAAAACATAATTTTGGAGAAG-TTT
1 GGGGTTAAAATATAATTTTAGA-AAGTTTT
29748504 GGGG
1 GGGG
29748508 ACTTTTAAGG
Statistics
Matches: 200, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 5 0.03
29 81 0.41
30 93 0.47
31 20 0.10
32 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTAGAAAGTTTT
Found at i:29748504 original size:29 final size:29
Alignment explanation
Indices: 29748237--29748507 Score: 176
Period size: 29 Copynumber: 9.1 Consensus size: 29
29748227 TGGTAAGATC
* * *
29748237 GGGGTTAAAAATAGAATTTTAGGA-AACTTA
1 GGGGTT-AAAATATAATTTT-GGAGAAGTTT
* * *
29748267 GGGGTAAAAATGTAATTTTAGA-AAGTTTT
1 GGGGTTAAAATATAATTTTGGAGAAG-TTT
* * *
29748296 AGGGTCAAAATATAATTTT-GAAAAGTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTT
* * * *
29748324 AAGGGTCAAAATTGTAA-TTTGTAGAAAGTTTT
1 -GGGGTTAAAA-TATAATTTTGGAG-AAG-TTT
* *
29748356 GGGGTCAAAATATAATTTTGGAAAAGTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTT
* *
29748385 AGGGGTTAAAATGTAA-TTTGTAGAAAGTTTT
1 -GGGGTTAAAATATAATTTTGGAG-AAG-TTT
*
29748416 GGGGTTAAAATATAATTTTAGAGAAGTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTT
* * * *
29748445 AAGGGTTAAAATGTAATTTT-CAAAAGTTTT
1 -GGGGTTAAAATATAATTTTGGAGAAG-TTT
* *
29748475 GAGGTTAAAACATAATTTTGGAGAAGTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTT
29748504 GGGG
1 GGGG
29748508 ACTTTTAAGG
Statistics
Matches: 192, Mismatches: 34, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
28 9 0.05
29 81 0.42
30 74 0.39
31 25 0.13
32 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTGGAGAAGTTT
Found at i:29748521 original size:60 final size:60
Alignment explanation
Indices: 29748237--29748507 Score: 331
Period size: 60 Copynumber: 4.6 Consensus size: 60
29748227 TGGTAAGATC
* * *
29748237 GGGGTTAAAAATAGAATTTTAGGA-AA-CTTAGGGGTAAAAATGTAATTT-TAGAAAGTTTT
1 GGGGTT-AAAATATAATTTT-GGAGAAGTTTAGGGGTTAAAATGTAATTTGTAGAAAGTTTT
* * * * *
29748296 AGGGTCAAAATATAATTTT-GAAAAGTTTAAGGGTCAAAATTGTAATTTGTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTTAGGGGTTAAAA-TGTAATTTGTAGAAAGTTTT
* *
29748356 GGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTGTAGAAAGTTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTGTAGAAAGTTTT
* *
29748416 GGGGTTAAAATATAATTTTAGAGAAGTTTAAGGGTTAAAATGTAATTT-TCA-AAAGTTTT
1 GGGGTTAAAATATAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTGT-AGAAAGTTTT
* *
29748475 GAGGTTAAAACATAATTTTGGAGAAGTTT-GGGG
1 GGGGTTAAAATATAATTTTGGAGAAGTTTAGGGG
29748508 ACTTTTAAGG
Statistics
Matches: 189, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
56 2 0.01
57 2 0.01
58 26 0.14
59 47 0.25
60 94 0.50
61 18 0.10
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
GGGGTTAAAATATAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTGTAGAAAGTTTT
Found at i:29748659 original size:11 final size:11
Alignment explanation
Indices: 29748643--29748668 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29748633 ATTAAGGGAT
29748643 TAAATTAAAAA
1 TAAATTAAAAA
29748654 TAAATTAAAAA
1 TAAATTAAAAA
29748665 TAAA
1 TAAA
29748669 AGGGATCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:29749993 original size:17 final size:17
Alignment explanation
Indices: 29749971--29750043 Score: 85
Period size: 17 Copynumber: 4.3 Consensus size: 17
29749961 GGACATTTTG
*
29749971 TTAAATTTATAA-TAATT
1 TTAAATTTA-AATTAAAT
29749988 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
* *
29750005 CTAAATTTAAATTTAAT
1 TTAAATTTAAATTAAAT
* *
29750022 TTAATTTTAAAATAAAT
1 TTAAATTTAAATTAAAT
29750039 TTAAA
1 TTAAA
29750044 ATGGTTTGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 2 0.04
17 45 0.96
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:29749998 original size:6 final size:6
Alignment explanation
Indices: 29749987--29750043 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
29749977 TTATAATAAT
* *
29749987 TTTAAA TTTAAA -TTAAA TCTAAA TTTAAA TTT-AA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29750033 -ATAAA TTTAAA
1 TTTAAA TTTAAA
29750044 ATGGTTTGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 14 0.33
6 28 0.67
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:29749998 original size:23 final size:23
Alignment explanation
Indices: 29749971--29750025 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
29749961 GGACATTTTG
*
29749971 TTAAATTTATAA-TAATTTTAAAT
1 TTAAATTTA-AACTAAATTTAAAT
29749994 TTAAA-TTAAATCTAAATTTAAAT
1 TTAAATTTAAA-CTAAATTTAAAT
29750017 TT-AATTTAA
1 TTAAATTTAA
29750026 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 5 0.18
23 21 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAATTTAAACTAAATTTAAAT
Found at i:29750045 original size:11 final size:11
Alignment explanation
Indices: 29749988--29750043 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
29749978 TATAATAATT
29749988 TTAAATTTAAA
1 TTAAATTTAAA
*
29749999 TTAAATCTAAA
1 TTAAATTTAAA
*
29750010 TTTAAATTTAAT
1 -TTAAATTTAAA
*
29750022 TTAATTTTAAA
1 TTAAATTTAAA
*
29750033 ATAAATTTAAA
1 TTAAATTTAAA
29750044 ATGGTTTGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:29752311 original size:21 final size:22
Alignment explanation
Indices: 29752268--29752314 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
29752258 TTTTCCTTCT
*
29752268 TTTCTTTCCCTTCTCTCTCTCC
1 TTTCTTTCCCTTCTCTATCTCC
29752290 TTTCTTTTCCCTTC-C-ATCTCC
1 TTTC-TTTCCCTTCTCTATCTCC
29752311 TTTC
1 TTTC
29752315 CACTCCATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTCTTTCCCTTCTCTATCTCC
Found at i:29758099 original size:10 final size:10
Alignment explanation
Indices: 29758084--29758108 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29758074 CTTAGCAGAA
29758084 GCAATATGGT
1 GCAATATGGT
29758094 GCAATATGGT
1 GCAATATGGT
29758104 GCAAT
1 GCAAT
29758109 CGACATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (10 bp):
GCAATATGGT
Found at i:29763235 original size:19 final size:20
Alignment explanation
Indices: 29763200--29763237 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29763190 AGGACTAGTT
29763200 TGGAACAAATTAGAAAATTA
1 TGGAACAAATTAGAAAATTA
29763220 TGGAA-AAATCTA-AAAATT
1 TGGAACAAAT-TAGAAAATT
29763238 TTAAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
TGGAACAAATTAGAAAATTA
Found at i:29767527 original size:119 final size:120
Alignment explanation
Indices: 29767403--29767624 Score: 410
Period size: 119 Copynumber: 1.9 Consensus size: 120
29767393 ATTTAAATTT
29767403 TTGCAAATGAAATAGTAAAAAAATTAAAAATAAAATATAAATTCTACAATATTCAAATAATATTA
1 TTGCAAATGAAATAGTAAAAAAATTAAAAATAAAATATAAATTCTACAATATTCAAATAATATTA
* *
29767468 AAAACGATAGTGAAACAACAGAAAAAAT-ACATTAAAAATTTTATATTAAGATAA
66 AAAACGACAGTGAAACAACAGAAAAAATAACAATAAAAATTTTATATTAAGATAA
29767522 TTGCAAATGAAATAGTAAAAAAATTAAAAATAAAATATAAATTCTACAATATTCAAATAATATTA
1 TTGCAAATGAAATAGTAAAAAAATTAAAAATAAAATATAAATTCTACAATATTCAAATAATATTA
*
29767587 AAAACGACAGTGAAATAACAGAAAAAATAACAATAAAA
66 AAAACGACAGTGAAACAACAGAAAAAATAACAATAAAA
29767625 TAACATAAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 91 0.92
120 8 0.08
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (120 bp):
TTGCAAATGAAATAGTAAAAAAATTAAAAATAAAATATAAATTCTACAATATTCAAATAATATTA
AAAACGACAGTGAAACAACAGAAAAAATAACAATAAAAATTTTATATTAAGATAA
Found at i:29767624 original size:11 final size:11
Alignment explanation
Indices: 29767599--29767650 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
29767589 AACGACAGTG
*
29767599 AAATAACAGAAA
1 AAATAACA-ATA
29767611 AAATAACAATA
1 AAATAACAATA
29767622 AAATAAC-ATAA
1 AAATAACAAT-A
*
29767633 AAACAACAA-A
1 AAATAACAATA
29767643 AAATAACA
1 AAATAACA
29767651 GCGAAAGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 10 0.29
11 16 0.46
12 9 0.26
ACGTcount: A:0.75, C:0.12, G:0.02, T:0.12
Consensus pattern (11 bp):
AAATAACAATA
Found at i:29771025 original size:31 final size:29
Alignment explanation
Indices: 29770960--29771025 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
29770950 GCCCAATATT
* *
29770960 GTATTTATTAATTTTTATTATTTTATTAT
1 GTATTTATTAATTTTTAATATTTTATTAA
*
29770989 TTATTTATTCTAATTTTTGAATATTTT-TTAA
1 GTATTTA-T-TAATTTTT-AATATTTTATTAA
29771020 GTATTT
1 GTATTT
29771026 TAAGTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 6 0.20
30 1 0.03
31 16 0.53
32 7 0.23
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
GTATTTATTAATTTTTAATATTTTATTAA
Found at i:29784396 original size:2 final size:2
Alignment explanation
Indices: 29784391--29784443 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
29784381 AAACTATTTA
29784391 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
29784433 AT AT AT AT AT A
1 AT AT AT AT AT A
29784444 GAATATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29785033 original size:25 final size:26
Alignment explanation
Indices: 29784981--29785056 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
29784971 TGTATTAATA
*
29784981 TTTAATATAAATATAATTTAATTATT
1 TTTAATATAAATATAATTTAAATATT
* *
29785007 TTTAA-ATAAATGTAATCTTAAATTTT
1 TTTAATATAAATATAAT-TTAAATATT
*
29785033 TGGTTAATATCAATATAATATTAA
1 T--TTAATATAAATATAAT-TTAA
29785057 TTAACATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 10 0.25
26 13 0.32
28 4 0.10
29 13 0.32
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTAATATAAATATAATTTAAATATT
Found at i:29785806 original size:7 final size:7
Alignment explanation
Indices: 29785796--29785820 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29785786 TAGGGTTTAA
29785796 AGTTATG
1 AGTTATG
29785803 AGTTATG
1 AGTTATG
29785810 AGTTATG
1 AGTTATG
29785817 AGTT
1 AGTT
29785821 TAGGGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (7 bp):
AGTTATG
Found at i:29791666 original size:30 final size:31
Alignment explanation
Indices: 29791610--29791668 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
29791600 TTTGTCCAAA
*
29791610 TTGGTACTTAAACTTGACACTTTTTTTTAAT
1 TTGGTACCTAAACTTGACACTTTTTTTTAAT
*
29791641 TTGGTACCTAAACTTGACATTTTTTTTT
1 TTGGTACCTAAACTTGACACTTTTTTTT
29791669 TATATTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTTTTAAT
Found at i:29791685 original size:30 final size:31
Alignment explanation
Indices: 29791618--29791679 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
29791608 AATTGGTACT
*
29791618 TAAACTTGACACTTTTTTTTAATTTGGTACC
1 TAAACTTGACACTTTTTTTTAATTTGATACC
* *
29791649 TAAACTTGACATTTTTTTTTTATATTGATAC
1 TAAACTTGACACTTTTTTTTAAT-TTGATAC
29791680 TAACTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (31 bp):
TAAACTTGACACTTTTTTTTAATTTGATACC
Found at i:29791968 original size:31 final size:31
Alignment explanation
Indices: 29791922--29792051 Score: 113
Period size: 31 Copynumber: 4.1 Consensus size: 31
29791912 GTTAAGAACT
* *
29791922 AAATTAGGAAAAAAATGCCAAGTTCAGGTACC
1 AAATTAAG-AAAAAATGTCAAGTTCAGGTACC
* *
29791954 AAGTTAAGAAAAAATGTCAACTTCAGGTTATACC
1 AAATTAAGAAAAAATGTCAAGTTCAGG---TACC
* * * *
29791988 AAATTAGGTAAAAAA---AAAGTTTAAGTACC
1 AAATTAAG-AAAAAATGTCAAGTTCAGGTACC
*
29792017 AAATTAAGAAAAAATGTCAAGTTCAGATACC
1 AAATTAAGAAAAAATGTCAAGTTCAGGTACC
29792048 AAAT
1 AAAT
29792052 GTTATATTAA
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
28 6 0.08
29 11 0.14
31 31 0.41
32 12 0.16
34 10 0.13
35 6 0.08
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (31 bp):
AAATTAAGAAAAAATGTCAAGTTCAGGTACC
Found at i:29803986 original size:98 final size:98
Alignment explanation
Indices: 29803854--29804078 Score: 306
Period size: 98 Copynumber: 2.3 Consensus size: 98
29803844 AGGATGGTTG
** * * *
29803854 GATATGTCTATAGCAAAAACCATTACTGTCGGGCTATCTAGGATGGTATAATGTATAGCTATTGA
1 GATATGTCTATAGTGAAAACCATTATTGTAGGGCTATCCAGGATGGTATAATGTATAGCTATTGA
29803919 ATGCCATCATTGTCAAGCTATCCGAGATGGTAA
66 ATGCCATCATTGTCAAGCTATCCGAGATGGTAA
* *
29803952 GATATGTCTATAGTGAAAACCATTATTGTAGGGCTATCCGGGATGGTATAATGTATAGGTATTGA
1 GATATGTCTATAGTGAAAACCATTATTGTAGGGCTATCCAGGATGGTATAATGTATAGCTATTGA
** * * * *
29804017 ATGCCATCATTGTTGAGCTATTCGGGATTGTAG
66 ATGCCATCATTGTCAAGCTATCCGAGATGGTAA
* **
29804050 GATAAGTAAATAGTGAAAACCATTATTGT
1 GATATGTCTATAGTGAAAACCATTATTGT
29804079 TGAGACATTC
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 111 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (98 bp):
GATATGTCTATAGTGAAAACCATTATTGTAGGGCTATCCAGGATGGTATAATGTATAGCTATTGA
ATGCCATCATTGTCAAGCTATCCGAGATGGTAA
Found at i:29804043 original size:49 final size:48
Alignment explanation
Indices: 29803894--29804044 Score: 153
Period size: 49 Copynumber: 3.1 Consensus size: 48
29803884 GGGCTATCTA
29803894 GGATGGTATAATGTATAGCTATTGAATGCCATCATTGTCA-AGCTATCCG
1 GGATGGTATAATGTATAG-TATTGAATGCCATCATTGT-AGAGCTATCCG
* * * * ** * *
29803943 AGATGGTAAGATATGTCTA-TAGTGAAAACCATTATTGTAGGGCTATCCG
1 GGATGGT-ATA-ATGTATAGTATTGAATGCCATCATTGTAGAGCTATCCG
* *
29803992 GGATGGTATAATGTATAGGTATTGAATGCCATCATTGTTGAGCTATTCG
1 GGATGGTATAATGTATA-GTATTGAATGCCATCATTGTAGAGCTATCCG
29804041 GGAT
1 GGAT
29804045 TGTAGGATAA
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
47 6 0.08
48 3 0.04
49 62 0.78
50 2 0.03
51 6 0.08
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (48 bp):
GGATGGTATAATGTATAGTATTGAATGCCATCATTGTAGAGCTATCCG
Found at i:29808341 original size:18 final size:18
Alignment explanation
Indices: 29808318--29808365 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
29808308 TAGCACTCTT
29808318 ACAAGCTAGTATGCTCAA
1 ACAAGCTAGTATGCTCAA
29808336 ACAAGCTAGTATGCTCAA
1 ACAAGCTAGTATGCTCAA
*
29808354 ACGAGCTAGTAT
1 ACAAGCTAGTAT
29808366 ACTACTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (18 bp):
ACAAGCTAGTATGCTCAA
Found at i:29809008 original size:18 final size:20
Alignment explanation
Indices: 29808985--29809023 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29808975 ATACGGACTC
29808985 AAAAACA-T-AGAAATCACT
1 AAAAACAGTGAGAAATCACT
29809003 AAAAACAGGTGAGAAATCACT
1 AAAAACA-GTGAGAAATCACT
29809024 CACCTATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAAACAGTGAGAAATCACT
Found at i:29810233 original size:272 final size:272
Alignment explanation
Indices: 29809747--29810291 Score: 1081
Period size: 272 Copynumber: 2.0 Consensus size: 272
29809737 TCCGATCTAT
29809747 ACCGTCTCAGCATCGAAACATGAAATACATTATGAATCTTCTCAAGTTCCGGAGGTAAATCCAAC
1 ACCGTCTCAGCATCGAAACATGAAATACATTATGAATCTTCTCAAGTTCCGGAGGTAAATCCAAC
29809812 TTATACGCTACAAGACCAACTTGCTCGATGATCTCATACGGCCTAATAAACCGAGGACTCAGCTT
66 TTATACGCTACAAGACCAACTTGCTCGATGATCTCATACGGCCTAATAAACCGAGGACTCAGCTT
29809877 TCCTTTCCTGCCAAAACGTAACACCTTTTTCCAAGGTGAAACCCTCAAGAAAACTCGATCTCCAA
131 TCCTTTCCTGCCAAAACGTAACACCTTTTTCCAAGGTGAAACCCTCAAGAAAACTCGATCTCCAA
29809942 CAGTAAACTCTATCTCTTTCCTTTTGAGATCTGCATATGACTTCTATCGGTCAGACGCTGCTTTT
196 CAGTAAACTCTATCTCTTTCCTTTTGAGATCTGCATATGACTTCTATCGGTCAGACGCTGCTTTT
29810007 AAACAGTCACGA
261 AAACAGTCACGA
29810019 ACCGTCTCAGCATCGAAACATGAAATACATTATGAATCTTCTCAAGTTCCGGAGGTAAATCCAAC
1 ACCGTCTCAGCATCGAAACATGAAATACATTATGAATCTTCTCAAGTTCCGGAGGTAAATCCAAC
29810084 TTATACGCTACAAGACCAACTTGCTCGATGATCTCATACGGCCTAATAAACCGAGGACTCAGCTT
66 TTATACGCTACAAGACCAACTTGCTCGATGATCTCATACGGCCTAATAAACCGAGGACTCAGCTT
29810149 TCCTTTCCTGCCAAAACGTAACACCTTTTTCCAAGGTGAAACCCTCAAGAAAACTCGATCTCCAA
131 TCCTTTCCTGCCAAAACGTAACACCTTTTTCCAAGGTGAAACCCTCAAGAAAACTCGATCTCCAA
29810214 CAGTAAACTCTATCTCTTTCCTTTTGAGATCTGCATATGACTTCTATCGGTCAGACGCTGCTTTT
196 CAGTAAACTCTATCTCTTTCCTTTTGAGATCTGCATATGACTTCTATCGGTCAGACGCTGCTTTT
*
29810279 AAATAGTCACGA
261 AAACAGTCACGA
29810291 A
1 A
29810292 TTACCCGAAC
Statistics
Matches: 272, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 272 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (272 bp):
ACCGTCTCAGCATCGAAACATGAAATACATTATGAATCTTCTCAAGTTCCGGAGGTAAATCCAAC
TTATACGCTACAAGACCAACTTGCTCGATGATCTCATACGGCCTAATAAACCGAGGACTCAGCTT
TCCTTTCCTGCCAAAACGTAACACCTTTTTCCAAGGTGAAACCCTCAAGAAAACTCGATCTCCAA
CAGTAAACTCTATCTCTTTCCTTTTGAGATCTGCATATGACTTCTATCGGTCAGACGCTGCTTTT
AAACAGTCACGA
Found at i:29815749 original size:19 final size:20
Alignment explanation
Indices: 29815713--29815751 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29815703 TAATTTCATC
*
29815713 TTATTTTTACTTTAACTATT
1 TTATTTTTAATTTAACTATT
29815733 TTATTTTTAATTT-ACTATT
1 TTATTTTTAATTTAACTATT
29815752 CTACCATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTAATTTAACTATT
Found at i:29818019 original size:52 final size:52
Alignment explanation
Indices: 29817938--29818105 Score: 257
Period size: 52 Copynumber: 3.2 Consensus size: 52
29817928 TTCACTTCAC
* * *
29817938 TCATATACTCACGATGACACATAGCCATCGGACCT-TATAATCCGCAAGGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCT-TAATCCGTAAAGGAT
*
29817990 TCATATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCGTAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAT
* *
29818042 TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCTGTAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAT
*
29818094 TAATATACTCAC
1 TCATATACTCAC
29818106 TGTAGAGACC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
52 106 0.99
53 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
TCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGAT
Found at i:29822500 original size:19 final size:19
Alignment explanation
Indices: 29822467--29822518 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
29822457 ACACACTATT
* *
29822467 AAAAGAAAAAAAAGAGAAG
1 AAAAGAAAGAAAAGAAAAG
29822486 AAGAAG-AAGAAAAGAAAAG
1 AA-AAGAAAGAAAAGAAAAG
29822505 AAAAGAAAGAAAAG
1 AAAAGAAAGAAAAG
29822519 GTCAACATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 23 0.79
20 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAAGAAAAGAAAAG
Found at i:29822513 original size:14 final size:14
Alignment explanation
Indices: 29822468--29822518 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
29822458 CACACTATTA
29822468 AAAGAAAA-AAAAG
1 AAAGAAAAGAAAAG
*
29822481 AGAAGAAGAAGAAGA-
1 A-AAGAA-AAGAAAAG
29822496 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
29822510 AAAGAAAAG
1 AAAGAAAAG
29822519 GTCAACATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 7 0.22
14 19 0.59
15 3 0.09
16 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:29822515 original size:4 final size:5
Alignment explanation
Indices: 29822467--29822518 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
29822457 ACACACTATT
*
29822467 AAAAG AAAAA AAAGAG AAGAAG AAGAAG AAAAG AAAAG AAAAG -AAAG
1 AAAAG AAAAG AAA-AG AA-AAG AA-AAG AAAAG AAAAG AAAAG AAAAG
29822514 AAAAG
1 AAAAG
29822519 GTCAACATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 24 0.57
6 13 0.31
7 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:29822597 original size:44 final size:43
Alignment explanation
Indices: 29822505--29822598 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 43
29822495 AAAAGAAAAG
* *
29822505 AAAAGAAAGAAAAGGTCAACATGAAAACCCGCAAAGGGCACATT
1 AAAAAAAAGAAAAGGTCAACATGAAAACCCGCAAA-GGAACATT
*
29822549 AAAAAAAAGGAAAA-GTCAAGATGAAAACCCGCAAA-GAACATCT
1 AAAAAAAA-GAAAAGGTCAACATGAAAACCCGCAAAGGAACAT-T
29822592 AAAAAAA
1 AAAAAAA
29822599 TCTCCTTTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
42 5 0.11
43 8 0.18
44 27 0.60
45 5 0.11
ACGTcount: A:0.59, C:0.16, G:0.17, T:0.09
Consensus pattern (43 bp):
AAAAAAAAGAAAAGGTCAACATGAAAACCCGCAAAGGAACATT
Found at i:29824622 original size:49 final size:49
Alignment explanation
Indices: 29824276--29824622 Score: 310
Period size: 49 Copynumber: 7.1 Consensus size: 49
29824266 CAGGTTTTAT
* * * *
29824276 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAAAGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
* * * * * *
29824325 TACCTCATAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
1 TACCAC-GAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTG
* *
29824374 TACCACGAAGATATGAAGGGAAAGGTTTAAGTCACAACGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
* * ** * * * * *
29824423 TACCTCAGAA-ACATGAAGGGAAATATTTAAGCCGCAACGACAAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
* * *
29824472 TACCACGAGGATAT-AGAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTG
1 TACCACGAAGATATGA-AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
* * * * * *
29824521 TACCTC-AAAAGCATGAAGGGAAAGATTTAAGTCGCAACGACGAATCC-AG
1 TACCACGAAGA-TATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTG
* *
29824570 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
29824619 TACC
1 TACC
29824623 TCAAAAACGT
Statistics
Matches: 230, Mismatches: 56, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
48 12 0.05
49 204 0.89
50 14 0.06
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (49 bp):
TACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
Found at i:29824670 original size:98 final size:98
Alignment explanation
Indices: 29824276--29824630 Score: 548
Period size: 98 Copynumber: 3.6 Consensus size: 98
29824266 CAGGTTTTAT
* * *
29824276 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAAAGGTGAACCTTGTACCTCATAAGCATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAAACATGA
*
29824341 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAG
* *
29824374 TACCACGAAGATATGAAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAGAAACATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAAACATGA
* * *
29824439 AGGGAAATATTTAAGCCGCAACGACAAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAG
* * * * *
29824472 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAATGGTGAACCTTGTACCTCAAAAGCATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAAACATGA
*
29824537 AGGGAAAGATTTAAGTCGCAACGACGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGACGAATCCAG
* **
29824570 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAAAAAC
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAAAC
29824631 GTAAAAGGAA
Statistics
Matches: 232, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 232 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (98 bp):
TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGTGAACCTTGTACCTCAAAAACATGA
AGGGAAAGATTTAAGCCGCAACGACGAATCCAG
Found at i:29824880 original size:19 final size:19
Alignment explanation
Indices: 29824858--29824895 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29824848 GCTTCGACAT
29824858 TAAATCCTATCTTCCTGAA
1 TAAATCCTATCTTCCTGAA
29824877 TAAATCCTATCTTCCTGAA
1 TAAATCCTATCTTCCTGAA
29824896 GTTGCAGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAATCCTATCTTCCTGAA
Found at i:29825719 original size:79 final size:80
Alignment explanation
Indices: 29825591--29825752 Score: 281
Period size: 79 Copynumber: 2.0 Consensus size: 80
29825581 CCCAAATCCT
* *
29825591 AAAACTACCCAAAATCTATTACAAAAAAACCTAAACCTAGCCCAAATATCCTAATCGGCCCAATA
1 AAAACTACCCAAAATCTATTACAAAAAAACCTAAACCTAGCCCAAATATCCTAACCGACCCAATA
29825656 AACCCAATCCACCCA
66 AACCCAATCCACCCA
*
29825671 AAAACTACCTAAAATCTATTAC-AAAAAACCTAAACCTAGCCCAAATATCCTAACCGACCCAATA
1 AAAACTACCCAAAATCTATTACAAAAAAACCTAAACCTAGCCCAAATATCCTAACCGACCCAATA
*
29825735 AGCCCAATCCACCCA
66 AACCCAATCCACCCA
29825750 AAA
1 AAA
29825753 TACCAGAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 57 0.73
80 21 0.27
ACGTcount: A:0.47, C:0.33, G:0.04, T:0.16
Consensus pattern (80 bp):
AAAACTACCCAAAATCTATTACAAAAAAACCTAAACCTAGCCCAAATATCCTAACCGACCCAATA
AACCCAATCCACCCA
Found at i:29835159 original size:52 final size:52
Alignment explanation
Indices: 29835097--29835290 Score: 234
Period size: 52 Copynumber: 3.7 Consensus size: 52
29835087 TTCACTTCAC
* * * *
29835097 TCATATACTCACAATGACATATAGCCA-CTGGACCT-TATAATCCGCAAGGGAT
1 TCATATACTCACGATGACATATAGTCATC-GGACCTCT-TAATCCGTAAAGGAT
* * *
29835149 TCATATACTCACGATGACACAGAGTCATCGGGCCTCTTAATCCGTAAAGGAT
1 TCATATACTCACGATGACATATAGTCATCGGACCTCTTAATCCGTAAAGGAT
* * *
29835201 TCATATACTTATGATGACACT-TAGTCATCGGACCTCTTAATCTGTAAAGGAT
1 TCATATACTCACGATGACA-TATAGTCATCGGACCTCTTAATCCGTAAAGGAT
29835253 TCATATACTCACGATGACACT-TAGTCATCGGACCTCTT
1 TCATATACTCACGATGACA-TATAGTCATCGGACCTCTT
29835291 CGTTTATGGC
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
52 122 0.98
53 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (52 bp):
TCATATACTCACGATGACATATAGTCATCGGACCTCTTAATCCGTAAAGGAT
Found at i:29842034 original size:49 final size:49
Alignment explanation
Indices: 29841960--29842053 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
29841950 TCCGTATAAA
*
29841960 ACTACAATTCTTCTATTTGAAATTGATTAGAATAAGGTGTTTCAACCTT
1 ACTACAATACTTCTATTTGAAATTGATTAGAATAAGGTGTTTCAACCTT
* * * *
29842009 ACTACACTACTTCTGTTTGACATTGATTAGAATAAGGTTTTTCAA
1 ACTACAATACTTCTATTTGAAATTGATTAGAATAAGGTGTTTCAA
29842054 TCTTTAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (49 bp):
ACTACAATACTTCTATTTGAAATTGATTAGAATAAGGTGTTTCAACCTT
Found at i:29843954 original size:3 final size:3
Alignment explanation
Indices: 29843948--29843980 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29843938 TTAAATTCTC
29843948 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29843981 AAACAAAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29846675 original size:20 final size:22
Alignment explanation
Indices: 29846652--29846697 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
29846642 AAAATAATAA
29846652 AAAAAACCCAAAAT-AA-TTTT
1 AAAAAACCCAAAATAAACTTTT
**
29846672 AAAAAATTCAAAATAAACTTTT
1 AAAAAACCCAAAATAAACTTTT
29846694 AAAA
1 AAAA
29846698 TTCAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 2 0.09
22 8 0.36
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAACCCAAAATAAACTTTT
Found at i:29846721 original size:20 final size:19
Alignment explanation
Indices: 29846660--29846723 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 19
29846650 AAAAAAAACC
29846660 CAAAATAATTTTAAAAAATT
1 CAAAATAATTTT-AAAAATT
29846680 CAAAATAAACTTTT-AAAATT
1 CAAAAT-AA-TTTTAAAAATT
29846700 CAAAAT-ATTTATAAAAATTT
1 CAAAATAATTT-TAAAAA-TT
29846720 CAAA
1 CAAA
29846724 TTATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 2 0.05
19 4 0.10
20 24 0.62
21 2 0.05
22 4 0.10
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
CAAAATAATTTTAAAAATT
Found at i:29846732 original size:20 final size:19
Alignment explanation
Indices: 29846673--29846732 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
29846663 AATAATTTTA
* *
29846673 AAAAATTCAAAATAAACTTT
1 AAAAATTCAAAATATA-TAT
* *
29846693 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATATAT
*
29846712 AAAAATTTCAAATTATATAT
1 AAAAA-TTCAAAATATATAT
29846732 A
1 A
29846733 TATATATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATATAT
Found at i:29846829 original size:3 final size:3
Alignment explanation
Indices: 29846821--29846873 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
29846811 AAAGTATCTC
*
29846821 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29846869 TTA TT
1 TTA TT
29846874 GTGCTTTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29847946 original size:23 final size:23
Alignment explanation
Indices: 29847876--29848046 Score: 125
Period size: 23 Copynumber: 7.3 Consensus size: 23
29847866 ACGGAACAAT
* *
29847876 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
29847897 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
29847922 CAGAGAGCACACATAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
29847945 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
29847968 CAGAGAGCATACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
29847991 TAGAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* * *
29848016 CAAAGAGCACGA-GATGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
29848039 CAGAGAGC
1 CAGAGAGC
29848047 GCACTAATGT
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
21 15 0.13
23 67 0.57
24 2 0.02
25 27 0.23
26 7 0.06
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:29847972 original size:46 final size:47
Alignment explanation
Indices: 29847921--29848046 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 47
29847911 GTGCTGGGCA
*
29847921 ACAGAGAGCACACATAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACATAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * ** * *
29847968 -CAGAGAGCATACAAAGTGCTAATTAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACATAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* *
29848014 AACAAAGAGCACGAGAT-GTGCTAAACAGAGAGC
1 -ACAGAGAGCAC-ACATAGTGCTAAACAGAGAGC
29848047 GCACTAATGT
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
46 39 0.62
48 22 0.35
49 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (47 bp):
ACAGAGAGCACACATAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:29847996 original size:69 final size:66
Alignment explanation
Indices: 29847876--29848012 Score: 170
Period size: 69 Copynumber: 2.0 Consensus size: 66
29847866 ACGGAACAAT
*
29847876 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACATAGTGC
1 CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCT--G-AACAGAGAGCACACACAGTGC
29847941 TAAA
63 TAAA
*
29847945 CAGAGAGTACACAAAGTACTAATCAGAGAGCATACA-AAGTGCT-AATTAGAGAGCACACACAGT
1 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGC--ACATAAGTGCTGAA-CAGAGAGCACACACAGT
29848008 GCTAA
61 GCTAA
29848013 TAACAAAGAG
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
68 2 0.03
69 30 0.49
70 11 0.18
71 8 0.13
72 7 0.11
73 3 0.05
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (66 bp):
CAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGAACAGAGAGCACACACAGTGCTAA
A
Found at i:29855123 original size:25 final size:23
Alignment explanation
Indices: 29855094--29855173 Score: 124
Period size: 23 Copynumber: 3.4 Consensus size: 23
29855084 TGTTGGGCAA
*
29855094 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
29855117 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
29855140 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
29855163 AACAGAGAGCA
1 --CAGAGAGCA
29855174 GGAGACGTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 44 0.83
25 9 0.17
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:29856540 original size:14 final size:13
Alignment explanation
Indices: 29856516--29856545 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
29856506 TCAAATTCTC
29856516 TAAAAATCTCACT
1 TAAAAATCTCACT
29856529 TAAAATATCTCACT
1 TAAAA-ATCTCACT
29856543 TAA
1 TAA
29856546 TAAAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATCTCACT
Found at i:29860226 original size:2 final size:2
Alignment explanation
Indices: 29860219--29860258 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29860209 AAGTAAAATA
29860219 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
29860259 TAATTGTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29863000 original size:40 final size:41
Alignment explanation
Indices: 29862937--29863055 Score: 150
Period size: 40 Copynumber: 2.9 Consensus size: 41
29862927 GCGGCACTTT
* * *
29862937 TAGCGGCGTTTAGACAGAAAACGCCGCAAAAGGTAAAACAA
1 TAGCAGCGTTTATACAAAAAACGCCGCAAAAGGTAAAACAA
* * *
29862978 TAGCAGCGTTT-TTCAACAAACGCCGCAAAAGGTAAAGCAA
1 TAGCAGCGTTTATACAAAAAACGCCGCAAAAGGTAAAACAA
* *
29863018 TAGCAGCGTTTATAGAAAAAACGCCGCTAAAAGTTAAA
1 TAGCAGCGTTTATACAAAAAACGCCGC-AAAAGGTAAA
29863056 GCATTAGCGG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
40 35 0.53
41 22 0.33
42 9 0.14
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (41 bp):
TAGCAGCGTTTATACAAAAAACGCCGCAAAAGGTAAAACAA
Found at i:29865006 original size:42 final size:42
Alignment explanation
Indices: 29864927--29865146 Score: 196
Period size: 42 Copynumber: 5.3 Consensus size: 42
29864917 AATATGAGAA
* * * * * *
29864927 AGAGCATTAGCGGCGTTTTTGGGGCAAATGCCGCTAAAGGTC
1 AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
* * *
29864969 AAAACATTAGCGGCGTTTATGGAGAAAACGCCACTAAAGGTC
1 AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
* * * *
29865011 AGAGCATTAGCGTCGCTTGTGGGGAAAACGTCACTAAAGGTC
1 AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
* * * *
29865053 AGAGCACTAGCGGCGCTTAT-GAGAAAGCGCCGCTAAAGGTT
1 AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
* ** * * *
29865094 A-AGCAATAGCAACGCTTAT-GAGAAAGCGCCACTAAACGTT
1 AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
*
29865134 A-AGCAATAGCGGC
1 AGAGCATTAGCGGC
29865147 ATTTTTCTCA
Statistics
Matches: 149, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
40 45 0.30
41 17 0.11
42 87 0.58
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.19
Consensus pattern (42 bp):
AGAGCATTAGCGGCGCTTATGGAGAAAACGCCACTAAAGGTC
Found at i:29865113 original size:40 final size:40
Alignment explanation
Indices: 29865066--29865143 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
29865056 GCACTAGCGG
* *
29865066 CGCTTATGAGAAAGCGCCGCTAAAGGTTAAGCAATAGCAA
1 CGCTTATGAGAAAGCGCCACTAAACGTTAAGCAATAGCAA
29865106 CGCTTATGAGAAAGCGCCACTAAACGTTAAGCAATAGC
1 CGCTTATGAGAAAGCGCCACTAAACGTTAAGCAATAGC
29865144 GGCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (40 bp):
CGCTTATGAGAAAGCGCCACTAAACGTTAAGCAATAGCAA
Found at i:29867623 original size:29 final size:28
Alignment explanation
Indices: 29867591--29867650 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
29867581 ATTTAATTAT
* *
29867591 TTAAATGTTTAATTA-TTAATAACATTTAA
1 TTAAATATTTAAATATTTAAT-A-ATTTAA
29867620 TTAAATATTTAAATATTTAATAATTTAA
1 TTAAATATTTAAATATTTAATAATTTAA
29867648 TTA
1 TTA
29867651 TTAAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 14 0.50
30 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TTAAATATTTAAATATTTAATAATTTAA
Found at i:29867673 original size:4 final size:4
Alignment explanation
Indices: 29867664--29867718 Score: 67
Period size: 4 Copynumber: 13.5 Consensus size: 4
29867654 AAAACAACTC
* *
29867664 AATT AATT AATT AATT AATT AATT AATT ATATTT AATT AAAT ATTT AATT
1 AATT AATT AATT AATT AATT AATT AATT A-A-TT AATT AATT AATT AATT
29867714 -ATT AA
1 AATT AA
29867719 AAATAACCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
3 3 0.07
4 36 0.82
5 2 0.05
6 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:29867743 original size:46 final size:45
Alignment explanation
Indices: 29867692--29867882 Score: 144
Period size: 46 Copynumber: 4.6 Consensus size: 45
29867682 TTAATTAATT
29867692 ATATTTAATTAAATATTTAATTATTAAAAATAACCCAAATATTTAA
1 ATATTTAATTAAATATTTAATTATTAAAAATAA-CCAAATATTTAA
** *
29867738 ATATTTAATTAGTTATTT-ATTA--AAAAAT--TCAAATATTT--
1 ATATTTAATTAAATATTTAATTATTAAAAATAACCAAATATTTAA
**
29867776 A-A-TTAA--AAATATTTAATTATT-----TAATTAAATATTTAA
1 ATATTTAATTAAATATTTAATTATTAAAAATAACCAAATATTTAA
* * *
29867812 TTATTTAATTAAATATTTAATTATTAAAAACAATCCAACTATTTAA
1 ATATTTAATTAAATATTTAATTATTAAAAATAA-CCAAATATTTAA
* * * *
29867858 TTATTTAGTTTAATAATTAATTATT
1 ATATTTAATTAAATATTTAATTATT
29867883 TATTAACAAC
Statistics
Matches: 114, Mismatches: 14, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
32 1 0.01
34 15 0.13
35 4 0.04
36 4 0.04
37 2 0.02
38 5 0.04
40 24 0.21
43 6 0.05
45 6 0.05
46 47 0.41
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (45 bp):
ATATTTAATTAAATATTTAATTATTAAAAATAACCAAATATTTAA
Found at i:29867787 original size:14 final size:14
Alignment explanation
Indices: 29867768--29867794 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29867758 TAAAAAATTC
29867768 AAATATTTAATTAA
1 AAATATTTAATTAA
29867782 AAATATTTAATTA
1 AAATATTTAATTA
29867795 TTTAATTAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATTTAATTAA
Found at i:29867788 original size:54 final size:54
Alignment explanation
Indices: 29867728--29867834 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
29867718 AAAATAACCC
**
29867728 AAATATTTAAATATTTAATTAGTTATTT-ATTAAAAAATTCAAATATTTAATTAA
1 AAATATTTAAATATTTAATTAAATATTTAATTAAAAAATT-AAATATTTAATTAA
* ***
29867782 AAATATTTAATTATTTAATTAAATATTTAATTATTTAATTAAATATTTAATTA
1 AAATATTTAAATATTTAATTAAATATTTAATTAAAAAATTAAATATTTAATTA
29867835 TTAAAAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 38 0.83
55 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (54 bp):
AAATATTTAAATATTTAATTAAATATTTAATTAAAAAATTAAATATTTAATTAA
Found at i:29867808 original size:12 final size:12
Alignment explanation
Indices: 29867734--29867834 Score: 71
Period size: 12 Copynumber: 9.2 Consensus size: 12
29867724 ACCCAAATAT
29867734 TTAAATATTTAA
1 TTAAATATTTAA
**
29867746 TTAGTTATTT-A
1 TTAAATATTTAA
29867757 TTAAA-A---AA
1 TTAAATATTTAA
29867765 TTCAAATATTTAA
1 TT-AAATATTTAA
* *
29867778 TTAAA-A-ATAT
1 TTAAATATTTAA
*
29867788 TTAATTATTTAA
1 TTAAATATTTAA
29867800 TTAAATATTTAA
1 TTAAATATTTAA
29867812 -T---TATTTAA
1 TTAAATATTTAA
29867820 TTAAATATTTAA
1 TTAAATATTTAA
29867832 TTA
1 TTA
29867835 TTAAAAACAA
Statistics
Matches: 67, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
8 10 0.15
9 4 0.06
10 8 0.12
11 7 0.10
12 34 0.51
13 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (12 bp):
TTAAATATTTAA
Found at i:29867836 original size:8 final size:8
Alignment explanation
Indices: 29867573--29867822 Score: 67
Period size: 8 Copynumber: 32.1 Consensus size: 8
29867563 AAATTAACTA
29867573 ATTTAATT
1 ATTTAATT
29867581 ATTTAATT
1 ATTTAATT
*
29867589 ATTTAAAT
1 ATTTAATT
*
29867597 GTTTAATT
1 ATTTAATT
*
29867605 A-TTAATAAC
1 ATTTAAT--T
29867614 ATTTAATT
1 ATTTAATT
29867622 A---AA-T
1 ATTTAATT
*
29867626 ATTTAAAT
1 ATTTAATT
*
29867634 ATTTAATA
1 ATTTAATT
29867642 ATTTAATT
1 ATTTAATT
* **
29867650 ATTAAAAACA
1 ATT--TAATT
* *
29867660 ACTCAATT
1 ATTTAATT
*
29867668 AATTAATT
1 ATTTAATT
*
29867676 AATTAATT
1 ATTTAATT
*
29867684 AATTAATT
1 ATTTAATT
*
29867692 A--TATTT
1 ATTTAATT
* *
29867698 AATTAAAT
1 ATTTAATT
29867706 ATTTAATT
1 ATTTAATT
* *
29867714 ATTAAAAATA
1 ATT--TAATT
*** *
29867724 ACCCAAAT
1 ATTTAATT
*
29867732 ATTTAAAT
1 ATTTAATT
29867740 ATTTAATT
1 ATTTAATT
* *
29867748 AGTTATTT
1 ATTTAATT
* **
29867756 ATTAAAAA
1 ATTTAATT
* *
29867764 ATTCAAAT
1 ATTTAATT
29867772 ATTTAATT
1 ATTTAATT
* *
29867780 A--AAAAT
1 ATTTAATT
29867786 ATTTAATT
1 ATTTAATT
29867794 ATTTAATT
1 ATTTAATT
29867802 A---AA-T
1 ATTTAATT
29867806 ATTTAATT
1 ATTTAATT
29867814 ATTTAATT
1 ATTTAATT
29867822 A
1 A
29867823 AATATTTAAT
Statistics
Matches: 174, Mismatches: 49, Indels: 38
0.67 0.19 0.15
Matches are distributed among these distances:
4 4 0.02
5 4 0.02
6 9 0.05
7 9 0.05
8 134 0.77
9 1 0.01
10 13 0.07
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (8 bp):
ATTTAATT
Found at i:29867901 original size:130 final size:120
Alignment explanation
Indices: 29867666--29867944 Score: 346
Period size: 120 Copynumber: 2.2 Consensus size: 120
29867656 AACAACTCAA
* * * *
29867666 TTAATTAATTAATTAATTAATTAATTATATTTAATTAAATATTTAATTATTAAAAATAACCCAAA
1 TTAATTATTTAATTAAATATTTAA-T-TATTTAATTAAATATTTAATTATTAAAAACAACCCAAA
* **
29867731 TATTTAAATATTTAATTAGTTATTTATTAAAAAATTCAAATATTTAATTAAAAATAT
64 TATTTAAATATTTAATTAATTATTTATTAAAAAACCCAAATATTTAATTAAAAATAT
* *
29867788 TTAATTATTTAATTAAATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAATCCAACTA
1 TTAATTATTTAATTAAATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATA
*
29867853 TTTAATTATTTAGTTTAATAATTAATTATTTATTAACAACAACCCAAATATTTAATTCAAAATAT
66 TTTAA--A--TA--TT--TAATTAATTATTTATTAA-AA-AACCCAAATATTTAATTAAAAATAT
29867918 TTAATTATTTAATT--ATATTTAATTATT
1 TTAATTATTTAATTAAATATTTAATTATT
29867945 AAAAACAACC
Statistics
Matches: 137, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
120 42 0.31
121 1 0.01
122 22 0.16
124 2 0.01
126 2 0.01
128 30 0.22
129 2 0.01
130 36 0.26
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (120 bp):
TTAATTATTTAATTAAATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATA
TTTAAATATTTAATTAATTATTTATTAAAAAACCCAAATATTTAATTAAAAATAT
Found at i:29867907 original size:50 final size:46
Alignment explanation
Indices: 29867802--29867909 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
29867792 TTATTTAATT
* *
29867802 AAATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAATCC
1 AAATATTTAATTATTTAATTAAATAATTAATTATTAAAAACAACCC
* * *
29867848 AACTATTTAATTATTTAGTTTAATAATTAATTATTTATTAACAACAACCC
1 AAATATTTAATTATTTAATTAAATAATTAATTA-TTA--AA-AACAACCC
29867898 AAATATTTAATT
1 AAATATTTAATT
29867910 CAAAATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 29 0.56
47 3 0.06
49 2 0.04
50 18 0.35
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (46 bp):
AAATATTTAATTATTTAATTAAATAATTAATTATTAAAAACAACCC
Found at i:29872863 original size:51 final size:53
Alignment explanation
Indices: 29872779--29872883 Score: 162
Period size: 51 Copynumber: 2.0 Consensus size: 53
29872769 CTATTAATTT
*
29872779 TAGCGGTGCTTGTGGGAGAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCG
1 TAGCGGCGCTTGTGGGAGAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCG
*
29872832 TAGCGGCGTTTGTGGG-G-AAAGCG-TCGCTAAAGACCATGTTCTTTAGCGGCG
1 TAGCGGCGCTTGTGGGAGAAAAGCGCT-GCTAAAGACCATGTTCTTTAGCGGCG
29872883 T
1 T
29872884 TTGTAGGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
50 1 0.02
51 33 0.67
52 1 0.02
53 14 0.29
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (53 bp):
TAGCGGCGCTTGTGGGAGAAAAGCGCTGCTAAAGACCATGTTCTTTAGCGGCG
Found at i:29872896 original size:43 final size:43
Alignment explanation
Indices: 29872832--29872987 Score: 208
Period size: 43 Copynumber: 3.7 Consensus size: 43
29872822 TTTAGCGGCG
*
29872832 TAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCTT
1 TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTT
* * *
29872875 TAGCGGCGTTTGTAGGAAAAGCGCTGCTAAAGA-C-TGTTCTT
1 TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTT
* * * *
29872916 TAGCAGCGTTTATGGGCAAAGCGCCGCTAAAGACTATGTTCTT
1 TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTT
* *
29872959 TAGCGACATTTGTGGGGAAAGCGCCGCTA
1 TAGCGGCGTTTGTGGGGAAAGCGCCGCTA
29872988 TAGGTTAAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
41 35 0.36
42 1 0.01
43 60 0.62
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTCTT
Found at i:29872980 original size:84 final size:84
Alignment explanation
Indices: 29872832--29872987 Score: 222
Period size: 84 Copynumber: 1.9 Consensus size: 84
29872822 TTTAGCGGCG
* * * * * *
29872832 TAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTAGGAAAAGC
1 TAGCAGCGTTTATGGGCAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACATTTGTAGGAAAAGC
*
29872897 GCTGCTAAAGACTGTTCTT
66 GCCGCTAAAGACTGTTCTT
* * *
29872916 TAGCAGCGTTTATGGGCAAAGCGCCGCTAAAGACTATGTTCTTTAGCGACATTTGTGGGGAAAGC
1 TAGCAGCGTTTATGGGCAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACATTTGTAGGAAAAGC
29872981 GCCGCTA
66 GCCGCTA
29872988 TAGGTTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (84 bp):
TAGCAGCGTTTATGGGCAAAGCGCCGCTAAAGACCATGTTCTTTAGCGACATTTGTAGGAAAAGC
GCCGCTAAAGACTGTTCTT
Found at i:29873371 original size:9 final size:9
Alignment explanation
Indices: 29873357--29873400 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
29873347 ACTTAAATCC
29873357 CTCTCAACT
1 CTCTCAACT
29873366 CTCTCAACT
1 CTCTCAACT
29873375 CTCTCAACT
1 CTCTCAACT
*
29873384 TTCTCAAACT
1 CTCTC-AACT
29873394 CTCTCAA
1 CTCTCAA
29873401 ATCCATTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (9 bp):
CTCTCAACT
Found at i:29874729 original size:25 final size:25
Alignment explanation
Indices: 29874701--29874764 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
29874691 AATTAAATTA
*
29874701 AATATAATATTAAGATAATCACT-TT
1 AATATAATATTAAGAAAAT-ACTATT
*
29874726 AATATTAA-ATTAATAAAATACTATT
1 AATA-TAATATTAAGAAAATACTATT
*
29874751 AACATAAGTATTAA
1 AATATAA-TATTAA
29874765 ATTTAATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.19
25 18 0.56
26 8 0.25
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (25 bp):
AATATAATATTAAGAAAATACTATT
Found at i:29874777 original size:37 final size:36
Alignment explanation
Indices: 29874693--29874799 Score: 94
Period size: 37 Copynumber: 2.9 Consensus size: 36
29874683 AAGATAAAAA
* * *
29874693 TTAAATTAA-ATATAA-TATTAAGATAATCACTTTAAT
1 TTAAATTAATATAAAACTATTAAAATAAT-A-TTAAAT
*
29874729 ATTAAATTAATA-AAATACTATTAACATAAGTATTAAAT
1 -TTAAATTAATATAAA-ACTATTAAAATAA-TATTAAAT
* *
29874767 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
29874800 TCTTTGGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
36 5 0.08
37 33 0.56
38 9 0.15
39 11 0.19
40 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:29880438 original size:15 final size:15
Alignment explanation
Indices: 29880414--29880538 Score: 103
Period size: 15 Copynumber: 8.3 Consensus size: 15
29880404 GTTTGGAAGA
*
29880414 TGCGAGCACTAGTGT
1 TGCGAACACTAGTGT
29880429 TGCGAACACTCA-TGT
1 TGCGAACACT-AGTGT
29880444 TGCGAACACT-GATGT
1 TGCGAACACTAG-TGT
*
29880459 TGTGAACACTAGTGT
1 TGCGAACACTAGTGT
* *
29880474 TGTGAGCACTCA-TGT
1 TGCGAACACT-AGTGT
* * * *
29880489 TGCGAACAATGGAGC
1 TGCGAACACTAGTGT
*
29880504 TGCGAACACTAATGT
1 TGCGAACACTAGTGT
* *
29880519 TGTGAACACTCGTGT
1 TGCGAACACTAGTGT
29880534 TGCGA
1 TGCGA
29880539 CCATGGATGA
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
15 83 0.97
16 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
TGCGAACACTAGTGT
Found at i:29880471 original size:45 final size:45
Alignment explanation
Indices: 29880414--29880538 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 45
29880404 GTTTGGAAGA
* * * *
29880414 TGCGAGCACTAGTGTTGCGAACACTCATGTTGCGAACACT-GATGT
1 TGCGAACACTAGTGTTGTGAACACTCATGTTGCGAACAATGGA-GC
* *
29880459 TGTGAACACTAGTGTTGTGAGCACTCATGTTGCGAACAATGGAGC
1 TGCGAACACTAGTGTTGTGAACACTCATGTTGCGAACAATGGAGC
* *
29880504 TGCGAACACTAATGTTGTGAACACTCGTGTTGCGA
1 TGCGAACACTAGTGTTGTGAACACTCATGTTGCGA
29880539 CCATGGATGA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
45 67 0.97
46 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (45 bp):
TGCGAACACTAGTGTTGTGAACACTCATGTTGCGAACAATGGAGC
Found at i:29887076 original size:18 final size:18
Alignment explanation
Indices: 29887049--29887087 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29887039 TGATTTAATT
29887049 GCACTAACATCCTTACTA
1 GCACTAACATCCTTACTA
*
29887067 GCACTGACATCCTTACTA
1 GCACTAACATCCTTACTA
29887085 GCA
1 GCA
29887088 TTTTCCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (18 bp):
GCACTAACATCCTTACTA
Found at i:29899001 original size:30 final size:30
Alignment explanation
Indices: 29898958--29899050 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
29898948 ACTCATGTTA
*
29898958 CGAACATTGATGTTGTGAACACTAGAGTTG
1 CGAACACTGATGTTGTGAACACTAGAGTTG
* * * * * *
29898988 CGAGCACTTATGTTGTGAATAATGGAGCTG
1 CGAACACTGATGTTGTGAACACTAGAGTTG
* *
29899018 CGAACACTGATGTTGTGAACACTCGTGTTG
1 CGAACACTGATGTTGTGAACACTAGAGTTG
29899048 CGA
1 CGA
29899051 CCATGGATGA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (30 bp):
CGAACACTGATGTTGTGAACACTAGAGTTG
Found at i:29899047 original size:15 final size:15
Alignment explanation
Indices: 29898945--29899040 Score: 61
Period size: 15 Copynumber: 6.4 Consensus size: 15
29898935 TAGTGTTGCA
* **
29898945 AACACTCATGTTACG
1 AACACTGATGTTGTG
*
29898960 AACATTGATGTTGTG
1 AACACTGATGTTGTG
*
29898975 AACACTAGA-GTTGCG
1 AACACT-GATGTTGTG
* *
29898990 AGCACTTATGTTGTG
1 AACACTGATGTTGTG
* * * *
29899005 AATAATGGA-GCTGCG
1 AACACT-GATGTTGTG
29899020 AACACTGATGTTGTG
1 AACACTGATGTTGTG
29899035 AACACT
1 AACACT
29899041 CGTGTTGCGA
Statistics
Matches: 58, Mismatches: 19, Indels: 8
0.68 0.22 0.09
Matches are distributed among these distances:
14 3 0.05
15 52 0.90
16 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (15 bp):
AACACTGATGTTGTG
Found at i:29901386 original size:31 final size:32
Alignment explanation
Indices: 29901323--29901386 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
29901313 AGATTCTTAA
* *
29901323 GATATCTGAAAAATAAGGATCACGATTCTTGG
1 GATATCTGAAAAATAAGGACCACGATTATTGG
* **
29901355 GATATTTG-AAAATAAGGACCGGGATTATTGG
1 GATATCTGAAAAATAAGGACCACGATTATTGG
29901386 G
1 G
29901387 TAGAATAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (32 bp):
GATATCTGAAAAATAAGGACCACGATTATTGG
Found at i:29902141 original size:22 final size:23
Alignment explanation
Indices: 29902103--29902148 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
29902093 AGCATTATTT
29902103 ATTAAACAAGGAAAAGGAAAGCC
1 ATTAAACAAGGAAAAGGAAAGCC
*
29902126 ATTAAAC-ATGAAAAGGAAAGCC
1 ATTAAACAAGGAAAAGGAAAGCC
29902148 A
1 A
29902149 AATCCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.57, C:0.13, G:0.20, T:0.11
Consensus pattern (23 bp):
ATTAAACAAGGAAAAGGAAAGCC
Found at i:29911399 original size:19 final size:19
Alignment explanation
Indices: 29911377--29911468 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 19
29911367 AATATAAAAT
*
29911377 AATTTAAAATAATTT-TTAA
1 AATTTAAAAT-ATTTATAAA
*
29911396 AATTAAAAATATTTATAAA
1 AATTTAAAATATTTATAAA
29911415 AATTCTAAAAT-TTTAT---
1 AATT-TAAAATATTTATAAA
*
29911431 ATTTTAAAA-A-TTATAAA
1 AATTTAAAATATTTATAAA
*
29911448 AATTTCAAAA-AATTATAAA
1 AATTT-AAAATATTTATAAA
29911467 AA
1 AA
29911469 AATATATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
14 4 0.07
15 5 0.08
16 3 0.05
17 4 0.07
18 9 0.15
19 30 0.50
20 5 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTAAAATATTTATAAA
Done.