Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 95 of 208
Found at i:28372785 original size:14 final size:15
Alignment explanation
Indices: 28372767--28372816 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
28372757 ATAAATATAA
28372767 AAAAATATTCATTA-
1 AAAAATATTCATTAG
**
28372781 AAAAATATAAATATAG
1 AAAAATATTCAT-TAG
*
28372797 AAAAATATTCGTTAG
1 AAAAATATTCATTAG
28372812 AAAAA
1 AAAAA
28372817 ATATAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.34
15 10 0.34
16 9 0.31
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (15 bp):
AAAAATATTCATTAG
Found at i:28372789 original size:32 final size:31
Alignment explanation
Indices: 28372755--28372827 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
28372745 ACGTGTATAT
28372755 ATATAAATATAAAAAAATATTCATT-AAAAA
1 ATATAAATATAAAAAAATATTCATTGAAAAA
* *
28372785 ATATAAATATAGAAAAATATTCGTTAGAAAAA
1 ATATAAATATAAAAAAATATTCATT-GAAAAA
28372817 ATATAAATATA
1 ATATAAATATA
28372828 TATACATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 23 0.59
32 16 0.41
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (31 bp):
ATATAAATATAAAAAAATATTCATTGAAAAA
Found at i:28374710 original size:44 final size:44
Alignment explanation
Indices: 28374653--28374770 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
28374643 GATGTGATCT
* *
28374653 ACTCTACTGTAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCC
1 ACTCCACTGTAACTTCAGAGAGATAAGAT-TAGTGGCTTTAATCC
* * *
28374697 ACTCCACTGTAACTTCA-AGGAGATAGGATTATTGGCTTTAATCT
1 ACTCCACTGTAACTTCAGA-GAGATAAGATTAGTGGCTTTAATCC
* * *
28374741 GCTCCACTGCAACTTCAGGGAGATAAGATT
1 ACTCCACTGTAACTTCAGAGAGATAAGATT
28374771 CGCCATCTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
43 2 0.03
44 60 0.97
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTCCACTGTAACTTCAGAGAGATAAGATTAGTGGCTTTAATCC
Found at i:28374954 original size:100 final size:100
Alignment explanation
Indices: 28374791--28374978 Score: 297
Period size: 100 Copynumber: 1.9 Consensus size: 100
28374781 AATCTTTCAT
* *
28374791 TGTTGGGGAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAA
1 TGTTGGGGAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAA
*
28374856 ATTCACTATTGCGGCTTCAATCTTTTTAATTGCAA
66 ATTCACCATTGCGGCTTCAATCTTTTTAATTGCAA
28374891 TGTTGGGGAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGG-AGTAA
1 TGTTGGGGAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAG-GGAAGTAA
* * * *
28374955 GATTCGCCGTTGCGGCTTTAATCT
65 AATTCACCATTGCGGCTTCAATCT
28374979 ATTCCACTGA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 78 0.98
101 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (100 bp):
TGTTGGGGAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAA
ATTCACCATTGCGGCTTCAATCTTTTTAATTGCAA
Found at i:28375011 original size:100 final size:100
Alignment explanation
Indices: 28374798--28375001 Score: 239
Period size: 100 Copynumber: 2.0 Consensus size: 100
28374788 CATTGTTGGG
* * *
28374798 GAAACGAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCACT
1 GAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCACC
* * * * ** *
28374863 ATTGCGGCTTCAATCTTTTTAATTGCAATGTTGGG
66 ATTGCGGCTTCAATCTATTCAACTGAAATGTAAGA
* *
28374898 GAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGAGG-AGTAAGATTCGC
1 GAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAG-GGAAGTAAAATTCAC
* * *
28374962 CGTTGCGGCTTTAATCTATTCCACTGAAATGCTAAAGA
65 CATTGCGGCTTCAATCTATTCAACTGAAATG-T-AAGA
28375000 GA
1 GA
28375002 TAGGATTCAC
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
100 80 0.93
101 3 0.03
102 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (100 bp):
GAAACGAGATTCACAGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAAATTCACC
ATTGCGGCTTCAATCTATTCAACTGAAATGTAAGA
Found at i:28383263 original size:170 final size:170
Alignment explanation
Indices: 28382981--28383326 Score: 692
Period size: 170 Copynumber: 2.0 Consensus size: 170
28382971 GTGCTAAATC
28382981 TCTCAATGAATTAATTTTGGTACGGCTCAATTGATTGTACCACTTGGATGCTGCCCTTGTGAGGC
1 TCTCAATGAATTAATTTTGGTACGGCTCAATTGATTGTACCACTTGGATGCTGCCCTTGTGAGGC
28383046 TATCCTGGAAGCAATGTATCAGCAGTTGGTCGTTGTTAACATACATAGTCATTCGTCTGCAAAAC
66 TATCCTGGAAGCAATGTATCAGCAGTTGGTCGTTGTTAACATACATAGTCATTCGTCTGCAAAAC
28383111 ATAGAAATATGAGCTTCGGGGCTACTAGTTCTGTTGTACT
131 ATAGAAATATGAGCTTCGGGGCTACTAGTTCTGTTGTACT
28383151 TCTCAATGAATTAATTTTGGTACGGCTCAATTGATTGTACCACTTGGATGCTGCCCTTGTGAGGC
1 TCTCAATGAATTAATTTTGGTACGGCTCAATTGATTGTACCACTTGGATGCTGCCCTTGTGAGGC
28383216 TATCCTGGAAGCAATGTATCAGCAGTTGGTCGTTGTTAACATACATAGTCATTCGTCTGCAAAAC
66 TATCCTGGAAGCAATGTATCAGCAGTTGGTCGTTGTTAACATACATAGTCATTCGTCTGCAAAAC
28383281 ATAGAAATATGAGCTTCGGGGCTACTAGTTCTGTTGTACT
131 ATAGAAATATGAGCTTCGGGGCTACTAGTTCTGTTGTACT
28383321 TCTCAA
1 TCTCAA
28383327 ACTCTGGCAT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 176 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (170 bp):
TCTCAATGAATTAATTTTGGTACGGCTCAATTGATTGTACCACTTGGATGCTGCCCTTGTGAGGC
TATCCTGGAAGCAATGTATCAGCAGTTGGTCGTTGTTAACATACATAGTCATTCGTCTGCAAAAC
ATAGAAATATGAGCTTCGGGGCTACTAGTTCTGTTGTACT
Found at i:28388000 original size:33 final size:31
Alignment explanation
Indices: 28387967--28388039 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 31
28387957 ATATATATAT
28387967 ATATAAATATA-AAAAATATTCATT-AAAAA
1 ATATAAATATAGAAAAATATTCATTGAAAAA
*
28387996 ATATAAATATAGAAAAATATTCGTTAGAAGAAA
1 ATATAAATATAGAAAAATATTCATT-GAA-AAA
28388029 ATATAAATATA
1 ATATAAATATA
28388040 TATACATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 11 0.28
30 12 0.31
32 2 0.05
33 14 0.36
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (31 bp):
ATATAAATATAGAAAAATATTCATTGAAAAA
Found at i:28388011 original size:16 final size:15
Alignment explanation
Indices: 28387967--28388015 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
28387957 ATATATATAT
28387967 ATATAAATATAAAAA
1 ATATAAATATAAAAA
**
28387982 ATATTCAT-TAAAAA
1 ATATAAATATAAAAA
28387996 ATATAAATATAGAAAA
1 ATATAAATATA-AAAA
28388012 ATAT
1 ATAT
28388016 TCGTTAGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATATAAATATAAAAA
Found at i:28388917 original size:20 final size:20
Alignment explanation
Indices: 28388892--28388930 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28388882 TTCGTTTATA
28388892 AAAAATA-AAACAATAAATAG
1 AAAAATAGAAA-AATAAATAG
28388912 AAAAATAGAAAAATAAATA
1 AAAAATAGAAAAATAAATA
28388931 AATATTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAATAGAAAAATAAATAG
Found at i:28390351 original size:26 final size:27
Alignment explanation
Indices: 28390322--28390385 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
28390312 TAATTTTTTA
28390322 TGAAAATTTTGTATTTTTTT-AAATTT
1 TGAAAATTTTGTATTTTTTTAAAATTT
* *
28390348 TG--AATTTGGAAATTTTTTTAAAATTT
1 TGAAAATTTTG-TATTTTTTTAAAATTT
28390374 T-AAAATATTTGT
1 TGAAAAT-TTTGT
28390386 TAACTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
24 6 0.21
25 8 0.28
26 9 0.31
27 3 0.10
28 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (27 bp):
TGAAAATTTTGTATTTTTTTAAAATTT
Found at i:28393654 original size:17 final size:17
Alignment explanation
Indices: 28393629--28393662 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28393619 AATGTTTCAA
28393629 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
* *
28393646 AAAAGGAAAAAACAAAG
1 AAAAAGAAAAAAAAAAG
28393663 TTACAAGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:28393655 original size:16 final size:17
Alignment explanation
Indices: 28393626--28393662 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28393616 ATCAATGTTT
28393626 CAAA-AAAAGAAAAAAA
1 CAAAGAAAAGAAAAAAA
*
28393642 -AAAGAAAAGGAAAAAA
1 CAAAGAAAAGAAAAAAA
28393658 CAAAG
1 CAAAG
28393663 TTACAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 11 0.61
17 4 0.22
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (17 bp):
CAAAGAAAAGAAAAAAA
Found at i:28405745 original size:51 final size:51
Alignment explanation
Indices: 28405678--28405809 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 51
28405668 TGATAGGTCG
*
28405678 CATGTGTAGTACTATGTGTAGGCTACTATGCGTA-CTGGATAGCCTTGATCA
1 CATGTGTAGTACTATGTGTAGGCTACTATGCGTATC-GGATAGCCATGATCA
* * * * ** *
28405729 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCA
1 CATGTGTAGTACTATGTGTAGGCTACTATGCGTATCGGATAGCCATGATCA
*
28405780 CATATGTAGTACTATGTGTAGGCTACTATG
1 CATGTGTAGTACTATGTGTAGGCTACTATG
28405810 TGAACCGGCA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 67 0.99
52 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGTAGGCTACTATGCGTATCGGATAGCCATGATCA
Found at i:28405808 original size:102 final size:99
Alignment explanation
Indices: 28405627--28405809 Score: 287
Period size: 102 Copynumber: 1.8 Consensus size: 99
28405617 AAAGTGATGG
* *
28405627 TCACGTGTGTTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTA
1 TCACGTGTGTTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATATGTAGTACTA
28405692 TGTGTAGGCTACTATGCGTACTGGATAGCCTTGA
66 TGTGTAGGCTACTATGCGTACTGGATAGCCTTGA
* *
28405726 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATATGTAGT
1 TCACGTGTGT--TACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCACATATGTAGT
28405790 ACTATGTGTAGGCTACTATG
62 ACTATGTGTAGGCTACTATG
28405810 TGAACCGGCA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
99 10 0.13
101 28 0.37
102 34 0.45
103 4 0.05
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (99 bp):
TCACGTGTGTTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATATGTAGTACTA
TGTGTAGGCTACTATGCGTACTGGATAGCCTTGA
Found at i:28406081 original size:37 final size:38
Alignment explanation
Indices: 28406012--28406084 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
28406002 ATGTGTGGAA
* **
28406012 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAATGACTTGAAAATGAAAAAGTGAATT
*
28406050 TTGAATTGAATAATGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAATGACTTGAAAATGAAAAAGTGAA
28406085 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAATGACTTGAAAATGAAAAAGTGAATT
Found at i:28409283 original size:29 final size:29
Alignment explanation
Indices: 28409251--28409359 Score: 107
Period size: 29 Copynumber: 3.7 Consensus size: 29
28409241 ACTTTGACTA
28409251 TCGAATATGAAAAGGGATGGTGACAACCT
1 TCGAATATGAAAAGGGATGGTGACAACCT
* * **
28409280 TCGAATATGAAAAGGGATAGCT-TC-GGCT
1 TCGAATATGAAAAGGGAT-GGTGACAACCT
* *
28409308 ATCGATTATGAAAAGGGATGGTGACAACCA
1 -TCGAATATGAAAAGGGATGGTGACAACCT
28409338 TC-AATTAATGAAAAGGGATGGT
1 TCGAA-T-ATGAAAAGGGATGGT
28409360 TTCAGCCAGC
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
28 5 0.08
29 40 0.63
30 18 0.29
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (29 bp):
TCGAATATGAAAAGGGATGGTGACAACCT
Found at i:28409318 original size:58 final size:59
Alignment explanation
Indices: 28409227--28409356 Score: 183
Period size: 58 Copynumber: 2.2 Consensus size: 59
28409217 ATCATCGACC
* * *
28409227 AATGAAAAAGGATAACTTTGACTATCGAATATGAAAAGGGATGGTGACAACCTTCGAA-T
1 AATGAAAAGGGATAACTTCGACTATCGAATATGAAAAGGGATGGTGACAACCATC-AATT
* * *
28409286 -ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACAACCATCAATT
1 AATGAAAAGGGATAACTTCGACTATCGAATATGAAAAGGGATGGTGACAACCATCAATT
28409344 AATGAAAAGGGAT
1 AATGAAAAGGGAT
28409357 GGTTTCAGCC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
57 2 0.03
58 49 0.78
59 12 0.19
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.23
Consensus pattern (59 bp):
AATGAAAAGGGATAACTTCGACTATCGAATATGAAAAGGGATGGTGACAACCATCAATT
Found at i:28418539 original size:50 final size:50
Alignment explanation
Indices: 28418406--28418550 Score: 166
Period size: 50 Copynumber: 2.9 Consensus size: 50
28418396 CCGAATCACC
* * * *
28418406 ATTTGTGGACAAGCCACCACTGATTTGAAGATAAACTGCCA-TTGATAACA
1 ATTTGTGGACAAGCCACCACTGATATGCAGATATACTGCCACAT-ATAACA
* * * *
28418456 CTTTGCGGACAAGCCACAACTTATATGCAGATATACTGCCACATATAACA
1 ATTTGTGGACAAGCCACCACTGATATGCAGATATACTGCCACATATAACA
* * * *
28418506 ATTTGTGGTCTAGCCACCACTGATATGCAGATATATTGCTACATA
1 ATTTGTGGACAAGCCACCACTGATATGCAGATATACTGCCACATA
28418551 CTTCCACCTT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
50 77 0.99
51 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (50 bp):
ATTTGTGGACAAGCCACCACTGATATGCAGATATACTGCCACATATAACA
Found at i:28419985 original size:92 final size:91
Alignment explanation
Indices: 28419858--28420067 Score: 312
Period size: 92 Copynumber: 2.3 Consensus size: 91
28419848 TTCAACAATA
* * *
28419858 TATATTCATATACGAATCAAATTTGACAACTTATCTTTATATACAAATCAATTTCGATAATGTAT
1 TATAATCATATACGAATC-AATTCGACAACTTATCTTCATATACAAATCAATTTCGATAA-GTAT
*
28419923 AACCATATGCAAATAAATTTCAGCAAAG
64 AACCATATACAAATAAATTTCAGCAAAG
*
28419951 TATAATCATATACGAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAAGTATAA
1 TATAATCATATACGAATCAATTCGACAACTTATCTTCATATACAAATCAATTTCGATAAGTATAA
*
28420016 CCATATACAAATAAATTTCAGCAATG
66 CCATATACAAATAAATTTCAGCAAAG
* * *
28420042 TAATACTTATATACGAATTAATTCGA
1 T-ATAATCATATACGAATCAATTCGA
28420068 AAATGTATAA
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 31 0.29
92 58 0.55
93 17 0.16
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (91 bp):
TATAATCATATACGAATCAATTCGACAACTTATCTTCATATACAAATCAATTTCGATAAGTATAA
CCATATACAAATAAATTTCAGCAAAG
Found at i:28420021 original size:30 final size:30
Alignment explanation
Indices: 28419896--28420034 Score: 131
Period size: 31 Copynumber: 4.6 Consensus size: 30
28419886 ACTTATCTTT
28419896 ATATACAAATCAATTTCGATAATGTATAACC
1 ATATACAAATCAATTTCGATAA-GTATAACC
* * *
28419927 ATATGCAAATAAATTTCAGCA-AAGTATAATC
1 ATATACAAATCAATTTC-G-ATAAGTATAACC
* ** * *
28419958 ATATACGAATCAA-TTCGGCAACT-TATCTTC
1 ATATACAAATCAATTTCGATAAGTATAAC--C
28419988 ATATACAAATCAATTTCGATAAGTATAACC
1 ATATACAAATCAATTTCGATAAGTATAACC
*
28420018 ATATACAAATAAATTTC
1 ATATACAAATCAATTTC
28420035 AGCAATGTAA
Statistics
Matches: 85, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
28 2 0.02
29 4 0.05
30 33 0.39
31 39 0.46
32 6 0.07
33 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (30 bp):
ATATACAAATCAATTTCGATAAGTATAACC
Found at i:28424479 original size:20 final size:20
Alignment explanation
Indices: 28424454--28424493 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28424444 TTAGAAACTA
28424454 AATTGAGCTCGAA-TGAGCTG
1 AATTGAGCTC-AAGTGAGCTG
28424474 AATTGAGCTCAAGTGAGCTG
1 AATTGAGCTCAAGTGAGCTG
28424494 GTTGGAGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (20 bp):
AATTGAGCTCAAGTGAGCTG
Found at i:28424535 original size:20 final size:19
Alignment explanation
Indices: 28424497--28424535 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28424487 TGAGCTGGTT
*
28424497 GGAGCTGAAACGAGGTAAA
1 GGAGCTGAAACGAGCTAAA
*
28424516 GGAGCTGGAATCGAGCTAAA
1 GGAGCT-GAAACGAGCTAAA
28424536 ATCAGCTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.38, C:0.13, G:0.36, T:0.13
Consensus pattern (19 bp):
GGAGCTGAAACGAGCTAAA
Found at i:28428429 original size:10 final size:10
Alignment explanation
Indices: 28428401--28428448 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
28428391 TGAATGCTTG
*
28428401 ATGGAATGAA
1 ATGGAATGGA
**
28428411 ATGCTATGGA
1 ATGGAATGGA
* *
28428421 ATGAAATGGT
1 ATGGAATGGA
28428431 ATGGAATGGA
1 ATGGAATGGA
28428441 ATGGAATG
1 ATGGAATG
28428449 AAATAAAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.25
Consensus pattern (10 bp):
ATGGAATGGA
Found at i:28428444 original size:15 final size:15
Alignment explanation
Indices: 28428401--28428444 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28428391 TGAATGCTTG
*
28428401 ATGGAATGAAATGCT
1 ATGGAATGAAATGGT
28428416 ATGGAATGAAATGGT
1 ATGGAATGAAATGGT
*
28428431 ATGGAATGGAATGG
1 ATGGAATGAAATGG
28428445 AATGAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (15 bp):
ATGGAATGAAATGGT
Found at i:28429339 original size:51 final size:50
Alignment explanation
Indices: 28429202--28429339 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 50
28429192 AAAGTGAAAG
* *
28429202 TGAT-GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAA
1 TGATCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAA
* * * * * *
28429251 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GGA
1 TGATCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAA
* *
28429300 TAGCTTCGATCACGTGTGTAGTACTATGTGCAAGCTACTA
1 T-G-ATCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
28429340 GGTGTATCGG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
49 7 0.10
50 36 0.49
51 30 0.41
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
TGATCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCAGAA
Found at i:28429369 original size:51 final size:49
Alignment explanation
Indices: 28429208--28429390 Score: 161
Period size: 51 Copynumber: 3.6 Consensus size: 49
28429198 AAAGTGATGA
* * * *
28429208 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTAGAATGATGGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGGATGATCGG
* * * * * *
28429258 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT-G-ATCGG
* * *
28429309 TCACGTGTGTAGTACTATGTGCAAGCTACTAGGTGTATCGGATGGAAAT-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT-G--ATCGG
** *
28429360 TCACATGTGTAGTACTACATGTAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
28429391 TGTGAACCGG
Statistics
Matches: 105, Mismatches: 25, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 34 0.32
51 67 0.64
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATCGG
Found at i:28429485 original size:33 final size:33
Alignment explanation
Indices: 28429448--28429600 Score: 138
Period size: 33 Copynumber: 4.5 Consensus size: 33
28429438 TCCCCCAAGG
28429448 GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
* * *
28429481 GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATTTGAAGGG
1 GGTTGCTAAGTGCTGATTTC-CCG--A-TT-CA-TT---GGT
* *
28429523 GGTTGCTAAGTGCTGA-TTCCC---CCA-AGG-
1 GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
28429550 GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
28429583 GGTTGCTAAGTGCTGATT
1 GGTTGCTAAGTGCTGATT
28429601 CCACCGTAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
27 16 0.17
28 7 0.07
31 2 0.02
32 2 0.02
33 38 0.40
34 3 0.03
36 1 0.01
37 2 0.02
38 1 0.01
39 2 0.02
40 2 0.02
41 2 0.02
42 18 0.19
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
Found at i:28429592 original size:102 final size:102
Alignment explanation
Indices: 28429416--28429708 Score: 514
Period size: 102 Copynumber: 2.9 Consensus size: 102
28429406 ATTGAATATA
28429416 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
*
28429481 GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATTTG
66 GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTG
28429518 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
28429583 GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTG
* * * * *
28429620 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
* *
28429685 GGTTGCTAAGTGTTGAATCCACCG
66 GGTTGCTAAGTGCTGATTCCACCG
28429709 ATAACGGATG
Statistics
Matches: 183, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 183 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTTCCCGATTCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTG
Found at i:28432145 original size:48 final size:47
Alignment explanation
Indices: 28432067--28432157 Score: 128
Period size: 48 Copynumber: 1.9 Consensus size: 47
28432057 TTATCTATGA
* * * *
28432067 TTATATGGTCGTTATTGGCAATTATGTGGTGGTTTGTCCACAATGTG
1 TTATATGGTCGTTATCGACAATAATGTGGTGGCTTGTCCACAATGTG
*
28432114 TTATGTGGTCGTTTATCGACAATAATGTGGTGGCTTGTCCACAA
1 TTATATGGTCG-TTATCGACAATAATGTGGTGGCTTGTCCACAA
28432158 ATGGTGTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 10 0.26
48 28 0.74
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (47 bp):
TTATATGGTCGTTATCGACAATAATGTGGTGGCTTGTCCACAATGTG
Found at i:28439226 original size:102 final size:101
Alignment explanation
Indices: 28439050--28439393 Score: 478
Period size: 102 Copynumber: 3.4 Consensus size: 101
28439040 TATCGATGAA
*
28439050 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * *
28439115 TAAGTGAAGGCTACAATGTGTATCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAACTTTGGT
*
28439152 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
28439217 TAAGTGAAGGCTACTATGTGTACCGAAAAACTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAACTTTGGT
*** * *
28439254 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CTG-TAAAACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATC-GATAAATGATGGTCACATGTGTAGTA
* * * *
28439317 CTATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
65 CTAAGTGAAGGCTACTATGTGTACCG-AAAACTTTGGT
* * *
28439354 CACGTGTGTAGTACTATGTGAAGACTATTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
28439394 ATGATAAAAG
Statistics
Matches: 221, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
100 38 0.17
101 49 0.22
102 133 0.60
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAACTTTGGT
Found at i:28439322 original size:50 final size:50
Alignment explanation
Indices: 28439050--28439392 Score: 384
Period size: 51 Copynumber: 6.8 Consensus size: 50
28439040 TATCGATGAA
* ***
28439050 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAAACTTGGT
* * * * * *
28439101 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTATCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTA-AAAC-TTGGT
* ***
28439152 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAAACTTGGT
* * * * * *
28439203 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAACTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAAC-TTGGT
*
28439254 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CTGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATC-GTAAAACTTGGT
* *
28439304 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGGT
* * *
28439354 CACGTGTGTAGTACTATGTGAAGACTATTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG
28439393 AATGATAAAA
Statistics
Matches: 247, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.00
50 93 0.38
51 150 0.61
52 2 0.01
53 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGGT
Found at i:28444901 original size:24 final size:24
Alignment explanation
Indices: 28444874--28444926 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
28444864 GGTCATTTTG
28444874 GTGGCTAATGTAATCTTTCATGAT
1 GTGGCTAATGTAATCTTTCATGAT
28444898 GTGGCTAATGTAATCTTTCATGAT
1 GTGGCTAATGTAATCTTTCATGAT
*
28444922 TTGGC
1 GTGGC
28444927 CATAACGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (24 bp):
GTGGCTAATGTAATCTTTCATGAT
Found at i:28454661 original size:40 final size:40
Alignment explanation
Indices: 28454588--28454664 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
28454578 ATACTAACAA
*
28454588 TTTATTTGCATTACTAGTGACTTGTCCACAATACTGGTAG
1 TTTATTTGCATTACTAGTGACTTGCCCACAATACTGGTAG
* * *
28454628 TTTATTTGCATTATTGGT-AGCTTGCCCATAATACTGG
1 TTTATTTGCATTACTAGTGA-CTTGCCCACAATACTGG
28454665 CAACTTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (40 bp):
TTTATTTGCATTACTAGTGACTTGCCCACAATACTGGTAG
Found at i:28457325 original size:27 final size:27
Alignment explanation
Indices: 28457295--28457353 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
28457285 TGGCATCATA
* *
28457295 GGTAGCCCACCGGGACACTAAACACGG
1 GGTAGCCCACCGAGACAATAAACACGG
* * *
28457322 GGTAGTCTACCGAGATAATAAACACGG
1 GGTAGCCCACCGAGACAATAAACACGG
28457349 GGTAG
1 GGTAG
28457354 ATCGCTAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.31, T:0.14
Consensus pattern (27 bp):
GGTAGCCCACCGAGACAATAAACACGG
Found at i:28460462 original size:18 final size:18
Alignment explanation
Indices: 28460439--28460473 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28460429 ATCCAATTAA
28460439 CATAGAGGTAGATGTAGT
1 CATAGAGGTAGATGTAGT
* *
28460457 CATAGATGTGGATGTAG
1 CATAGAGGTAGATGTAG
28460474 AAGTAGATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.29
Consensus pattern (18 bp):
CATAGAGGTAGATGTAGT
Found at i:28463240 original size:26 final size:26
Alignment explanation
Indices: 28463191--28463245 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
28463181 CTTGTAAAAG
* *
28463191 AAACTCAAGAGAAATTCTTAAAAGGA
1 AAACTCAAGAGAAATTATTAAAAGCA
*
28463217 AAACTCAAAGAGAATTTATT-AAAGCA
1 AAACTC-AAGAGAAATTATTAAAAGCA
28463243 AAA
1 AAA
28463246 GAGAAGTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (26 bp):
AAACTCAAGAGAAATTATTAAAAGCA
Found at i:28468764 original size:28 final size:28
Alignment explanation
Indices: 28468724--28468791 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
28468714 GATTTTCTAG
*
28468724 AGCTCATGTAGCTTACATTCCAACCCAC
1 AGCTCGTGTAGCTTACATTCCAACCCAC
*
28468752 AGCTCGTGTAGCTTACATTCCAACCTAC
1 AGCTCGTGTAGCTTACATTCCAACCCAC
28468780 AGCTCGTGTAGC
1 AGCTCGTGTAGC
28468792 AGGCCCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.26
Consensus pattern (28 bp):
AGCTCGTGTAGCTTACATTCCAACCCAC
Found at i:28469745 original size:127 final size:126
Alignment explanation
Indices: 28469520--28469775 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 126
28469510 AAGGGCCCAA
*
28469520 ATTATTATTATCATCACTACTACTACTATTTTTAAATATTATTATCATTTTTTACAAATAAACAA
1 ATTATTATTATCATCACTACTACTACTATTATTAAATATTATTATCATTTTTTACAAATAAACAA
28469585 GATTAAAAAACAACATATATACATGAAATGAAATGAAAGAAAAAAAAAGGAAGGTTTTTCAT
66 GATTAAAAAACAACATATATACATGAAATGAAATGAAAG-AAAAAAAAGGAAGGTTTTTCAT
28469647 ATTATTATTATCATCACTACTACTACTATTATTAAATATTATTATCATTTTTTACAAATAAACAA
1 ATTATTATTATCATCACTACTACTACTATTATTAAATATTATTATCATTTTTTACAAATAAACAA
* *
28469712 GATTAAAAAACAATATATATACATGAAATGAAATGAAAGAAAAAAAAGGGAGGTTTTTCAT
66 GATTAAAAAACAACATATATACATGAAATGAAATGAAAGAAAAAAAAGGAAGGTTTTTCAT
28469773 ATT
1 ATT
28469776 TTGTTCTTAA
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
126 24 0.19
127 102 0.81
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (126 bp):
ATTATTATTATCATCACTACTACTACTATTATTAAATATTATTATCATTTTTTACAAATAAACAA
GATTAAAAAACAACATATATACATGAAATGAAATGAAAGAAAAAAAAGGAAGGTTTTTCAT
Found at i:28469803 original size:3 final size:3
Alignment explanation
Indices: 28469795--28469820 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28469785 AAAAAGGTAA
28469795 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
28469821 ACATTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:28470224 original size:23 final size:22
Alignment explanation
Indices: 28470198--28470246 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
28470188 AAAAATATGT
* **
28470198 TTTTTAATCATTTTAAAGGAAAA
1 TTTTAAAT-ATTTTAAAACAAAA
*
28470221 TTTTAAATTTTTTAAAACAAAA
1 TTTTAAATATTTTAAAACAAAA
28470243 TTTT
1 TTTT
28470247 GATCTCTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTAAATATTTTAAAACAAAA
Found at i:28470257 original size:142 final size:141
Alignment explanation
Indices: 28470030--28470323 Score: 425
Period size: 142 Copynumber: 2.1 Consensus size: 141
28470020 AAAAAAAGAT
*
28470030 AAAGTTTAGATTTCTAAAATAAAATTTTTTTTAGTCATATTAAAGGAAAAGTTTAAATTTTTAAA
1 AAAGTTTAGATTTCTAAAATAAAATTTTTTTTAATCATATTAAAGGAAAAGTTTAAATTTTTAAA
* * * * *
28470095 ATAAAGTTTTGATCTTTTTCAACTATTTTGAAATGAAGTTTTGATTTTTAAGAAAAATAGTGA-T
66 ACAAAATTTTGATCTCTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAAATAGTGATT
28470159 -TTTTAAAAAA
131 CTTTTAAAAAA
* *
28470169 AAAGTTTAGATTT-TAAAATAAAAATATGTTTTTTAATCATTTTAAAGGAAAATTTTAAATTTTT
1 AAAGTTTAGATTTCTAAAAT-AAAAT-T-TTTTTTAATCATATTAAAGGAAAAGTTTAAA-TTTT
*
28470233 TAAAACAAAATTTTGATCTCTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGACAAATAGT
62 TAAAACAAAATTTTGATCTCTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAAATAGT
*
28470298 GATTCTTTTAAAAGA
127 GATTCTTTTAAAAAA
*
28470313 AAACTTT-GATT
1 AAAGTTTAGATT
28470324 CTACCAAAAA
Statistics
Matches: 138, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
138 6 0.04
139 18 0.13
140 1 0.01
141 28 0.20
142 65 0.47
143 5 0.04
144 15 0.11
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (141 bp):
AAAGTTTAGATTTCTAAAATAAAATTTTTTTTAATCATATTAAAGGAAAAGTTTAAATTTTTAAA
ACAAAATTTTGATCTCTTTCAACTATTTCGAAATAAAGTTTTGATTTTTAAGAAAAATAGTGATT
CTTTTAAAAAA
Found at i:28472627 original size:17 final size:19
Alignment explanation
Indices: 28472587--28472629 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 19
28472577 TTAATTTCAC
*
28472587 ATTTTTTTCATTTGACTTT
1 ATTTTTTTCATTTGAATTT
28472606 A-TTTTTT-A-TTGAATTT
1 ATTTTTTTCATTTGAATTT
28472622 ATTTTTTT
1 ATTTTTTT
28472630 TGTGTCTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 6 0.27
19 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (19 bp):
ATTTTTTTCATTTGAATTT
Found at i:28475266 original size:27 final size:27
Alignment explanation
Indices: 28475237--28475622 Score: 425
Period size: 27 Copynumber: 14.4 Consensus size: 27
28475227 GGTATAACAA
* *
28475237 TCATTTTATCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * * *
28475264 TCATGTTACCTTATGAGGATATTTCTG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
28475291 TCATTTTACCCTAT-GGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
28475317 TCATTTTACCCTATGGAGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
* ** * *
28475344 TTATTTTACCCTATAAGGGTTTTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
28475371 TCATTTTACCCTATGAGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
28475398 TCATTTTACCCTATAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28475425 T-AATTTACCCTATGGGGTTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28475451 TCATTATACCCTATGGCGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
** *
28475478 TCATTTTACCCTATTAGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
28475505 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
**
28475532 TCATTTTACTGTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28475559 TCATTTTACCTTATGGAGGTATTTCTG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
28475586 TCATTTTATCCTATGGGGGTTTTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
28475613 TCATTTTACC
1 TCATTTTACC
28475623 TATTTTTGGG
Statistics
Matches: 298, Mismatches: 59, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
26 45 0.15
27 253 0.85
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:28476354 original size:24 final size:25
Alignment explanation
Indices: 28476310--28476356 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
28476300 CCCAAATCTC
*
28476310 AATATTCTCTCCTCAAATCTCTCCA
1 AATATTCTCTCATCAAATCTCTCCA
*
28476335 AATATTC-CTCATCAATTCTCTC
1 AATATTCTCTCATCAAATCTCTC
28476357 TATGACCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATTCTCTCATCAAATCTCTCCA
Found at i:28477397 original size:3 final size:3
Alignment explanation
Indices: 28477389--28477415 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28477379 AAGCTCATAG
28477389 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
28477416 CAACGAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28477600 original size:12 final size:12
Alignment explanation
Indices: 28477585--28477625 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
28477575 TTTCAATCAA
*
28477585 TCATTCATTCAT
1 TCATTCATTCGT
*
28477597 TCATCCATTCGT
1 TCATTCATTCGT
*
28477609 TCACTCATTCGT
1 TCATTCATTCGT
28477621 TCATT
1 TCATT
28477626 TGTTTATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (12 bp):
TCATTCATTCGT
Found at i:28479126 original size:28 final size:28
Alignment explanation
Indices: 28479094--28479150 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28479084 TTAAGAACTG
*
28479094 CTTAGCGTTAAAATACAAGGTACAAGAT
1 CTTAGCGTTAAAATACAAGGTAAAAGAT
28479122 CTTAGCGTTAAAATACAAGGTAAAAGAT
1 CTTAGCGTTAAAATACAAGGTAAAAGAT
28479150 C
1 C
28479151 ATACCATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (28 bp):
CTTAGCGTTAAAATACAAGGTAAAAGAT
Found at i:28481563 original size:26 final size:27
Alignment explanation
Indices: 28481534--28481586 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28481524 ACCAATGAAA
* *
28481534 TCGGG-GAATCAGCACTTAGCAACCCC
1 TCGGGTGAATCAGCACATAACAACCCC
28481560 TCGGGTGAATCAGCACATAACAACCCC
1 TCGGGTGAATCAGCACATAACAACCCC
28481587 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (27 bp):
TCGGGTGAATCAGCACATAACAACCCC
Found at i:28481577 original size:104 final size:104
Alignment explanation
Indices: 28481398--28481709 Score: 563
Period size: 104 Copynumber: 3.0 Consensus size: 104
28481388 TAACCGTTAT
** *
28481398 TGGTGGATCCCGCACTTAGCACCACCACTG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
28481462 GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
*
28481501 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGT
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
28481566 GAATCAGCACATAACAACCCCCTTTTCATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
28481605 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
28481670 GAATCAGCACATAGCAACCCCCTTTCTCATTTCAAAGATA
66 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
28481710 GCACCACCCA
Statistics
Matches: 200, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 27 0.14
104 159 0.80
105 14 0.07
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:28482112 original size:29 final size:29
Alignment explanation
Indices: 28482079--28482142 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
28482069 TAATCCACCA
28482079 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
28482108 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
28482138 CCCAA
1 CCCAA
28482143 GCTCGGANNN
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:28482116 original size:30 final size:30
Alignment explanation
Indices: 28482086--28482142 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28482076 CCACCCAACT
28482086 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
28482115 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
28482143 GCTCGGANNN
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:28486070 original size:34 final size:34
Alignment explanation
Indices: 28486027--28486094 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
28486017 AAAGAAGAAA
*
28486027 ACCAGTTAGCATATGCATTAGCTACTCTAGCCAC
1 ACCAGTTAGCAGATGCATTAGCTACTCTAGCCAC
28486061 ACCAGTTAGCAGATGCATTAGCTACTCTAGCCAC
1 ACCAGTTAGCAGATGCATTAGCTACTCTAGCCAC
28486095 CATGTTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (34 bp):
ACCAGTTAGCAGATGCATTAGCTACTCTAGCCAC
Found at i:28487912 original size:42 final size:42
Alignment explanation
Indices: 28487852--28488322 Score: 561
Period size: 42 Copynumber: 11.3 Consensus size: 42
28487842 AATGAAATTA
* * * *
28487852 TTCATTCCATTTAGAGGCCCAGGTGTGTATGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
28487894 TTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28487936 TTCATTACATTTAGAGGCCTAAGTGT-G-GGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28487976 TTTATTACATTTAAAGGACCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
28488018 TTCGTTGAATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTAT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACT-T
* *
28488061 TT-ATTGCATTTAAAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
28488102 TTCCTTGCATTTAGAGGCCCAAGTGTGGAGGCCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
28488144 TTCATTGCATTTAGAGGCCTAGGTGTGAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * **
28488186 TTTATTGTATTTAGAGGCTCAAGTGTAAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
28488228 TTCATTGCATCTAGAGGCCTAGGTGTGGTGGTTCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
28488270 TTCATTGCATTTAAAGGCCCAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
28488312 TTCATTGCATT
1 TTCATTGCATT
28488323 GTATATTAAG
Statistics
Matches: 361, Mismatches: 64, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
40 33 0.09
41 5 0.01
42 320 0.89
43 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:28489354 original size:22 final size:22
Alignment explanation
Indices: 28489299--28489355 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
28489289 AAAATATGTT
* * **
28489299 TTTTAGTCATTTTAAAGGAAAA
1 TTTTAATCTTTTTAAAACAAAA
28489321 TTTTAAAT-TTTTTAAAACAAAA
1 TTTT-AATCTTTTTAAAACAAAA
28489343 TTTTAATCTTTTT
1 TTTTAATCTTTTT
28489356 CAACTATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTAATCTTTTTAAAACAAAA
Found at i:28489371 original size:151 final size:149
Alignment explanation
Indices: 28489106--28489404 Score: 476
Period size: 151 Copynumber: 2.0 Consensus size: 149
28489096 ATTTTTAAAA
* *
28489106 AAAATAAAGATAAAGTTTAGGTTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAG
1 AAAATAAAGAAAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAG
* * *
28489171 TTTAAATTTTTAAAATAAAGTTTTAATCTTTTTCAACTATTTCGAAAATAAAGTTTTGATTTTCA
66 TTTAAATTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAAATAAAATTTTGATTTTCA
28489236 AGAAAAAATAGTGATTTTTTTT
131 AG-AAAAATAGT--TTTTTTTT
* *
28489258 AAAA-AAAGAAAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAT
1 AAAATAAAGAAAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAG
*
28489322 TTTAAATTTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCG-AAATAAAATTTTGATTTTT
66 TTTAAA-TTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAAATAAAATTTTGATTTTC
28489386 AAGAAAAATAGTTTTTTTT
130 AAGAAAAATAGTTTTTTTT
28489405 AAGAAAACTT
Statistics
Matches: 138, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
148 7 0.05
150 9 0.07
151 82 0.59
152 40 0.29
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (149 bp):
AAAATAAAGAAAAAGTTTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAAGGAAAAG
TTTAAATTTTTAAAACAAAATTTTAATCTTTTTCAACTATTTCGAAAATAAAATTTTGATTTTCA
AGAAAAATAGTTTTTTTTT
Found at i:28489393 original size:19 final size:18
Alignment explanation
Indices: 28489371--28489421 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
28489361 ATTTCGAAAT
28489371 AAAATTTTGATTTTTAAG
1 AAAATTTTGATTTTTAAG
28489389 AAAAATAGTTT--TTTTTAAG
1 -AAAAT--TTTGATTTTTAAG
*
28489408 AAAACTTTGATTTT
1 AAAATTTTGATTTT
28489422 GCAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 3 0.11
18 8 0.30
19 13 0.48
21 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (18 bp):
AAAATTTTGATTTTTAAG
Found at i:28489771 original size:21 final size:21
Alignment explanation
Indices: 28489747--28489788 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28489737 ATTATTCACA
28489747 CTTATATAATTTTTATTTATT
1 CTTATATAATTTTTATTTATT
* **
28489768 CTTATTTTGTTTTTATTTATT
1 CTTATATAATTTTTATTTATT
28489789 TTCATGTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
CTTATATAATTTTTATTTATT
Found at i:28500950 original size:30 final size:30
Alignment explanation
Indices: 28500914--28500975 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
28500904 TATATAAAAG
28500914 TATGAAAAGATAAAAATGTCATAAAAATAA
1 TATGAAAAGATAAAAATGTCATAAAAATAA
28500944 TATGAAAAGATAAAAATGTCATAAAAATAA
1 TATGAAAAGATAAAAATGTCATAAAAATAA
28500974 TA
1 TA
28500976 ATAGTAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.24
Consensus pattern (30 bp):
TATGAAAAGATAAAAATGTCATAAAAATAA
Found at i:28505304 original size:28 final size:28
Alignment explanation
Indices: 28505273--28505359 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
28505263 ATATTCCCAC
28505273 TTTTAGTTGTCCATGATTATATATTTTA
1 TTTTAGTTGTCCATGATTATATATTTTA
* * **
28505301 TTTTA-TTAT---TTATTACTATATTCCCA
1 TTTTAGTTGTCCATGATTA-TATATT-TTA
28505327 CTTTTAGTTGTCCATGATTATATATTTTA
1 -TTTTAGTTGTCCATGATTATATATTTTA
28505356 TTTT
1 TTTT
28505360 CTTTATGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 5 0.11
25 6 0.14
26 1 0.02
27 8 0.18
28 12 0.27
29 1 0.02
30 6 0.14
31 5 0.11
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTAGTTGTCCATGATTATATATTTTA
Found at i:28505332 original size:55 final size:55
Alignment explanation
Indices: 28505251--28505359 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
28505241 CATTGTTCTC
28505251 TTATTTATTACTATATTCCCACTTTTAGTTGTCCATGATTATATATTTTATTTTA
1 TTATTTATTACTATATTCCCACTTTTAGTTGTCCATGATTATATATTTTATTTTA
28505306 TTATTTATTACTATATTCCCACTTTTAGTTGTCCATGATTATATATTTTATTTT
1 TTATTTATTACTATATTCCCACTTTTAGTTGTCCATGATTATATATTTTATTTT
28505360 CTTTATGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.57
Consensus pattern (55 bp):
TTATTTATTACTATATTCCCACTTTTAGTTGTCCATGATTATATATTTTATTTTA
Found at i:28506989 original size:26 final size:27
Alignment explanation
Indices: 28506951--28507008 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
28506941 AATATTAAAT
* *
28506951 TATTTATATAATTT-TATTATATATTA
1 TATTTTTAAAATTTGTATTATATATTA
* *
28506977 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTTTAAAATTTGTATTATATATTA
28507004 T-TTTT
1 TATTTT
28507009 AATGATGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (27 bp):
TATTTTTAAAATTTGTATTATATATTA
Found at i:28515513 original size:55 final size:55
Alignment explanation
Indices: 28515447--28515553 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
28515437 GTAACAAACA
* *
28515447 GATTCTTAATGGTGTTGAAAAGTTCGGTTTTAGATCAAATTTATTGAGTTGATTT
1 GATTCTTAATGGTATTGAAAAATTCGGTTTTAGATCAAATTTATTGAGTTGATTT
* *
28515502 GATTCTTAATGGTATTGAAAAATTCGGTTTTCGATCAGATTTATTGAGTTGA
1 GATTCTTAATGGTATTGAAAAATTCGGTTTTAGATCAAATTTATTGAGTTGA
28515554 GTTAGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (55 bp):
GATTCTTAATGGTATTGAAAAATTCGGTTTTAGATCAAATTTATTGAGTTGATTT
Found at i:28523795 original size:27 final size:26
Alignment explanation
Indices: 28523724--28523797 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
28523714 GTAAATGGTA
* * * *
28523724 ATTTTACCCCTAGGGGTATTTTGGTC
1 ATTTTACCCTTTGGGGTATTTCGATC
28523750 ATTTTA-CCTTTCGGAGGTATTTCGATC
1 ATTTTACCCTTT-GG-GGTATTTCGATC
28523777 ATTTTACCCTTTGAGGGTATT
1 ATTTTACCCTTTG-GGGTATT
28523798 ACGGTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.08
26 8 0.20
27 23 0.57
28 6 0.15
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.45
Consensus pattern (26 bp):
ATTTTACCCTTTGGGGTATTTCGATC
Found at i:28523834 original size:53 final size:54
Alignment explanation
Indices: 28523719--28523850 Score: 126
Period size: 53 Copynumber: 2.5 Consensus size: 54
28523709 TAGGGGTAAA
* ** * * *
28523719 TGGTAATTTTACCCCTAG-GGGTATTTTGGTCATTTTACCTTTCGGAGGTATTT
1 TGGTAATTTTACCCTTAGAGGGTATTACGGTAAATTTACCTGTCGGAGGTATTT
* * * * *
28523772 CGATCATTTTACCCTTTGAGGGTATTACGGTAAATTTACCTGTC-GAGGTGTTT
1 TGGTAATTTTACCCTTAGAGGGTATTACGGTAAATTTACCTGTCGGAGGTATTT
*
28523825 TGGTAATTTTATCCTTCA-AGGGTATT
1 TGGTAATTTTACCCTT-AGAGGGTATT
28523851 TCGATAATTC
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
53 41 0.67
54 20 0.33
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (54 bp):
TGGTAATTTTACCCTTAGAGGGTATTACGGTAAATTTACCTGTCGGAGGTATTT
Found at i:28523858 original size:27 final size:26
Alignment explanation
Indices: 28523750--28523891 Score: 87
Period size: 27 Copynumber: 5.3 Consensus size: 26
28523740 TATTTTGGTC
*
28523750 ATTTTACCTTTCG-GAGGTATTTCGATC
1 ATTTTACC-TTCGAG-GGTATTTCGATA
* * *
28523777 ATTTTACCCTTTGAGGGTATTACGGTA
1 ATTTTA-CCTTCGAGGGTATTTCGATA
* *
28523804 AATTTACCTGTCGAGGTGT-TTT-GGTA
1 ATTTTACCT-TCGAGG-GTATTTCGATA
*
28523830 ATTTTATCCTTCAAGGGTATTTCGATA
1 ATTTTA-CCTTCGAGGGTATTTCGATA
* * *
28523857 ATTCTACTCTTAG-GGTGTATTTCGGTA
1 ATTTTAC-CTTCGAGG-GTATTTCGATA
28523884 A-TTTACCT
1 ATTTTACCT
28523892 ACGAATCGCA
Statistics
Matches: 91, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
25 4 0.04
26 27 0.30
27 55 0.60
28 5 0.05
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCTTCGAGGGTATTTCGATA
Found at i:28528211 original size:24 final size:24
Alignment explanation
Indices: 28528184--28528240 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28528174 GTGGGCATGT
**
28528184 CACTCAATAGTGTTGTGGTC-AAGC
1 CACTCAATAACGTTGTGG-CAAAGC
28528208 CACTCAATAACGTTGTGGCAAAGC
1 CACTCAATAACGTTGTGGCAAAGC
*
28528232 CACTTAATA
1 CACTCAATA
28528241 TTTTAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (24 bp):
CACTCAATAACGTTGTGGCAAAGC
Found at i:28531474 original size:50 final size:50
Alignment explanation
Indices: 28531333--28531524 Score: 260
Period size: 50 Copynumber: 3.8 Consensus size: 50
28531323 ATTTGGGTAA
*
28531333 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
28531383 AGAGGTCCCATGAAAG-CAATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
28531432 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
28531482 AGAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28531525 TGTTATTATC
Statistics
Matches: 122, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
49 43 0.35
50 46 0.38
51 33 0.27
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28539821 original size:13 final size:14
Alignment explanation
Indices: 28539799--28539827 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28539789 ATAATCTCTG
28539799 TTCATAATCATAAA
1 TTCATAATCATAAA
28539813 TTCAT-ATCATAAA
1 TTCATAATCATAAA
28539826 TT
1 TT
28539828 TATACACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
TTCATAATCATAAA
Found at i:28543589 original size:45 final size:45
Alignment explanation
Indices: 28543521--28543613 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
28543511 ACAGATACTC
* * *
28543521 GGTGGATTTAGCACATAGAAACCATCTTATTAATCAATGATGTCT
1 GGTGGAATTAGCACATAGAAACCACCTTACTAATCAATGATGTCT
*
28543566 GGTGGAATTAGCACATA-ACAACCACCTTACTAATCAATGATGTTT
1 GGTGGAATTAGCACATAGA-AACCACCTTACTAATCAATGATGTCT
28543611 GGT
1 GGT
28543614 TCACATAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (45 bp):
GGTGGAATTAGCACATAGAAACCACCTTACTAATCAATGATGTCT
Found at i:28543786 original size:50 final size:48
Alignment explanation
Indices: 28543609--28543805 Score: 157
Period size: 50 Copynumber: 4.0 Consensus size: 48
28543599 TCAATGATGT
* * * * * * *
28543609 TTGGTTCACATAGTAGTCTGCATATAGTACTATACATTTGACCATTACCA
1 TTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC--TATCA
* * *
28543659 TCTGATACACGTAGTAGCCTGCACATAGTACTACACGTGATCGAAACTAT--
1 T-TGGTACACGTAGTAGCCTGCACATAGTACTACACATG-T-G-ACCTATCA
***
28543709 TTGGTACGTATAGTAGCCTGCACATAGTACTACACATGTGACCTATCA
1 TTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCTATCA
* * *
28543757 TTCCGGTACACGTAGTAGCTTGCACATAGTACTACAAACGTGACC-ATCA
1 TT--GGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCTATCA
28543806 CTTTCAGTTT
Statistics
Matches: 117, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
46 5 0.04
47 1 0.01
48 3 0.03
49 36 0.31
50 37 0.32
51 29 0.25
52 3 0.03
53 1 0.01
54 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (48 bp):
TTGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCTATCA
Found at i:28547395 original size:50 final size:50
Alignment explanation
Indices: 28547282--28547448 Score: 167
Period size: 50 Copynumber: 3.3 Consensus size: 50
28547272 GATAATAACA
* * ** *
28547282 TGCCAA-AGCCATGTCTCA-AACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACA-CCATGTCCCAGAA-ATGGTCTTACAGGGGA-CCTCTCATCTCGG
* ** *
28547333 TGCCCATTCCATGTCCCAGAAATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACACCATGTCCCAGAAATGGTCTTACAGGGGACCTCTCATCTCGG
* ** *
28547383 TGCCAACACCATGCCCCAGGCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACACCATGTCCCAGAAATGGTCTTACAGGGGACCTCTCATCTCGG
*
28547433 TGCCAACGCCATGTCC
1 TGCCAACACCATGTCC
28547449 TAGACATCAA
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 66 0.69
51 28 0.29
52 2 0.02
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACACCATGTCCCAGAAATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:28552071 original size:50 final size:50
Alignment explanation
Indices: 28551956--28552248 Score: 388
Period size: 50 Copynumber: 5.8 Consensus size: 50
28551946 GATAATAACA
* ** * *
28551956 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATTTTCTCATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
** ** * **
28552007 TGCCCTTGCCATGTCTTAGGCATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
28552057 TACCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
28552107 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * *
28552157 TGCTAATGTCATGTCCCAAACATGGTCGTACATGGGACCTCTCATCTGGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
28552207 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28552249 TTACCCAAAT
Statistics
Matches: 207, Mismatches: 35, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
50 178 0.86
51 29 0.14
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:28557401 original size:17 final size:17
Alignment explanation
Indices: 28557379--28557421 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
28557369 GAATGGGCCG
*
28557379 TGTGGGCTCAATGGGCT
1 TGTGGGCCCAATGGGCT
28557396 TGTGGGCCCAATGGGCT
1 TGTGGGCCCAATGGGCT
28557413 TGTGGGCCC
1 TGTGGGCCC
28557422 CACACGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.09, C:0.23, G:0.42, T:0.26
Consensus pattern (17 bp):
TGTGGGCCCAATGGGCT
Found at i:28557789 original size:27 final size:27
Alignment explanation
Indices: 28557668--28557789 Score: 140
Period size: 27 Copynumber: 4.5 Consensus size: 27
28557658 TATCTAAATG
* *
28557668 AAAATTACCGAAATACCCTCGAAGTGT
1 AAAATTACTGAAATACCCTCGAAGGGT
* * *
28557695 AAAATTACTGAAATACCTTTGAAGGAT
1 AAAATTACTGAAATACCCTCGAAGGGT
28557722 AAAATTACTGGAAA-ACCCTCGAAGGGT
1 AAAATTACT-GAAATACCCTCGAAGGGT
* *
28557749 AAAATTA-TCGAAATACTCTCAAAGGGT
1 AAAATTACT-GAAATACCCTCGAAGGGT
*
28557776 AAAATTACTAAAAT
1 AAAATTACTGAAAT
28557790 GCCCCTATAG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.06
27 70 0.88
28 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.25
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTCGAAGGGT
Found at i:28557805 original size:27 final size:27
Alignment explanation
Indices: 28557775--28558082 Score: 124
Period size: 27 Copynumber: 11.4 Consensus size: 27
28557765 TCTCAAAGGG
*
28557775 TAAAATTACTAAAATGCCCCTATAGGC
1 TAAAATGACTAAAATGCCCCTATAGGC
* * *
28557802 TAAAATGACTATAATGCCCCTGTAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* *** * * *
28557829 TAAAATGGCCGCAACGCCCCTGTAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* *** * *
28557856 TAAAATGGCCGTAATGCCCCTGTAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* *** ** *
28557883 TAAAATGGCCGTAATGCCCCTGCAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* *** * *
28557910 TAAAATAACCGTAATGCCCCTGTAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* * * *
28557937 TAAAATGACCATAATGCCCTTATAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
* *
28557964 TAAAATGATCGT--AATGCCCCTGTAGGG
1 TAAAATGA-C-TAAAATGCCCCTATAGGC
** * *
28557991 TAAAATGACTGTAATGCCCCTGTAGGG
1 TAAAATGACTAAAATGCCCCTATAGGC
*
28558018 TAAAATGAACGT--AATGCCCCTATAGGG
1 TAAAATG-AC-TAAAATGCCCCTATAGGC
* * *
28558045 TAAAATGATCGT--AATGCTCCTGTAGGG
1 TAAAATGA-C-TAAAATGCCCCTATAGGC
28558072 TAAAATGACTA
1 TAAAATGACTA
28558083 TTTTACCACT
Statistics
Matches: 248, Mismatches: 25, Indels: 17
0.86 0.09 0.06
Matches are distributed among these distances:
25 2 0.01
26 3 0.01
27 239 0.96
28 3 0.01
29 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (27 bp):
TAAAATGACTAAAATGCCCCTATAGGC
Found at i:28557829 original size:54 final size:54
Alignment explanation
Indices: 28557787--28558080 Score: 408
Period size: 54 Copynumber: 5.4 Consensus size: 54
28557777 AAATTACTAA
* * ** * *
28557787 AATGCCCCTATAGGCTAAAATGACTATAATGCCCCTGTAGGGTAAAATGGCCGC
1 AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
* * *
28557841 AACGCCCCTGTAGGGTAAAATGGCCGTAATGCCCCTGTAGGGTAAAATGGCCGT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
* * *
28557895 AATGCCCCTGCAGGGTAAAATAACCGTAATGCCCCTGTAGGGTAAAATGACCAT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
* * * *
28557949 AATGCCCTTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACTGT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
* * *
28558003 AATGCCCCTGTAGGGTAAAATGAACGTAATGCCCCTATAGGGTAAAATGATCGT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
*
28558057 AATGCTCCTGTAGGGTAAAATGAC
1 AATGCCCCTGTAGGGTAAAATGAC
28558081 TATTTTACCA
Statistics
Matches: 212, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 212 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (54 bp):
AATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGT
Found at i:28558081 original size:81 final size:81
Alignment explanation
Indices: 28557787--28558080 Score: 428
Period size: 81 Copynumber: 3.6 Consensus size: 81
28557777 AAATTACTAA
* * * * *
28557787 AATGCCCCTATAGGCTAAAATGA-CTATAATGCCCCTGTAGGGTAAAATGGCCGCAACGCCCCTG
1 AATGCCCCTATAGGGTAAAATGATC-GTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTG
*
28557851 TAGGGTAAAATGGCCGT
65 TAGGGTAAAATGACCGT
* ** * *
28557868 AATGCCCCTGTAGGGTAAAATGGCCGTAATGCCCCTGCAGGGTAAAATAACCGTAATGCCCCTGT
1 AATGCCCCTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGT
*
28557933 AGGGTAAAATGACCAT
66 AGGGTAAAATGACCGT
* *
28557949 AATGCCCTTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACTGTAATGCCCCTGT
1 AATGCCCCTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGT
*
28558014 AGGGTAAAATGAACGT
66 AGGGTAAAATGACCGT
*
28558030 AATGCCCCTATAGGGTAAAATGATCGTAATGCTCCTGTAGGGTAAAATGAC
1 AATGCCCCTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGAC
28558081 TATTTTACCA
Statistics
Matches: 190, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 189 0.99
82 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (81 bp):
AATGCCCCTATAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTGT
AGGGTAAAATGACCGT
Found at i:28558129 original size:24 final size:24
Alignment explanation
Indices: 28558099--28558162 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
28558089 CACTCGGGGT
*
28558099 TAAATGATTAATTT-TCCTATGATG
1 TAAATGATTAATTTGTCCGA-GATG
*
28558123 TAAATGATTGATTTGTCCGAGATG
1 TAAATGATTAATTTGTCCGAGATG
* *
28558147 TAAATGACTGATTTGT
1 TAAATGATTAATTTGT
28558163 TGTGATTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 32 0.89
25 4 0.11
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (24 bp):
TAAATGATTAATTTGTCCGAGATG
Found at i:28558198 original size:24 final size:24
Alignment explanation
Indices: 28558118--28558230 Score: 129
Period size: 24 Copynumber: 4.8 Consensus size: 24
28558108 AATTTTCCTA
* * *
28558118 TGATGTAAATGATTGATTTGTCCG
1 TGATTTAAATGACTGATTTGTCTG
* *
28558142 AGATGTAAATGACTGATTTGT-TG
1 TGATTTAAATGACTGATTTGTCTG
* *
28558165 TGATTGAAATGACTGATTTGTTTG
1 TGATTTAAATGACTGATTTGTCTG
*
28558189 TGATTTAAATGACTGATTTGTCTA
1 TGATTTAAATGACTGATTTGTCTG
**
28558213 TGATTTGTATGACTGATT
1 TGATTTAAATGACTGATT
28558231 CCGGGCATGG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 19 0.25
24 58 0.75
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (24 bp):
TGATTTAAATGACTGATTTGTCTG
Found at i:28558333 original size:27 final size:27
Alignment explanation
Indices: 28558295--28558359 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
28558285 ATGGAGGAAG
28558295 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
28558320 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
28558348 TACTATTACTGG
1 TACTGTTACTGG
28558360 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:28558365 original size:27 final size:26
Alignment explanation
Indices: 28558313--28558391 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 26
28558303 TGGTGGCTCT
* **
28558313 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAAT-ACTATTACTGGCAGCTTG
*
28558340 GCCACATATACTATTACTGGCAGCTTT
1 GCCACA-ATACTATTACTGGCAGCTTG
** * *
28558367 GCTGCGATACTATTGCTGGCAGCTT
1 GCCACAATACTATTACTGGCAGCTT
28558392 TGCTGCGATG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 18 0.42
27 23 0.53
28 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (26 bp):
GCCACAATACTATTACTGGCAGCTTG
Found at i:28558384 original size:14 final size:14
Alignment explanation
Indices: 28558365--28558410 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
28558355 ACTGGCAGCT
*
28558365 TTGCTGCGATACTA
1 TTGCTGCGATGCTA
28558379 TTGCTG-GCA-GCT-
1 TTGCTGCG-ATGCTA
28558391 TTGCTGCGATGCTA
1 TTGCTGCGATGCTA
28558405 TTGCTG
1 TTGCTG
28558411 GATTTGTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
12 7 0.26
13 7 0.26
14 13 0.48
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (14 bp):
TTGCTGCGATGCTA
Found at i:28558385 original size:26 final size:26
Alignment explanation
Indices: 28558347--28558411 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
28558337 TTGGCCACAT
*
28558347 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTGCTGGCAGCTTTGCTGCG
28558373 ATACTATTGCTGGCAGCTTTGCTGCG
1 ATACTATTGCTGGCAGCTTTGCTGCG
*
28558399 ATGCTATTGCTGG
1 ATACTATTGCTGG
28558412 ATTTGTACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (26 bp):
ATACTATTGCTGGCAGCTTTGCTGCG
Found at i:28558457 original size:32 final size:32
Alignment explanation
Indices: 28558415--28558608 Score: 187
Period size: 32 Copynumber: 6.1 Consensus size: 32
28558405 TTGCTGGATT
* * *
28558415 TGTACTGATCATATTACCATTACTGATGGTTG
1 TGTACCGATCATATTACTATTACTGATGGCTG
*
28558447 TGTACCGATCATATTACCATTACTGATGGCTG
1 TGTACCGATCATATTACTATTACTGATGGCTG
* * * *
28558479 TGTGCCGATTATATTACTACTACTGATGGCTT
1 TGTACCGATCATATTACTATTACTGATGGCTG
* * *
28558511 TGTGCCGATCATACTATTATTACTGATGGCTG
1 TGTACCGATCATATTACTATTACTGATGGCTG
* * * *
28558543 TATACC-AGTCATATTACTACTACTGATGACTT
1 TGTACCGA-TCATATTACTATTACTGATGGCTG
* * * *
28558575 TGTGCCAATCATATTACT-GTACTTATGGCT-
1 TGTACCGATCATATTACTATTACTGATGGCTG
28558605 TGTA
1 TGTA
28558609 GTCATTCTGT
Statistics
Matches: 135, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
30 3 0.02
31 10 0.07
32 121 0.90
33 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (32 bp):
TGTACCGATCATATTACTATTACTGATGGCTG
Found at i:28558579 original size:96 final size:95
Alignment explanation
Indices: 28558433--28558605 Score: 231
Period size: 96 Copynumber: 1.8 Consensus size: 95
28558423 TCATATTACC
* * * * * *
28558433 ATTACTGATGGTTGTGTACCGATCATATTACCATTACTGATGGCTGTGTGCCGATTATATTACTA
1 ATTACTGATGGCTGTATACCGATCATATTACCACTACTGATGACTGTGTGCCAATCATATTACT-
28558498 CTACTGATGGCTTTGTGCCGATCATACTATT
65 CTACTGATGGCTTTGTGCCGATCATACTATT
* *
28558529 ATTACTGATGGCTGTATACC-AGTCATATTACTACTACTGATGACTTTGTGCCAATCATATTACT
1 ATTACTGATGGCTGTATACCGA-TCATATTACCACTACTGATGACTGTGTGCCAATCATATTACT
* *
28558593 GTACTTATGGCTT
65 CTACTGATGGCTT
28558606 GTAGTCATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
95 12 0.18
96 54 0.82
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (95 bp):
ATTACTGATGGCTGTATACCGATCATATTACCACTACTGATGACTGTGTGCCAATCATATTACTC
TACTGATGGCTTTGTGCCGATCATACTATT
Found at i:28561707 original size:14 final size:14
Alignment explanation
Indices: 28561684--28561713 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28561674 CATCCCTCAT
*
28561684 TCACATCTCTTCTC
1 TCACAACTCTTCTC
28561698 TCACAACTCTTCTC
1 TCACAACTCTTCTC
28561712 TC
1 TC
28561714 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:28563899 original size:15 final size:15
Alignment explanation
Indices: 28563879--28563909 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28563869 AATAACATGT
28563879 TTATCTTTATAAATA
1 TTATCTTTATAAATA
28563894 TTATCTTTATAAATA
1 TTATCTTTATAAATA
28563909 T
1 T
28563910 GTTTTATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATCTTTATAAATA
Found at i:28568932 original size:50 final size:50
Alignment explanation
Indices: 28568852--28568988 Score: 211
Period size: 50 Copynumber: 2.7 Consensus size: 50
28568842 ATTTGGGTAA
* **
28568852 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
28568902 AGAGGTCCCATGTAACACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
**
28568952 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT
28568989 GGGAACCTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:28574750 original size:18 final size:20
Alignment explanation
Indices: 28574727--28574770 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
28574717 AATTTTTGTC
28574727 ATAAAATAATT-AATT-TTT
1 ATAAAATAATTAAATTGTTT
28574745 ATAAAATAATTAAATTGTTT
1 ATAAAATAATTAAATTGTTT
28574765 -TAAAAT
1 ATAAAAT
28574771 TTTGAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.46
19 10 0.42
20 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAAAATAATTAAATTGTTT
Found at i:28575391 original size:14 final size:14
Alignment explanation
Indices: 28575368--28575397 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28575358 CATCCCTCAT
*
28575368 TCACATCTCTTCTC
1 TCACAACTCTTCTC
28575382 TCACAACTCTTCTC
1 TCACAACTCTTCTC
28575396 TC
1 TC
28575398 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:28584980 original size:25 final size:25
Alignment explanation
Indices: 28584924--28584981 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
28584914 CTATTAAATT
*
28584924 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
*
28584949 TTTATTAAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
28584974 TTAATTAA
1 TTAATTAA
28584982 TTTTTTGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:28602755 original size:39 final size:41
Alignment explanation
Indices: 28602647--28602782 Score: 131
Period size: 40 Copynumber: 3.4 Consensus size: 41
28602637 TGTTTGGACA
* * * *
28602647 AAAAACGCCGA-TAAGAATCGAGCATTAGCTGCGCTTTA-TG
1 AAAAACGCC-ACTAAAAATCGAGCATTAGCGGCGTTTTACAG
* * * *
28602687 GAAATCGCCACTAAATATCGAGCATTAGCGGTGTTTTTA-A-
1 AAAAACGCCACTAAAAATCGAGCATTAGCGGCG-TTTTACAG
*
28602727 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTACAG
1 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGTTTTACAG
28602767 AAAAACGCCAC-AAAAA
1 AAAAACGCCACTAAAAA
28602783 CCAAAAGCCC
Statistics
Matches: 78, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
38 5 0.06
39 20 0.26
40 49 0.63
41 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (41 bp):
AAAAACGCCACTAAAAATCGAGCATTAGCGGCGTTTTACAG
Found at i:28603218 original size:15 final size:14
Alignment explanation
Indices: 28603199--28603247 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
28603189 ACTATTTTAA
*
28603199 GGTTTAGGGAGTAT
1 GGTTTAGGGATTAT
28603213 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
*
28603228 GGATTAGGGATTAT
1 GGTTTAGGGATTAT
28603242 GGTTTA
1 GGTTTA
28603248 AGGTTTGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:28603276 original size:7 final size:7
Alignment explanation
Indices: 28603266--28603324 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
28603256 GATTTAAGGT
28603266 TTAGGGG
1 TTAGGGG
**
28603273 TTAGACG
1 TTAGGGG
28603280 TTAGGGG
1 TTAGGGG
* *
28603287 TTAAGAG
1 TTAGGGG
28603294 TTAGGGG
1 TTAGGGG
28603301 TTTAGGGG
1 -TTAGGGG
*
28603309 TTAGGGA
1 TTAGGGG
28603316 TTCAGGGG
1 TT-AGGGG
28603324 T
1 T
28603325 CGAGTTAGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
7 28 0.70
8 12 0.30
ACGTcount: A:0.20, C:0.03, G:0.46, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:28603541 original size:21 final size:22
Alignment explanation
Indices: 28603504--28603571 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
28603494 GGAGTATGGA
* *
28603504 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAGGGG
28603525 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAGGGG
*
28603546 TTAGGG-TTTATGGGTTTAGGGG
1 TTAGGGATTTA-AGGTTTAGGGG
28603568 TTAG
1 TTAG
28603572 ATGCGTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.10
21 20 0.49
22 17 0.41
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAGGGG
Found at i:28603560 original size:8 final size:7
Alignment explanation
Indices: 28603504--28603571 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
28603494 GGAGTATGGA
*
28603504 TTAGGGA
1 TTAGGGT
*
28603511 TTATGGT
1 TTAGGGT
28603518 TTAAGGG-
1 TT-AGGGT
28603525 TT-GGGAT
1 TTAGGG-T
*
28603532 TTAAGGT
1 TTAGGGT
*
28603539 TTAGGGG
1 TTAGGGT
28603546 TTAGGGT
1 TTAGGGT
28603553 TTATGGGT
1 TTA-GGGT
*
28603561 TTAGGGG
1 TTAGGGT
28603568 TTAG
1 TTAG
28603572 ATGCGTTAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 3 0.06
7 33 0.69
8 12 0.25
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:28603804 original size:15 final size:14
Alignment explanation
Indices: 28603766--28603800 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28603756 CATATTTTAA
28603766 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
28603780 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
28603795 GGTTTA
1 GGTTTA
28603801 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:28603821 original size:21 final size:20
Alignment explanation
Indices: 28603787--28603827 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28603777 TATGGATTTA
*
28603787 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
28603807 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
28603828 AGACATTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:28604562 original size:103 final size:102
Alignment explanation
Indices: 28604447--28604649 Score: 311
Period size: 104 Copynumber: 2.0 Consensus size: 102
28604437 AAAACGCTGC
*
28604447 AAAAATAAATCAATTAAT-AAAATACAAAATAAAAAATTTTTAGCATAAG-AAAACGACGTCATT
1 AAAAATAAATCAATTAATAAAAAAACAAAATAAAAAATTTTTAGCAT-AGCAAAACGACGTCATT
28604510 TTGTTCAAAATGAAATAATTTCATAAAAACGCCGCAAACA
65 TTGTTCAAAATGAAATAATTT--TAAAAACGCCGCAAACA
* * * * *
28604550 AAAAATAAATCAATTTATAAAAAAATAAAATAAAAATTTTTTAGCATAGCAAAATGGCGTCATTT
1 AAAAATAAATCAATTAATAAAAAAACAAAATAAAAAATTTTTAGCATAGCAAAACGACGTCATTT
28604615 TGTTCAAAATGAAATAATTTTAAAAACGCCGCAAA
66 TGTTCAAAATGAAATAATTTTAAAAACGCCGCAAA
28604650 AGATAAGCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
102 15 0.16
103 19 0.21
104 58 0.63
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.27
Consensus pattern (102 bp):
AAAAATAAATCAATTAATAAAAAAACAAAATAAAAAATTTTTAGCATAGCAAAACGACGTCATTT
TGTTCAAAATGAAATAATTTTAAAAACGCCGCAAACA
Found at i:28604767 original size:240 final size:233
Alignment explanation
Indices: 28604323--28604770 Score: 614
Period size: 240 Copynumber: 1.9 Consensus size: 233
28604313 ATTTTATAAA
*** **
28604323 AAATCAATTTATAAAAAACAAAATAATTTTTTTTTAGTGTAGCAAAACGGCGTCATTTTGTTCAA
1 AAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
** * * * *
28604388 AATAAAATAATTTTTTGCTGAAAATAAAGCAATAGCGGCGTTTTTATAAAAAACGCTGCAAAAAT
66 AATAAAATAATTTTACGCCGAAAAGAAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAAT
28604453 AAATCAATTAATAAAATACAAAATAAAAAATTTTTAGCATAAGAAAACGACGTCATTTTGTTCAA
131 AAATCAATTAATAAAATACAAAATAAAAAATTTTTAGCATAAGAAAACGACGTCATTTTGTTCAA
28604518 AATGAAATAATTTCATAAAAACGCCGCAAACAAAAAAT
196 AATGAAATAATTTCATAAAAACGCCGCAAACAAAAAAT
* *
28604556 AAATCAATTTATAAAAAAATAAAATAAAAATTTTTTAGCATAGCAAAATGGCGTCATTTTGTTCA
1 AAATCAATTTAT-AAAAAACAAAATAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* *
28604621 AAATGAAATAATTTTAAAAACGCCGCAAAAGATAAGCAATAGCGGCGTTTTTATGAAAAACACCG
65 AAATAAAATAATTTT----ACGCCG-AAAAGA-AAGCAATAGCGGCGTTTTTATAAAAAACACCG
* * * *
28604686 CAAAAAATAAATCAATTTATAAAA-ATCAAAAT-AAAATTTTTTTG-ATAAGAAGAACGGCGTCA
124 C-AAAAATAAATCAATTAATAAAATA-CAAAATAAAAAATTTTTAGCATAAGAA-AACGACGTCA
28604748 TTTTGTTCAAAATGAAATAATTT
186 TTTTGTTCAAAATGAAATAATTT
28604771 TTTACGGCGT
Statistics
Matches: 186, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
233 12 0.06
234 59 0.32
238 3 0.02
239 12 0.06
240 73 0.39
241 27 0.15
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (233 bp):
AAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAA
AATAAAATAATTTTACGCCGAAAAGAAAGCAATAGCGGCGTTTTTATAAAAAACACCGCAAAAAT
AAATCAATTAATAAAATACAAAATAAAAAATTTTTAGCATAAGAAAACGACGTCATTTTGTTCAA
AATGAAATAATTTCATAAAAACGCCGCAAACAAAAAAT
Found at i:28606696 original size:2 final size:2
Alignment explanation
Indices: 28606689--28606725 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28606679 TGTTTAACAG
28606689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28606726 GATTTACCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28609046 original size:15 final size:14
Alignment explanation
Indices: 28609013--28609039 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28609003 TATCATAGAA
28609013 ATAAAAATTATTTG
1 ATAAAAATTATTTG
28609027 ATAAAAATTATTT
1 ATAAAAATTATTT
28609040 TTTTAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
ATAAAAATTATTTG
Found at i:28609152 original size:43 final size:43
Alignment explanation
Indices: 28609057--28609365 Score: 320
Period size: 43 Copynumber: 7.3 Consensus size: 43
28609047 GATATGTTTT
* *
28609057 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGT-TTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * *
28609099 CAGTGGCGTTTGTGGAAAATGCGCCGCTAAAGGTCTTGATTTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * *
28609142 TAGCGGCGTTTGTGG-GAAATCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * * *
28609184 TAGCGGTGTTTTTGTAAAAAGTGTCGTTAAAGGTTCTT-ATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGG-TCTTGATCTA
* *
28609227 TAGTGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * **
28609269 CAGCGGCGTTTGTTGAAAAAGTGCCGCTAAAGGTCCCGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * * *
28609312 TAGCGGCGTTTGTTGTATAAGCGACGCTAAAGGTCATGACCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
28609355 TAGCGGCGTTT
1 TAGCGGCGTTT
28609366 TTAGAAATAA
Statistics
Matches: 218, Mismatches: 44, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
41 3 0.01
42 93 0.43
43 118 0.54
44 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:28609215 original size:85 final size:84
Alignment explanation
Indices: 28609057--28609372 Score: 330
Period size: 85 Copynumber: 3.7 Consensus size: 84
28609047 GATATGTTTT
* * * * *
28609057 TAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGT-TTGATCTACAGTGGCGTTTGTGGAAAATGC
1 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGATCTACAGCGGCGTTT-TTGAAAAAGT
*
28609121 GCCGCTAAAGGTCTTGATTTA
64 GCCGCTAAAGGTCTTGATCTA
* * * * *
28609142 TAGCGGCGTTTGTGGGAAATCGCCGCTAAAGATCTTGAGCTATAGCGGTGTTTTTGTAAAAAGTG
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGATCTACAGCGGCGTTTTTG-AAAAAGTG
* *
28609207 TCGTTAAAGGTTCTT-ATCTA
65 CCGCTAAAGG-TCTTGATCTA
* ** *
28609227 TAGTGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCCTGATCTACAGCGGCGTTTGTTGAAAAAGTG
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGATCTACAGCGGCGTTT-TTGAAAAAGTG
**
28609292 CCGCTAAAGGTCCCGATCTA
65 CCGCTAAAGGTCTTGATCTA
* * * * * *
28609312 TAGCGGCGTTTGTTGTATAAGCGACGCTAAAGGTCATGACCTATAGCGGCGTTTTTAGAAA
1 TAGCGGCGTTTGTGGGA-AAGCGCCGCTAAAGGTCTTGATCTACAGCGGCGTTTTT-GAAA
28609373 TAAACGCCGC
Statistics
Matches: 190, Mismatches: 34, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
84 18 0.09
85 129 0.68
86 43 0.23
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (84 bp):
TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGATCTACAGCGGCGTTTTTGAAAAAGTGC
CGCTAAAGGTCTTGATCTA
Found at i:28616119 original size:36 final size:37
Alignment explanation
Indices: 28616079--28616151 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
28616069 TCAAAAACCT
28616079 GCAAAACAAACAC-TCAA-CACTCAAAAAGAAAAATTA
1 GCAAAACAAAC-CGTCAATCACTCAAAAAGAAAAATTA
* ** *
28616115 GCAAACCTCACCGTTAATCACTCAAAAAGAAAAATTA
1 GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
28616152 AATTCTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 1 0.03
36 11 0.35
37 19 0.61
ACGTcount: A:0.55, C:0.23, G:0.07, T:0.15
Consensus pattern (37 bp):
GCAAAACAAACCGTCAATCACTCAAAAAGAAAAATTA
Found at i:28619540 original size:5 final size:5
Alignment explanation
Indices: 28619530--28619565 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
28619520 AAAAAGATAG
28619530 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA ATAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A-AGAA
28619566 TGCTTGTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:28620243 original size:42 final size:42
Alignment explanation
Indices: 28620187--28620486 Score: 402
Period size: 42 Copynumber: 7.1 Consensus size: 42
28620177 ATATACAATA
* * *
28620187 CAATGAAAAGTAAATGGACCTCCACACCCGTGCCTTTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
28620229 TAATGAAAAATAAATGGACCTCCACACCTAGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
28620271 CAATGAAAAGTAAATGGACCTTCAGACCTGGGTCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
*
28620313 CAATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * **
28620355 CAATGAAAAGTTAATGGACCTCCACACTTAGGTTTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
28620397 CAATGAAAAATGAATGGACCTCCACACCTGGGACTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * **
28620439 CAATAAAAAGTTAATGGACCTCCACACCTAAGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
28620481 CAATGA
1 CAATGA
28620487 TTGCTTTCCT
Statistics
Matches: 225, Mismatches: 33, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 225 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
Found at i:28629517 original size:18 final size:18
Alignment explanation
Indices: 28629507--28629548 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
28629497 GAACAAAAAG
28629507 AAAAGATAGAAAAATAAA
1 AAAAGATAGAAAAATAAA
28629525 AAAAGAGT-GAAAAA-ACAA
1 AAAAGA-TAGAAAAATA-AA
28629543 AAAAGA
1 AAAAGA
28629549 AAAAGTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (18 bp):
AAAAGATAGAAAAATAAA
Found at i:28632817 original size:28 final size:28
Alignment explanation
Indices: 28632764--28632817 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28632754 ATTTTTTTTA
* *
28632764 AATGCATGTTCTTAATTTGTCTAAGTTT
1 AATGCATGTTCTTAATTGGTCCAAGTTT
28632792 AATGCATG-TCTTAATGTGGTCCAAGT
1 AATGCATGTTCTTAAT-TGGTCCAAGT
28632818 CCAGCCGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (28 bp):
AATGCATGTTCTTAATTGGTCCAAGTTT
Found at i:28634932 original size:25 final size:23
Alignment explanation
Indices: 28634904--28635038 Score: 90
Period size: 25 Copynumber: 5.4 Consensus size: 23
28634894 ATCCTGTACA
28634904 TGTATGCTCATACAAGATGTAAACC
1 TGTATGCTC-TACAAGATGTAAA-C
* *
28634929 TGTATGCTCTATCAAGCTGTAAAT
1 TGTATGCTCTA-CAAGATGTAAAC
*
28634953 TGGTATGCTCTCACGAGATGTAAATC
1 T-GTATGCTCT-ACAAGATGTAAA-C
* * * *
28634979 GGTATGCTCTCACGAGCTGTAAAT
1 TGTATGCTCT-ACAAGATGTAAAC
* *
28635003 TGGTATGCTCTTACGAGCTGTAAATC
1 T-GTATGCTC-TACAAGATGTAAA-C
*
28635029 GGTATGCTCT
1 TGTATGCTCT
28635039 CACGAGCTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
24 4 0.04
25 86 0.93
26 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (23 bp):
TGTATGCTCTACAAGATGTAAAC
Found at i:28634959 original size:50 final size:50
Alignment explanation
Indices: 28634905--28635078 Score: 208
Period size: 50 Copynumber: 3.5 Consensus size: 50
28634895 TCCTGTACAT
* * *
28634905 GTATGCTCATACAAGATGTAAACCTGTATGCTCT-ATCAAGCTGTAAATTG
1 GTATGCTCATACAAGATGTAAATCGGTATGCTCTCA-CGAGCTGTAAATTG
*
28634955 GTATGCTC-TCACGAGATGTAAATCGGTATGCTCTCACGAGCTGTAAATTG
1 GTATGCTCAT-ACAAGATGTAAATCGGTATGCTCTCACGAGCTGTAAATTG
* * * * *
28635005 GTATGCTCTTACGAGCTGTAAATCGGTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCATACAAGATGTAAATCGGTATGCTCTCACGAGCTGTAAATTG
* * *
28635055 GTAAGCTCATACAAGTTGTGAATC
1 GTATGCTCATACAAGATGTAAATC
28635079 AGCAAGCTCA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 106 0.97
51 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (50 bp):
GTATGCTCATACAAGATGTAAATCGGTATGCTCTCACGAGCTGTAAATTG
Found at i:28635043 original size:25 final size:25
Alignment explanation
Indices: 28634921--28635062 Score: 187
Period size: 25 Copynumber: 5.7 Consensus size: 25
28634911 TCATACAAGA
* * *
28634921 TGTAAACCTGTATGCTCT-ATCAAGC
1 TGTAAATCGGTATGCTCTCA-CGAGC
* *
28634946 TGTAAATTGGTATGCTCTCACGAGA
1 TGTAAATCGGTATGCTCTCACGAGC
28634971 TGTAAATCGGTATGCTCTCACGAGC
1 TGTAAATCGGTATGCTCTCACGAGC
* *
28634996 TGTAAATTGGTATGCTCTTACGAGC
1 TGTAAATCGGTATGCTCTCACGAGC
28635021 TGTAAATCGGTATGCTCTCACGAGC
1 TGTAAATCGGTATGCTCTCACGAGC
* *
28635046 TATAAATCGGTAAGCTC
1 TGTAAATCGGTATGCTC
28635063 ATACAAGTTG
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
25 102 0.99
26 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (25 bp):
TGTAAATCGGTATGCTCTCACGAGC
Found at i:28635096 original size:75 final size:75
Alignment explanation
Indices: 28634943--28635096 Score: 175
Period size: 75 Copynumber: 2.1 Consensus size: 75
28634933 TGCTCTATCA
* * * * ** *
28634943 AGCTGTAAATTGGTATGCTCTCACGAGATGTAAATCGGTATGCTCTCACGAGCTGTAAATTGGTA
1 AGCTGTAAATCGGTATGCTCTCACGAGATATAAATCGGTAAGCTCTCACAAGCTGTAAATCAGCA
* *
28635008 TGCTCTTACG
66 AGCTCATACG
* * *
28635018 AGCTGTAAATCGGTATGCTCTCACGAGCTATAAATCGGTAAGCTCAT-ACAAGTTGTGAATCAGC
1 AGCTGTAAATCGGTATGCTCTCACGAGATATAAATCGGTAAGCTC-TCACAAGCTGTAAATCAGC
*
28635082 AAGCTCATATG
65 AAGCTCATACG
28635093 AGCT
1 AGCT
28635097 ATGAGGCGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
75 64 0.98
76 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (75 bp):
AGCTGTAAATCGGTATGCTCTCACGAGATATAAATCGGTAAGCTCTCACAAGCTGTAAATCAGCA
AGCTCATACG
Found at i:28639846 original size:18 final size:20
Alignment explanation
Indices: 28639825--28639872 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
28639815 AAAGGAAGAC
28639825 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
28639843 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
28639863 AGCAAAAAGA
1 AG-AAAAAGA
28639873 TATTGAGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 2 0.08
21 7 0.27
ACGTcount: A:0.73, C:0.04, G:0.19, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:28644983 original size:102 final size:102
Alignment explanation
Indices: 28644791--28645085 Score: 457
Period size: 102 Copynumber: 2.9 Consensus size: 102
28644781 ACTTTTATCA
* * * * ** *
28644791 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCATGTTTTA-CGGTTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTATCGATTCACGTAG
* * *
28644855 TAGCCTTCAAATAGAACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
*
28644892 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTATCGATTCACGTAG
28644957 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * *
28644994 ATCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTATCGATACACGTAG
1 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTATCGATTCACGTAG
28645059 TAGCCTTCACACAGTACTACACACGTG
66 TAGCCTTCACACAGTACTACACACGTG
28645086 TTCATCGATA
Statistics
Matches: 178, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
101 45 0.25
102 133 0.75
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (102 bp):
TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:28645078 original size:153 final size:151
Alignment explanation
Indices: 28644792--28645081 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 151
28644782 CTTTTATCAT
* * * * * *
28644792 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCATGTTTTACGGTTCACGTAGTA
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTATACGGTACACATAGTA
* **
28644857 GCCTTCAAATAGAACTACACACGTGACCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCAAATAGAACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAGTA
28644922 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* *
28644944 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTAT-CGGTACACATTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTATACGGTACACATAG
** * * * * *
28645008 TAGCCTTCACTTAGTACTACACATGTGATC-ATCATTTATCGATACACGTAGTAGCCTTCACACA
64 TAGCCTTCAAATAGAACTACACACGTGACCAAAC-TTT-TCGATACACATAGTAGCCTTCACACA
28645072 GTACTACACA
127 GTACTACACA
28645082 CGTGTTCATC
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
151 1 0.01
152 44 0.38
153 68 0.59
154 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (151 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTATACGGTACACATAGTA
GCCTTCAAATAGAACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACACAGTAC
TACACATGTGACCATCATTTA
Found at i:28645091 original size:51 final size:51
Alignment explanation
Indices: 28644792--28645085 Score: 326
Period size: 51 Copynumber: 5.8 Consensus size: 51
28644782 CTTTTATCAT
* **
28644792 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCATGTTTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCATTTA
* * * * *
28644843 -CGGTTCACGTAGTAGCCTTCAAATAGAACTACACACGTGACCA-AAGCTTT-
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCA--TTTA
* * * *
28644893 TCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCATTTA
* * * *
28644944 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA-AAGCTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCA-TTTA
* * * * * *
28644995 TCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGATCATCATTTA
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCATTTA
*
28645046 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
28645086 TTCATCGATA
Statistics
Matches: 198, Mismatches: 38, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
50 42 0.21
51 154 0.78
52 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (51 bp):
TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATCATTTA
Found at i:28654431 original size:24 final size:23
Alignment explanation
Indices: 28654404--28654452 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
28654394 TTAAAACTAC
28654404 TTCTAA-AGAAAACTCAAGAGAGAA
1 TTCTAAGAG-AAACTCAA-AGAGAA
**
28654428 TTCTTGGAGAAACTCAAAGAGAA
1 TTCTAAGAGAAACTCAAAGAGAA
28654451 TT
1 TT
28654453 TTCACTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (23 bp):
TTCTAAGAGAAACTCAAAGAGAA
Found at i:28659561 original size:27 final size:25
Alignment explanation
Indices: 28659519--28659577 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
28659509 GCAGTCAACC
28659519 TATAAA-TAGTTCATTTGTAAACATTT
1 TATAAATTAGTTCATTT-T-AACATTT
* *
28659545 TATAAATTAGTTGATTTTGACATTT
1 TATAAATTAGTTCATTTTAACATTT
28659570 TATGAAAT
1 TAT-AAAT
28659578 ATATAGACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
26 11 0.38
27 9 0.31
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (25 bp):
TATAAATTAGTTCATTTTAACATTT
Found at i:28659589 original size:26 final size:25
Alignment explanation
Indices: 28659539--28659589 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
28659529 TCATTTGTAA
* *
28659539 ACATTTTATAAATTAGTTGATTTTG
1 ACATTTTATAAATTAGTAGACTTTG
28659564 ACATTTTATGAAATATA-TAGACTTTG
1 ACATTTTAT-AAAT-TAGTAGACTTTG
28659590 TGAGTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (25 bp):
ACATTTTATAAATTAGTAGACTTTG
Done.