Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 85 of 433
Found at i:25158722 original size:21 final size:21
Alignment explanation
Indices: 25158681--25158735 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
25158671 ATTTATAATT
* *
25158681 TTTTTTATA-TTCCTTAGTAC
1 TTTTTTATATTTTCATAGTAC
*
25158701 TTTTTTATATTTTCATATTAC
1 TTTTTTATATTTTCATAGTAC
*
25158722 TTTTGTAGTATTTT
1 TTTTTTA-TATTTT
25158736 TACCGGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.31
21 14 0.48
22 6 0.21
ACGTcount: A:0.20, C:0.09, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTTATATTTTCATAGTAC
Found at i:25160808 original size:17 final size:17
Alignment explanation
Indices: 25160786--25160821 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25160776 GTTTAGCAAG
25160786 AATTTGTTAATAATTTT
1 AATTTGTTAATAATTTT
25160803 AATTTGTTAATAATTTT
1 AATTTGTTAATAATTTT
25160820 AA
1 AA
25160822 GTATTGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AATTTGTTAATAATTTT
Found at i:25166747 original size:12 final size:12
Alignment explanation
Indices: 25166730--25166756 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25166720 AAATCCTTAA
25166730 TTTCTTCTTCTT
1 TTTCTTCTTCTT
25166742 TTTCTTCTTCTT
1 TTTCTTCTTCTT
25166754 TTT
1 TTT
25166757 AAAAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTCTTCTT
Found at i:25176923 original size:33 final size:33
Alignment explanation
Indices: 25176886--25176951 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
25176876 TGAATAGGTT
*
25176886 GCTCCCCCT-TAATAAAAGTCATTTTCAATTTAA
1 GCTCCCCCTAT-ATAAAAATCATTTTCAATTTAA
25176919 GCTCCCCCTATATAAAAATCATTTTCAATTTAA
1 GCTCCCCCTATATAAAAATCATTTTCAATTTAA
25176952 CGCATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (33 bp):
GCTCCCCCTATATAAAAATCATTTTCAATTTAA
Found at i:25179424 original size:76 final size:76
Alignment explanation
Indices: 25179298--25179445 Score: 287
Period size: 76 Copynumber: 1.9 Consensus size: 76
25179288 GCACCTATGG
*
25179298 ATAAATACCTCTTTTAGCACCAAGCAAGGGCTCTCATTGTTTACACTCTACTCAAACTCAACCCC
1 ATAAATACCTCTTTTAACACCAAGCAAGGGCTCTCATTGTTTACACTCTACTCAAACTCAACCCC
25179363 AACTTCCCTCT
66 AACTTCCCTCT
25179374 ATAAATACCTCTTTTAACACCAAGCAAGGGCTCTCATTGTTTACACTCTACTCAAACTCAACCCC
1 ATAAATACCTCTTTTAACACCAAGCAAGGGCTCTCATTGTTTACACTCTACTCAAACTCAACCCC
25179439 AACTTCC
66 AACTTCC
25179446 TTAAAATAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.30, C:0.34, G:0.07, T:0.28
Consensus pattern (76 bp):
ATAAATACCTCTTTTAACACCAAGCAAGGGCTCTCATTGTTTACACTCTACTCAAACTCAACCCC
AACTTCCCTCT
Found at i:25184461 original size:29 final size:29
Alignment explanation
Indices: 25184423--25184507 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
25184413 CTAGAACAAC
25184423 TCATATTTGACATCCTACAGATTCAAACT
1 TCATATTTGACATCCTACAGATTCAAACT
*
25184452 TCATATTTGACATCCTACAGATACAAACT
1 TCATATTTGACATCCTACAGATTCAAACT
25184481 TCATATTTGACATCCTACAGATTCAAA
1 TCATATTTGACATCCTACAGATTCAAA
25184508 AACTATGTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (29 bp):
TCATATTTGACATCCTACAGATTCAAACT
Found at i:25184855 original size:2 final size:2
Alignment explanation
Indices: 25184848--25184900 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
25184838 GCCAAAACAA
*
25184848 AT AT AT AT AT AT AC 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
25184890 AT AT AT AT AT A
1 AT AT AT AT AT A
25184901 CCAAAAGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25187447 original size:24 final size:24
Alignment explanation
Indices: 25187411--25187460 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
25187401 TTCACGTTAC
25187411 ATGTTTGGAATGGTTT-ATATGGT
1 ATGTTTGGAATGGTTTAATATGGT
*
25187434 ATGTTTTGAGATGGTTTGAATATGGT
1 ATGTTTGGA-ATGGTTT-AATATGGT
25187460 A
1 A
25187461 AGATTATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 7 0.30
26 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (24 bp):
ATGTTTGGAATGGTTTAATATGGT
Found at i:25189833 original size:19 final size:19
Alignment explanation
Indices: 25189809--25189847 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
25189799 TTACAAAATG
25189809 CCTAAACACAAGTATTCAT
1 CCTAAACACAAGTATTCAT
25189828 CCTAAACACAAGTATTCAT
1 CCTAAACACAAGTATTCAT
25189847 C
1 C
25189848 ACATGTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.28, G:0.05, T:0.26
Consensus pattern (19 bp):
CCTAAACACAAGTATTCAT
Found at i:25191479 original size:29 final size:29
Alignment explanation
Indices: 25191447--25191548 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
25191437 CTTCGAGCTC
* *
25191447 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
25191476 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
25191505 GCACACTCAGTGCCATATATTTCCAGCAC
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
25191534 GCACACTTAGTGCCA
1 GCACACTCAGTGCCA
25191549 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (29 bp):
GCACACTCAGTGCCATATATTTCCAGCAT
Found at i:25191487 original size:58 final size:58
Alignment explanation
Indices: 25191420--25191548 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 58
25191410 TTAAGCCCGT
* * * * *
25191420 ACACATAGTGCCATAGCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCATGC
1 ACACTTAGTGCCATAGACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCACGC
* * *
25191478 ACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCACGC
1 ACACTTAGTGCCATAGACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCACGC
25191536 ACACTTAGTGCCA
1 ACACTTAGTGCCA
25191549 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 61 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (58 bp):
ACACTTAGTGCCATAGACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCACGC
Found at i:25205285 original size:39 final size:39
Alignment explanation
Indices: 25205197--25205310 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 39
25205187 TATCACGATT
*
25205197 TGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
1 TGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAAC
* * ***
25205236 TGCACGAATGCCTTC-GGTCTTAGCTCGGATATATTTAC
1 TGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAAC
* * *
25205274 TAGCATAAATGCC-TCGGGACTTAGCCCGG-TATCACAA
1 T-GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAA
25205311 TTGCTCATGC
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
38 25 0.42
39 34 0.58
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (39 bp):
TGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAAC
Found at i:25209944 original size:55 final size:53
Alignment explanation
Indices: 25209857--25210064 Score: 249
Period size: 55 Copynumber: 3.8 Consensus size: 53
25209847 ATTAGGGTTT
*
25209857 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGCTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * * *
25209912 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * * *
25209967 AAAGG-TCCCATGTAAGACCATGCCAAGGCACGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
25210020 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
25210065 TCAAAAGGAT
Statistics
Matches: 129, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
52 6 0.05
53 43 0.33
54 8 0.06
55 68 0.53
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:25210063 original size:108 final size:110
Alignment explanation
Indices: 25209864--25210064 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
25209854 TTTAAGGATA
* *
25209864 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGCTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCACGGCAATTGGTAAGGCTTCTAAGGCAAGGAAACCATGTAAGA
*
25209929 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
25209974 CCATGTAAGACCATGCCAAGGCACGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCACGGCAATTGGTAAGGCTTC-TAAGGCAAGGAAACCATGTAAG
*
25210036 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
25210065 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCACGGCAATTGGTAAGGCTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:25210324 original size:16 final size:16
Alignment explanation
Indices: 25210303--25210333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25210293 ATAAATTTGA
25210303 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
25210319 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
25210334 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:25212806 original size:45 final size:45
Alignment explanation
Indices: 25212756--25212846 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
25212746 CCAAAACATG
*
25212756 TGTCACATACATCATGAACCCAGACCATAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACCCAGACCACAACTCAATGAGTTCAGA
* * *
25212801 TGTCACATATATCATGAACTCATACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACCCAGACCACAACTCAATGAGTTCAGA
25212846 T
1 T
25212847 CACATAGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (45 bp):
TGTCACATACATCATGAACCCAGACCACAACTCAATGAGTTCAGA
Found at i:25216286 original size:50 final size:53
Alignment explanation
Indices: 25216212--25216310 Score: 177
Period size: 53 Copynumber: 1.9 Consensus size: 53
25216202 GGAATGTATG
25216212 TGAATGAATGTGATA-T-TATATATA-TTTTTATATAATTATTATTTTTGACA
1 TGAATGAATGTGATATTATATATATATTTTTTATATAATTATTATTTTTGACA
25216262 TGAATGAATGTGATATTATATATATATTTTTTATATAATTATTATTTTT
1 TGAATGAATGTGATATTATATATATATTTTTTATATAATTATTATTTTT
25216311 TGTCAAGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 15 0.33
51 1 0.02
52 8 0.17
53 22 0.48
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (53 bp):
TGAATGAATGTGATATTATATATATATTTTTTATATAATTATTATTTTTGACA
Found at i:25216623 original size:2 final size:2
Alignment explanation
Indices: 25216616--25216643 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25216606 TATAATTATG
25216616 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
25216644 GTATGTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25218748 original size:43 final size:43
Alignment explanation
Indices: 25218656--25218771 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
25218646 TGTGATTACA
* * *
25218656 TGTAAGACCATGTCTGGGACATTGGCATTGCATTGAGATTATG
1 TGTAAGACCATGTCTGGGACATTGGCATCGCAATCAGATTATG
* *
25218699 TATAAGACCATGTCTGGGACATTGGCATCGTTAATCA-ATT-TCG
1 TGTAAGACCATGTCTGGGACATTGGCATCG-CAATCAGATTAT-G
* *
25218742 TGTAAGACCCTGTCTGGGACAGTGGCATCG
1 TGTAAGACCATGTCTGGGACATTGGCATCG
25218772 ATATGTGATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.02
43 59 0.94
44 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGCAATCAGATTATG
Found at i:25230415 original size:38 final size:38
Alignment explanation
Indices: 25230372--25230462 Score: 173
Period size: 38 Copynumber: 2.4 Consensus size: 38
25230362 ATTTATATTC
*
25230372 ATACATTTATTCTTTGCCATTTTAGTCAATGCTTTCTG
1 ATACATTCATTCTTTGCCATTTTAGTCAATGCTTTCTG
25230410 ATACATTCATTCTTTGCCATTTTAGTCAATGCTTTCTG
1 ATACATTCATTCTTTGCCATTTTAGTCAATGCTTTCTG
25230448 ATACATTCATTCTTT
1 ATACATTCATTCTTT
25230463 TTGTGTGTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (38 bp):
ATACATTCATTCTTTGCCATTTTAGTCAATGCTTTCTG
Found at i:25231892 original size:20 final size:21
Alignment explanation
Indices: 25231853--25231892 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25231843 TTTTATTCTA
*
25231853 TTTTAAGACTACTTTTTATTT
1 TTTTAAGACTACTTTCTATTT
*
25231874 TTTTAAGCCTA-TTTCTATT
1 TTTTAAGACTACTTTCTATT
25231893 AGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTAAGACTACTTTCTATTT
Found at i:25235040 original size:42 final size:43
Alignment explanation
Indices: 25234922--25235092 Score: 155
Period size: 43 Copynumber: 4.0 Consensus size: 43
25234912 ACCAGATTTT
* * ** *
25234922 GATATGTGATTTCGTGTAAGACCATGTTTGGGATGTTGGCTTC
1 GATATATGATTTCGTGTAAGACCATGTATGGGACATTGGCATC
* *
25234965 GATTTGTGATTTACGTGTAAGACCATGTATGGGACATTGGCATC
1 GATATATGATTT-CGTGTAAGACCATGTATGGGACATTGGCATC
* * * *
25235009 G-TATATGATTTTGTGTAAGACCTTGTCTGGGACAGTGGCATC
1 GATATATGATTTCGTGTAAGACCATGTATGGGACATTGGCATC
* * * * * * * *
25235051 AACATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATATGATTTCGTGTAAGACCATGTATGGGACATTGGCAT
25235093 TGTAAGAGCT
Statistics
Matches: 105, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 27 0.26
43 50 0.48
44 28 0.27
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (43 bp):
GATATATGATTTCGTGTAAGACCATGTATGGGACATTGGCATC
Found at i:25244932 original size:46 final size:45
Alignment explanation
Indices: 25244788--25244958 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 45
25244778 TTTGTTAGCT
* * *
25244788 AGTGTAAGACATGTCTGGGACTTGCATCGGCCAT-ATTATGAAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TGA-GACGAAAGCC
* * * * * *
25244834 AATGTAAGACCATGGCTAGGACATGGCATCGACATTGAGACGAAAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTGAGACGAAAGCC
* *
25244882 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAGGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGACGAAAGCC
*
25244928 AGTGTAAGACTTGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
25244959 TATTGTAAGA
Statistics
Matches: 102, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
45 1 0.01
46 54 0.53
47 23 0.23
48 23 0.23
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGACGAAAGCC
Found at i:25244979 original size:79 final size:80
Alignment explanation
Indices: 25244879--25245039 Score: 202
Period size: 79 Copynumber: 2.0 Consensus size: 80
25244869 TGAGACGAAA
* * *
25244879 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGAGGTAAGCCAGTGTAAGA-CTTGT
1 GCTAGTGTAAGACATGTCTGGGACATGGCATC-GACTCGAGAGATAAGCCAGTGTAAGACCATGT
25244942 CTGGGACAT-GCATCG
65 CTGGGACATGGCATCG
* * * * **
25244957 GCTATTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGAGTTAGTGTAAGACCATGT
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGACTCGAGAGATAAGCCAGTGTAAGACCATGT
25245022 CTGGGACATGGCATCG
65 CTGGGACATGGCATCG
25245038 GC
1 GC
25245040 ACCTTACCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
78 11 0.16
79 33 0.47
80 18 0.26
81 8 0.11
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (80 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGACTCGAGAGATAAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCG
Found at i:25247184 original size:13 final size:13
Alignment explanation
Indices: 25247166--25247231 Score: 105
Period size: 13 Copynumber: 5.1 Consensus size: 13
25247156 GCTCGGCAGG
25247166 GACACGCCCGTGT
1 GACACGCCCGTGT
*
25247179 GACACGCTCGTGT
1 GACACGCCCGTGT
25247192 GACACGCCCGTGT
1 GACACGCCCGTGT
*
25247205 GACACGCTCGTGT
1 GACACGCCCGTGT
*
25247218 GACACGCCCTTGT
1 GACACGCCCGTGT
25247231 G
1 G
25247232 CGATTACTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:25247196 original size:26 final size:26
Alignment explanation
Indices: 25247166--25247231 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
25247156 GCTCGGCAGG
25247166 GACACGCCCGTGTGACACGCTCGTGT
1 GACACGCCCGTGTGACACGCTCGTGT
25247192 GACACGCCCGTGTGACACGCTCGTGT
1 GACACGCCCGTGTGACACGCTCGTGT
*
25247218 GACACGCCCTTGTG
1 GACACGCCCGTGTG
25247232 CGATTACTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (26 bp):
GACACGCCCGTGTGACACGCTCGTGT
Found at i:25255085 original size:14 final size:13
Alignment explanation
Indices: 25255062--25255093 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
25255052 GGGATATCAA
25255062 AACAATAATTAAG
1 AACAATAATTAAG
25255075 AACACATAATTAAG
1 AACA-ATAATTAAG
25255089 AACAA
1 AACAA
25255094 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:25280360 original size:17 final size:17
Alignment explanation
Indices: 25280334--25280377 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
25280324 AAATATATCA
*
25280334 TTTATCACATTAGACCT
1 TTTATAACATTAGACCT
25280351 TTTATAACATTAGACCT
1 TTTATAACATTAGACCT
25280368 TTTATAACAT
1 TTTATAACAT
25280378 CATGATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (17 bp):
TTTATAACATTAGACCT
Found at i:25283027 original size:49 final size:49
Alignment explanation
Indices: 25282927--25283097 Score: 186
Period size: 49 Copynumber: 3.5 Consensus size: 49
25282917 ATAGTAAAAC
* *
25282927 TATGGTCTTAAACA-AAGTCACATAATCACAAACCGATGCCATAGCCCAGA
1 TATGGTCTTATACAGAA-TCACAT-ATCACAAACCGATGCCATATCCCAGA
* * *
25282977 TATGGTCTTATACAGAATTACATATCACATACCGATGCCATATCCTAGA
1 TATGGTCTTATACAGAATCACATATCACAAACCGATGCCATATCCCAGA
** * * * *
25283026 TATGGAATTATACGGAA--ACATATAATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGAATCACATATCA-CAAACCGATGCCATATCCCAGA
*
25283074 TATGGTCTTATACAGGATCACATA
1 TATGGTCTTATACAGAATCACATA
25283098 ATCATATAGT
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
47 7 0.07
48 32 0.32
49 37 0.37
50 23 0.23
51 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (49 bp):
TATGGTCTTATACAGAATCACATATCACAAACCGATGCCATATCCCAGA
Found at i:25283099 original size:48 final size:49
Alignment explanation
Indices: 25282927--25283101 Score: 203
Period size: 48 Copynumber: 3.6 Consensus size: 49
25282917 ATAGTAAAAC
* *
25282927 TATGGTCTTAAACA-AAGTCACATAATCACAAACCGATGCCATAGCCCAGA
1 TATGGTCTTATACAGAA-TCACATAATCAC-AACCGATGCCATATCCCAGA
* *
25282977 TATGGTCTTATACAGAATTACAT-ATCACATACCGATGCCATATCCTAGA
1 TATGGTCTTATACAGAATCACATAATCACA-ACCGATGCCATATCCCAGA
** * * * *
25283026 TATGGAATTATACGGAAACATATAATCAC-ACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGAATCACATAATCACAACCGATGCCATATCCCAGA
*
25283074 TATGGTCTTATACAGGATCACATAATCA
1 TATGGTCTTATACAGAATCACATAATCA
25283102 TATAGTCACA
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
48 40 0.38
49 39 0.38
50 23 0.22
51 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (49 bp):
TATGGTCTTATACAGAATCACATAATCACAACCGATGCCATATCCCAGA
Found at i:25284043 original size:11 final size:11
Alignment explanation
Indices: 25284027--25284058 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
25284017 ATTACCCTTT
25284027 TAATTTCAAAC
1 TAATTTCAAAC
25284038 TAATTTCAAAC
1 TAATTTCAAAC
25284049 TAATTTCAAA
1 TAATTTCAAA
25284059 AATACCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATTTCAAAC
Found at i:25287356 original size:46 final size:45
Alignment explanation
Indices: 25287195--25287365 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 45
25287185 TGAGCATCCG
* * *
25287195 AACTCGTTGAGTTGCGTCCGAGTTCAC-TATGGATGCGAGCGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCC
* * *
25287240 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC--CC
25287286 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 -AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
25287332 AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25287366 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 9, Indels: 23
0.77 0.07 0.17
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 28 0.27
46 34 0.32
47 25 0.24
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
Found at i:25287357 original size:93 final size:92
Alignment explanation
Indices: 25287188--25287357 Score: 288
Period size: 92 Copynumber: 1.8 Consensus size: 92
25287178 GGATGGTTGA
* * *
25287188 GCATCCGAACTCGTTGAGTTGCGTCCGAGTTCACTATGGATGCGAGCGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGTCCCAACTCGTTGAGTT
25287253 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
25287280 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGTCCCAA-CTCGTTGAG
25287344 TTGAGTCCGAGTTC
64 TTGAGTCCGAGTTC
25287358 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
92 37 0.51
93 36 0.49
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGTCCCAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:25292442 original size:48 final size:48
Alignment explanation
Indices: 25292279--25292481 Score: 204
Period size: 48 Copynumber: 4.2 Consensus size: 48
25292269 TAAACAGAGT
* *
25292279 CACATAATCACAAACCGATGCCATAGCCCAGCTATGGTCTTATAC-GAAA
1 CACATAATCAC--ACCGATGCCATATCCCAGATATGGTCTTATACGGAAA
* *
25292328 TCACAT-TTCACAGACCGATGCCATATCCCAG--A--GTCTTAT-CGGAAT
1 -CACATAATCAC--ACCGATGCCATATCCCAGATATGGTCTTATACGGAAA
* * *
25292373 CACATATTACATACAGATGCCATATCCCAGATATGGTCTTATACGGAAA
1 CACATAAT-CACACCGATGCCATATCCCAGATATGGTCTTATACGGAAA
* * * *
25292422 CATATAATCACACCGATGCCATATCCCAGATATGGTCTTATATGGGAT
1 CACATAATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAA
25292470 CACATAATCACA
1 CACATAATCACA
25292482 TATTCACATG
Statistics
Matches: 130, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
44 23 0.18
45 12 0.09
46 3 0.02
47 1 0.01
48 53 0.41
49 33 0.25
50 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (48 bp):
CACATAATCACACCGATGCCATATCCCAGATATGGTCTTATACGGAAA
Found at i:25300338 original size:4 final size:4
Alignment explanation
Indices: 25300329--25300354 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25300319 AAGAAGGAAT
25300329 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
25300355 TTGTAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:25304668 original size:14 final size:13
Alignment explanation
Indices: 25304647--25304679 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
25304637 AAATATTTAA
25304647 CTTGTTCTTAATT
1 CTTGTTCTTAATT
25304660 CTGTGTTCTTAATT
1 CT-TGTTCTTAATT
25304674 CTTGTT
1 CTTGTT
25304680 TTGATATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:25307814 original size:80 final size:80
Alignment explanation
Indices: 25307650--25307802 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 80
25307640 TCGAATGATG
*
25307650 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAGCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAGCATAACCGGACTAAGATCCGAAGGCATTT
*
25307715 GTGCGAGTTCCCAAA
66 GAGCGAGTTCCCAAA
* ** * * *
25307730 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-AAGCT-ATTATAACCGGGCTATG-TCCCGAAGGCT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAGCATAACCGGACTAAGAT-CCGAAGGCA
25307792 TTTGAGCGAGT
63 TTTGAGCGAGT
25307803 CGCTATATCC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
79 1 0.02
80 53 0.85
81 8 0.13
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAGCATAACCGGACTAAGATCCGAAGGCATTT
GAGCGAGTTCCCAAA
Found at i:25312404 original size:40 final size:40
Alignment explanation
Indices: 25312359--25312523 Score: 201
Period size: 40 Copynumber: 4.1 Consensus size: 40
25312349 AATACAACCA
25312359 GATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCG
* * * *
25312399 GATATAACGACTCGCACAAATGCCTTCGGGTATTAGCCCG
1 GATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCG
* **
25312439 GATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCG
* *
25312479 GATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAACCCG
1 GATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGCCCG
25312519 GATAT
1 GATAT
25312524 CATTCAATTG
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 105 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCG
Found at i:25312496 original size:80 final size:80
Alignment explanation
Indices: 25312372--25312523 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 80
25312362 ATAACCACAC
* *
25312372 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGCC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
25312437 CGGATATAACAACTT
66 CGGATATAACAACTT
* *
25312452 GCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAATTGCCTTCGGGTCTTAA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAATGCCTTCGGGTATTAA
25312515 CCCGGATAT
64 CCCGGATAT
25312524 CATTCAATTG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
78 1 0.02
79 2 0.03
80 63 0.95
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
CGGATATAACAACTT
Found at i:25317955 original size:40 final size:40
Alignment explanation
Indices: 25317830--25317981 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
25317820 TCGAATGATG
* * *
25317830 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAGCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACCAAA
* * *
25317870 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACCAAA
* **
25317910 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCA-AA
* * *
25317951 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
25317982 TCGCTATATC
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 80 0.87
41 11 0.12
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACCAAA
Found at i:25323924 original size:28 final size:29
Alignment explanation
Indices: 25323866--25323927 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
25323856 GAAAGCATGT
*
25323866 ATATGAATGTGATTTGGGCCTAATGGACC
1 ATATGAATGAGATTTGGGCCTAATGGACC
* * *
25323895 ATATGAATGAGA-TTGGTCCTAGTGGGCC
1 ATATGAATGAGATTTGGGCCTAATGGACC
25323923 ATATG
1 ATATG
25323928 CATGTATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (29 bp):
ATATGAATGAGATTTGGGCCTAATGGACC
Found at i:25328228 original size:23 final size:24
Alignment explanation
Indices: 25328178--25328362 Score: 85
Period size: 24 Copynumber: 7.8 Consensus size: 24
25328168 CTTGTAACGA
* *
25328178 GAAGCTCACACAGAGCCATTTCGG
1 GAAGCTCACAAAGAGCCATATCGG
*
25328202 GAAGCTCATAAAGAGCC-TATCGG
1 GAAGCTCACAAAGAGCCATATCGG
* * *** *
25328225 GAAGATTATTCAG-GCTATATAACGG
1 GAAGCTCACAAAGAGCCATAT--CGG
* * *
25328250 GAAGCTCA-TAACAGCTATAATCGG
1 GAAGCTCACAAAGAGCCAT-ATCGG
* * *
25328274 GAAGTTCACAAAGAACCATATCGA
1 GAAGCTCACAAAGAGCCATATCGG
* *
25328298 GAAGCTC-CAGATAGCCAATATCGG
1 GAAGCTCACAAAGAGCC-ATATCGG
* ** * *
25328322 GAAGTTCA-AGCG-GGCACTATCAG
1 GAAGCTCACAAAGAGCCA-TATCGG
25328345 GAAGCTCACAAAGAGCCA
1 GAAGCTCACAAAGAGCCA
25328363 ATTAACTGGA
Statistics
Matches: 118, Mismatches: 32, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
22 3 0.03
23 37 0.31
24 53 0.45
25 23 0.19
26 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (24 bp):
GAAGCTCACAAAGAGCCATATCGG
Found at i:25328296 original size:24 final size:25
Alignment explanation
Indices: 25328269--25328387 Score: 66
Period size: 24 Copynumber: 4.9 Consensus size: 25
25328259 AACAGCTATA
25328269 ATCGGGAAGTTCACAAAGAACC-AT
1 ATCGGGAAGTTCACAAAGAACCAAT
* * * * *
25328293 ATCGAGAAGCTC-CAGATAGCCAAT
1 ATCGGGAAGTTCACAAAGAACCAAT
** ** *
25328317 ATCGGGAAGTTCA-AGCG-GGCACT
1 ATCGGGAAGTTCACAAAGAACCAAT
* * *
25328340 ATCAGGAAGCTCACAAAGAGCCAATT
1 ATCGGGAAGTTCACAAAGAACCAA-T
* *
25328366 AACTGGAAGTTCACAAAGAACC
1 ATCGGGAAGTTCACAAAGAACC
25328388 TTTAATCGGG
Statistics
Matches: 69, Mismatches: 21, Indels: 8
0.70 0.21 0.08
Matches are distributed among these distances:
23 21 0.30
24 26 0.38
25 3 0.04
26 19 0.28
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGTTCACAAAGAACCAAT
Found at i:25336683 original size:31 final size:31
Alignment explanation
Indices: 25336646--25336714 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
25336636 GACTTTTTTT
* *
25336646 ATTTAATTGTGATATATTAACTAATGTAATA
1 ATTTAATTGGGATATATTAACTAATGCAATA
* * *
25336677 ATTTAATTGGGATGTATTAACTATTGCAGTA
1 ATTTAATTGGGATATATTAACTAATGCAATA
25336708 ATTTAAT
1 ATTTAAT
25336715 ATGGTCAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (31 bp):
ATTTAATTGGGATATATTAACTAATGCAATA
Found at i:25339128 original size:46 final size:46
Alignment explanation
Indices: 25339061--25339235 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
25339051 TGTAACCCGC
25339061 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
25339107 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
25339157 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
25339200 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
25339236 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 63 0.58
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:25339181 original size:93 final size:93
Alignment explanation
Indices: 25339069--25339239 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
25339059 GCCCATAAGT
** *
25339069 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
25339134 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
25339162 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
25339227 CGAGTTCGGATGC
66 CGAGCTCGGATGC
25339240 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:25339827 original size:20 final size:18
Alignment explanation
Indices: 25339793--25339829 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
25339783 GCAACTCATA
25339793 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
25339811 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
25339830 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:25343277 original size:12 final size:12
Alignment explanation
Indices: 25343251--25343282 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25343241 ATAAATGATA
25343251 AATA-TATTTTT
1 AATATTATTTTT
25343262 -ATATTATTTTT
1 AATATTATTTTT
25343273 AATATTATTT
1 AATATTATTT
25343283 ATACATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 7 0.37
12 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATATTATTTTT
Found at i:25345053 original size:24 final size:23
Alignment explanation
Indices: 25345026--25345073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
25345016 CATTATAATC
* *
25345026 AACTTTTCACCTTTCATATTCCTT
1 AACTCTTCACATTTCAT-TTCCTT
25345050 AACTCTTCACATTTCATTTCCTT
1 AACTCTTCACATTTCATTTCCTT
25345073 A
1 A
25345074 TAACCTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (23 bp):
AACTCTTCACATTTCATTTCCTT
Found at i:25345131 original size:2 final size:2
Alignment explanation
Indices: 25345126--25345160 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25345116 AATCTCTCCT
25345126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25345161 GAATATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25346151 original size:30 final size:30
Alignment explanation
Indices: 25346110--25346182 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
25346100 GGTCACGCTA
25346110 GTAGTCGTGGTTGAGGACATAAGTGCAATC
1 GTAGTCGTGGTTGAGGACATAAGTGCAATC
*
25346140 GTAGTCATGGTTGAGGACATAAGTGCAATC
1 GTAGTCGTGGTTGAGGACATAAGTGCAATC
25346170 GTAGTCGTGGTTG
1 GTAGTCGTGGTTG
25346183 TGGTCGCGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.12, G:0.34, T:0.29
Consensus pattern (30 bp):
GTAGTCGTGGTTGAGGACATAAGTGCAATC
Found at i:25349134 original size:41 final size:41
Alignment explanation
Indices: 25349077--25349158 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
25349067 ATATTTTCCA
25349077 TCTAAGAATCTTTTGATGTATTGTATATGTTCCGATTGCTC
1 TCTAAGAATCTTTTGATGTATTGTATATGTTCCGATTGCTC
* *
25349118 TCTAAGAATTTTTTGATGTATTGTATATGTTTCGATTGCTC
1 TCTAAGAATCTTTTGATGTATTGTATATGTTCCGATTGCTC
25349159 CACAACAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (41 bp):
TCTAAGAATCTTTTGATGTATTGTATATGTTCCGATTGCTC
Found at i:25353970 original size:14 final size:15
Alignment explanation
Indices: 25353951--25353987 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
25353941 CAGAAATGAC
25353951 AAGAGAAATTAGGG-
1 AAGAGAAATTAGGGA
25353965 AAGAG-AA-TAGGGA
1 AAGAGAAATTAGGGA
25353978 AAGAGAAATT
1 AAGAGAAATT
25353988 TGTGCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.25
13 7 0.35
14 7 0.35
15 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.32, T:0.14
Consensus pattern (15 bp):
AAGAGAAATTAGGGA
Found at i:25357411 original size:18 final size:17
Alignment explanation
Indices: 25357388--25357430 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
25357378 GGCCCAGAAT
*
25357388 CCCACACACCCGTGTGGG
1 CCCACACACCCGTGT-AG
* *
25357406 CCCACACGCTCGTGTAG
1 CCCACACACCCGTGTAG
25357423 CCCACACA
1 CCCACACA
25357431 GCCCAAAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.12
Consensus pattern (17 bp):
CCCACACACCCGTGTAG
Found at i:25374461 original size:34 final size:35
Alignment explanation
Indices: 25374418--25374485 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
25374408 TTCAATTTTG
*
25374418 GAAAGTGAT-AATTATAATTTAATAAATACATTTA
1 GAAAGTGATAAATTATAATTCAATAAATACATTTA
* **
25374452 GAAAGTGATAAATTATCATTCAATGGATACATTT
1 GAAAGTGATAAATTATAATTCAATAAATACATTT
25374486 TTATGGGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (35 bp):
GAAAGTGATAAATTATAATTCAATAAATACATTTA
Found at i:25379843 original size:2 final size:2
Alignment explanation
Indices: 25379838--25379873 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25379828 GATATATTTG
25379838 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
25379874 GCGAAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25381218 original size:26 final size:26
Alignment explanation
Indices: 25381188--25381238 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
25381178 TCCTTATATT
*
25381188 TTAATATAATATAATT-TTATCATTAA
1 TTAATATAA-ATAATTAATATCATTAA
*
25381214 TTAATTTAAATAATTAATATCATTA
1 TTAATATAAATAATTAATATCATTA
25381239 TTATTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
TTAATATAAATAATTAATATCATTAA
Found at i:25385871 original size:20 final size:20
Alignment explanation
Indices: 25385826--25385917 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 20
25385816 TTTATTAAAT
* *
25385826 TTTATAATTTTTT-CTATATA
1 TTTATAATTTTTTAC-AGATG
25385846 TATTATATATTTTTTACA-ATG
1 T-TTATA-ATTTTTTACAGATG
** *
25385867 TTTATAAAATTTTACAGATT
1 TTTATAATTTTTTACAGATG
* *
25385887 TTTATAATTTTTTA-TGATT
1 TTTATAATTTTTTACAGATG
25385906 TTTATAATTTTT
1 TTTATAATTTTT
25385918 AATAAATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 24 0.39
20 20 0.33
21 8 0.13
22 8 0.13
23 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATAATTTTTTACAGATG
Found at i:25385926 original size:20 final size:20
Alignment explanation
Indices: 25385884--25385958 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
25385874 AATTTTACAG
* *
25385884 ATTTTTATAATTTTTTAT-G
1 ATTTTTATAATTTTTAATAA
25385903 ATTTTTATAATTTTTAATAA
1 ATTTTTATAATTTTTAATAA
*
25385923 ATTTTTA-ATATTTTTATTAA
1 ATTTTTATA-ATTTTTAATAA
* * *
25385943 AATTTAATCATTTTTA
1 ATTTTTATAATTTTTA
25385959 TATTTTTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (20 bp):
ATTTTTATAATTTTTAATAA
Found at i:25385927 original size:19 final size:19
Alignment explanation
Indices: 25385886--25385936 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
25385876 TTTTACAGAT
* * *
25385886 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTAATAAA
25385905 TTTTATAATTTTTAATAAA
1 TTTTATAATTTTTAATAAA
25385924 TTTT-TAATATTTT
1 TTTTATAAT-TTTT
25385937 TATTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAA
Found at i:25385927 original size:48 final size:48
Alignment explanation
Indices: 25385856--25386000 Score: 125
Period size: 48 Copynumber: 3.0 Consensus size: 48
25385846 TATTATATAT
* * * *
25385856 TTTTTACAATGTTT-ATAAAATTTTACAGATTTTTATAATTTTTTATGA
1 TTTTTATAATTTTTAAT-AAATTTTACATATTTTTATAATTTTTTATCA
** *
25385904 TTTTTATAATTTTTAATAAATTTTTA-ATATTTTTATTAAAATTTAATCA
1 TTTTTATAATTTTTAATAAA-TTTTACATATTTTTA-TAATTTTTTATCA
* * * * *
25385953 TTTTTATATTTTTTATTGATTTTTAC-TTTTTTTATCAATTTTTTATCA
1 TTTTTATAATTTTTAATAAATTTTACATATTTTTAT-AATTTTTTATCA
25386001 CATGTTATGC
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
47 1 0.01
48 44 0.57
49 32 0.42
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTTTATAATTTTTAATAAATTTTACATATTTTTATAATTTTTTATCA
Found at i:25385937 original size:10 final size:10
Alignment explanation
Indices: 25385884--25385977 Score: 70
Period size: 9 Copynumber: 9.7 Consensus size: 10
25385874 AATTTTACAG
25385884 ATTTTT-ATA
1 ATTTTTAATA
* *
25385893 ATTTTTTATG
1 ATTTTTAATA
25385903 ATTTTT-ATA
1 ATTTTTAATA
25385912 ATTTTTAATAA
1 ATTTTTAAT-A
25385923 ATTTTTAAT-
1 ATTTTTAATA
*
25385932 ATTTTTATTA
1 ATTTTTAATA
** *
25385942 AAATTTAATC
1 ATTTTTAATA
25385952 ATTTTT-ATA
1 ATTTTTAATA
* * *
25385961 TTTTTTATTG
1 ATTTTTAATA
25385971 ATTTTTA
1 ATTTTTA
25385978 CTTTTTTTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
9 29 0.44
10 27 0.41
11 10 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:25385949 original size:30 final size:27
Alignment explanation
Indices: 25385890--25385965 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 27
25385880 ACAGATTTTT
**
25385890 ATAATTTTTTATGATTTTTATAATTTTTA
1 ATAA-TTTTTAT-ATTTTTATAAAATTTA
25385919 ATAAATTTTTAATATTTTTATTAAAATTTA
1 AT-AATTTTT-ATATTTTTA-TAAAATTTA
*
25385949 ATCATTTTTATATTTTT
1 ATAATTTTTATATTTTT
25385966 TATTGATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 8 0.20
29 20 0.49
30 13 0.32
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (27 bp):
ATAATTTTTATATTTTTATAAAATTTA
Found at i:25385967 original size:19 final size:19
Alignment explanation
Indices: 25385945--25385995 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
25385935 TTTATTAAAA
25385945 TTTAATCATTTTTA-TATTT
1 TTTAATCATTTTTACT-TTT
* *
25385964 TTTATTGATTTTTACTTTT
1 TTTAATCATTTTTACTTTT
25385983 TTT-ATCAATTTTT
1 TTTAATC-ATTTTT
25385996 TATCACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTAATCATTTTTACTTTT
Found at i:25387743 original size:2 final size:2
Alignment explanation
Indices: 25387731--25387760 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25387721 TATGAATAAA
25387731 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25387761 GAAAAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25389664 original size:135 final size:135
Alignment explanation
Indices: 25389492--25390092 Score: 685
Period size: 135 Copynumber: 4.5 Consensus size: 135
25389482 TGTTCAGTAG
* * *
25389492 AGATAAGATCTGATATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGTCTGATGATTGGA
1 AGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGA
* * * *
25389557 ATCTGCTCCATCG-CTAGTACAGGGAGATAAGATTCACCAAAATTCGATCTAC-TCTGCTCCTGC
66 ATCTGCTCCATCGCCGA-TACAGGGAGATAAGACTCACCAAAATTCGATCTGCTTC-ACTCCTGC
25389620 TCAGCGA
129 TCAGCGA
* *
25389627 AGATAAGATCTGCTGTACTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGA
1 AGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGA
* ** * *
25389692 ATCTGCTCCATTGCCGATACATAGAGATAAGATTCACCAAAATTCGATCTGC-TCTGCTCCTGCT
66 ATCTGCTCCATCGCCGATACAGGGAGATAAGACTCACCAAAATTCGATCTGCTTC-ACTCCTGCT
25389756 CAGCGA
130 CAGCGA
* *
25389762 AGATAAGATCTGCTATACTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGTTGATGATTAGA
1 AGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGA
* * * * * * * *
25389827 ATCTACTCTATTGCCGATACATGGAGATAAGACTCGCTAAAATTTGATCTGCTTCACTCCTGTTC
66 ATCTGCTCCATCGCCGATACAGGGAGATAAGACTCACCAAAATTCGATCTGCTTCACTCCTGCTC
*
25389892 AGTGA
131 AGCGA
* * * * ** * **
25389897 AGAAAAGATCGGGTATGTTTAGCCTGC-TCTACTCCTGTTCAGTGAAGATAAGGCTGGTGGCT-G
1 AGATAAGATCTGCTATATTTAGCCTGCTTC-ACTCCTACTCAGTGAAGATAAGGCTGATGATTAG
* * * * *
25389960 AAATCTGCTCCACTC-CTGCT-CAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCCT
65 -AATCTGCTCCA-TCGCCGATACAG-GGAGATAAGACTCACCAAAATTCGATCTGCTTCACTCCT
**
25390023 GCTCAATGA
127 GCTCAGCGA
* * * *
25390032 AGATAAGATCGGGTATGTTTAGCCCGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGAT
1 AGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGAT
25390093 ATCTGTCTTT
Statistics
Matches: 409, Mismatches: 50, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
134 5 0.01
135 397 0.97
136 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (135 bp):
AGATAAGATCTGCTATATTTAGCCTGCTTCACTCCTACTCAGTGAAGATAAGGCTGATGATTAGA
ATCTGCTCCATCGCCGATACAGGGAGATAAGACTCACCAAAATTCGATCTGCTTCACTCCTGCTC
AGCGA
Found at i:25390022 original size:46 final size:45
Alignment explanation
Indices: 25389851--25390083 Score: 136
Period size: 45 Copynumber: 5.2 Consensus size: 45
25389841 CGATACATGG
* *
25389851 AGATAAGACTCGCTAAAATTTGATCTGCTTCACTCCTGTTCAGTGA
1 AGATAAGACTCGCCAAAATTT-ATCTGCTTCACTCCTGCTCAGTGA
* *** ** * *
25389897 AGAAAAGA-TCGGGTATGTTTAGCCTGC-TCTACTCCTGTTCAGTGA
1 AGATAAGACTCGCCAAAATTTA-TCTGCTTC-ACTCCTGCTCAGTGA
* * * ** *
25389942 AGATAAGGCTGGTGGCTGAA---ATCTGCTCCACTCCTGCTCAGTGA
1 AGATAAGACT--CGCCAAAATTTATCTGCTTCACTCCTGCTCAGTGA
*
25389986 AGATAAGACTCGCCAAAATTTGATCTGCTTCACTCCTGCTCAATGA
1 AGATAAGACTCGCCAAAATTT-ATCTGCTTCACTCCTGCTCAGTGA
*** ** * * *
25390032 AGATAAGA-TCGGGTATGTTTAGCCCGCTTCACTCCTACTCAGTGA
1 AGATAAGACTCGCCAAAATTTA-TCTGCTTCACTCCTGCTCAGTGA
25390077 AGATAAG
1 AGATAAG
25390084 GCTGATGATA
Statistics
Matches: 143, Mismatches: 33, Indels: 23
0.72 0.17 0.12
Matches are distributed among these distances:
42 4 0.03
44 31 0.22
45 67 0.47
46 38 0.27
48 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
AGATAAGACTCGCCAAAATTTATCTGCTTCACTCCTGCTCAGTGA
Found at i:25397849 original size:20 final size:20
Alignment explanation
Indices: 25397826--25397874 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
25397816 TGTTAGCTGG
* *
25397826 CTCATCATGTTGTTCTGTGA
1 CTCAGCATGTTGTTCTGGGA
*
25397846 CTCAGCATGTTTTTCTGGGA
1 CTCAGCATGTTGTTCTGGGA
25397866 CTCTAGCAT
1 CTC-AGCAT
25397875 TTGATCCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.41
Consensus pattern (20 bp):
CTCAGCATGTTGTTCTGGGA
Found at i:25400728 original size:38 final size:38
Alignment explanation
Indices: 25400686--25400762 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
25400676 TCACGAAGGC
25400686 ATAGCTTTTCACTCCCACTTAAGGTGCGACCACAACAG
1 ATAGCTTTTCACTCCCACTTAAGGTGCGACCACAACAG
25400724 ATAGCTTTTCACTCCCACTTAAGGTGCGACCACAACAG
1 ATAGCTTTTCACTCCCACTTAAGGTGCGACCACAACAG
25400762 A
1 A
25400763 CATGCAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (38 bp):
ATAGCTTTTCACTCCCACTTAAGGTGCGACCACAACAG
Found at i:25405788 original size:3 final size:3
Alignment explanation
Indices: 25405780--25405824 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
25405770 TATGGTCCAT
*
25405780 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25405825 AAGAGATAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:25407316 original size:13 final size:13
Alignment explanation
Indices: 25407300--25407344 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
25407290 TTATTTTGTT
25407300 TTATTTAGTTTTA
1 TTATTTAGTTTTA
*
25407313 TTATTTATTTTTA
1 TTATTTAGTTTTA
25407326 -T-TTTA-TTTTA
1 TTATTTAGTTTTA
25407336 TTAATTTAG
1 TT-ATTTAG
25407345 AATTAGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 1 0.04
13 16 0.59
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TTATTTAGTTTTA
Found at i:25407317 original size:23 final size:23
Alignment explanation
Indices: 25407288--25407343 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
25407278 AAATAGAAGA
25407288 TATTATTT-TGTTTTA-TTTAGTTT
1 TATTATTTAT-TTTTATTTTA-TTT
25407311 TATTATTTATTTTTATTTTATTT
1 TATTATTTATTTTTATTTTATTT
25407334 TATTAATTTA
1 TATT-ATTTA
25407344 GAATTAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (23 bp):
TATTATTTATTTTTATTTTATTT
Found at i:25413610 original size:24 final size:24
Alignment explanation
Indices: 25413582--25413628 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
25413572 AAAATGGCGA
* *
25413582 TGATAACGTAGACAATAATAATAG
1 TGATAACATAAACAATAATAATAG
*
25413606 TGATAACATAAATAATAATAATA
1 TGATAACATAAACAATAATAATA
25413629 TAAAACGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (24 bp):
TGATAACATAAACAATAATAATAG
Found at i:25413740 original size:2 final size:2
Alignment explanation
Indices: 25413718--25413771 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
25413708 AAAAAGGAAA
* *
25413718 AT AT AC AT A- AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25413758 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
25413772 GAGATATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:25415394 original size:23 final size:23
Alignment explanation
Indices: 25415343--25415396 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
25415333 TAGGTTTAAT
*
25415343 GTTTTAGGTAAATTGGGTTAGGG
1 GTTTTGGGTAAATTGGGTTAGGG
25415366 GTTTTGGGTAAATTGGGTTAGGG
1 GTTTTGGGTAAATTGGGTTAGGG
25415389 GTTTTGGG
1 GTTTTGGG
25415397 CCCAAAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.41
Consensus pattern (23 bp):
GTTTTGGGTAAATTGGGTTAGGG
Found at i:25415948 original size:43 final size:43
Alignment explanation
Indices: 25415800--25416109 Score: 171
Period size: 43 Copynumber: 7.2 Consensus size: 43
25415790 TGTCATCATC
* * *
25415800 GATCTGTGAATTCAACCTGTTACCCTACTACTTA-GGGTTTAA
1 GATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
* * *** * * *
25415842 GGTCTGTAAGTTTGGCTTGCTACCCTACTGCTTAGGGGGTTGA
1 GATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
** * ** ** * *
25415885 GCCCAT-CATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAA
1 GATC-TGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
** **
25415928 GATCTGTAAATTCAACCTGTTTCACTGTAACT--TTAGGGGGACAA
1 GATCTGTAAATTCAACCTG-TT-ACCCT-ACTGCTTAGGGGGTTAA
* * * * *
25415972 AATCTGTAATTTTTAGCCTATTACCCTACTGCTTA-GGGGTTAA
1 GATCTGTAA-ATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
* * ** *
25416015 GGTCTGCAAATTCGGCTTGTTACCCTACTGCTTAGGGGGTTAAA
1 GATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTT-AA
** * * *
25416059 GCCCTTTGAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAA
1 GATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
*
25416102 GGTCTGTA
1 GATCTGTA
25416110 CATTTAGTTT
Statistics
Matches: 192, Mismatches: 65, Indels: 21
0.69 0.23 0.08
Matches are distributed among these distances:
42 49 0.26
43 72 0.38
44 60 0.31
45 8 0.04
46 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (43 bp):
GATCTGTAAATTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
Found at i:25416040 original size:42 final size:42
Alignment explanation
Indices: 25415992--25416107 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 42
25415982 TTTTAGCCTA
** *
25415992 TTACCCTACTGCTTAGGGGTTAAGGTCTGCAAATTCGGCTTG
1 TTACCCTACTGCTTAGGGGTTAAGGTCTGCAAATTCAACCTG
** ***
25416034 TTACCCTACTGCTTAGGGGGTTAAAGCCCTTTGAATTCAACCTG
1 TTACCCTACTGCTTA-GGGGTT-AAGGTCTGCAAATTCAACCTG
25416078 TTACCCTACTGCTTAGGGGTTTAAGGTCTG
1 TTACCCTACTGCTTAGGGG-TTAAGGTCTG
25416108 TACATTTAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 15 0.25
43 15 0.25
44 30 0.50
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (42 bp):
TTACCCTACTGCTTAGGGGTTAAGGTCTGCAAATTCAACCTG
Found at i:25416358 original size:44 final size:44
Alignment explanation
Indices: 25416246--25416408 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 44
25416236 ATTTGTAATT
* * * ** *
25416246 TTCAGCCTATTACCCTACTACTTAGGGGGTT-AAGGCCTGCAAA
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAAGATCTGCGAA
*** * *
25416289 TTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCAT-C-AA
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAAGATC-TGCGAA
* * **
25416332 CTTCGATCTGTTTTCCTACTGCTTAGGGGGTT-AAGATCTGCGAA
1 -TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAAGATCTGCGAA
25416376 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAA
25416409 GGTCTGGTGA
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
42 1 0.01
43 61 0.64
44 33 0.34
45 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (44 bp):
TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAAGATCTGCGAA
Found at i:25424466 original size:9 final size:9
Alignment explanation
Indices: 25424448--25424479 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
25424438 TGCAATGCTG
25424448 ATGC-ATGA
1 ATGCAATGA
25424456 ATGCAATGA
1 ATGCAATGA
25424465 ATGCAATGA
1 ATGCAATGA
25424474 ATGCAA
1 ATGCAA
25424480 AAAAGCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (9 bp):
ATGCAATGA
Found at i:25429814 original size:20 final size:21
Alignment explanation
Indices: 25429789--25429828 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25429779 CTCTTGAAAC
*
25429789 AGGGC-ACATGCCCATGTGGA
1 AGGGCAACACGCCCATGTGGA
*
25429809 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCATGTGG
25429829 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:25431260 original size:45 final size:46
Alignment explanation
Indices: 25431196--25431285 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
25431186 TATCTCATAA
* *
25431196 TACGGGACTCGGATGATGTTCTCGTCTATTTATCATG-AAATAGAT
1 TACGGGACTCAGATGATGTTCCCGTCTATTTATCATGAAAATAGAT
* *
25431241 TACGGGACTCAGATGATGTTCCCTTCTATTTATTATGAAAATAGA
1 TACGGGACTCAGATGATGTTCCCGTCTATTTATCATGAAAATAGA
25431286 CTCATTAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 33 0.82
46 7 0.17
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (46 bp):
TACGGGACTCAGATGATGTTCCCGTCTATTTATCATGAAAATAGAT
Found at i:25458523 original size:26 final size:26
Alignment explanation
Indices: 25458492--25458599 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
25458482 TGAAATTCCC
*
25458492 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
25458518 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
25458544 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
25458570 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
25458596 ATCA
1 ATCA
25458600 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:25465570 original size:26 final size:26
Alignment explanation
Indices: 25465539--25465646 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
25465529 TGAAATTCCC
*
25465539 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
25465565 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
25465591 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
25465617 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
25465643 ATCA
1 ATCA
25465647 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:25469465 original size:29 final size:29
Alignment explanation
Indices: 25469420--25469492 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
25469410 GTGACAAGAT
25469420 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
*
25469449 TGTCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
25469478 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
25469493 GAATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCAAGCTTGAAAAGTA
Found at i:25469511 original size:29 final size:29
Alignment explanation
Indices: 25469479--25469551 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
25469469 TGAAAAGTAT
* * *
25469479 GGCACTAAGTGTGCGAATTTAAATTATAC
1 GGCACTAAGTGTGCGAACTTAAATCACAC
* * *
25469508 GGCACTATGTGTGCGAGCTTAAATCACAT
1 GGCACTAAGTGTGCGAACTTAAATCACAC
25469537 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
25469552 TGATCGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAACTTAAATCACAC
Found at i:25473934 original size:29 final size:29
Alignment explanation
Indices: 25473901--25474032 Score: 210
Period size: 29 Copynumber: 4.6 Consensus size: 29
25473891 CCTTCGAGCT
** * *
25473901 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
25473930 TGCACACTTAGTGTCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25473959 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25473988 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25474017 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
25474033 ATCTCGTCAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:25473935 original size:58 final size:58
Alignment explanation
Indices: 25473872--25474032 Score: 178
Period size: 58 Copynumber: 2.8 Consensus size: 58
25473862 AATTTAAGCC
* * * * * *
25473872 CGCACACATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * * * **
25473930 TGCACACTTAGTGTCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * **
25473988 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCA
25474033 ATCTCGTCAC
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:25481957 original size:29 final size:29
Alignment explanation
Indices: 25481896--25482056 Score: 223
Period size: 29 Copynumber: 5.6 Consensus size: 29
25481886 AATTTAAGCC
* *** * *
25481896 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
** * *
25481925 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
25481954 CGCACACTTAGTGTCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25481983 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25482012 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
25482041 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
25482057 ATCTCGTCAC
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 118 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:25487957 original size:29 final size:29
Alignment explanation
Indices: 25487915--25487986 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
25487905 GTGACAAGAT
25487915 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
25487944 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
25487973 TGGCACTAAGTGTG
1 TGGCACTAAGTGTG
25487987 TGAATTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCAAGCTTGAAAAGTA
Found at i:25488006 original size:29 final size:29
Alignment explanation
Indices: 25487974--25488046 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
25487964 TGAAAAGTAT
* * * *
25487974 GGCACTAAGTGTGTGAATTTAAATTATAC
1 GGCACTAAGTGTGCGAACTTAAATCACAC
* * *
25488003 GGCACTATGTGTGCGAGCTTAAATCACAT
1 GGCACTAAGTGTGCGAACTTAAATCACAC
25488032 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
25488047 TGATCGATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAACTTAAATCACAC
Found at i:25493688 original size:25 final size:25
Alignment explanation
Indices: 25493660--25493729 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
25493650 CCCTTTTAAT
25493660 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
25493685 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
25493710 AACTAGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
25493730 GCACTTCCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:25493788 original size:10 final size:10
Alignment explanation
Indices: 25493775--25493814 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
25493765 CATATATGAA
25493775 CATATCATGG
1 CATATCATGG
*
25493785 CATATCAGGTG
1 CATATCATG-G
*
25493796 AATATCATGG
1 CATATCATGG
25493806 CATATCATG
1 CATATCATG
25493815 TACAAAACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (10 bp):
CATATCATGG
Found at i:25493882 original size:25 final size:25
Alignment explanation
Indices: 25493854--25493904 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
25493844 ATAACATATC
* *
25493854 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCAAAATGGTCATTTTCA
25493879 CCTAGGGGCAAAATGGTCATTTTCA
1 CCTAGGGGCAAAATGGTCATTTTCA
25493904 C
1 C
25493905 ATTATAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTCA
Found at i:25503959 original size:29 final size:27
Alignment explanation
Indices: 25503925--25504027 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
25503915 TACTCAATCA
*
25503925 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
25503954 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
25503983 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
25504012 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
25504028 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:25506213 original size:30 final size:29
Alignment explanation
Indices: 25506152--25506254 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
25506142 AAAATTGTAC
*
25506152 AGCACTAAGTGTGCGAGCTGAAAAAATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
25506181 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
25506211 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
25506240 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
25506255 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 44 0.61
30 28 0.39
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:25506218 original size:59 final size:60
Alignment explanation
Indices: 25506122--25506254 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
25506112 GACAAGATTG
* * *
25506122 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAGCTGAAAAAATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAGCTGAAAAAATATA
* * *
25506182 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAGCTGAAAAAATATA
25506241 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
25506255 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAGCTGAAAAAATATA
Found at i:25510973 original size:40 final size:40
Alignment explanation
Indices: 25510769--25510973 Score: 198
Period size: 40 Copynumber: 5.1 Consensus size: 40
25510759 AATACAACCT
* *
25510769 GATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGCCCG
1 GATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGCCCG
* * * *
25510809 GATAGAACGACTTGCACAAATGCCTTCGGGTATTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* * * **
25510849 GATTTAACAACTTGCACGAATGCCTTTAGGTCTTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
* * * *
25510889 GATGTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 GATATA-ACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
** * * *
25510929 GATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCG
1 GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
25510969 GATAT
1 GATAT
25510974 CATTCAATTG
Statistics
Matches: 134, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
40 133 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
GATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCG
Found at i:25514273 original size:27 final size:27
Alignment explanation
Indices: 25514243--25514431 Score: 236
Period size: 27 Copynumber: 7.0 Consensus size: 27
25514233 AAAAGGTGAT
*
25514243 TGAAATACCCCCATAGGGTAAAATGAC
1 TGAAATACCCCTATAGGGTAAAATGAC
*
25514270 TGAAATACCCCTTCTAGGGTAAAATGAC
1 TGAAATACCCC-TATAGGGTAAAATGAC
*
25514298 TGAAATACCCCCATAGGGTAAAATGATC
1 TGAAATACCCCTATAGGGTAAAATGA-C
*
25514326 T-AAATACCCTTATAGGGTAAAATGAC
1 TGAAATACCCCTATAGGGTAAAATGAC
* * *
25514352 TGAAATACCCTTATAAGTTAAAATGAC
1 TGAAATACCCCTATAGGGTAAAATGAC
* *
25514379 TGTAATACCCCTATAAGGTAAAATGAC
1 TGAAATACCCCTATAGGGTAAAATGAC
* * * *
25514406 TGTAATACTCCTGTAAGGTAAAATGA
1 TGAAATACCCCTATAGGGTAAAATGA
25514432 TTGATTTGCC
Statistics
Matches: 146, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.01
27 117 0.80
28 27 0.18
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (27 bp):
TGAAATACCCCTATAGGGTAAAATGAC
Found at i:25517265 original size:31 final size:31
Alignment explanation
Indices: 25517224--25517287 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
25517214 CCTTCTCATA
*
25517224 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
25517255 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
25517286 TT
1 TT
25517288 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:25517533 original size:24 final size:24
Alignment explanation
Indices: 25517481--25517646 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
25517471 GCTTTATCAT
*
25517481 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
25517506 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
25517530 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
25517553 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
25517577 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
25517601 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
25517624 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25517647 TCACTTCCTC
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
23 43 0.33
24 74 0.57
25 12 0.09
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:25517557 original size:47 final size:48
Alignment explanation
Indices: 25517480--25517646 Score: 241
Period size: 47 Copynumber: 3.5 Consensus size: 48
25517470 TGCTTTATCA
* *
25517480 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
25517529 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
25517576 GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
25517623 AATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT
25517647 TCACTTCCTC
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
47 70 0.64
48 26 0.24
49 13 0.12
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:25517581 original size:71 final size:71
Alignment explanation
Indices: 25517481--25517646 Score: 262
Period size: 71 Copynumber: 2.3 Consensus size: 71
25517471 GCTTTATCAT
* *
25517481 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
25517545 GCCCTTTA
64 GCCCTTTA
* * *
25517553 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
25517618 CCTTTA
66 CCTTTA
25517624 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
25517647 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:25517719 original size:9 final size:9
Alignment explanation
Indices: 25517705--25517761 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
25517695 ATCTCGTGTG
25517705 CATATCATA
1 CATATCATA
*
25517714 CATATCATGTG
1 CATATCA--TA
25517725 CATATCATA
1 CATATCATA
* *
25517734 CATGTCATGTG
1 CATATCA--TA
25517745 CATATCATA
1 CATATCATA
25517754 CATATCAT
1 CATATCAT
25517762 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:25517724 original size:20 final size:20
Alignment explanation
Indices: 25517701--25517763 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
25517691 GAACATCTCG
25517701 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
25517721 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
25517741 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
25517761 TGT
1 TGT
25517764 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:25519151 original size:27 final size:27
Alignment explanation
Indices: 25519121--25519341 Score: 147
Period size: 27 Copynumber: 8.1 Consensus size: 27
25519111 GTAAATCTAC
* *
25519121 AAACTAAGGGTATTTCAGTAATTTTGT
1 AAACTAAGGGTATTTCGGTAATTTTAT
* * ** *
25519148 AAACCAATGGTATTTCTATAATTTTTAG
1 AAACTAAGGGTATTTCGGTAA-TTTTAT
* * * * *
25519176 AAAGTCAAGGGTGTTTCTGTAACTTTGT
1 AAACT-AAGGGTATTTCGGTAATTTTAT
* * *
25519204 AAA-TCAGGGGTATTTTGGTAATTTTAC
1 AAACT-AAGGGTATTTCGGTAATTTTAT
* * *
25519231 AAATTAAGGGTATTTCGGTAATTTCAC
1 AAACTAAGGGTATTTCGGTAATTTTAT
* * * *
25519258 AAACCAATGGTATTTTGGTAATTTTAA
1 AAACTAAGGGTATTTCGGTAATTTTAT
* * * *
25519285 AAACTAGGGGTATTTTGGTACTTTTAC
1 AAACTAAGGGTATTTCGGTAATTTTAT
** *
25519312 AAACTAAGGGTATTTTAGTAATTTTGT
1 AAACTAAGGGTATTTCGGTAATTTTAT
25519339 AAA
1 AAA
25519342 TCGAGGGTAA
Statistics
Matches: 151, Mismatches: 40, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
27 124 0.82
28 14 0.09
29 13 0.09
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACTAAGGGTATTTCGGTAATTTTAT
Found at i:25519273 original size:54 final size:54
Alignment explanation
Indices: 25519098--25519336 Score: 210
Period size: 54 Copynumber: 4.4 Consensus size: 54
25519088 TTTCATCCTA
* * * * **
25519098 CAAGGGTGTTTTGGTAAATCTACAAACTAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
* * * * * * * ** *
25519152 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTGTTTCTGTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAA-TTTTACAAACT-AAGGGTATTTCGGTAATTTTACAAAC
* * *
25519208 CAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
* * * * *
25519262 CAATGGTATTTTGGTAATTTTAAAAACTAGGGGTATTTTGGTACTTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
* *
25519316 TAAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
25519337 GTAAATCGAG
Statistics
Matches: 147, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
54 95 0.65
55 18 0.12
56 34 0.23
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
Found at i:25519348 original size:27 final size:27
Alignment explanation
Indices: 25519126--25519404 Score: 127
Period size: 27 Copynumber: 10.3 Consensus size: 27
25519116 TCTACAAACT
* *
25519126 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
25519153 AATGGTATTTCTA-TAATTTT-TAGAAAGTC
1 AAGGGTATTT-TAGTAATTTTGT--AAA-TC
* *
25519182 AAGGGTGTTTCT-GTAACTTTGTAAATC
1 AAGGGTATTT-TAGTAATTTTGTAAATC
* * ** *
25519209 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTGTAAATC
** *** *
25519236 AAGGGTATTTCGGTAATTTCACAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
* * * *
25519263 AATGGTATTTTGGTAATTTT-AAAAAC
1 AAGGGTATTTTAGTAATTTTGTAAATC
* * * **
25519289 TAGGGGTATTTTGGTACTTTTACAAA-C
1 -AAGGGTATTTTAGTAATTTTGTAAATC
25519316 TAAGGGTATTTTAGTAATTTTGTAAATC
1 -AAGGGTATTTTAGTAATTTTGTAAATC
* **** *
25519344 GAGGGTAAAACAGTAATTCTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*** * *
25519371 AAGGGTAAAATAGTAATTCTATAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
25519398 GAGGGTA
1 AAGGGTA
25519405 AAATGATAAT
Statistics
Matches: 201, Mismatches: 41, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
26 6 0.03
27 166 0.83
28 11 0.05
29 17 0.08
30 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAATC
Found at i:25519405 original size:27 final size:27
Alignment explanation
Indices: 25519327--25519539 Score: 225
Period size: 27 Copynumber: 7.9 Consensus size: 27
25519317 AAGGGTATTT
*
25519327 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
25519354 CAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
25519381 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
25519408 T-GATAATTCTGTAAATCGAGGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
* *
25519435 TGGTAATTCTGTAAGTCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* * *
25519462 -CGATAATTATGTAAAT-TAGGGGTAAAA
1 TAG-TAATTCTGTAAATCGA-GGGTAAAA
** * * *
25519489 CGGTAATTATATAAATCGGGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** *
25519516 CGGTAATTCTGTAAATCGGGGGTA
1 TAGTAATTCTGTAAATCGAGGGTA
25519540 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.02
27 157 0.97
28 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:25519469 original size:81 final size:81
Alignment explanation
Indices: 25519330--25519539 Score: 253
Period size: 81 Copynumber: 2.6 Consensus size: 81
25519320 GGTATTTTAG
* * * * *
25519330 TAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAA
1 TAATTATGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAGAGTAATTATATAA
*
25519395 ATCGA-GGGTAAAATGA
66 AT-GAGGGGTAAAACGA
* * * *
25519411 TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAGTCGAGGGTAAAACGA-TAATTATGTA
1 TAATTATGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-GAGTAATTATATA
* *
25519475 AATTAGGGGTAAAACGG
65 AATGAGGGGTAAAACGA
* * *
25519492 TAATTATATAAATCGGGGGTAAAACGGTAATTCTGTAAATCGGGGGTA
1 TAATTATGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
25519540 CTTTGGTAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 108 0.98
82 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.29
Consensus pattern (81 bp):
TAATTATGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAGAGTAATTATATAA
ATGAGGGGTAAAACGA
Found at i:25519550 original size:54 final size:54
Alignment explanation
Indices: 25519329--25519532 Score: 266
Period size: 54 Copynumber: 3.8 Consensus size: 54
25519319 GGGTATTTTA
* * *
25519329 GTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAACGA-TAATTCTGTAAATCAAGGGTAAAATG
* *
25519383 GTAATTCTATAAATCGAGGGTAAAATGATAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAATG
* * * * * *
25519437 GTAATTCTGTAAGTCGAGGGTAAAACGATAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAATG
* * *
25519491 GTAATTATATAAATCGGGGGTAAAACGGTAATTCTGTAAATC
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATC
25519533 GGGGGTACTT
Statistics
Matches: 129, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
54 128 0.99
55 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (54 bp):
GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAATG
Found at i:25519575 original size:27 final size:27
Alignment explanation
Indices: 25519545--25519634 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
25519535 GGGTACTTTG
* *
25519545 GTAATTTTACAAGTCGAAAGTATTTTA
1 GTAATTTTACAAATCGAAAGTATTTCA
**
25519572 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAAGTATTTCA
* * * *
25519599 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-AGTATTTCA
25519626 GTAATTTTA
1 GTAATTTTA
25519635 GTAAACTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 2 0.04
27 51 0.96
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAAGTATTTCA
Found at i:25519641 original size:28 final size:27
Alignment explanation
Indices: 25519564--25519643 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
25519554 CAAGTCGAAA
* *
25519564 GTATTTTAGTAATTTTACAAA-TCGAGG
1 GTATTTCAGTAATTTTACAAACT-AAGG
*
25519591 GTATTTCAGTATTTTTACAAACTAAGG
1 GTATTTCAGTAATTTTACAAACTAAGG
* *
25519618 GTATTTCGGTAATTTTAGTAAACTAA
1 GTATTTCAGTAATTTTA-CAAACTAA
25519644 AGTATTCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 37 0.82
28 8 0.18
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAACTAAGG
Found at i:25519648 original size:27 final size:27
Alignment explanation
Indices: 25519545--25519649 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
25519535 GGGTACTTTG
* * *
25519545 GTAATTTTACAAGTCGAA-AGTATTTTA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
25519572 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
25519599 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
25519626 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
25519650 CTAAACATGG
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.02
27 54 0.86
28 8 0.13
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:25534166 original size:46 final size:46
Alignment explanation
Indices: 25534112--25534287 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
25534102 TGGTTGAGCA
25534112 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
25534158 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
25534203 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
25534251 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25534288 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 27 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:25534268 original size:93 final size:93
Alignment explanation
Indices: 25534109--25534279 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
25534099 GGATGGTTGA
* *
25534109 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
25534174 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
25534202 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
25534267 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
25534280 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:25538755 original size:2 final size:2
Alignment explanation
Indices: 25538748--25538779 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25538738 ACCAGAATAG
25538748 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
25538780 GTGGCGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25543220 original size:12 final size:12
Alignment explanation
Indices: 25543203--25543227 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25543193 CTTTTTATTC
25543203 TATAAGTTTCCA
1 TATAAGTTTCCA
25543215 TATAAGTTTCCA
1 TATAAGTTTCCA
25543227 T
1 T
25543228 TTGTCTGACT
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TATAAGTTTCCA
Found at i:25544136 original size:221 final size:221
Alignment explanation
Indices: 25543753--25544197 Score: 863
Period size: 221 Copynumber: 2.0 Consensus size: 221
25543743 ATTCGGTATA
*
25543753 AGACTTCTGCAGTATGTAGAATCATTCAAAATAGTGGAATTCATAGCCCTAGAAATGGGTAAATC
1 AGACTTCTGCAGTATGTAGAACCATTCAAAATAGTGGAATTCATAGCCCTAGAAATGGGTAAATC
25543818 ATATCATCTCATTTTTATTACATGATATATGAAAAGTAATCGTAGCTACCATCGTTTGTCTGTTT
66 ATATCATCTCATTTTTATTACATGATATATGAAAAGTAATCGTAGCTACCATCGTTTGTCTGTTT
*
25543883 GGTGAATGACTTAACTACTATTTGATAATAATTGGCTTTTCATGAAATAAATTGTAATGGTTACC
131 GGTGAATGACTTAACTACTATTTGATAATAATTGGCTTTTCATGAAAGAAATTGTAATGGTTACC
*
25543948 ATGAGATAAAATAAGATCATGTTGAG
196 ATGAGATAAAATAAGATCATATTGAG
25543974 AGACTTCTGCAGTATGTAGAACCATTCAAAATAGTGGAATTCATAGCCCTAGAAATGGGTAAATC
1 AGACTTCTGCAGTATGTAGAACCATTCAAAATAGTGGAATTCATAGCCCTAGAAATGGGTAAATC
25544039 ATATCATCTCATTTTTATTACATGATATATGAAAAGTAATCGTAGCTACCATCGTTTGTCTGTTT
66 ATATCATCTCATTTTTATTACATGATATATGAAAAGTAATCGTAGCTACCATCGTTTGTCTGTTT
25544104 GGTGAATGACTTAACTACTATTTGATAATAATTGGCTTTTCATGAAAGAAATTGTAATGGTTACC
131 GGTGAATGACTTAACTACTATTTGATAATAATTGGCTTTTCATGAAAGAAATTGTAATGGTTACC
25544169 ATGAGATAAAATAAGATCATATTGAG
196 ATGAGATAAAATAAGATCATATTGAG
25544195 AGA
1 AGA
25544198 ACAAAATTAT
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
221 221 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (221 bp):
AGACTTCTGCAGTATGTAGAACCATTCAAAATAGTGGAATTCATAGCCCTAGAAATGGGTAAATC
ATATCATCTCATTTTTATTACATGATATATGAAAAGTAATCGTAGCTACCATCGTTTGTCTGTTT
GGTGAATGACTTAACTACTATTTGATAATAATTGGCTTTTCATGAAAGAAATTGTAATGGTTACC
ATGAGATAAAATAAGATCATATTGAG
Found at i:25561206 original size:30 final size:30
Alignment explanation
Indices: 25561170--25561236 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
25561160 CACACGGTTA
*
25561170 GACACACGAGCATGTGTCTTGGCCGTGTGG
1 GACACACGAGCATATGTCTTGGCCGTGTGG
* *
25561200 GACACACGGGCATATGTCTTGGTCGTGTGG
1 GACACACGAGCATATGTCTTGGCCGTGTGG
25561230 GACACAC
1 GACACAC
25561237 CGTTTGCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.22
Consensus pattern (30 bp):
GACACACGAGCATATGTCTTGGCCGTGTGG
Found at i:25566115 original size:173 final size:173
Alignment explanation
Indices: 25565826--25566171 Score: 649
Period size: 173 Copynumber: 2.0 Consensus size: 173
25565816 CGTATGTCAT
25565826 ATCGGATTGAATCTCAATCTCAGAGGTAAAAATCACATGCGAGGGATCGGATCTGTAACATCGAA
1 ATCGGATTGAATCTCAATCTCAGAGGTAAAAATCACATGCGAGGGATCGGATCTGTAACATCGAA
*
25565891 GCATTGATACGTGAAATACATTATGAATCTTTTCTAACTCAGGTGGCAACAAAAATTTATAAGCA
66 GCATTGATACGTAAAATACATTATGAATCTTTTCTAACTCAGGTGGCAACAAAAATTTATAAGCA
25565956 ACC-GACCCAATACGCTCAACAATCTCGTACGACCCAATGAATC
131 ACCTG-CCCAATACGCTCAACAATCTCGTACGACCCAATGAATC
*
25565999 ATCGGATTGAATCTCAATCTCAGAGGTAAAAATCATATGCGAGGGATCGGATCTGTAACATCGAA
1 ATCGGATTGAATCTCAATCTCAGAGGTAAAAATCACATGCGAGGGATCGGATCTGTAACATCGAA
25566064 GCATTGATACGTAAAATACATTATGAATCTTTTCTAACTCAGGTGGCAACAAAAATTTATAAGCA
66 GCATTGATACGTAAAATACATTATGAATCTTTTCTAACTCAGGTGGCAACAAAAATTTATAAGCA
*
25566129 ACCTGCCCAATACGCTCAACAATCTCGTACGACCTAATGAATC
131 ACCTGCCCAATACGCTCAACAATCTCGTACGACCCAATGAATC
25566172 TAGGACTTAA
Statistics
Matches: 169, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
173 168 0.99
174 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (173 bp):
ATCGGATTGAATCTCAATCTCAGAGGTAAAAATCACATGCGAGGGATCGGATCTGTAACATCGAA
GCATTGATACGTAAAATACATTATGAATCTTTTCTAACTCAGGTGGCAACAAAAATTTATAAGCA
ACCTGCCCAATACGCTCAACAATCTCGTACGACCCAATGAATC
Done.