Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 74 of 145
Found at i:25135701 original size:24 final size:23
Alignment explanation
Indices: 25135652--25135701 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
25135642 TAAAGTAGGT
* *
25135652 TATATATTATTTTTTTAATATTA
1 TATATATGATTTTTTTAATATCA
25135675 TATATTATGATTTTTATTAA-ATCA
1 TATA-TATGATTTTT-TTAATATCA
25135699 TAT
1 TAT
25135702 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTTTAATATCA
Found at i:25135939 original size:16 final size:16
Alignment explanation
Indices: 25135918--25135968 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
25135908 TGAATTACTG
25135918 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
**
25135934 ATTACATATCTATTCC
1 ATTACAGCTCTATTCC
* *
25135950 ATTACAGCCCTATTTC
1 ATTACAGCTCTATTCC
25135966 ATT
1 ATT
25135969 GACTCCACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:25136745 original size:19 final size:19
Alignment explanation
Indices: 25136709--25136745 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25136699 AAAAATAAAA
**
25136709 AAAATTGTAAAATTTTATG
1 AAAATTGTAAAAAGTTATG
25136728 AAAATTGTAAAAAGTTAT
1 AAAATTGTAAAAAGTTAT
25136746 AAATTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
AAAATTGTAAAAAGTTATG
Found at i:25136803 original size:57 final size:58
Alignment explanation
Indices: 25136680--25136824 Score: 154
Period size: 57 Copynumber: 2.5 Consensus size: 58
25136670 AAAAAATTAG
* * * *
25136680 AAAAA-TATAAAAATCGTAAAAAAATA-AAAAAAATTGTAAAATTTTATGAAAATTGTA
1 AAAAATTATAAAAAT-ATAAAGAAATATAAAAAAATTATAAAATTTTATGAAAATCGTA
* * * * *
25136737 AAAAGTTAT-AAATTATATAGAAATATAAAAAAATTATAGAATTTTAT-AAAGTCGTA
1 AAAAATTATAAAAATATAAAGAAATATAAAAAAATTATAAAATTTTATGAAAATCGTA
25136793 AGAAAATTATACAAAATATAAAGAAATATAAA
1 A-AAAATTATA-AAAATATAAAGAAATATAAA
25136825 TTTTGTAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
56 16 0.23
57 34 0.48
58 3 0.04
59 18 0.25
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (58 bp):
AAAAATTATAAAAATATAAAGAAATATAAAAAAATTATAAAATTTTATGAAAATCGTA
Found at i:25143933 original size:10 final size:10
Alignment explanation
Indices: 25143907--25143952 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
25143897 TATATTCTGA
25143907 CACATATCAAT
1 CACATAT-AAT
*
25143918 CACATATAAG
1 CACATATAAT
25143928 CACATATAAT
1 CACATATAAT
*
25143938 TACATATAAT
1 CACATATAAT
25143948 CACAT
1 CACAT
25143953 TTAGTCATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (10 bp):
CACATATAAT
Found at i:25144367 original size:36 final size:36
Alignment explanation
Indices: 25144327--25144438 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
25144317 CTATTTATTG
25144327 TCACATGGCATGATTAACATACTTTCATATTCACTT
1 TCACATGGCATGATTAACATACTTTCATATTCACTT
* * *
25144363 TCACATGGCATGA-AAACATACCCTTC-TATTTA-TT
1 TCACATGGCATGATTAACATA-CTTTCATATTCACTT
25144397 GTCACATGGCATGATTAACATACTTTCATATTCACTT
1 -TCACATGGCATGATTAACATACTTTCATATTCACTT
25144434 TCACA
1 TCACA
25144439 ACAGTGAACA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
34 2 0.03
35 28 0.43
36 33 0.51
37 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (36 bp):
TCACATGGCATGATTAACATACTTTCATATTCACTT
Found at i:25144374 original size:71 final size:71
Alignment explanation
Indices: 25144297--25144438 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
25144287 CTCTGACATG
25144297 TGGCATGAAAACATACCCTTCTATTTATTGTCACATGGCATGATTAACATACTTTCATATTCACT
1 TGGCATGAAAACATACCCTTCTATTTATTGTCACATGGCATGATTAACATACTTTCATATTCACT
25144362 TTCACA
66 TTCACA
25144368 TGGCATGAAAACATACCCTTCTATTTATTGTCACATGGCATGATTAACATACTTTCATATTCACT
1 TGGCATGAAAACATACCCTTCTATTTATTGTCACATGGCATGATTAACATACTTTCATATTCACT
25144433 TTCACA
66 TTCACA
25144439 ACAGTGAACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (71 bp):
TGGCATGAAAACATACCCTTCTATTTATTGTCACATGGCATGATTAACATACTTTCATATTCACT
TTCACA
Found at i:25144402 original size:35 final size:36
Alignment explanation
Indices: 25144297--25144419 Score: 164
Period size: 35 Copynumber: 3.5 Consensus size: 36
25144287 CTCTGACATG
25144297 TGGCATGA-AAACATACCCTTCTATTTATTGTCACA
1 TGGCATGATAAACATACCCTTCTATTTATTGTCACA
* * *
25144332 TGGCATGATTAACATA-CTTTCATATTCACTT-TCACA
1 TGGCATGATAAACATACCCTTC-TATTTA-TTGTCACA
25144368 TGGCATGA-AAACATACCCTTCTATTTATTGTCACA
1 TGGCATGATAAACATACCCTTCTATTTATTGTCACA
*
25144403 TGGCATGATTAACATAC
1 TGGCATGATAAACATAC
25144420 TTTCATATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
34 2 0.03
35 36 0.48
36 35 0.47
37 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (36 bp):
TGGCATGATAAACATACCCTTCTATTTATTGTCACA
Found at i:25146229 original size:25 final size:25
Alignment explanation
Indices: 25146195--25146253 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
25146185 TTCTCATCAC
*
25146195 AATTTTACCCCAGTAAAATTATGGT
1 AATTTTACCCCAATAAAATTATGGT
25146220 AATTTTACCCCAATAAAATTATGGT
1 AATTTTACCCCAATAAAATTATGGT
25146245 AATTTTACC
1 AATTTTACC
25146254 TCGGGTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTTTACCCCAATAAAATTATGGT
Found at i:25148563 original size:11 final size:11
Alignment explanation
Indices: 25148529--25148566 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
25148519 ACAATAGCTT
25148529 ATAAATCTTTG
1 ATAAATCTTTG
*
25148540 AGAAATCTTTG
1 ATAAATCTTTG
*
25148551 ATAAACCTTTG
1 ATAAATCTTTG
25148562 ATAAA
1 ATAAA
25148567 AACTGACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (11 bp):
ATAAATCTTTG
Found at i:25152337 original size:30 final size:30
Alignment explanation
Indices: 25152301--25152363 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
25152291 TGTATATGTA
25152301 AGTCAATAGTTGCTCAATTAATAATTGGCT
1 AGTCAATAGTTGCTCAATTAATAATTGGCT
25152331 AGTCAATAGTTGCTCAATTAATAATTGGCT
1 AGTCAATAGTTGCTCAATTAATAATTGGCT
25152361 AGT
1 AGT
25152364 TGGTGATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (30 bp):
AGTCAATAGTTGCTCAATTAATAATTGGCT
Found at i:25162753 original size:69 final size:69
Alignment explanation
Indices: 25162592--25162735 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
25162582 GATGTATATA
* * * * * **
25162592 ATGTAACACCATAGCTCGTCTATGGAAACTAATAGATTTTGTCGAGATAGTAAACATGGGGATTA
1 ATGTAATACCATAGCTCGACTATGGCAACTAATAGAGTTTGTCGAGACAGTAAACACAGGGATTA
25162657 TAAG
66 TAAG
*
25162661 ATGTAATACCATAGCTCAACTATGGCAACTAATAGAGTTTGTC-AGGACAGTAAACACAGGGATT
1 ATGTAATACCATAGCTCGACTATGGCAACTAATAGAGTTTGTCGA-GACAGTAAACACAGGGATT
25162725 ATAAG
65 ATAAG
*
25162730 GTGTAA
1 ATGTAA
25162736 GTTTATAGCT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (69 bp):
ATGTAATACCATAGCTCGACTATGGCAACTAATAGAGTTTGTCGAGACAGTAAACACAGGGATTA
TAAG
Found at i:25165784 original size:16 final size:17
Alignment explanation
Indices: 25165751--25165784 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25165741 AAAGAAAAAA
25165751 TAATAATAGAAGAGTTG
1 TAATAATAGAAGAGTTG
*
25165768 TAATATTAGAA-AGTTG
1 TAATAATAGAAGAGTTG
25165784 T
1 T
25165785 TACAAGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
TAATAATAGAAGAGTTG
Found at i:25172601 original size:342 final size:342
Alignment explanation
Indices: 25171972--25172657 Score: 1070
Period size: 342 Copynumber: 2.0 Consensus size: 342
25171962 GCACTTTCAT
* *
25171972 CACTATTTCTTGAGTTTAATGCATGTTGTGTTTGCCTTTTAGGCAGCATGTTTTTTGCATGAGAA
1 CACTATTTCTTGAGTTCAATACATGTTGTGTTTGCCTTTTAGGCAGCATGTTTTTTGCATGAGAA
* ** *
25172037 GGTTCACTTATGTAGTTGAATTTTGAGACAATCATAGGAGCTGTTTTAGTTGCATCATGATTTTC
66 GGTTCACTTATGTAGTTGAATTTTGAGACAATCACACCAGCTGTTTTAGTTGCATCATGACTTTC
* * * *
25172102 TGGACCATCACATACAGTCCTGTTCTTTTCTCCACTAGCATTATCTCTTTTCACAACTATATTTT
131 CGGACCATCACATACAGTCCTATTCTTTCCTCCACTAGCATTATCTCTTTTCACAACAATATTTT
*
25172167 CATTTTGTTGACTCACTTCGCATCGTACATTATTAAATCTGCTAAAATGATGTCCAACTGTCTGA
196 CATTTTGTTGACTCACTTCGCATCGTACATTATTAAATCTGCTAAAATGATGTCCAACTGCCTGA
*
25172232 TCTGCATTATGTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCTTCAAAGCATGCATCTCT
261 TCTGCATTATCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCTTCAAAGCATGCATCTCT
25172297 ATTTGAATCACCAAAAC
326 ATTTGAATCACCAAAAC
* *
25172314 CACTATTTCTTGAGTTCAATACATGTTTTGTTTGCCTTTTAGGCAGTATGTTTTTTGCACT-AGA
1 CACTATTTCTTGAGTTCAATACATGTTGTGTTTGCCTTTTAGGCAGCATGTTTTTTGCA-TGAGA
* * *
25172378 AGGTTCACTTCTTTGGTTGAATTTTGAGACAATCACACCAGCT-TTTTCAGTTGCATCATGACTT
65 AGGTTCACTTATGTAGTTGAATTTTGAGACAATCACACCAGCTGTTTT-AGTTGCATCATGACTT
*** *
25172442 TCCGGACCATCACATGTGGTCCTATTGTTTCCTCCACTAGCATTATCTCTTTTCACAACAATATT
129 TCCGGACCATCACATACAGTCCTATTCTTTCCTCCACTAGCATTATCTCTTTTCACAACAATATT
* * * *
25172507 TTCATTTTGTTGACTCACTTGGGATCGTATATTATTAAATCTGCTGAAATGATGTCCAACTGCCT
194 TTCATTTTGTTGACTCACTTCGCATCGTACATTATTAAATCTGCTAAAATGATGTCCAACTGCCT
* ** * *
25172572 GATCTGCATTGTCTGAGTGGTAGTGTGTGCTTCTCCAGCCACCTTTTTCTTCAAAGCATGCATCT
259 GATCTGCATTATCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCTTCAAAGCATGCATCT
25172637 CTATTTGAATCACCAAAAC
324 CTATTTGAATCACCAAAAC
25172656 CA
1 CA
25172658 TTAGCTTCCA
Statistics
Matches: 312, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
341 4 0.01
342 307 0.98
343 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (342 bp):
CACTATTTCTTGAGTTCAATACATGTTGTGTTTGCCTTTTAGGCAGCATGTTTTTTGCATGAGAA
GGTTCACTTATGTAGTTGAATTTTGAGACAATCACACCAGCTGTTTTAGTTGCATCATGACTTTC
CGGACCATCACATACAGTCCTATTCTTTCCTCCACTAGCATTATCTCTTTTCACAACAATATTTT
CATTTTGTTGACTCACTTCGCATCGTACATTATTAAATCTGCTAAAATGATGTCCAACTGCCTGA
TCTGCATTATCTGAGCAGTAATGTGTGCTTCTCCAGCCACCTTTTCCTTCAAAGCATGCATCTCT
ATTTGAATCACCAAAAC
Found at i:25175534 original size:17 final size:17
Alignment explanation
Indices: 25175512--25175544 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
25175502 ATACATTTCA
25175512 AAATTTAAAATTCAATG
1 AAATTTAAAATTCAATG
25175529 AAATTTAAAATTCAAT
1 AAATTTAAAATTCAAT
25175545 CCTGACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATTTAAAATTCAATG
Found at i:25176095 original size:11 final size:11
Alignment explanation
Indices: 25176081--25176115 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
25176071 GGTGAGATTA
*
25176081 GATATTGTAGC
1 GATACTGTAGC
25176092 GATACTGTAGC
1 GATACTGTAGC
25176103 GATACTGTAGC
1 GATACTGTAGC
25176114 GA
1 GA
25176116 GACTAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (11 bp):
GATACTGTAGC
Found at i:25190002 original size:42 final size:43
Alignment explanation
Indices: 25189956--25190041 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
25189946 ATTTATATGC
* * *
25189956 CACACGGCCTTGACACACGCCCGTGTCCT-TGCCTATGTGGTT
1 CACACGGCCTGGACACACGCCCGTGTCCTCTACCCATGTGGTT
*
25189998 CACACGGCCTGGACACATGCCCGTGTCCTCTACCCATGTGGTT
1 CACACGGCCTGGACACACGCCCGTGTCCTCTACCCATGTGGTT
25190041 C
1 C
25190042 CAAAACATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 27 0.69
43 12 0.31
ACGTcount: A:0.15, C:0.37, G:0.23, T:0.24
Consensus pattern (43 bp):
CACACGGCCTGGACACACGCCCGTGTCCTCTACCCATGTGGTT
Found at i:25192916 original size:21 final size:22
Alignment explanation
Indices: 25192892--25192935 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
25192882 TGGCTCGGTT
*
25192892 TGTT-GCCTTTATGGCATACTC
1 TGTTGGCCCTTATGGCATACTC
25192913 TGTTGGCCCTTATGGCATACTC
1 TGTTGGCCCTTATGGCATACTC
25192935 T
1 T
25192936 AGTAAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTTGGCCCTTATGGCATACTC
Found at i:25195101 original size:53 final size:54
Alignment explanation
Indices: 25195021--25195141 Score: 147
Period size: 53 Copynumber: 2.3 Consensus size: 54
25195011 GTCGAGAAAA
* *
25195021 TAAACACGAGATAGCCCAATGAGACATTAAACACAAGATAGTCTGAA-GGGACAT
1 TAAACACGAGATAGCCCAACGAGACATTAAACACAAGATAGTCT-AACGAGACAT
* * **
25195075 TAAACATG-GATAGTCCAACGAGACATTAAACATGAGATAGTCTAACGAGACAT
1 TAAACACGAGATAGCCCAACGAGACATTAAACACAAGATAGTCTAACGAGACAT
* *
25195128 TAAAAACGGGATAG
1 TAAACACGAGATAG
25195142 TCCGTCGAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
52 2 0.04
53 43 0.75
54 12 0.21
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.18
Consensus pattern (54 bp):
TAAACACGAGATAGCCCAACGAGACATTAAACACAAGATAGTCTAACGAGACAT
Found at i:25195140 original size:27 final size:27
Alignment explanation
Indices: 25195021--25195143 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
25195011 GTCGAGAAAA
* * *
25195021 TAAACACGAGATAGCCCAATGAGACAT
1 TAAACACGAGATAGTCTAACGAGACAT
* *
25195048 TAAACACAAGATAGTCTGAA-GGGACAT
1 TAAACACGAGATAGTCT-AACGAGACAT
* *
25195075 TAAACATG-GATAGTCCAACGAGACAT
1 TAAACACGAGATAGTCTAACGAGACAT
*
25195101 TAAACATGAGATAGTCTAACGAGACAT
1 TAAACACGAGATAGTCTAACGAGACAT
* *
25195128 TAAAAACGGGATAGTC
1 TAAACACGAGATAGTC
25195144 CGTCGAGGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.02
26 21 0.26
27 56 0.69
28 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (27 bp):
TAAACACGAGATAGTCTAACGAGACAT
Found at i:25205027 original size:115 final size:117
Alignment explanation
Indices: 25204823--25205054 Score: 317
Period size: 115 Copynumber: 2.0 Consensus size: 117
25204813 CAAAATCTGG
* * *
25204823 TAGGGAAAAAAATAAAACCTGCTATTCCTAAAAGTAGTCAAACTTGGGTCCCCCAAGTCTCCAAG
1 TAGGGAAAAAAATAAAACCTACTATTCCTAAAAGAAGTCAAACCTGGGTCCCCCAAGTCTCCAAG
* * *
25204888 GTTGTTTAACCGCTCATCTACCCACAAACCATTGCTAGTTTATGTCAAGAAA
66 GTTGTTTAACCACTCATCTACCCACAAACCATTACTAATTTATGTCAAGAAA
* * * * * *
25204940 TAGGG-AAAAAATTAAACTTACTATTCCTAGAAGAAGTCAAACCTGGGT-CTCCATGT-TACCAT
1 TAGGGAAAAAAATAAAACCTACTATTCCTAAAAGAAGTCAAACCTGGGTCCCCCAAGTCT-CCAA
*
25205002 GGTTGTTTAACCACTCATCTACCCACAAACCATTACTAATTTATGTTAAGAAA
65 GGTTGTTTAACCACTCATCTACCCACAAACCATTACTAATTTATGTCAAGAAA
25205055 CTTATAAAAC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
114 1 0.01
115 58 0.57
116 37 0.37
117 5 0.05
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (117 bp):
TAGGGAAAAAAATAAAACCTACTATTCCTAAAAGAAGTCAAACCTGGGTCCCCCAAGTCTCCAAG
GTTGTTTAACCACTCATCTACCCACAAACCATTACTAATTTATGTCAAGAAA
Found at i:25212564 original size:41 final size:41
Alignment explanation
Indices: 25212519--25212602 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 41
25212509 GTGTAAATAT
*
25212519 GCTGATGCTCAGATCTTTAGCGGCGTTTTT-GAAAATGCGCC
1 GCTGATGCTCAGATCTTTAGCGGCATTTTTAGAAAA-GCGCC
25212560 GCTGATGCTCAGATCTTTAGCGGCATTTTTAGAAAAGCGCC
1 GCTGATGCTCAGATCTTTAGCGGCATTTTTAGAAAAGCGCC
25212601 GC
1 GC
25212603 AAAAACATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 36 0.88
42 5 0.12
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (41 bp):
GCTGATGCTCAGATCTTTAGCGGCATTTTTAGAAAAGCGCC
Found at i:25213041 original size:14 final size:15
Alignment explanation
Indices: 25213008--25213041 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
25212998 TAAGTTTTAT
25213008 AGATTATGGAATTAG
1 AGATTATGGAATTAG
25213023 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
25213037 GGATT
1 AGATT
25213042 TTTGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:25213100 original size:12 final size:12
Alignment explanation
Indices: 25213083--25213107 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25213073 ATGGGTTAGG
25213083 GGTTAGGGGTTA
1 GGTTAGGGGTTA
25213095 GGTTAGGGGTTA
1 GGTTAGGGGTTA
25213107 G
1 G
25213108 ATGTTAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:25213107 original size:7 final size:7
Alignment explanation
Indices: 25213075--25213107 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
25213065 TAAGGTTTAT
25213075 GGGTTAG
1 GGGTTAG
25213082 GGGTTAG
1 GGGTTAG
25213089 GGGTTA-
1 GGGTTAG
25213095 -GGTTAG
1 GGGTTAG
25213101 GGGTTAG
1 GGGTTAG
25213108 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.21
7 19 0.79
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:25213113 original size:19 final size:20
Alignment explanation
Indices: 25213076--25213123 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
25213066 AAGGTTTATG
*
25213076 GGTTAGGGGTTAGGGGTT-A
1 GGTTAGGGGTTAGAGGTTAA
*
25213095 GGTTAGGGGTTAGATGTTAA
1 GGTTAGGGGTTAGAGGTTAA
25213115 GAGTTAGGG
1 G-GTTAGGG
25213124 ATTTAGGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.64
20 2 0.08
21 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (20 bp):
GGTTAGGGGTTAGAGGTTAA
Found at i:25213233 original size:56 final size:57
Alignment explanation
Indices: 25213162--25213280 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 57
25213152 TTAGAGTTTC
*
25213162 GGGTTTAGATTAATTAGTGTGTTTTAA-GTATATATTAAATAAGGTTTAGGGGTTAG
1 GGGTTAAGATTAATTAGTGTGTTTTAATGTATATATTAAATAAGGTTTAGGGGTTAG
* * *
25213218 GGGTTAAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGTTAG
1 GGGTTAAGATTAATTAGTGTGTTTTAATGTATATATTAAATAAGGTTTAGGGGTTAG
25213275 GGGTTA
1 GGGTTA
25213281 GGGATTTAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
56 25 0.43
57 33 0.57
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (57 bp):
GGGTTAAGATTAATTAGTGTGTTTTAATGTATATATTAAATAAGGTTTAGGGGTTAG
Found at i:25214096 original size:108 final size:105
Alignment explanation
Indices: 25213978--25214187 Score: 228
Period size: 108 Copynumber: 1.9 Consensus size: 105
25213968 TCACTTAACT
*
25213978 AATAATTTTTAAC-AAACAAAATAAAAT-ATTTTTAGCATAGCAAAACAGTGTCGTTTTATTCCA
1 AATAATTTTT-ACTAAA-AAAAT-AAATCA-TTTTA-CATAGCAAAACAGTGTCATTTTATTCCA
*
25214041 AATGAAATAATTTTTTAGCGGCATTTTTATAAAAAACGCCACGAAA
61 AATAAAATAATTTTTT-GCGGCATTTTTATAAAAAACGCCACGAAA
** * *
25214087 AATAA-TTTTACTTTAAAAAAATAGCTCCATTTTATATAGCAAAACAGTGTCATTTTATTCCGAA
1 AATAATTTTTAC--TAAAAAAATAAAT-CATTTTACATAGCAAAACAGTGTCATTTTATTCCAAA
* * **
25214151 TAAAATAATTTTTTGCTGCGTTTTTATGGAAAACGCC
63 TAAAATAATTTTTTGCGGCATTTTTATAAAAAACGCC
25214188 GCAAAAGTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
107 21 0.24
108 46 0.53
109 15 0.17
110 4 0.05
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (105 bp):
AATAATTTTTACTAAAAAAATAAATCATTTTACATAGCAAAACAGTGTCATTTTATTCCAAATAA
AATAATTTTTTGCGGCATTTTTATAAAAAACGCCACGAAA
Found at i:25214330 original size:146 final size:146
Alignment explanation
Indices: 25214056--25214413 Score: 466
Period size: 146 Copynumber: 2.4 Consensus size: 146
25214046 AATAATTTTT
* * *
25214056 TAGCGGCATTTTTATAAAAAACGCCACGAAAAATAATTTTACTTTAAAAAAATAGCTCCATTTTA
1 TAGCGGCGTTTTTATAAAAAACGCCAC-AAAAAAAATTTTACTTTAAAAAAATAGCGCCATTTTA
* * * * *** *
25214121 TATAGCAAAACAGTGTCATTTTATTCCGAATAAAATAATTTTTTGCTGCGTTTTTATGGAAAACG
65 CATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTGTAACAAAAACA
*
25214186 CCGCAAAAGTTAAGCAA
130 CCGCAAAAGATAAGCAA
*
25214203 TAGCGGCGTTTTTAT-AAAAACGCCACAAAAAAAATTTTACTTTAAAAAAATAGCGCCCTTTTAG
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAAAATTTTACTTTAAAAAAATAGCGCCATTTTA-
* ** *
25214267 CATAGCAAAACAGTGTCGTTTTATTTTAAATGAAATAATTTTTTGCGGCGTTTGTAACAAAAACA
65 CATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTGTAACAAAAACA
* * *
25214332 CTGCAAAAGATCAGCTA
130 CCGCAAAAGATAAGCAA
* * *
25214349 TAGCGGCGTTTTTATCAAAAACGCCACAAAAAATAATTTGACTTTAAAAAAACAGGCGCCATTTT
1 TAGCGGCGTTTTTATAAAAAACGCCACAAAAAA-AATTTTACTTTAAAAAAATA-GCGCCATTTT
25214414 GTAAAATTCC
Statistics
Matches: 184, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
145 34 0.18
146 92 0.50
147 31 0.17
148 18 0.10
149 9 0.05
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (146 bp):
TAGCGGCGTTTTTATAAAAAACGCCACAAAAAAAATTTTACTTTAAAAAAATAGCGCCATTTTAC
ATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAATTTTTTGCGGCGTTTGTAACAAAAACAC
CGCAAAAGATAAGCAA
Found at i:25214706 original size:20 final size:20
Alignment explanation
Indices: 25214681--25214722 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25214671 TTTCAATTTG
25214681 GTATTTGGGGGTTTTTCATT
1 GTATTTGGGGGTTTTTCATT
25214701 GTATTTGGGGGTTTTTCATT
1 GTATTTGGGGGTTTTTCATT
25214721 GT
1 GT
25214723 TACTGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.05, G:0.31, T:0.55
Consensus pattern (20 bp):
GTATTTGGGGGTTTTTCATT
Found at i:25217293 original size:43 final size:43
Alignment explanation
Indices: 25217246--25217471 Score: 362
Period size: 43 Copynumber: 5.3 Consensus size: 43
25217236 GATATGTTTT
* *
25217246 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
25217289 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * *
25217332 TAGCGGCATTTGTGGGAAATGCACCGCTAAAGGTCCTAATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
25217375 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
25217418 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGCTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
25217461 TAGCGGCGTTT
1 TAGCGGCGTTT
25217472 ATTTCTATAA
Statistics
Matches: 170, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 170 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:25219598 original size:36 final size:36
Alignment explanation
Indices: 25219558--25219635 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
25219548 ATGATGATTG
* * *
25219558 ATGTGAAAATGAATATGAGGGTGTGCTATTTATGCC
1 ATGTGAAAATAAATATGAGGGTATGCTATTCATGCC
* * * *
25219594 ATGTGACAGTAAATATGTGGGTATGTTATTCATGCC
1 ATGTGAAAATAAATATGAGGGTATGCTATTCATGCC
25219630 ATGTGA
1 ATGTGA
25219636 CAGTTTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.35
Consensus pattern (36 bp):
ATGTGAAAATAAATATGAGGGTATGCTATTCATGCC
Found at i:25219636 original size:36 final size:36
Alignment explanation
Indices: 25219569--25219639 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
25219559 TGTGAAAATG
* *
25219569 AATATGAGGGTGTGCTATTTATGCCATGTGACAGTA
1 AATATGAGGGTATGCTATTCATGCCATGTGACAGTA
* *
25219605 AATATGTGGGTATGTTATTCATGCCATGTGACAGT
1 AATATGAGGGTATGCTATTCATGCCATGTGACAGT
25219640 TTTTATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (36 bp):
AATATGAGGGTATGCTATTCATGCCATGTGACAGTA
Found at i:25225800 original size:152 final size:150
Alignment explanation
Indices: 25225560--25225867 Score: 472
Period size: 152 Copynumber: 2.0 Consensus size: 150
25225550 ATTGGTCAAC
* * * **
25225560 TAGTCAAGGTATAAGTGATGGTACCGAAAGTCAAGTGGTTTTGAAAATGAGGTATCGGGACCTCA
1 TAGTGAAGGTAGAAGTGATGGTACCGAAAGTCAAGCGGTTTTGAAAATGAGGTATCAAGACCTCA
* * * * * *
25225625 TTTTTGTAAATCGAGCCCGTGAATATTTTTATTAAATATTTATGGAGCTTTTATATAGGTGAATT
66 TTTTCGTAAATCGAACCCATGAATATTGTTATTAAATATTTACGAAGCTTTTATATAGGTGAATT
25225690 GAAGTTTGGTCAAAAAATTT
131 GAAGTTTGGTCAAAAAATTT
*
25225710 TAGTGAAGGTAGAAGTGGTGAGTACCGAAAGTCAAGCGGTTTTGAAAAATGAGGTATCAAGACCT
1 TAGTGAAGGTAGAAGTGATG-GTACCGAAAGTCAAGCGGTTTTG-AAAATGAGGTATCAAGACCT
*
25225775 CATTTTCGTAAATCGAACCCATGAATATTGTTATTAAATATTTACGAAGTTTTTATATAGGTGAA
64 CATTTTCGTAAATCGAACCCATGAATATTGTTATTAAATATTTACGAAGCTTTTATATAGGTGAA
*
25225840 TTGAAGTTTGGTCCAAAAATTT
129 TTGAAGTTTGGTCAAAAAATTT
25225862 TAGTGA
1 TAGTGA
25225868 TTGAATGATT
Statistics
Matches: 142, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
150 17 0.12
151 22 0.15
152 103 0.73
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.34
Consensus pattern (150 bp):
TAGTGAAGGTAGAAGTGATGGTACCGAAAGTCAAGCGGTTTTGAAAATGAGGTATCAAGACCTCA
TTTTCGTAAATCGAACCCATGAATATTGTTATTAAATATTTACGAAGCTTTTATATAGGTGAATT
GAAGTTTGGTCAAAAAATTT
Found at i:25229414 original size:21 final size:20
Alignment explanation
Indices: 25229390--25229429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
25229380 ATAATAGAAA
* *
25229390 GCAATTCAAAGTAAATAATAT
1 GCAATGCAAAATAAA-AATAT
25229411 GCAATGCAAAATAAAAATA
1 GCAATGCAAAATAAAAATA
25229430 ACATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (20 bp):
GCAATGCAAAATAAAAATAT
Found at i:25229442 original size:23 final size:23
Alignment explanation
Indices: 25229402--25229449 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
25229392 AATTCAAAGT
* * *
25229402 AAATAATATGCAATGCAAAATAA
1 AAATAACATACAAAGCAAAATAA
*
25229425 AAATAACATACAAAGCAAATTAA
1 AAATAACATACAAAGCAAAATAA
25229448 AA
1 AA
25229450 TAAATAACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (23 bp):
AAATAACATACAAAGCAAAATAA
Found at i:25230006 original size:26 final size:26
Alignment explanation
Indices: 25229972--25230042 Score: 108
Period size: 25 Copynumber: 2.7 Consensus size: 26
25229962 TGAAAAACTT
*
25229972 AAATAAATAATAATAAAAAAATTTTA
1 AAATAAATAATAATAAAAAAAGTTTA
25229998 AAATAAATAAT-ATAAAAAAAGTTTA
1 AAATAAATAATAATAAAAAAAGTTTA
25230023 AAATAAATAAATAAATAAAA
1 AAATAAAT-AAT-AATAAAA
25230043 TTGCAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 21 0.51
26 14 0.34
28 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (26 bp):
AAATAAATAATAATAAAAAAAGTTTA
Found at i:25230805 original size:17 final size:17
Alignment explanation
Indices: 25230757--25230826 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 17
25230747 TTTTCTTTTT
*
25230757 AAAAT-GAAAAATAAAAA
1 AAAATAGAAAAA-AGAAA
*
25230774 AAACAGAGAAGAAAAGAAAA
1 AAA-ATAGAA-AAAAG-AAA
*
25230794 AAAATAGAAAAAAGAAC
1 AAAATAGAAAAAAGAAA
25230811 AAAATAGAAAAAAGAA
1 AAAATAGAAAAAAGAA
25230827 CACATTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 21 0.47
18 6 0.13
19 9 0.20
20 9 0.20
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.06
Consensus pattern (17 bp):
AAAATAGAAAAAAGAAA
Found at i:25230827 original size:17 final size:17
Alignment explanation
Indices: 25230780--25230828 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
25230770 AAAAAAACAG
*
25230780 AGAAGAAAAGAAAAAAAAT
1 AGAA-AAAAG-AACAAAAT
25230799 AGAAAAAAGAACAAAAT
1 AGAAAAAAGAACAAAAT
25230816 AGAAAAAAGAACA
1 AGAAAAAAGAACA
25230829 CATTTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 20 0.69
18 5 0.17
19 4 0.14
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (17 bp):
AGAAAAAAGAACAAAAT
Found at i:25230939 original size:14 final size:15
Alignment explanation
Indices: 25230916--25230945 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25230906 TTTATAACCG
25230916 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
25230931 AAAAG-AAAAAGAAA
1 AAAAGAAAAAAGAAA
25230945 A
1 A
25230946 GAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:25231741 original size:21 final size:22
Alignment explanation
Indices: 25231710--25231760 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
25231700 ACACGGTTTG
*
25231710 CTCACACGGTCGTGTGACCCAT
1 CTCACATGGTCGTGTGACCCAT
* * *
25231732 C-CACATGGTCTTGTGGCCTAT
1 CTCACATGGTCGTGTGACCCAT
25231753 CTCACATG
1 CTCACATG
25231761 AGCACGGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.27
Consensus pattern (22 bp):
CTCACATGGTCGTGTGACCCAT
Found at i:25239256 original size:27 final size:27
Alignment explanation
Indices: 25239218--25239294 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
25239208 TAGTATTGGC
25239218 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
25239245 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
25239272 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
25239295 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:25239493 original size:19 final size:19
Alignment explanation
Indices: 25239471--25239508 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25239461 AATTTAATTT
*
25239471 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
25239490 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
25239509 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:25239659 original size:22 final size:24
Alignment explanation
Indices: 25239557--25239672 Score: 98
Period size: 22 Copynumber: 4.8 Consensus size: 24
25239547 TTATAAAATA
25239557 ATTACAATATTCATAC-AAA-AA-
1 ATTACAATATTCATACAAAATAAT
* * *** *
25239578 ATTACAATATTACAATATATACCGAC
1 ATTACAATATT-C-ATACAAAATAAT
25239604 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATAC-AAA--ATAAT
25239631 ATTACAATATTCATACAAAA-AA-
1 ATTACAATATTCATACAAAATAAT
25239653 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
25239673 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
21 11 0.14
22 21 0.27
23 5 0.06
24 5 0.06
25 4 0.05
26 14 0.18
27 17 0.22
ACGTcount: A:0.53, C:0.15, G:0.01, T:0.31
Consensus pattern (24 bp):
ATTACAATATTCATACAAAATAAT
Found at i:25239880 original size:16 final size:16
Alignment explanation
Indices: 25239859--25239900 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
25239849 AATAATTTGA
*
25239859 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
25239875 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
25239891 TAGTTTTAAT
1 TAATTTTAAT
25239901 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:25240151 original size:27 final size:27
Alignment explanation
Indices: 25240079--25240140 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
25240069 GGTCTAGTAA
*
25240079 TGGCGCCTCTCTATAAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
25240106 TGGCGCCTCTCTATGAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
25240133 TGGCGCCT
1 TGGCGCCT
25240141 ACCTGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCTCTATGAGGCACCTTCAT
Found at i:25243061 original size:24 final size:24
Alignment explanation
Indices: 25243034--25243088 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
25243024 TTAACTCGCT
25243034 TTAGGGTTTGTAATTATCTTTAGA
1 TTAGGGTTTGTAATTATCTTTAGA
25243058 TTAGGGTTTGTAATTATCTTTAGA
1 TTAGGGTTTGTAATTATCTTTAGA
25243082 TTAGGGT
1 TTAGGGT
25243089 GGATTAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.49
Consensus pattern (24 bp):
TTAGGGTTTGTAATTATCTTTAGA
Found at i:25248922 original size:30 final size:30
Alignment explanation
Indices: 25248871--25249019 Score: 182
Period size: 30 Copynumber: 5.1 Consensus size: 30
25248861 ATTTCTTATA
*
25248871 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
25248902 CCAATATTTGATACCAATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
25248931 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
25248957 CCATTATTTGATACCCAAATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
25248987 CTATTATTTGATACCCATATATTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
25249017 CCA
1 CCA
25249020 TAAATATGGA
Statistics
Matches: 104, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
25 22 0.21
26 2 0.02
29 2 0.02
30 71 0.68
31 7 0.07
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:25248926 original size:15 final size:15
Alignment explanation
Indices: 25248868--25248927 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
25248858 CAGATTTCTT
*
25248868 ATACCAATATC-TCG
1 ATACCAATATCTTTG
*
25248882 ATACCCATATCTTTG
1 ATACCAATATCTTTG
*
25248897 ACTTTCCAATA--TTTG
1 A--TACCAATATCTTTG
25248912 ATACCAATATCTTTG
1 ATACCAATATCTTTG
25248927 A
1 A
25248928 CTTTATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
13 7 0.19
14 10 0.28
15 13 0.36
17 6 0.17
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (15 bp):
ATACCAATATCTTTG
Found at i:25248934 original size:25 final size:25
Alignment explanation
Indices: 25248906--25248956 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
25248896 GACTTTCCAA
25248906 TATTTGATACCAATATCTTTGACTT
1 TATTTGATACCAATATCTTTGACTT
*
25248931 TATTTGATACCCATATCTTTGACTT
1 TATTTGATACCAATATCTTTGACTT
25248956 T
1 T
25248957 CCATTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (25 bp):
TATTTGATACCAATATCTTTGACTT
Found at i:25248947 original size:55 final size:57
Alignment explanation
Indices: 25248881--25249019 Score: 194
Period size: 55 Copynumber: 2.4 Consensus size: 57
25248871 CCAATATCTC
25248881 GATACCCATATCTTTGACTTTCCAATATTTGATA-CCAATATCTTTGA-CT-TTATTT
1 GATACCCATATCTTTGACTTTCCAATATTTGATACCCAA-ATCTTTGATCTATTATTT
*
25248936 GATACCCATATCTTTGACTTTCCATTATTTGATACCCAAATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCCAATATTTGATACCCAAATCTTTGA---TCTATTATTT
* *
25248996 GATACCCATATATTTGATTTTCCA
1 GATACCCATATCTTTGACTTTCCA
25249020 TAAATATGGA
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
55 41 0.55
56 4 0.05
59 2 0.03
60 28 0.37
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (57 bp):
GATACCCATATCTTTGACTTTCCAATATTTGATACCCAAATCTTTGATCTATTATTT
Found at i:25253402 original size:30 final size:31
Alignment explanation
Indices: 25253351--25253414 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
25253341 ATTTCTTATA
* *
25253351 CCAATATCTCGATACCTATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTCT
*
25253382 CCAATAT-TTGATACCCATATCTTTGACTCT
1 CCAATATCTCGATACCCATATCTTTGACTCT
25253412 CCA
1 CCA
25253415 TAAATATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATCTTTGACTCT
Found at i:25254499 original size:80 final size:81
Alignment explanation
Indices: 25254409--25254623 Score: 249
Period size: 86 Copynumber: 2.6 Consensus size: 81
25254399 ATTTTATTCG
* * *
25254409 ATTTTATTTCCAAATTAAAAGTGAATAAAATCTATTTCGGGATTTATTCCCT-CAGTTCAACGAA
1 ATTTTATTTCCAAATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCTGCAGCTCAACGAA
*
25254473 TTTTATTCCATTTTTT
66 CTTTATTCCATTTTTT
* *
25254489 ATTTTATTTCCAAACGAGAATT-AAAGTTAAATAAAATCTGTTTCAGGATTTATT-CCTGCCGCT
1 ATTTTATTT-C---C-A-AATTAAAAG-TAAATAAAATCTGTTTCGGGATTTATTCCCTGCAGCT
25254552 CAACGAACTTTATTCCATTTTTT
59 CAACGAACTTTATTCCATTTTTT
* * *
25254575 ATTTGATTTCCAAA-CAAGAATTAAATAAAATCTGTTTCGGGATTTATTC
1 ATTTTATTTCCAAATTAA-AAGTAAATAAAATCTGTTTCGGGATTTATTC
25254624 TTGCCATTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
80 38 0.33
81 4 0.04
82 1 0.01
84 1 0.01
85 9 0.08
86 61 0.54
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (81 bp):
ATTTTATTTCCAAATTAAAAGTAAATAAAATCTGTTTCGGGATTTATTCCCTGCAGCTCAACGAA
CTTTATTCCATTTTTT
Found at i:25254544 original size:86 final size:85
Alignment explanation
Indices: 25254432--25254712 Score: 326
Period size: 86 Copynumber: 3.3 Consensus size: 85
25254422 ATTAAAAGTG
25254432 AATAAAATCTATTTCGGGATTTATTCCCT-CAGTTCAACGAATTTTATTCCATTTTTTATTTTAT
1 AATAAAATCTATTTCGGGATTTATT-CCTGCAGTTCAACGAATTTTATTCCATTTTTTATTTTAT
25254496 TTCCAAACGAGAATTAAAGTTA
65 TTCCAAACGAGAATTAAA-TTA
* * * * * *
25254518 AATAAAATCTGTTTCAGGATTTATTCCTGCCGCTCAACGAACTTTATTCCATTTTTTATTTGATT
1 AATAAAATCTATTTCGGGATTTATTCCTGCAGTTCAACGAATTTTATTCCATTTTTTATTTTATT
*
25254583 TCCAAAC---AA--GAATTA
66 TCCAAACGAGAATTAAATTA
* * * * *
25254598 AATAAAATCTGTTTCGGGATTTATTCTTGCCA-TTC-ACCAGATTTTATTCTATTTTTTATTTTG
1 AATAAAATCTATTTCGGGATTTATTCCTG-CAGTTCAACGA-ATTTTATTCCATTTTTTATTTTA
*
25254661 TTGCCAAAACGAGAAATTAAAATTA
64 TTTCC-AAACGAG-AATT-AAATTA
25254686 AATAAAATCTATTTCGGGATTTATTCC
1 AATAAAATCTATTTCGGGATTTATTCC
25254713 CGCCATTTAA
Statistics
Matches: 164, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
79 3 0.02
80 55 0.34
81 7 0.04
83 2 0.01
85 5 0.03
86 62 0.38
88 30 0.18
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (85 bp):
AATAAAATCTATTTCGGGATTTATTCCTGCAGTTCAACGAATTTTATTCCATTTTTTATTTTATT
TCCAAACGAGAATTAAATTA
Found at i:25266165 original size:95 final size:95
Alignment explanation
Indices: 25265963--25266138 Score: 280
Period size: 95 Copynumber: 1.9 Consensus size: 95
25265953 ACAATTGAGC
* * *
25265963 TATCACCTTTTGTTCACTGTTATTGGTGTAGTTCAAAATATCATAAGGCTTTCCAATGTCCAATT
1 TATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGGCTTTCCAATGTCCAATT
*
25266028 AAATATTCAAATAGAGGAATACGATTGAAA
66 AAATATCCAAATAGAGGAATACGATTGAAA
* * *
25266058 TATCACCTTTTGTGCAATGTTGTTGGTGTAGTTCAAAAGATCATAAGGGTTTCCAATGTCTAATT
1 TATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGGCTTTCCAATGTCCAATT
*
25266123 AAATATCCAACTAGAG
66 AAATATCCAAATAGAG
25266139 ATGAAAGTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (95 bp):
TATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGGCTTTCCAATGTCCAATT
AAATATCCAAATAGAGGAATACGATTGAAA
Found at i:25269812 original size:62 final size:62
Alignment explanation
Indices: 25269655--25269812 Score: 201
Period size: 62 Copynumber: 2.5 Consensus size: 62
25269645 AATTAGAGGT
* * * * * * *
25269655 ACACGGGCTAGGCGAACAGATGTGTCTCCAGGCCGTGTAACTTACTATTTGTATTTTTGGTC
1 ACACGGGCTAGGGGCACAGGTGTGTGTCTAGGCCGTGGAACTCACTATTTGTATTTTTGGTC
* * * *
25269717 ACACGAGCTAGGGACATAGGCGTGTGT-TCAGGCCGTGGAACTCACTATTTGTATTTTTGGTC
1 ACACGGGCTAGGGGCACAGGTGTGTGTCT-AGGCCGTGGAACTCACTATTTGTATTTTTGGTC
25269779 ACACGGGCTAGGGGCACAGGTGTGTGTCTAGGCC
1 ACACGGGCTAGGGGCACAGGTGTGTGTCTAGGCC
25269813 ATGTGTAGGG
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
62 78 0.99
63 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (62 bp):
ACACGGGCTAGGGGCACAGGTGTGTGTCTAGGCCGTGGAACTCACTATTTGTATTTTTGGTC
Found at i:25276736 original size:82 final size:83
Alignment explanation
Indices: 25276598--25276762 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
25276588 ACATATATGA
25276598 ATATTTAGCTAGCATGGGTTACATTAAAAATGGATCACACGACCATTGCCAATTTGGGTCGAGTG
1 ATATTTAGCTAGCATGGGTTACATTAAAAATGGATCACACGACCATTGCCAATTTGGGTCGAGTG
25276663 GGCTACACGGGCACACAC
66 GGCTACACGGGCACACAC
25276681 ATATTTAGCT-GCATGGGTTACATTAAAAATGGATCACACGACCATTGCCAATTTGGGTCGAGTG
1 ATATTTAGCTAGCATGGGTTACATTAAAAATGGATCACACGACCATTGCCAATTTGGGTCGAGTG
25276745 GGCTACACGGGCACACAC
66 GGCTACACGGGCACACAC
25276763 GGGCGTGTGG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 72 0.88
83 10 0.12
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (83 bp):
ATATTTAGCTAGCATGGGTTACATTAAAAATGGATCACACGACCATTGCCAATTTGGGTCGAGTG
GGCTACACGGGCACACAC
Found at i:25278016 original size:26 final size:26
Alignment explanation
Indices: 25277973--25278027 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
25277963 AAGTGTTTTA
*
25277973 AAACTGATACATGCTATGATATTCTG
1 AAACTAATACATGCTATGATATTCTG
* *
25277999 AAACTAATATATGTTATGATATTCTG
1 AAACTAATACATGCTATGATATTCTG
25278025 AAA
1 AAA
25278028 TTACTGTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (26 bp):
AAACTAATACATGCTATGATATTCTG
Found at i:25288010 original size:9 final size:9
Alignment explanation
Indices: 25287998--25288023 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25287988 TTTTTAGATT
25287998 ATTTAAATA
1 ATTTAAATA
25288007 ATTTAAATA
1 ATTTAAATA
25288016 ATTTAAAT
1 ATTTAAAT
25288024 TTGTATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTTAAATA
Found at i:25309124 original size:9 final size:9
Alignment explanation
Indices: 25309110--25309148 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
25309100 TTAATTTTTA
25309110 ATTTTATTT
1 ATTTTATTT
*
25309119 ATTTTATTC
1 ATTTTATTT
25309128 A-TTTATTT
1 ATTTTATTT
*
25309136 ATTTGATTT
1 ATTTTATTT
25309145 ATTT
1 ATTT
25309149 CACTAACGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (9 bp):
ATTTTATTT
Found at i:25309569 original size:132 final size:132
Alignment explanation
Indices: 25309433--25309818 Score: 664
Period size: 132 Copynumber: 2.9 Consensus size: 132
25309423 ACCTGTAATT
* * * * *
25309433 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTCGGTGGCTTAGATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
* * *
25309498 CTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGCTA
66 TTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTA
25309563 TC
131 TC
25309565 TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
* * *
25309630 TTGGAAAGATAAGATTTTCCATCTTTGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGCTA
66 TTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTA
25309695 TC
131 TC
25309697 TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
*
25309762 TTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAG
66 TTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAG
25309819 GCCCGGTGGC
Statistics
Matches: 241, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 241 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
TTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATC
TTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCTA
TC
Found at i:25309698 original size:44 final size:44
Alignment explanation
Indices: 25309504--25310052 Score: 129
Period size: 44 Copynumber: 12.5 Consensus size: 44
25309494 TATCCTGGAA
* ** * * *
25309504 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTACTTAAGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
* * * * * * *
25309548 AGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTGAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
* * * ** * *
25309592 AGACAAGGTTCAG-TGGCTTAAATCTGCTTCC-C-ACTATCTT-GGAA
1 AGATAA-GATCTGCTATCTTTAATCTGC-TCCACTACT-TCTTAGG-G
* * * *
25309636 AGATAAGATTTTCCATCTTTGATCTGCTCCACTACTTCTTAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
* * * * * * *
25309680 AGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTGAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
* * * ** * *
25309724 AGACAAGGTTCAG-TGGCTTAAATCTGCTTCC-C-ACTATCTT-GGAA
1 AGATAA-GATCTGCTATCTTTAATCTGC-TCCACTACT-TCTTAGG-G
* * ** * *
25309768 AGATAAGATTTACCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
** * * ** * ** *
25309812 AGATAAGGCCCGGTGGCTTAAATCTATTTCC-C-ACTATCTT-GGAA
1 AGATAAGATCTGCTATCTTTAATCT-GCTCCACTACT-TCTTAGG-G
* * * * *
25309856 AGATAAGATTTG-TCGTCCTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTGCT-ATCTTTAATCTGCTCCACTACTTCTTAGGG
* * * * * * * * *
25309900 AGATAAGATCTGGTGTCTTCAACCTACTTCGCTACTGCTCAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
* ** * ** * *
25309944 AGACAAGGCCTGGTGGCTTAAATCTGCTTCTCACTA--TCTT-GGAA
1 AGATAAGATCTGCTATCTTTAATCTGC-TC-CACTACTTCTTAGG-G
* ** * *
25309988 AGATAAGATTTGCCGTCTTTGATTTGCTCCACTACTTCTTAGGG
1 AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
25310032 AGATAAGATCTGCTATCTTTA
1 AGATAAGATCTGCTATCTTTA
25310053 CTGATCTGTT
Statistics
Matches: 344, Mismatches: 131, Indels: 60
0.64 0.24 0.11
Matches are distributed among these distances:
42 5 0.01
43 31 0.09
44 268 0.78
45 36 0.10
46 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (44 bp):
AGATAAGATCTGCTATCTTTAATCTGCTCCACTACTTCTTAGGG
Found at i:25309812 original size:88 final size:88
Alignment explanation
Indices: 25309714--25309902 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 88
25309704 TACTCCGCTG
* ** *
25309714 CTGCTGAGGGAGACAAGGTTCAGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTT
1 CTGCTTAGGGAGACAAGGCCCAGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTT
*
25309779 ACCGTCTTTGATCTGCTCCACTA
66 ACCGTCCTTGATCTGCTCCACTA
* * *
25309802 CTGCTTAGGGAGATAAGGCCCGGTGGCTTAAATCTATTTCCCACTATCTTGGAAAGATAAGATTT
1 CTGCTTAGGGAGACAAGGCCCAGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTT
**
25309867 GTCGTCCTTGATCTGCTCCACTA
66 ACCGTCCTTGATCTGCTCCACTA
25309890 CTGCTTAGGGAGA
1 CTGCTTAGGGAGA
25309903 TAAGATCTGG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (88 bp):
CTGCTTAGGGAGACAAGGCCCAGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTT
ACCGTCCTTGATCTGCTCCACTA
Found at i:25309853 original size:220 final size:220
Alignment explanation
Indices: 25309604--25310038 Score: 694
Period size: 220 Copynumber: 2.0 Consensus size: 220
25309594 ACAAGGTTCA
* *
25309604 GTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTT-TCCATCTTTGATCTGCTCCAC
1 GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGT-CATCCTTGATCTGCTCCAC
* * *
25309668 TACTTCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCGCTGCTGCTGAGGGAGACAAGG-
65 TACTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCGCTACTGCTCAGGGAGACAAGGC
*
25309732 TTCAGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTC
130 CT-AGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTC
25309797 CACTACTGCTTAGGGAGATAAGGCCCG
194 CACTACTGCTTAGGGAGATAAGGCCCG
* *
25309824 GTGGCTTAAATCTATTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCCTTGATCTGCTCCACT
1 GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCATCCTTGATCTGCTCCACT
* * *
25309889 ACTGCTTAGGGAGATAAGATCTGGTGTCTTCAACCTACTTCGCTACTGCTCAGGGAGACAAGGCC
66 ACTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCGCTACTGCTCAGGGAGACAAGGCC
* * * *
25309954 TGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATTTGCTCCA
131 TAGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCA
*
25310019 CTACTTCTTAGGGAGATAAG
196 CTACTGCTTAGGGAGATAAG
25310039 ATCTGCTATC
Statistics
Matches: 197, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
220 195 0.99
221 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (220 bp):
GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCATCCTTGATCTGCTCCACT
ACTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCGCTACTGCTCAGGGAGACAAGGCC
TAGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCA
CTACTGCTTAGGGAGATAAGGCCCG
Found at i:25309881 original size:132 final size:133
Alignment explanation
Indices: 25309745--25310042 Score: 345
Period size: 132 Copynumber: 2.3 Consensus size: 133
25309735 AGTGGCTTAA
* ** * *
25309745 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACTACTGCT
1 ATCTGCTT-CCACTACTGCTTAGG-AAGATAAGATCTACCGTCTTCAACCTACTCCACTACTGCT
* * * *
25309807 TAGGGAGATAAGGCCCGGTGGCTTAAATCTATTTCCCACTATCTTGGAAAGATAAGATTTGTCGT
64 CAGGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGT
25309872 CCTTG
129 CCTTG
* *** * *
25309877 ATCTGC-TCCACTACTGCTTAGGGAGATAAGATCTGGTGTCTTCAACCTACTTCGCTACTGCTCA
1 ATCTGCTTCCACTACTGCTTAGGAAGATAAGATCTACCGTCTTCAACCTACTCCACTACTGCTCA
* * * *
25309941 GGGAGACAAGGCCTGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATTTGCCGTCT
66 GGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCC
25310006 TTG
131 TTG
* * *
25310009 ATTTGC-TCCACTACTTCTTAGGGAGATAAGATCT
1 ATCTGCTTCCACTACTGCTTAGGAAGATAAGATCT
25310043 GCTATCTTTA
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
130 6 0.04
131 2 0.01
132 132 0.93
133 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (133 bp):
ATCTGCTTCCACTACTGCTTAGGAAGATAAGATCTACCGTCTTCAACCTACTCCACTACTGCTCA
GGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCC
TTG
Found at i:25309903 original size:88 final size:88
Alignment explanation
Indices: 25309736--25309906 Score: 297
Period size: 88 Copynumber: 1.9 Consensus size: 88
25309726 ACAAGGTTCA
* *
25309736 GTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTTGATCTGCTCCACT
1 GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTACCGTCCTTGATCTGCTCCACT
25309801 ACTGCTTAGGGAGATAAGGCCCG
66 ACTGCTTAGGGAGATAAGGCCCG
* **
25309824 GTGGCTTAAATCTATTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCCTTGATCTGCTCCACT
1 GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTACCGTCCTTGATCTGCTCCACT
25309889 ACTGCTTAGGGAGATAAG
66 ACTGCTTAGGGAGATAAG
25309907 ATCTGGTGTC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (88 bp):
GTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGATTTACCGTCCTTGATCTGCTCCACT
ACTGCTTAGGGAGATAAGGCCCG
Found at i:25310043 original size:132 final size:132
Alignment explanation
Indices: 25309799--25310043 Score: 400
Period size: 132 Copynumber: 1.9 Consensus size: 132
25309789 ATCTGCTCCA
* * *
25309799 CTACTGCTTAGGGAGATAAGGCCCGGTGGCTTAAATCTATTTCCCACTATCTTGGAAAGATAAGA
1 CTACTGCTCAGGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGA
*
25309864 TTTGTCGTCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTGTCTTCAACCTACTT
66 TTTGCCGTCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTGTCTTCAACCTACTT
25309929 CG
131 CG
* * *
25309931 CTACTGCTCAGGGAGACAAGGCCTGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGA
1 CTACTGCTCAGGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGA
* * *
25309996 TTTGCCGTCTTTGATTTGCTCCACTACTTCTTAGGGAGATAAGATCTG
66 TTTGCCGTCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
25310044 CTATCTTTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 103 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (132 bp):
CTACTGCTCAGGGAGACAAGGCCCGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAGA
TTTGCCGTCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGGTGTCTTCAACCTACTT
CG
Found at i:25314730 original size:11 final size:11
Alignment explanation
Indices: 25314714--25314744 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
25314704 GGGAATATCA
25314714 AAGAATATACC
1 AAGAATATACC
25314725 AAGAATATACC
1 AAGAATATACC
25314736 AAGAATATA
1 AAGAATATA
25314745 TAAATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.13, G:0.10, T:0.19
Consensus pattern (11 bp):
AAGAATATACC
Found at i:25315283 original size:16 final size:16
Alignment explanation
Indices: 25315241--25315284 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
25315231 CAAACGTGCC
25315241 CTTCTTCT-CTTTTGT
1 CTTCTTCTACTTTTGT
* *
25315256 CTTTTCTCTACTTTTTT
1 CTTCT-TCTACTTTTGT
25315273 CTTCTTCTACTT
1 CTTCTTCTACTT
25315285 CATGTCTGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.05, C:0.27, G:0.02, T:0.66
Consensus pattern (16 bp):
CTTCTTCTACTTTTGT
Found at i:25323347 original size:9 final size:9
Alignment explanation
Indices: 25323333--25323371 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
25323323 TTAATTTTTA
25323333 ATTTTATTT
1 ATTTTATTT
*
25323342 ATTTTATTC
1 ATTTTATTT
25323351 ATTTT-TTT
1 ATTTTATTT
*
25323359 ATTTGATTT
1 ATTTTATTT
25323368 ATTT
1 ATTT
25323372 CACTAACGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:25323371 original size:17 final size:18
Alignment explanation
Indices: 25323333--25323371 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
25323323 TTAATTTTTA
*
25323333 ATTTTATTTATTTTATTC
1 ATTTTATTTATTTGATTC
*
25323351 ATTTT-TTTATTTGATTT
1 ATTTTATTTATTTGATTC
25323368 ATTT
1 ATTT
25323372 CACTAACGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTATTTATTTGATTC
Found at i:25324196 original size:10 final size:10
Alignment explanation
Indices: 25324177--25324231 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
25324167 AAATATATCG
25324177 AAAA-TAATC
1 AAAATTAATC
25324186 AAAATTAATC
1 AAAATTAATC
*
25324196 AAAATTAATTAT
1 AAAATTAA-T-C
*
25324208 AAAATTAATT
1 AAAATTAATC
25324218 AAAATT--TC
1 AAAATTAATC
25324226 AAAATT
1 AAAATT
25324232 TTATAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 7 0.17
9 4 0.10
10 20 0.49
11 2 0.05
12 8 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTAATC
Found at i:25328988 original size:70 final size:70
Alignment explanation
Indices: 25328871--25329064 Score: 236
Period size: 70 Copynumber: 2.8 Consensus size: 70
25328861 GGACTAGTTG
25328871 AACAAGTCGAC-AA--ATTGTGTCCAGCGCTAGTTAGATAACTGATGATAGTTGTGCCC-ATCAC
1 AACAAGTCGACAAATTATTGTGTCCAGCGCTAGTTAGATAACTGATGATAGTTGTGCCCGA-CAC
25328932 TAGTCA
65 TAGTCA
* * *
25328938 AACAAGTCGACAAATTATTGTGCCCAGCGCTGGTTTGATAACCT-ATGATAGTTGTGCCCGACAC
1 AACAAGTCGACAAATTATTGTGTCCAGCGCTAGTTAGATAA-CTGATGATAGTTGTGCCCGACAC
**
25329002 TAGTTG
65 TAGTCA
* * * ** *
25329008 AACGAGTCAACAAATTATTGTGTCCAACGCTAGTCGGATAACTGACGATAGTTGTGC
1 AACAAGTCGACAAATTATTGTGTCCAGCGCTAGTTAGATAACTGATGATAGTTGTGC
25329065 TCACCAAGAA
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
67 11 0.10
68 2 0.02
69 2 0.02
70 90 0.83
71 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (70 bp):
AACAAGTCGACAAATTATTGTGTCCAGCGCTAGTTAGATAACTGATGATAGTTGTGCCCGACACT
AGTCA
Found at i:25332935 original size:5 final size:5
Alignment explanation
Indices: 25332927--25332959 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
25332917 ATAGAAAGAG
25332927 AAATA AAATA ATAAT- AAATA AAATA AAATA AAA
1 AAATA AAATA A-AATA AAATA AAATA AAATA AAA
25332960 ACAAAAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.12
5 20 0.77
6 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:25334196 original size:14 final size:14
Alignment explanation
Indices: 25334177--25334221 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
25334167 TTGTGTGAGG
*
25334177 GTTTAAAATATTAA
1 GTTTAAAAAATTAA
25334191 GTTTAAAAAATTAA
1 GTTTAAAAAATTAA
* *
25334205 CTTGAAAAAGATTAA
1 GTTTAAAAA-ATTAA
25334220 GT
1 GT
25334222 CTACTTACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (14 bp):
GTTTAAAAAATTAA
Found at i:25334423 original size:32 final size:32
Alignment explanation
Indices: 25334387--25334456 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
25334377 AGGTGACTAT
* *
25334387 ATATAAA-A-TTATTAAATATTTAATTAAAATTA
1 ATATAAATATTTATTAAAT-TTTAA-AAAAAATA
*
25334419 ATATAAATATTTATTTAATTTTAAAAAAAATA
1 ATATAAATATTTATTAAATTTTAAAAAAAATA
25334451 ATATAA
1 ATATAA
25334457 GTAAACCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 19 0.58
33 6 0.18
34 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAAATATTTATTAAATTTTAAAAAAAATA
Found at i:25334442 original size:23 final size:23
Alignment explanation
Indices: 25334390--25334436 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25334380 TGACTATATA
25334390 TAAAATT-AT-TAAATATTTAAT
1 TAAAATTAATATAAATATTTAAT
*
25334411 TAAAATTAATATAAATATTTATT
1 TAAAATTAATATAAATATTTAAT
25334434 TAA
1 TAA
25334437 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAATTAATATAAATATTTAAT
Found at i:25334449 original size:23 final size:23
Alignment explanation
Indices: 25334400--25334450 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
25334390 TAAAATTATT
* *
25334400 AAATATTTAATTAAAATTAATAT
1 AAATATTTAATTAAAATTAAAAA
* **
25334423 AAATATTTATTTAATTTTAAAAA
1 AAATATTTAATTAAAATTAAAAA
25334446 AAATA
1 AAATA
25334451 ATATAAGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATTTAATTAAAATTAAAAA
Found at i:25338711 original size:42 final size:42
Alignment explanation
Indices: 25338652--25338736 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
25338642 TTTAAGTTTA
25338652 AAACTTAAATCTAATTAAACATAAAATTCTAAACCTAGTTGC
1 AAACTTAAATCTAATTAAACATAAAATTCTAAACCTAGTTGC
25338694 AAACTTAAATCTAATTAAACATAAAATTCTAAACCTAGTTGC
1 AAACTTAAATCTAATTAAACATAAAATTCTAAACCTAGTTGC
25338736 A
1 A
25338737 CCTTATTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (42 bp):
AAACTTAAATCTAATTAAACATAAAATTCTAAACCTAGTTGC
Found at i:25348993 original size:15 final size:15
Alignment explanation
Indices: 25348975--25349006 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25348965 CAATTTACCT
25348975 AAAATCTAAATCTAA
1 AAAATCTAAATCTAA
*
25348990 AAAATTTAAATCTAA
1 AAAATCTAAATCTAA
25349005 AA
1 AA
25349007 CTTAAAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATCTAAATCTAA
Found at i:25349006 original size:14 final size:14
Alignment explanation
Indices: 25348975--25349020 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
25348965 CAATTTACCT
*
25348975 AAAATCTAAATCTAA
1 AAAATTTAAATCT-A
25348990 AAAATTTAAATCTA
1 AAAATTTAAATCTA
* *
25349004 AAACTTAAAATCTA
1 AAAATTTAAATCTA
25349018 AAA
1 AAA
25349021 GTATGAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTTAAATCTA
Found at i:25349059 original size:18 final size:18
Alignment explanation
Indices: 25349036--25349073 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25349026 AAACATAATT
*
25349036 CTAAAAATCCAATTTAAA
1 CTAAAAATCAAATTTAAA
*
25349054 CTAAAAATCAAATTTGAA
1 CTAAAAATCAAATTTAAA
25349072 CT
1 CT
25349074 TAATAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (18 bp):
CTAAAAATCAAATTTAAA
Found at i:25350485 original size:12 final size:12
Alignment explanation
Indices: 25350456--25350486 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
25350446 AGAAAAAAAA
25350456 AATTTGGGTACC
1 AATTTGGGTACC
25350468 AA-TTGGGTACC
1 AATTTGGGTACC
25350479 AATTTGGG
1 AATTTGGG
25350487 AAAAGTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (12 bp):
AATTTGGGTACC
Found at i:25353407 original size:42 final size:41
Alignment explanation
Indices: 25353336--25353581 Score: 180
Period size: 42 Copynumber: 5.9 Consensus size: 41
25353326 TTGTGTTTAC
* * * *
25353336 TTTCCGTTTAGCTCTCA-TGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCT-ATTGAGCTTTTGTTTAAC-CTTATGGG
*
25353378 TTTTCGTTCAGCTCTATTGAGCTTTTGTTTAAGCCTTATGGG
1 TTTCCGTTCAGCTCTATTGAGCTTTTGTTTAA-CCTTATGGG
* *
25353420 TTTCCGTTCAGCTTTATTAAGCTTTTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTATTGAGCTTTTGTTTAA-CCTTATGGG
* *** *
25353462 TTTCCGTTCAACTC-ACACAAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTA-TTGAGCTTTTGTTTAA-CCTTATGGG
* * ** *
25353504 TTTTTC-TTCAGTTCT-TATGAGCTTCCGTTCAACCCTTATGGG
1 -TTTCCGTTCAGCTCTAT-TGAGCTTTTGTTTAA-CCTTATGGG
* *
25353546 TTTCTGGTT-AGCTCT-TATGAGCTTTTGTTTAGCCTT
1 TTTC-CGTTCAGCTCTAT-TGAGCTTTTGTTTAACCTT
25353582 CGAGCTCCTA
Statistics
Matches: 167, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
41 9 0.05
42 151 0.90
43 7 0.04
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.45
Consensus pattern (41 bp):
TTTCCGTTCAGCTCTATTGAGCTTTTGTTTAACCTTATGGG
Found at i:25354346 original size:45 final size:46
Alignment explanation
Indices: 25354281--25354371 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 46
25354271 AATCGAATTA
25354281 AAATAAATCAGATCTGTAATTAAATTCCCAAATTCAATTAAATGAG
1 AAATAAATCAGATCTGTAATTAAATTCCCAAATTCAATTAAATGAG
25354327 AAATAAATCA-ATCTGTAATTAAATTCCCAAATTCAATTAAATGAG
1 AAATAAATCAGATCTGTAATTAAATTCCCAAATTCAATTAAATGAG
25354372 CAGCAAGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 35 0.78
46 10 0.22
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (46 bp):
AAATAAATCAGATCTGTAATTAAATTCCCAAATTCAATTAAATGAG
Found at i:25365218 original size:17 final size:18
Alignment explanation
Indices: 25365192--25365226 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25365182 AGAGTTAGGC
25365192 CGTGTCGG-CCACATGGG
1 CGTGTCGGCCCACATGGG
*
25365209 CGTGTGGGCCCACATGGG
1 CGTGTCGGCCCACATGGG
25365227 TGAACCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.11, C:0.29, G:0.43, T:0.17
Consensus pattern (18 bp):
CGTGTCGGCCCACATGGG
Found at i:25371980 original size:20 final size:20
Alignment explanation
Indices: 25371955--25371993 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25371945 CAGACTGAGT
*
25371955 TTATTCTGTTTACTGTTTGA
1 TTATTCTGTATACTGTTTGA
25371975 TTATTCTGTATACTGTTTG
1 TTATTCTGTATACTGTTTG
25371994 TTTGTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (20 bp):
TTATTCTGTATACTGTTTGA
Found at i:25377576 original size:41 final size:41
Alignment explanation
Indices: 25377490--25377616 Score: 103
Period size: 41 Copynumber: 3.1 Consensus size: 41
25377480 TTTGTTTAAC
* * * * ** *
25377490 CCTTATGGGTTTCTGTTCAACTCACACGA-CTTCTGTTTAA
1 CCTTATCGGTTTCCGTTCAACTCTCATGAGCTTCCATTCAA
* * *
25377530 CCCTTATCGGTTTTCGTTCAATTCTTATGAGCTTCCATTCAA
1 -CCTTATCGGTTTCCGTTCAACTCTCATGAGCTTCCATTCAA
* * * * *
25377572 CCTTATGGGTTTCCGTTTAGCTCTCATGAGCTTCTATTCAG
1 CCTTATCGGTTTCCGTTCAACTCTCATGAGCTTCCATTCAA
25377613 CCTT
1 CCTT
25377617 CGGGCTTTTG
Statistics
Matches: 67, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
41 59 0.88
42 8 0.12
ACGTcount: A:0.17, C:0.26, G:0.15, T:0.42
Consensus pattern (41 bp):
CCTTATCGGTTTCCGTTCAACTCTCATGAGCTTCCATTCAA
Found at i:25379006 original size:18 final size:18
Alignment explanation
Indices: 25378983--25379020 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25378973 TGGTGCAAAC
*
25378983 TATTTATTTTATTTTATT
1 TATTTATTTAATTTTATT
25379001 TATTTATTTAATTTTATT
1 TATTTATTTAATTTTATT
25379019 TA
1 TA
25379021 CATTTTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTATTTAATTTTATT
Found at i:25379752 original size:27 final size:27
Alignment explanation
Indices: 25379719--25379865 Score: 199
Period size: 27 Copynumber: 5.5 Consensus size: 27
25379709 TACCAAACTA
* *
25379719 TTATAAAATAACAATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
**
25379746 TTATAAAATGACTATTATG-CTTTATG
1 TTATAAAATGACTATTATGCCCCTATG
*
25379772 TTATAAAATGA-TGGTTATGCCCCTATG
1 TTATAAAATGACT-ATTATGCCCCTATG
* *
25379799 TTATAAAATGACTGTTATGGCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
25379826 TTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
*
25379853 TTATATAATGACT
1 TTATAAAATGACT
25379866 GTATGCTTAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.01
26 21 0.20
27 83 0.78
28 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (27 bp):
TTATAAAATGACTATTATGCCCCTATG
Found at i:25379850 original size:54 final size:53
Alignment explanation
Indices: 25379719--25379871 Score: 211
Period size: 53 Copynumber: 2.9 Consensus size: 53
25379709 TACCAAACTA
* * * **
25379719 TTATAAAATAACAATTATGCCCCTATGTTATAAAATGACTATTATGCTTTATG
1 TTATAAAATGACTATTATGCCCCTATGTTATAAAATGACTGTTATGCCCTATG
*
25379772 TTATAAAATGA-TGGTTATGCCCCTATGTTATAAAATGACTGTTATGGCCCTATG
1 TTATAAAATGACT-ATTATGCCCCTATGTTATAAAATGACTGTTAT-GCCCTATG
*
25379826 TTATAAAATGACTATTATGCCCCTATGTTATATAATGACTG-TATGC
1 TTATAAAATGACTATTATGCCCCTATGTTATAAAATGACTGTTATGC
25379872 TTAATGTTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
52 2 0.02
53 43 0.48
54 43 0.48
55 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (53 bp):
TTATAAAATGACTATTATGCCCCTATGTTATAAAATGACTGTTATGCCCTATG
Found at i:25387310 original size:27 final size:27
Alignment explanation
Indices: 25387278--25387537 Score: 412
Period size: 27 Copynumber: 9.6 Consensus size: 27
25387268 ACCCCCAACC
* *
25387278 TGTTATAAAATAACGGTTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
25387305 TGTTATAAAATGACTGTTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387332 TGTTATAAAATGACGGTTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387359 TGTTATAAAATGACGGTTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387386 TGTTATAAAATGACGGTTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387413 TGTTATAAAATGACTGTTATACCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387440 TGTTATAAAATGACTATTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387467 TGTTATAAAATGACTGTTATGCCCTTA
1 TGTTATAAAATGACTGTTATGCCCCTA
* * *
25387494 TGTTATTAAATGTCTATTATGCCCCTA
1 TGTTATAAAATGACTGTTATGCCCCTA
*
25387521 TGTTATAAAATAACTGT
1 TGTTATAAAATGACTGT
25387538 GTGCTTAATG
Statistics
Matches: 216, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 216 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (27 bp):
TGTTATAAAATGACTGTTATGCCCCTA
Found at i:25389877 original size:38 final size:39
Alignment explanation
Indices: 25389835--25389913 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
25389825 ATAGTTAAAA
*
25389835 TTAGTA-AAAAGAAAA-AAATAATATGAATTTAATAATTT
1 TTAGTAGAAAAGAAAATAAATAAT-TGAATATAATAATTT
*
25389873 TTAGTAGAAAAGAAAATAAATAATTGAATATATTAATTT
1 TTAGTAGAAAAGAAAATAAATAATTGAATATAATAATTT
25389912 TT
1 TT
25389914 TTTATAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 6 0.16
39 24 0.65
40 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (39 bp):
TTAGTAGAAAAGAAAATAAATAATTGAATATAATAATTT
Found at i:25394582 original size:21 final size:21
Alignment explanation
Indices: 25394556--25394600 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
25394546 ACATGTTTTT
25394556 CATATAACAAATCATACTCAG
1 CATATAACAAATCATACTCAG
* *
25394577 CATATAACATATCATACTTAG
1 CATATAACAAATCATACTCAG
25394598 CAT
1 CAT
25394601 GTAATAGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.29
Consensus pattern (21 bp):
CATATAACAAATCATACTCAG
Found at i:25398884 original size:26 final size:25
Alignment explanation
Indices: 25398828--25398884 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
25398818 AATCTAAAAT
*
25398828 AAATTC-AAAATCTAATTTCATTTA
1 AAATTCTAAAATCTAATTTCACTTA
* *
25398852 AAGTTCTAAAATCTATTTTACACTTA
1 AAATTCTAAAATCTAATTT-CACTTA
25398878 AAATTCT
1 AAATTCT
25398885 TATAACGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 11 0.41
26 11 0.41
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATTCTAAAATCTAATTTCACTTA
Found at i:25399333 original size:2 final size:2
Alignment explanation
Indices: 25399326--25399359 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25399316 NNNNNNNNNN
25399326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25399360 AAATAGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25400555 original size:13 final size:13
Alignment explanation
Indices: 25400537--25400567 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
25400527 TCCGAAAAAA
25400537 TAGAATTTATACT
1 TAGAATTTATACT
25400550 TAGAATTTATACT
1 TAGAATTTATACT
25400563 TAGAA
1 TAGAA
25400568 ATCAGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (13 bp):
TAGAATTTATACT
Found at i:25403345 original size:15 final size:15
Alignment explanation
Indices: 25403325--25403353 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25403315 TGATTAAATT
25403325 AAATTATCTAAATGA
1 AAATTATCTAAATGA
25403340 AAATTATCTAAATG
1 AAATTATCTAAATG
25403354 TATGAATGAA
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:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
AAATTATCTAAATGA
Found at i:25406126 original size:27 final size:27
Alignment explanation
Indices: 25406096--25406211 Score: 169
Period size: 27 Copynumber: 4.3 Consensus size: 27
25406086 CCCACATAGG
*
25406096 TAAAATGACGGTTATGCCCTTATGTTA
1 TAAAATGACGGTTATGCCCCTATGTTA
* * *
25406123 TAAAATAATGGTTATGCCCTTATGTTA
1 TAAAATGACGGTTATGCCCCTATGTTA
*
25406150 TAAAATGACTGTTATGCCCCTATGTTA
1 TAAAATGACGGTTATGCCCCTATGTTA
**
25406177 TAAAATGACTATTATGCCCCTATGTTA
1 TAAAATGACGGTTATGCCCCTATGTTA
25406204 TAAAATGA
1 TAAAATGA
25406212 TTGTATGCTT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (27 bp):
TAAAATGACGGTTATGCCCCTATGTTA
Found at i:25406533 original size:34 final size:33
Alignment explanation
Indices: 25406490--25406560 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
25406480 TCTGAACTAT
*
25406490 TACTGTCACTGTAATGGGCTAAGGCCCACACTGA
1 TACTGTCACTATAATGGGCTAAGGCCCA-ACTGA
* *
25406524 TACTGTCACTATTATGGGCTAAGGCTCAACTGA
1 TACTGTCACTATAATGGGCTAAGGCCCAACTGA
25406557 -ACTG
1 TACTG
25406561 AACTGTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 4 0.12
33 5 0.15
34 25 0.74
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (33 bp):
TACTGTCACTATAATGGGCTAAGGCCCAACTGA
Found at i:25407594 original size:20 final size:20
Alignment explanation
Indices: 25407569--25407608 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25407559 CGTAAAATGA
*
25407569 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
25407589 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
25407609 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:25407598 original size:34 final size:34
Alignment explanation
Indices: 25407555--25407620 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
25407545 AGTAAAATAT
*
25407555 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
25407588 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
25407621 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:25411317 original size:30 final size:28
Alignment explanation
Indices: 25411283--25411338 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
25411273 GTGATTAAAT
25411283 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
25411313 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
25411339 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:25413582 original size:18 final size:17
Alignment explanation
Indices: 25413559--25413597 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
25413549 CTCTTTTTGC
25413559 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
25413577 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
25413595 TCT
1 TCT
25413598 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:25415295 original size:30 final size:28
Alignment explanation
Indices: 25415261--25415316 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
25415251 GTGATTAAAT
25415261 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
25415291 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
25415317 TAAGTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:25415740 original size:203 final size:203
Alignment explanation
Indices: 25415391--25415785 Score: 745
Period size: 203 Copynumber: 1.9 Consensus size: 203
25415381 CCCTCCAAAG
*
25415391 GAATATCAATGGCAAGAATAAGGCTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTT
1 GAATATCAATGGCAAGAAGAAGGCTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTT
25415456 CTAAAGAAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAGGAGAATTCTGCACTTAAACAAAT
66 CTAAAGAAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAGGAGAATTCTGCACTTAAACAAAT
25415521 ATGAAATTTTTAATATATTTGAGAAGTTTAAACAAGGGGTGGCCGGCCATCACTTATATAGGAGA
131 ATGAAATTTTTAATATATTTGAGAAGTTTAAACAAGGGGTGGCCGGCCATCACTTATATAGGAGA
25415586 AGGCTGAA
196 AGGCTGAA
25415594 GAATATCAATGGCAAGAAGAAGGCTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTT
1 GAATATCAATGGCAAGAAGAAGGCTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTT
*
25415659 CTAAAGAAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAGGAGAATTCTGTACTTAAACAAAT
66 CTAAAGAAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAGGAGAATTCTGCACTTAAACAAAT
* * *
25415724 CTGAACTTTTTAATATATTTGAGAAGTTTATACAAGGGGTGGCCGGCCATCACTTATATAGG
131 ATGAAATTTTTAATATATTTGAGAAGTTTAAACAAGGGGTGGCCGGCCATCACTTATATAGG
25415786 CCTCAAACTA
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 187 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (203 bp):
GAATATCAATGGCAAGAAGAAGGCTGAAGATGACTCCCACAATCAAAAGATTGTTAAAACAACTT
CTAAAGAAAACTCAAGAGAGAATTCTTGGAGAAAAACTCAAGGAGAATTCTGCACTTAAACAAAT
ATGAAATTTTTAATATATTTGAGAAGTTTAAACAAGGGGTGGCCGGCCATCACTTATATAGGAGA
AGGCTGAA
Found at i:25417178 original size:17 final size:18
Alignment explanation
Indices: 25417147--25417180 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25417137 CATGTTGTCG
25417147 GCCCGTGTAGGCCCACAC
1 GCCCGTGTAGGCCCACAC
25417165 GCCCGTGT-GGCCCACA
1 GCCCGTGTAGGCCCACA
25417181 AGGCCCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (18 bp):
GCCCGTGTAGGCCCACAC
Found at i:25417186 original size:18 final size:18
Alignment explanation
Indices: 25417146--25417186 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25417136 CCATGTTGTC
25417146 GGCCCGTGTAGGCCCACA
1 GGCCCGTGTAGGCCCACA
*
25417164 CGCCCGTGT-GGCCCACAA
1 GGCCCGTGTAGGCCCAC-A
25417182 GGCCC
1 GGCCC
25417187 AAAATGACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.15, C:0.44, G:0.32, T:0.10
Consensus pattern (18 bp):
GGCCCGTGTAGGCCCACA
Found at i:25422053 original size:19 final size:19
Alignment explanation
Indices: 25422007--25422045 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25421997 AAATAAGAGC
* *
25422007 TCATTTCTCACTTTTTCAA
1 TCATCTCTCACTCTTTCAA
25422026 TCATCTCTCACTCTTTCAA
1 TCATCTCTCACTCTTTCAA
25422045 T
1 T
25422046 ATTCTCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (19 bp):
TCATCTCTCACTCTTTCAA
Found at i:25429747 original size:10 final size:10
Alignment explanation
Indices: 25429731--25429760 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
25429721 TCAGGTCAAG
25429731 TCAGATCGGA
1 TCAGATCGGA
*
25429741 TCGGATCGGA
1 TCAGATCGGA
25429751 TCAGATCGGA
1 TCAGATCGGA
25429761 ATGAGTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (10 bp):
TCAGATCGGA
Found at i:25434993 original size:22 final size:22
Alignment explanation
Indices: 25434967--25435012 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
25434957 TGTTAAGAAT
25434967 GAACAGATATATGATGTTGATA
1 GAACAGATATATGATGTTGATA
25434989 GAACAGATATATGATGTTGATA
1 GAACAGATATATGATGTTGATA
25435011 GA
1 GA
25435013 CTTACTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (22 bp):
GAACAGATATATGATGTTGATA
Found at i:25435304 original size:2 final size:2
Alignment explanation
Indices: 25435297--25435326 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25435287 TGTGCTCATG
25435297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25435327 AGTTGACGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25440320 original size:21 final size:21
Alignment explanation
Indices: 25440296--25440341 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
25440286 CTAAACTGTT
25440296 TTATTCA-CACAAAAAAAAACA
1 TTATTCATCACAAAAAAAAA-A
* *
25440317 TTA-TCATTACAAAAATAAAA
1 TTATTCATCACAAAAAAAAAA
25440337 TTATT
1 TTATT
25440342 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
TTATTCATCACAAAAAAAAAA
Found at i:25440473 original size:42 final size:42
Alignment explanation
Indices: 25440427--25440509 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
25440417 CACAACAAAT
25440427 ATTTAAAATATAAAAATTTAATGTTAAAAATCTCAAAAAAAA
1 ATTTAAAATATAAAAATTTAATGTTAAAAATCTCAAAAAAAA
* *
25440469 ATTTAATATATAAAAATTTAATGTTAAAAATCTGAAAAAAA
1 ATTTAAAATATAAAAATTTAATGTTAAAAATCTCAAAAAAA
25440510 TTATAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (42 bp):
ATTTAAAATATAAAAATTTAATGTTAAAAATCTCAAAAAAAA
Found at i:25440490 original size:15 final size:15
Alignment explanation
Indices: 25440427--25440499 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
25440417 CACAACAAAT
*
25440427 ATTTAAAATATAAAA
1 ATTTAATATATAAAA
*
25440442 ATTTAATGT-TAAAA
1 ATTTAATATATAAAA
*
25440456 ATCTCAA-A-A-AAAA
1 AT-TTAATATATAAAA
25440469 ATTTAATATATAAAA
1 ATTTAATATATAAAA
*
25440484 ATTTAATGT-TAAAA
1 ATTTAATATATAAAA
25440498 AT
1 AT
25440500 CTGAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
12 3 0.06
13 7 0.15
14 15 0.32
15 22 0.47
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
ATTTAATATATAAAA
Found at i:25452092 original size:14 final size:14
Alignment explanation
Indices: 25452073--25452100 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25452063 AGTAGAAATC
25452073 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
25452087 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
25452101 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:25452098 original size:19 final size:18
Alignment explanation
Indices: 25452076--25452120 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
25452066 AGAAATCTGG
25452076 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
25452095 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
25452112 AGAAAAGAA
1 AGAAAAGAA
25452121 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:25452491 original size:39 final size:42
Alignment explanation
Indices: 25452448--25452538 Score: 98
Period size: 45 Copynumber: 2.2 Consensus size: 42
25452438 TTACAACATC
* *
25452448 ATTCCATGCAACCAA-ACACAA-GAA-TACTATTACGCCTCT
1 ATTCCATACAACCAACAAACAATGAATTACTATTACGCCTCT
**
25452487 ATTCCATTACATTCAACTAAACAATTGAATTACTATTACGCCTCT
1 ATTCCA-TACAACCAAC-AAACAA-TGAATTACTATTACGCCTCT
25452532 ATTCCAT
1 ATTCCAT
25452539 TACAGCTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 6 0.14
40 6 0.14
42 5 0.12
44 4 0.10
45 21 0.50
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.31
Consensus pattern (42 bp):
ATTCCATACAACCAACAAACAATGAATTACTATTACGCCTCT
Found at i:25452540 original size:16 final size:16
Alignment explanation
Indices: 25452528--25452560 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25452518 ACTATTACGC
25452528 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
25452544 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
25452560 C
1 C
25452561 GAACCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:25471474 original size:55 final size:55
Alignment explanation
Indices: 25471407--25471517 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
25471397 ATTCAATAGA
*
25471407 GAAAGAATGGTGTGTGGCAATTCAAAAGCTCCTACATGGTCAATATCATAGTCTT
1 GAAAGAATGGTGTGTGGCAATTCAAAAGCTCCTACATGGTCAACATCATAGTCTT
*
25471462 GAAAGAATGGTGTGTGGCAATTCAAATGCTCCTACATGGTCAACATCATAGTCTT
1 GAAAGAATGGTGTGTGGCAATTCAAAAGCTCCTACATGGTCAACATCATAGTCTT
25471517 G
1 G
25471518 GCACTTATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (55 bp):
GAAAGAATGGTGTGTGGCAATTCAAAAGCTCCTACATGGTCAACATCATAGTCTT
Done.